[
  {"_key":"60c20a727723bebd8664533a","_id":"annotations/60c20a727723bebd8664533a","_rev":"_cfFmUDa---","document":{"$oid":"60c20a727723bebd86645338"},"type":"software","software-name":{"offsetStart":27,"normalizedForm":"Molecular Evolutionary Genetic Analysis","offsetEnd":66,"rawForm":"Molecular Evolutionary Genetic Analysis","boundingBoxes":[{"x":90.5685,"h":9.584000000000003,"y":205.126,"p":3,"w":186.297}]},"context":"Sequences were aligned by Molecular Evolutionary Genetic Analysis version 7.0 (MEGA7) [6] and a search of homologous sequences was performed using Basic Local Alignment Search Tool (BLAST) [7]."},
  {"_key":"60c20a727723bebd8664533b","_id":"annotations/60c20a727723bebd8664533b","_rev":"_cfFmUDm---","document":{"$oid":"60c20a727723bebd86645338"},"context":"Sequences were aligned by Molecular Evolutionary Genetic Analysis version 7.0 (MEGA7) [6] and a search of homologous sequences was performed using Basic Local Alignment Search Tool (BLAST) [7].","references":[{"offsetStart":7252,"normalizedForm":"[6]","refKey":5,"label":"[6]","reference_id":{"$oid":"60c20a727723bebd86645339"},"offsetEnd":7256,"boundingBoxes":[{"x":377.305,"h":9.584000000000003,"y":205.126,"p":3,"w":11.752399999999966}]}],"type":"software","software-name":{"offsetStart":79,"normalizedForm":"(MEGA","offsetEnd":84,"rawForm":"(MEGA","boundingBoxes":[{"x":331.211,"h":9.584000000000003,"y":205.126,"p":3,"w":37.14008571428576}]},"version":{"offsetStart":84,"normalizedForm":"7","offsetEnd":85,"rawForm":"7","boundingBoxes":[{"x":337.4010142857143,"h":9.584,"y":205.126,"p":3,"w":30.95007142857143}]}},
  {"_key":"60c20a727723bebd8664533c","_id":"annotations/60c20a727723bebd8664533c","_rev":"_cfFmUDu---","document":{"$oid":"60c20a727723bebd86645338"},"type":"software","software-name":{"offsetStart":149,"normalizedForm":"Basic Local Alignment Search Tool (BLAST)","offsetEnd":190,"rawForm":"Basic Local Alignment Search Tool (BLAST)","boundingBoxes":[{"x":220.096,"h":9.584000000000003,"y":218.636,"p":3,"w":192.22770000000003}]},"context":"Sequences were aligned by Molecular Evolutionary Genetic Analysis version 7.0 (MEGA7) [6] and a search of homologous sequences was performed using Basic Local Alignment Search Tool (BLAST) [7]."},
  {"_key":"60c20a747723bebd8664533e","_id":"annotations/60c20a747723bebd8664533e","_rev":"_cfFmUD6---","document":{"$oid":"60c20a747723bebd8664533d"},"context":"The phylogenetic trees were constructed by MEGA 7.0 with the best bases substitution model consideration, neighbour-joining, maximum likelihood and bootstrap values adjustment.","type":"software","software-name":{"offsetStart":44,"normalizedForm":"MEGA","offsetEnd":48,"rawForm":"MEGA","boundingBoxes":[{"x":224.109,"h":8.9767,"y":172.722,"p":4,"w":28.7725}]},"version":{"offsetStart":49,"normalizedForm":"7.0","offsetEnd":52,"rawForm":"7.0","boundingBoxes":[{"x":256.821,"h":8.976699999999994,"y":172.722,"p":4,"w":11.936300000000017}]}},
  {"_key":"60c20a747723bebd8664533f","_id":"annotations/60c20a747723bebd8664533f","_rev":"_cfFmUEG---","wikipediaExternalRef":179088,"document":{"$oid":"60c20a747723bebd8664533d"},"context":"The statistical significance of the data was evaluated with SPSS 20.0.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":61,"wikidataId":"Q181596","offsetEnd":65,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":56.6929,"h":8.9767,"y":112.742,"p":4,"w":20.5014}]},"version":{"offsetStart":66,"normalizedForm":"20.0","offsetEnd":70,"rawForm":"20.0","boundingBoxes":[{"x":81.6376,"h":8.976699999999994,"y":112.742,"p":4,"w":15.178080000000008}]}},
  {"_key":"60c20a757723bebd86645341","_id":"annotations/60c20a757723bebd86645341","_rev":"_cfFmUES---","wikipediaExternalRef":179088,"document":{"$oid":"60c20a757723bebd86645340"},"context":"Analyses were conducted in SPSS version 18. Statistical significance was set at P < 0.05, and all tests were 2-tailed.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":27,"wikidataId":"Q181596","offsetEnd":31,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":244.287,"h":8.8468,"y":471.04,"p":4,"w":17.072}]},"version":{"offsetStart":41,"normalizedForm":"18","offsetEnd":43,"rawForm":"18","boundingBoxes":[{"x":37.5874,"h":8.8468,"y":481.529,"p":4,"w":7.470666666666666}]}},
  {"_key":"60c20a787723bebd86645343","_id":"annotations/60c20a787723bebd86645343","_rev":"_cfFmUEe---","wikipediaExternalRef":179088,"document":{"$oid":"60c20a787723bebd86645342"},"publisher":{"offsetStart":33,"normalizedForm":"IBM","offsetEnd":36,"rawForm":"IBM","boundingBoxes":[{"x":172.174,"h":8.8468,"y":170.569,"p":6,"w":14.4339}]},"context":"All analyses were conducted with IBM SPSS® Statistics version 26.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":37,"wikidataId":"Q181596","offsetEnd":41,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":189.295,"h":8.8468,"y":170.569,"p":6,"w":23.1292}]},"version":{"offsetStart":62,"normalizedForm":"26","offsetEnd":64,"rawForm":"26","boundingBoxes":[{"x":277.452,"h":8.8468,"y":170.569,"p":6,"w":7.470666666666666}]}},
  {"_key":"60c20a787723bebd86645344","_id":"annotations/60c20a787723bebd86645344","_rev":"_cfFmUEq---","document":{"$oid":"60c20a787723bebd86645342"},"publisher":{"offsetStart":72,"normalizedForm":"Globalpark","offsetEnd":82,"rawForm":"Globalpark","boundingBoxes":[{"x":41.4029,"h":8.8468,"y":212.408,"p":4,"w":38.155}]},"context":"The survey was carried out via the online platform Unipark/Questback® (Globalpark AG).","type":"software","software-name":{"offsetStart":51,"normalizedForm":"Unipark/Questback","offsetEnd":68,"rawForm":"Unipark/Questback","boundingBoxes":[{"x":213.56,"h":8.846800000000002,"y":201.92,"p":4,"w":75.1182}]}},
  {"_key":"60c20a7b7723bebd86645348","_id":"annotations/60c20a7b7723bebd86645348","_rev":"_cfFmUE2---","document":{"$oid":"60c20a7b7723bebd86645345"},"context":"TaxIt aims to overcome the problem of inaccurate species and strain resolution when proteomics data are searched against reference databases that lack taxonomic depth.","references":[{"offsetStart":13555,"normalizedForm":"33","refKey":28,"label":"33","reference_id":{"$oid":"60c20a7b7723bebd86645346"},"offsetEnd":13559,"boundingBoxes":[{"x":293.215,"h":5.9927,"y":551.781,"p":3,"w":7.1399}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"TaxIt","offsetEnd":5,"rawForm":"TaxIt","boundingBoxes":[{"x":107.774,"h":8.9901,"y":587.491,"p":3,"w":20.6202}]}},
  {"_key":"60c20a7b7723bebd86645349","_id":"annotations/60c20a7b7723bebd86645349","_rev":"_cfFmUFC---","document":{"$oid":"60c20a7b7723bebd86645345"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"PeptidePicker","offsetEnd":13,"rawForm":"PeptidePicker","boundingBoxes":[{"x":504.34,"h":8.9901,"y":375.913,"p":3,"w":52.8605}]},"context":"PeptidePicker 37 is a web-based application for selecting peptides after submission of the protein accession identifier and was specifically designed for human and mouse proteomes."},
  {"_key":"60c20a7b7723bebd8664534a","_id":"annotations/60c20a7b7723bebd8664534a","_rev":"_cfFmUFO---","document":{"$oid":"60c20a7b7723bebd86645345"},"context":"For example, Skyline 34 is one of the most widely used software tools in the field.","references":[{"offsetStart":14252,"normalizedForm":"34","refKey":29,"label":"34","reference_id":{"$oid":"60c20a7b7723bebd86645347"},"offsetEnd":14255,"boundingBoxes":[{"x":285.051,"h":5.9927,"y":685.236,"p":3,"w":7.1399}]}],"type":"software","software-name":{"offsetStart":13,"normalizedForm":"Skyline","offsetEnd":20,"rawForm":"Skyline","boundingBoxes":[{"x":257.56,"h":8.9901,"y":687.611,"p":3,"w":27.5103}]}},
  {"_key":"60c20a7b7723bebd8664534b","_id":"annotations/60c20a7b7723bebd8664534b","_rev":"_cfFmUFe---","document":{"$oid":"60c20a7b7723bebd86645345"},"context":"In a first step, TaxIt applies reference sequence data for the identification of species candidates and, in a second step, it performs an automated acquisition of relevant strain sequences for low-level classification.","references":[{"offsetStart":13555,"normalizedForm":"33","refKey":28,"label":"33","reference_id":{"$oid":"60c20a7b7723bebd86645346"},"offsetEnd":13559,"boundingBoxes":[{"x":293.215,"h":5.9927,"y":551.781,"p":3,"w":7.1399}]}],"type":"software","software-name":{"offsetStart":17,"normalizedForm":"TaxIt","offsetEnd":22,"rawForm":"TaxIt","boundingBoxes":[{"x":142.867,"h":8.9901,"y":620.883,"p":3,"w":20.6202}]}},
  {"_key":"60c20a7b7723bebd8664534c","_id":"annotations/60c20a7b7723bebd8664534c","_rev":"_cfFmUFq---","document":{"$oid":"60c20a7b7723bebd86645345"},"type":"software","software-name":{"offsetStart":56,"normalizedForm":"Unique Peptide Finder","offsetEnd":78,"rawForm":"Unique \nPeptide Finder","boundingBoxes":[{"x":536.092,"h":8.9901,"y":419.906,"p":3,"w":28.4003},{"x":324.453,"h":8.990099999999984,"y":430.904,"p":3,"w":58.44630000000001}]},"context":"As a specific use case of targeted metaproteomics, the Unique Peptide Finder of the UniPept web application 38 allows the selection of unique peptides for user-defined taxa and can therefore be interesting for the proteome-based analysis of viral samples."},
  {"_key":"60c20a7b7723bebd8664534d","_id":"annotations/60c20a7b7723bebd8664534d","_rev":"_cfFmUF6---","document":{"$oid":"60c20a7b7723bebd86645345"},"context":"For example, the recently published taxonomic identification tool TaxIt 33 was also tested on virus samples (e.g., cowpoxvirus and adenovirus strains) that have been measured by shotgun proteomics.","references":[{"offsetStart":13555,"normalizedForm":"33","refKey":28,"label":"33","reference_id":{"$oid":"60c20a7b7723bebd86645346"},"offsetEnd":13559,"boundingBoxes":[{"x":293.215,"h":5.9927,"y":551.781,"p":3,"w":7.1399}]}],"type":"software","software-name":{"offsetStart":67,"normalizedForm":"TaxIt","offsetEnd":72,"rawForm":"TaxIt","boundingBoxes":[{"x":272.581,"h":8.9901,"y":554.1,"p":3,"w":20.6202}]}},
  {"_key":"60c20a7b7723bebd8664534e","_id":"annotations/60c20a7b7723bebd8664534e","_rev":"_cfFmUGG---","wikipediaExternalRef":47612960,"document":{"$oid":"60c20a7b7723bebd86645345"},"context":"As a specific use case of targeted metaproteomics, the Unique Peptide Finder of the UniPept web application 38 allows the selection of unique peptides for user-defined taxa and can therefore be interesting for the proteome-based analysis of viral samples.","wikidataId":"Q22673960","type":"software","confidence":0.4764,"software-name":{"wikipediaExternalRef":47612960,"normalizedForm":"UniPept","offsetStart":86,"wikidataId":"Q22673960","offsetEnd":93,"lang":"en","confidence":0.4764,"rawForm":"UniPept","boundingBoxes":[{"x":415.333,"h":8.9901,"y":430.904,"p":3,"w":31.9303}]},"lang":"en"},
  {"_key":"60c20a7b7723bebd86645350","_id":"annotations/60c20a7b7723bebd86645350","_rev":"_cfFmUGS---","document":{"$oid":"60c20a7b7723bebd8664534f"},"type":"software","software-name":{"offsetStart":28,"normalizedForm":"OSRATY","offsetEnd":34,"rawForm":"OSRATY","boundingBoxes":[{"x":125.412,"h":12,"y":128.54,"p":4,"w":38.472}]},"context":"However, unfortunately the OSRATY platform was not completely functional and few services were not available."},
  {"_key":"60c20a7b7723bebd86645351","_id":"annotations/60c20a7b7723bebd86645351","_rev":"_cfFmUGi---","document":{"$oid":"60c20a7b7723bebd8664534f"},"type":"software","software-name":{"offsetStart":148,"normalizedForm":"OSRATY","offsetEnd":154,"rawForm":"OSRATY","boundingBoxes":[{"x":94.344,"h":12,"y":128.54,"p":3,"w":38.592}]},"context":"The Family Medicine department with the support of the Information Technology (IT) department developed a Virtual Clinic website, by the name of OSRATY platform; a secure online website that gives 24-hour access."},
  {"_key":"60c20a817723bebd86645353","_id":"annotations/60c20a817723bebd86645353","_rev":"_cfFmUGu---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20a817723bebd86645352"},"context":"For alpha, kappa, PPV and NPV, we pooled data across studies using DerSimonian-Laird random effects models, imple- mented in STATA version 13 (Colleges Station, TX) [34].","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7367,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"STATA","offsetStart":127,"wikidataId":"Q1204300","offsetEnd":132,"lang":"en","confidence":0.7367,"rawForm":"STATA","boundingBoxes":[{"x":106.582,"h":8.9767,"y":604.722,"p":4,"w":32.0035}]},"version":{"offsetStart":141,"normalizedForm":"13","offsetEnd":143,"rawForm":"13","boundingBoxes":[{"x":179.206,"h":8.9767,"y":604.722,"p":4,"w":9.7999}]}},
  {"_key":"60c20a817723bebd86645354","_id":"annotations/60c20a817723bebd86645354","_rev":"_cfFmUG6---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20a817723bebd86645352"},"context":"Add- itionally, for sensitivity and specificity, we used hierarch- ical logistic regression models, implemented using the metandi command in STATA, to account for the correl- ation between the two measures (i.e., trade-off between sensitivity and specificity) [36-38].","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7367,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"STATA","offsetStart":142,"wikidataId":"Q1204300","offsetEnd":147,"lang":"en","confidence":0.7367,"rawForm":"STATA","boundingBoxes":[{"x":396.339,"h":8.9767,"y":124.758,"p":4,"w":28.387083333333337}]},"version":{"offsetStart":141,"normalizedForm":"13","offsetEnd":143,"rawForm":"13","boundingBoxes":[{"x":179.206,"h":8.9767,"y":604.722,"p":4,"w":9.7999}]}},
  {"_key":"60c20a827723bebd86645357","_id":"annotations/60c20a827723bebd86645357","_rev":"_cfFmUHK---","document":{"$oid":"60c20a827723bebd86645355"},"context":"For encoding the cardinality constraints, we use cardinality networks [1] as implemented in PySAT [10].","references":[{"offsetStart":12789,"normalizedForm":"[10]","refKey":9,"label":"[10]","reference_id":{"$oid":"60c20a827723bebd86645356"},"offsetEnd":12793,"boundingBoxes":[{"x":152.777,"h":8.936500000000024,"y":363.74,"p":5,"w":14.61712}]}],"type":"software","software-name":{"offsetStart":93,"normalizedForm":"PySAT","offsetEnd":98,"rawForm":"PySAT","boundingBoxes":[{"x":123.032,"h":8.4981,"y":364.408,"p":5,"w":26.1478}]}},
  {"_key":"60c20a827723bebd86645359","_id":"annotations/60c20a827723bebd86645359","_rev":"_cfFmUHW---","document":{"$oid":"60c20a827723bebd86645358"},"type":"software","software-name":{"offsetStart":42,"normalizedForm":"Reply All Storm Protection","offsetEnd":68,"rawForm":"Reply All Storm Protection","boundingBoxes":[{"x":48.9332,"h":7.336000000000013,"y":339.358,"p":2,"w":90.0958}]},"context":"According to a story in Gizmodo, its new Reply All Storm Protection software \"detects possible reply-all screw-ups and essentially puts all recipients on a temporary time-out\"."},
  {"_key":"60c20a877723bebd8664535b","_id":"annotations/60c20a877723bebd8664535b","_rev":"_cfFmUHi---","wikipediaExternalRef":9804129,"document":{"$oid":"60c20a877723bebd8664535a"},"context":"P p 1 For phylogenetic analysis, first the Tree-Puzzle program (ver- sion 5.0) was used to generate approximate quartet-likelihood trees, with 1000 puzzling steps [9].","wikidataId":"Q7837628","type":"software","lang":"en","confidence":0.6343,"software-name":{"wikipediaExternalRef":9804129,"normalizedForm":"Tree-Puzzle","offsetStart":44,"wikidataId":"Q7837628","offsetEnd":55,"lang":"en","confidence":0.6343,"rawForm":"Tree-Puzzle","boundingBoxes":[{"x":453.701,"h":8.413800000000037,"y":714.117,"p":1,"w":44.089399999999955}]},"version":{"offsetStart":75,"normalizedForm":"5.0","offsetEnd":78,"rawForm":"5.0","boundingBoxes":[{"x":75.7588,"h":8.41379999999998,"y":453.204,"p":2,"w":11.142075000000006}]}},
  {"_key":"60c20a877723bebd8664535c","_id":"annotations/60c20a877723bebd8664535c","_rev":"_cfFmUHu---","wikipediaExternalRef":26578372,"document":{"$oid":"60c20a877723bebd8664535a"},"context":"The parsimony-based partition-homogeneity test was performed by the PAUP* program [8].","wikidataId":"Q7118292","type":"software","confidence":0.8451,"software-name":{"wikipediaExternalRef":26578372,"normalizedForm":"PAUP*","offsetStart":69,"wikidataId":"Q7118292","offsetEnd":74,"lang":"en","confidence":0.8451,"rawForm":"PAUP*","boundingBoxes":[{"x":387.332,"h":8.413800000000037,"y":610.111,"p":1,"w":26.904200000000003}]},"lang":"en"},
  {"_key":"60c20a877723bebd8664535d","_id":"annotations/60c20a877723bebd8664535d","_rev":"_cfFmUH6---","document":{"$oid":"60c20a877723bebd8664535a"},"context":"The amino acid sequences of the 3CL pro , POL, HEL, S, E, M, and N proteins were individually aligned by the Clustral X program (version 1.83).","type":"software","software-name":{"offsetStart":111,"normalizedForm":"Clustral X","offsetEnd":121,"rawForm":"Clustral X","boundingBoxes":[{"x":374.343,"h":8.413800000000037,"y":519.454,"p":1,"w":40.05340000000001}]},"version":{"offsetStart":139,"normalizedForm":"1.83","offsetEnd":143,"rawForm":"1.83","boundingBoxes":[{"x":490.28,"h":8.413800000000037,"y":519.454,"p":1,"w":14.445666666666625}]}},
  {"_key":"60c20a877723bebd8664535e","_id":"annotations/60c20a877723bebd8664535e","_rev":"_cfFmUIG---","document":{"$oid":"60c20a877723bebd8664535a"},"type":"software","software-name":{"offsetStart":167,"normalizedForm":"ProML","offsetEnd":172,"rawForm":"ProML","boundingBoxes":[{"x":395.663,"h":8.4138,"y":466.155,"p":2,"w":27.0215}]},"context":"JTT + F + G  inv  Parameters that had been established on the basis of the puz- zling analysis were then applied to a true maximum-likelihood (ML) analysis by the ProML program included in the PHYLIP package [10], with the sequence input order randomized and with global rearrangements enabled during the tree search."},
  {"_key":"60c20a877723bebd8664535f","_id":"annotations/60c20a877723bebd8664535f","_rev":"_cfFmUIS---","wikipediaExternalRef":4500351,"document":{"$oid":"60c20a877723bebd8664535a"},"context":"JTT + F + G  inv  Parameters that had been established on the basis of the puz- zling analysis were then applied to a true maximum-likelihood (ML) analysis by the ProML program included in the PHYLIP package [10], with the sequence input order randomized and with global rearrangements enabled during the tree search.","wikidataId":"Q4046201","type":"software","confidence":0.8108,"software-name":{"wikipediaExternalRef":4500351,"normalizedForm":"PHYLIP","offsetStart":197,"wikidataId":"Q4046201","offsetEnd":203,"lang":"en","confidence":0.8108,"rawForm":"PHYLIP","boundingBoxes":[{"x":521.37,"h":8.4138,"y":466.155,"p":2,"w":31.6534}]},"lang":"en"},
  {"_key":"60c20a8a7723bebd86645361","_id":"annotations/60c20a8a7723bebd86645361","_rev":"_cfFmUIa---","wikipediaExternalRef":179088,"document":{"$oid":"60c20a8a7723bebd86645360"},"publisher":{"offsetStart":53,"normalizedForm":"IBM","offsetEnd":56,"rawForm":"IBM","boundingBoxes":[{"x":520.39,"h":8.9767,"y":652.743,"p":4,"w":18.1592}]},"context":"Statistical analysis of the data was performed using IBM SPSS 23 data analysis software.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":58,"wikidataId":"Q181596","offsetEnd":62,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":304.724,"h":8.9767,"y":664.757,"p":4,"w":20.5014}]},"version":{"offsetStart":63,"normalizedForm":"23","offsetEnd":65,"rawForm":"23","boundingBoxes":[{"x":329.331,"h":8.9767,"y":664.757,"p":4,"w":9.7999}]}},
  {"_key":"60c20a8c7723bebd86645363","_id":"annotations/60c20a8c7723bebd86645363","_rev":"_cfFmUIm---","wikipediaExternalRef":179088,"document":{"$oid":"60c20a8c7723bebd86645362"},"context":"The data from the questionnaire survey were exported to the SPSS 22.0 statistical software for data logical verification and statistical analysis.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":60,"wikidataId":"Q181596","offsetEnd":64,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":470.759,"h":9.584,"y":114.22,"p":4,"w":22.1427}]},"version":{"offsetStart":65,"normalizedForm":"22.0","offsetEnd":69,"rawForm":"22.0","boundingBoxes":[{"x":496.143,"h":9.584000000000003,"y":114.22,"p":4,"w":17.783200000000022}]}},
  {"_key":"60c20a977723bebd86645365","_id":"annotations/60c20a977723bebd86645365","_rev":"_cfFmUIy---","wikipediaExternalRef":179088,"document":{"$oid":"60c20a977723bebd86645364"},"context":"SPSS 15.0 for Windows was used for statistical analysis.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":0,"wikidataId":"Q181596","offsetEnd":4,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":509.634,"h":9.702,"y":717.777,"p":2,"w":21.1155}]},"version":{"offsetStart":5,"normalizedForm":"15.0","offsetEnd":9,"rawForm":"15.0","boundingBoxes":[{"x":533.595,"h":9.701999999999998,"y":717.777,"p":2,"w":18.33299999999997}]}},
  {"_key":"60c20a977723bebd86645366","_id":"annotations/60c20a977723bebd86645366","_rev":"_cfFmUJ----","document":{"$oid":"60c20a977723bebd86645364"},"context":"The sample size was calculated with the G * PowerVersion 3.1.6","type":"software","software-name":{"offsetStart":40,"normalizedForm":"G * PowerVersion","offsetEnd":56,"rawForm":"G * PowerVersion","boundingBoxes":[{"x":490.659,"h":9.701999999999998,"y":665.151,"p":2,"w":76.27099999999996}]},"version":{"offsetStart":58,"normalizedForm":"3.1.6","offsetEnd":63,"rawForm":"3.1.6","boundingBoxes":[{"x":311.811,"h":9.701999999999998,"y":678.308,"p":2,"w":20.50649999999996}]}},
  {"_key":"60c20a997723bebd86645368","_id":"annotations/60c20a997723bebd86645368","_rev":"_cfFmUJK---","document":{"$oid":"60c20a997723bebd86645367"},"type":"software","software-name":{"offsetStart":121,"normalizedForm":"Clinical Record Interactive Search (CRIS)","offsetEnd":164,"rawForm":"Clinical \n\nRecord Interactive Search (CRIS)","boundingBoxes":[{"x":477.486,"h":10.2023,"y":615.416,"p":2,"w":35.9073},{"x":94.1402,"h":10.202300000000037,"y":634.856,"p":2,"w":152.5011}]},"context":"SLaM's BRC Case Register was set up  in 2008, providing researcher access to de-identified data from SLaM's EHR via the Clinical  Record Interactive Search (CRIS) platform and within a robust security model and  governance framework (10)."},
  {"_key":"60c20a9c7723bebd8664536a","_id":"annotations/60c20a9c7723bebd8664536a","_rev":"_cfFmUJW---","document":{"$oid":"60c20a9c7723bebd86645369"},"context":"Software MDI Jade 5.0 was used for the calculation of the structural and microstructural param- eters.","type":"software","software-name":{"offsetStart":9,"normalizedForm":"MDI Jade","offsetEnd":17,"rawForm":"MDI Jade","boundingBoxes":[{"x":408.856,"h":11.480000000000018,"y":358.157,"p":3,"w":42.579999999999984}]},"version":{"offsetStart":18,"normalizedForm":"5.0","offsetEnd":21,"rawForm":"5.0","boundingBoxes":[{"x":455.266,"h":11.480000000000018,"y":358.157,"p":3,"w":13.180000000000007}]}},
  {"_key":"60c20aa07723bebd8664536c","_id":"annotations/60c20aa07723bebd8664536c","_rev":"_cfFmUJi---","wikipediaExternalRef":20412,"document":{"$oid":"60c20aa07723bebd8664536b"},"context":"Based on the theory described in the previous section, the Jacobi-based moment invariants were implemented in MATLAB.","wikidataId":"Q169478","type":"software","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":111,"wikidataId":"Q169478","offsetEnd":117,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":168.021,"h":8.7571,"y":554.861,"p":4,"w":37.229057142857144}]},"lang":"en"},
  {"_key":"60c20aa37723bebd8664536e","_id":"annotations/60c20aa37723bebd8664536e","_rev":"_cfFmUJu---","wikipediaExternalRef":990677,"document":{"$oid":"60c20aa37723bebd8664536d"},"publisher":{"offsetStart":71,"normalizedForm":"SAS Institute","offsetEnd":84,"rawForm":"SAS Institute","boundingBoxes":[{"x":127.791,"h":8.789999999999964,"y":527.561,"p":4,"w":53.489000000000004}]},"context":"The statistical analyses were done with statistics software (SAS 9.2, SAS Institute, Cary, North Carolina).","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":62,"wikidataId":"Q2003932","offsetEnd":65,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":89.7441,"h":8.79,"y":527.561,"p":4,"w":16.2525}]},"version":{"offsetStart":66,"normalizedForm":"9.2","offsetEnd":69,"rawForm":"9.2","boundingBoxes":[{"x":109.393,"h":8.789999999999964,"y":527.561,"p":4,"w":11.25}]}},
  {"_key":"60c20aa77723bebd86645370","_id":"annotations/60c20aa77723bebd86645370","_rev":"_cfFmUJ6---","wikipediaExternalRef":179088,"document":{"$oid":"60c20aa77723bebd8664536f"},"publisher":{"offsetStart":33,"normalizedForm":"IBM","offsetEnd":36,"rawForm":"IBM","boundingBoxes":[{"x":158.571,"h":6.9978,"y":538.239,"p":16,"w":14.7999}]},"context":"Code Availability Software used: IBM SPSS Statistics 26.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.4875,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS Statistics","offsetStart":37,"wikidataId":"Q181596","offsetEnd":52,"lang":"en","confidence":0.4875,"rawForm":"SPSS Statistics","boundingBoxes":[{"x":175.523,"h":6.997799999999984,"y":538.239,"p":16,"w":46.89259999999999}]},"version":{"offsetStart":53,"normalizedForm":"26","offsetEnd":55,"rawForm":"26","boundingBoxes":[{"x":224.733,"h":6.9978,"y":538.239,"p":16,"w":6.4685999999999995}]}},
  {"_key":"60c20aae7723bebd86645372","_id":"annotations/60c20aae7723bebd86645372","_rev":"_cfFmUKG---","wikipediaExternalRef":363695,"document":{"$oid":"60c20aae7723bebd86645371"},"context":"We performed a BLAST engine search for other proteins with similarities to the N-terminal portion of PV 2C, and identified the hepatitis C virus (HCV) NS5A protein, with scores comparable to those of the cardio-or aphthovirus 2C homologs (Fig. 1A, data not shown.).","wikidataId":"Q286820","type":"software","confidence":0.2888,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":16,"wikidataId":"Q286820","offsetEnd":21,"lang":"en","confidence":0.2888,"rawForm":"BLAST","boundingBoxes":[{"x":301.721,"h":8.7372,"y":721.29,"p":3,"w":31.3224}]},"lang":"en"},
  {"_key":"60c20aae7723bebd86645373","_id":"annotations/60c20aae7723bebd86645373","_rev":"_cfFmUKS---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20aae7723bebd86645371"},"context":"Sequence alignments were generated using the ClustalX 1.64 and 1.81, a Windows-based interface of the ClustalW program (Thompson et al., 1997, 1994), and the Dialign2 program (Morgenstern, 1999), both assisted by the Blossum scoring matrices of the amino acid similarities (Henikoff and Henikoff, 1994).","wikidataId":"Q866737","type":"software","lang":"en","confidence":0.2972,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"ClustalX","offsetStart":46,"wikidataId":"Q866737","offsetEnd":54,"lang":"en","confidence":0.2972,"rawForm":"ClustalX","boundingBoxes":[{"x":73.3592,"h":8.7372,"y":589.768,"p":13,"w":35.1162}]},"version":{"offsetStart":55,"normalizedForm":"1.64 and 1.81","offsetEnd":68,"rawForm":"1.64 and 1.81","boundingBoxes":[{"x":112.079,"h":8.73720000000003,"y":589.768,"p":13,"w":54.83116}]}},
  {"_key":"60c20aae7723bebd86645374","_id":"annotations/60c20aae7723bebd86645374","_rev":"_cfFmUKe---","wikipediaExternalRef":18890,"document":{"$oid":"60c20aae7723bebd86645371"},"context":"Sequence alignments were generated using the ClustalX 1.64 and 1.81, a Windows-based interface of the ClustalW program (Thompson et al., 1997, 1994), and the Dialign2 program (Morgenstern, 1999), both assisted by the Blossum scoring matrices of the amino acid similarities (Henikoff and Henikoff, 1994).","wikidataId":"Q1406","type":"software","confidence":0.275,"software-name":{"wikipediaExternalRef":18890,"normalizedForm":"Windows","offsetStart":72,"wikidataId":"Q1406","offsetEnd":79,"lang":"en","confidence":0.275,"rawForm":"Windows","boundingBoxes":[{"x":182.378,"h":8.7372,"y":589.768,"p":13,"w":34.18886153846154}]},"lang":"en"},
  {"_key":"60c20aae7723bebd86645375","_id":"annotations/60c20aae7723bebd86645375","_rev":"_cfFmUKq---","wikipediaExternalRef":363695,"document":{"$oid":"60c20aae7723bebd86645371"},"context":"GenBank searches with 2C and NS5A sequences as queries were performed using the original BLAST program (Altschul et al., 1990).","wikidataId":"Q286820","type":"software","confidence":0.2901,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":90,"wikidataId":"Q286820","offsetEnd":95,"lang":"en","confidence":0.2901,"rawForm":"BLAST","boundingBoxes":[{"x":175.008,"h":8.7372,"y":541.976,"p":13,"w":31.4161}]},"lang":"en"},
  {"_key":"60c20aae7723bebd86645376","_id":"annotations/60c20aae7723bebd86645376","_rev":"_cfFmUK2---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20aae7723bebd86645371"},"context":"Sequence alignments were generated using the ClustalX 1.64 and 1.81, a Windows-based interface of the ClustalW program (Thompson et al., 1997, 1994), and the Dialign2 program (Morgenstern, 1999), both assisted by the Blossum scoring matrices of the amino acid similarities (Henikoff and Henikoff, 1994).","wikidataId":"Q866737","type":"software","confidence":0.7779,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"ClustalW","offsetStart":104,"wikidataId":"Q866737","offsetEnd":112,"lang":"en","confidence":0.7779,"rawForm":"ClustalW","boundingBoxes":[{"x":60.2066,"h":8.7372,"y":601.73,"p":13,"w":37.298}]},"lang":"en"},
  {"_key":"60c20aae7723bebd86645377","_id":"annotations/60c20aae7723bebd86645377","_rev":"_cfFmULC---","wikipediaExternalRef":6793394,"document":{"$oid":"60c20aae7723bebd86645371"},"context":"Sequence alignments were generated using the ClustalX 1.64 and 1.81, a Windows-based interface of the ClustalW program (Thompson et al., 1997, 1994), and the Dialign2 program (Morgenstern, 1999), both assisted by the Blossum scoring matrices of the amino acid similarities (Henikoff and Henikoff, 1994).","wikidataId":"Q5205081","type":"software","lang":"en","confidence":0.4603,"software-name":{"wikipediaExternalRef":6793394,"normalizedForm":"Dialign","offsetStart":161,"wikidataId":"Q5205081","offsetEnd":168,"lang":"en","confidence":0.4603,"rawForm":"Dialign","boundingBoxes":[{"x":47.1107,"h":8.7372,"y":613.692,"p":13,"w":34.631}]},"version":{"offsetStart":168,"normalizedForm":"2","offsetEnd":169,"rawForm":"2","boundingBoxes":[{"x":47.1107,"h":8.7372,"y":613.692,"p":13,"w":34.631}]}},
  {"_key":"60c20ab17723bebd86645379","_id":"annotations/60c20ab17723bebd86645379","_rev":"_cfFmULO---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20ab17723bebd86645378"},"context":"Statistical data analyses were done using GraphPad Prism 6 software.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":42,"wikidataId":"Q5597066","offsetEnd":56,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":213.841,"h":8.854000000000042,"y":625.713,"p":3,"w":66.27729999999997}]},"version":{"offsetStart":57,"normalizedForm":"6","offsetEnd":58,"rawForm":"6","boundingBoxes":[{"x":284.593,"h":8.854,"y":625.713,"p":3,"w":4.5505}]}},
  {"_key":"60c20ab67723bebd8664537b","_id":"annotations/60c20ab67723bebd8664537b","_rev":"_cfFmULa---","document":{"$oid":"60c20ab67723bebd8664537a"},"type":"software","software-name":{"offsetStart":32,"normalizedForm":"maTilDA: Multi-Purpose Toolkit for TDA","offsetEnd":71,"rawForm":"maTilDA: Multi-Purpose Toolkit for \nTDA","boundingBoxes":[{"x":197.452,"h":8.86669999999998,"y":401.515,"p":7,"w":187.73560000000003},{"x":39.4023,"h":8.8667,"y":413.476,"p":7,"w":20.9028}]},"context":"We used our own implementation, maTilDA: Multi-Purpose Toolkit for TDA, for the construction of the Weighted Vietoris-Rips complex, its persistent homology, barcode computations, persistence landscapes and discrete sampling."},
  {"_key":"60c20ab67723bebd8664537c","_id":"annotations/60c20ab67723bebd8664537c","_rev":"_cfFmULm---","document":{"$oid":"60c20ab67723bebd8664537a"},"type":"software","software-name":{"offsetStart":37,"normalizedForm":"scikit-learn python","offsetEnd":56,"rawForm":"scikit-learn python","boundingBoxes":[{"x":209.51,"h":8.936499999999995,"y":220.182,"p":7,"w":81.74370000000005}]},"context":"These methods were applied using the scikit-learn python library [23]."},
  {"_key":"60c20ab67723bebd8664537d","_id":"annotations/60c20ab67723bebd8664537d","_rev":"_cfFmULy---","wikipediaExternalRef":51650259,"document":{"$oid":"60c20ab67723bebd8664537a"},"context":"In the TDA-CNN approach, for a given resolution r y , we fed each subject's vectorized persistence landscape as a tensor of shape (r x , r y , 2), one channel per homology degree, into a Convolutional Neural Network (CNN) [20] implemented using the Keras library [12] with the Tensorflow [1] backend.","wikidataId":"Q28470421","type":"software","confidence":0.7048,"software-name":{"wikipediaExternalRef":51650259,"normalizedForm":"Keras","offsetStart":252,"wikidataId":"Q28470421","offsetEnd":257,"lang":"en","confidence":0.7048,"rawForm":"Keras","boundingBoxes":[{"x":84.6547,"h":8.9365,"y":267.997,"p":7,"w":24.9862}]},"lang":"en"},
  {"_key":"60c20ab77723bebd8664537f","_id":"annotations/60c20ab77723bebd8664537f","_rev":"_cfFmUM----","wikipediaExternalRef":1976990,"document":{"$oid":"60c20ab77723bebd8664537e"},"context":"The sequences were aligned by Clustal W method using MEGA 4.0 software (Tamura et al., 2007).","wikidataId":"Q866737","type":"software","confidence":0.8955,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"Clustal W","offsetStart":30,"wikidataId":"Q866737","offsetEnd":39,"lang":"en","confidence":0.8955,"rawForm":"Clustal W","boundingBoxes":[{"x":456.218,"h":9.79649999999998,"y":485.367,"p":3,"w":46.3895}]},"lang":"en"},
  {"_key":"60c20ab77723bebd86645380","_id":"annotations/60c20ab77723bebd86645380","_rev":"_cfFmUMK---","wikipediaExternalRef":363695,"document":{"$oid":"60c20ab77723bebd8664537e"},"context":"Aligned nucleotide sequences were subject- ed to BLAST analysis (http://www.ncbi.nlm.nih.gov) to confirm their identity.","wikidataId":"Q286820","type":"software","confidence":0.2946,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":49,"wikidataId":"Q286820","offsetEnd":54,"lang":"en","confidence":0.2946,"rawForm":"BLAST","boundingBoxes":[{"x":344.456,"h":9.7965,"y":425.359,"p":3,"w":35.28}]},"url":{"offsetStart":65,"normalizedForm":"http://www.ncbi.nlm.nih.gov","offsetEnd":92,"rawForm":"http://www.ncbi.nlm.nih.gov","boundingBoxes":[{"x":430.21237931034483,"h":9.79649999999998,"y":425.359,"p":3,"w":131.90524137931033}]},"lang":"en"},
  {"_key":"60c20ab77723bebd86645381","_id":"annotations/60c20ab77723bebd86645381","_rev":"_cfFmUMa---","document":{"$oid":"60c20ab77723bebd8664537e"},"context":"The sequences were aligned by Clustal W method using MEGA 4.0 software (Tamura et al., 2007).","type":"software","software-name":{"offsetStart":54,"normalizedForm":"MEGA","offsetEnd":58,"rawForm":"MEGA","boundingBoxes":[{"x":315.004,"h":9.7965,"y":497.368,"p":3,"w":32.865}]},"version":{"offsetStart":59,"normalizedForm":"4.0","offsetEnd":62,"rawForm":"4.0","boundingBoxes":[{"x":352.615,"h":9.79649999999998,"y":497.368,"p":3,"w":13.41900000000004}]}},
  {"_key":"60c20ab97723bebd86645383","_id":"annotations/60c20ab97723bebd86645383","_rev":"_cfFmUMi---","wikipediaExternalRef":179088,"document":{"$oid":"60c20ab97723bebd86645382"},"publisher":{"offsetStart":41,"normalizedForm":"SPSS Inc","offsetEnd":50,"rawForm":"SPSS \nInc","boundingBoxes":[{"x":271.609,"h":7.1652,"y":289.915,"p":4,"w":17.0483},{"x":37.588,"h":7.1652,"y":300.346,"p":4,"w":9.17688}]},"context":"The SPSS software program (Version 15.0, SPSS Inc., Chicago, IL, USA) was used for statistical analysis.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7466,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":4,"wikidataId":"Q181596","offsetEnd":8,"lang":"en","confidence":0.7466,"rawForm":"SPSS","boundingBoxes":[{"x":136.458,"h":7.1652,"y":289.915,"p":4,"w":17.0483}]},"version":{"offsetStart":35,"normalizedForm":"15.0","offsetEnd":39,"rawForm":"15.0","boundingBoxes":[{"x":251.654,"h":7.165200000000027,"y":289.915,"p":4,"w":14.308080000000018}]}},
  {"_key":"60c20abd7723bebd86645385","_id":"annotations/60c20abd7723bebd86645385","_rev":"_cfFmUMu---","document":{"$oid":"60c20abd7723bebd86645384"},"context":"Para a análise descritiva foi usado o programa Graph Pad Prism versão 8.4 (https://www.graphpad.com/scientific-software/prism/)","type":"software","software-name":{"offsetStart":47,"normalizedForm":"Graph Pad Prism","offsetEnd":62,"rawForm":"Graph Pad Prism","boundingBoxes":[{"x":442.501,"h":8.780499999999961,"y":546.052,"p":4,"w":68.16149999999999}]},"url":{"offsetStart":76,"normalizedForm":"https://www.graphpad.com/scientific-software/prism","offsetEnd":126,"rawForm":"https://www.graphpad.com/scientific-software/prism","boundingBoxes":[{"x":162.78224528301888,"h":8.780499999999961,"y":558.452,"p":4,"w":210.8122641509434}]},"version":{"offsetStart":71,"normalizedForm":"8.4","offsetEnd":74,"rawForm":"8.4","boundingBoxes":[{"x":144.567,"h":8.780499999999961,"y":558.452,"p":4,"w":11.906800000000004}]}},
  {"_key":"60c20abd7723bebd86645386","_id":"annotations/60c20abd7723bebd86645386","_rev":"_cfFmUM6---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20abd7723bebd86645384"},"context":"e para a análise de tendência foi utiliza- do o programa Stata versão 11.0 (https://www.stata.com).","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":57,"wikidataId":"Q1204300","offsetEnd":62,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":204.619,"h":8.7805,"y":570.852,"p":4,"w":19.6331}]},"url":{"offsetStart":76,"normalizedForm":"https://www.stata.com","offsetEnd":97,"rawForm":"https://www.stata.com","boundingBoxes":[{"x":276.9908916666667,"h":8.780499999999961,"y":570.852,"p":4,"w":85.84572499999996}]},"version":{"offsetStart":70,"normalizedForm":"11.0","offsetEnd":74,"rawForm":"11.0","boundingBoxes":[{"x":254.001,"h":8.780499999999961,"y":570.852,"p":4,"w":16.83590000000001}]}},
  {"_key":"60c20abd7723bebd86645387","_id":"annotations/60c20abd7723bebd86645387","_rev":"_cfFmUNG---","wikipediaExternalRef":20268,"publisher":{"offsetStart":52,"normalizedForm":"Microsoft","offsetEnd":61,"rawForm":"Microsoft","boundingBoxes":[{"x":185.384,"h":8.7805,"y":409.652,"p":4,"w":39.5087}]},"context":"Para o cálculo das taxas, foi utilizado o programa Microsoft Office Excel 2010.","confidence":0.3543,"url":{"offsetStart":88,"normalizedForm":"https://products. office.com","offsetEnd":117,"rawForm":"https://products. \noffice.com","boundingBoxes":[{"x":472.6051777777778,"h":8.78049999999999,"y":223.652,"p":4,"w":66.0480222222223},{"x":144.567,"h":8.78049999999999,"y":236.052,"p":4,"w":38.56507692307693}]},"version":{"offsetStart":75,"normalizedForm":"2010","offsetEnd":79,"rawForm":"2010","boundingBoxes":[{"x":277.314,"h":8.7805,"y":409.652,"p":4,"w":17.411920000000002}]},"document":{"$oid":"60c20abd7723bebd86645384"},"wikidataId":"Q11272","type":"software","software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Office Excel","offsetStart":62,"wikidataId":"Q11272","offsetEnd":74,"lang":"en","confidence":0.3543,"rawForm":"Office Excel","boundingBoxes":[{"x":227.047,"h":8.780500000000018,"y":409.652,"p":4,"w":48.11300000000003}]},"lang":"en"},
  {"_key":"60c20abd7723bebd86645388","_id":"annotations/60c20abd7723bebd86645388","_rev":"_cfFmUNS---","wikipediaExternalRef":20268,"publisher":{"offsetStart":59,"normalizedForm":"Microsoft","offsetEnd":68,"rawForm":"Microsoft","boundingBoxes":[{"x":354.819,"h":8.7805,"y":223.652,"p":4,"w":39.5087}]},"context":"Para a criação do banco de dados foi utilizado o programa Microsoft Office Excel 2010 (https://products. office.com/).","confidence":0.3543,"url":{"offsetStart":88,"normalizedForm":"https://products. office.com","offsetEnd":117,"rawForm":"https://products. \noffice.com","boundingBoxes":[{"x":472.6051777777778,"h":8.78049999999999,"y":223.652,"p":4,"w":66.0480222222223},{"x":144.567,"h":8.78049999999999,"y":236.052,"p":4,"w":38.56507692307693}]},"version":{"offsetStart":82,"normalizedForm":"2010","offsetEnd":86,"rawForm":"2010","boundingBoxes":[{"x":446.823,"h":8.7805,"y":223.652,"p":4,"w":19.7163}]},"document":{"$oid":"60c20abd7723bebd86645384"},"wikidataId":"Q11272","type":"software","software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Office Excel","offsetStart":69,"wikidataId":"Q11272","offsetEnd":81,"lang":"en","confidence":0.3543,"rawForm":"Office Excel","boundingBoxes":[{"x":396.508,"h":8.78049999999999,"y":223.652,"p":4,"w":48.13570000000004}]},"lang":"en"},
  {"_key":"60c20ac67723bebd8664538a","_id":"annotations/60c20ac67723bebd8664538a","_rev":"_cfFmUNe---","wikipediaExternalRef":6732927,"document":{"$oid":"60c20ac67723bebd86645389"},"context":"The ClogP values, calcu- lated using ChemDraw, together with the molecular weights of in- hibitors 1-10 are summarized in Table 1.","wikidataId":"Q898716","type":"software","confidence":0.7984,"software-name":{"wikipediaExternalRef":6732927,"normalizedForm":"ChemDraw","offsetStart":37,"wikidataId":"Q898716","offsetEnd":45,"lang":"en","confidence":0.7984,"rawForm":"ChemDraw","boundingBoxes":[{"x":82.3752,"h":7.1652,"y":415.434,"p":5,"w":36.811733333333336}]},"lang":"en"},
  {"_key":"60c20ac67723bebd8664538b","_id":"annotations/60c20ac67723bebd8664538b","_rev":"_cfFmUNq---","document":{"$oid":"60c20ac67723bebd86645389"},"type":"software","software-name":{"offsetStart":56,"normalizedForm":"AMBER","offsetEnd":61,"rawForm":"AMBER","boundingBoxes":[{"x":369.861,"h":7.1652,"y":353.979,"p":12,"w":26.9632}]},"context":"Molecular docking calculations and MD simulations with AMBER led to the development of the more potent GIIA sPLA 2 inhibitor GK241 (Fig. 10) [94,140]."},
  {"_key":"60c20aca7723bebd8664538d","_id":"annotations/60c20aca7723bebd8664538d","_rev":"_cfFmUN2---","wikipediaExternalRef":179088,"document":{"$oid":"60c20aca7723bebd8664538c"},"publisher":{"offsetStart":48,"normalizedForm":"IBM Corp","offsetEnd":56,"rawForm":"IBM Corp","boundingBoxes":[{"x":50.8026,"h":7.880000000000003,"y":63.0448,"p":4,"w":30.789600000000007}]},"context":"The statistical program SPSS Statistics v.25  (IBM Corp) was used for data processing.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.4875,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS Statistics","offsetStart":24,"wikidataId":"Q181596","offsetEnd":39,"lang":"en","confidence":0.4875,"rawForm":"SPSS Statistics","boundingBoxes":[{"x":217.119,"h":7.880000000000003,"y":50.0448,"p":4,"w":53.92339999999999}]},"version":{"offsetStart":42,"normalizedForm":"25","offsetEnd":46,"rawForm":"25","boundingBoxes":[{"x":281.79139999999995,"h":7.88,"y":50.0448,"p":4,"w":7.6824}]}},
  {"_key":"60c20ad27723bebd86645390","_id":"annotations/60c20ad27723bebd86645390","_rev":"_cfFmUOC---","document":{"$oid":"60c20ad27723bebd8664538e"},"publisher":{"offsetStart":65,"normalizedForm":"StataCorp","offsetEnd":74,"rawForm":"StataCorp","boundingBoxes":[{"x":465.7260909090909,"h":11.48,"y":432.755,"p":4,"w":39.33081818181818}]},"context":"Analyses were performed using the statistical software StataIC (StataCorp, College Station, TX) or R (R Foundation for Statistical Computing, Vienna, Austria).","type":"software","software-name":{"offsetStart":56,"normalizedForm":"StataIC","offsetEnd":63,"rawForm":"StataIC","boundingBoxes":[{"x":427.386,"h":11.48,"y":432.755,"p":4,"w":31.23}]}},
  {"_key":"60c20ad27723bebd86645391","_id":"annotations/60c20ad27723bebd86645391","_rev":"_cfFmUOO---","document":{"$oid":"60c20ad27723bebd8664538e"},"context":"The change in Δ U at 3 versus 12 months was assessed by the t test for partially overlap- ping samples (R package Partiallyoverlapping [41]).","references":[{"offsetStart":12807,"normalizedForm":"[41]","refKey":41,"label":"[41]","reference_id":{"$oid":"60c20ad27723bebd8664538f"},"offsetEnd":12811,"boundingBoxes":[{"x":235.956,"h":11.480000000000018,"y":532.755,"p":4,"w":15.02666666666667}]}],"type":"software","software-name":{"offsetStart":105,"normalizedForm":"R package Partiallyoverlapping","offsetEnd":135,"rawForm":"R package Partiallyoverlapping","boundingBoxes":[{"x":110.62899999999999,"h":11.480000000000018,"y":532.755,"p":4,"w":123.05699999999999}]}},
  {"_key":"60c20ad27723bebd86645392","_id":"annotations/60c20ad27723bebd86645392","_rev":"_cfFmUOa---","document":{"$oid":"60c20ad27723bebd8664538e"},"context":"For the stroke survivors, who may have persisting problems, and their caregivers, the EQ-5D-3L dimensions were also ana- lysed separately, and changes over time in the proportion experiencing problems with each dimension were assessed with the z-test for partially overlapping samples (R package Partiallyoverlapping [41]).","references":[{"offsetStart":13136,"normalizedForm":"[41]","refKey":41,"label":"[41]","reference_id":{"$oid":"60c20ad27723bebd8664538f"},"offsetEnd":13140,"boundingBoxes":[{"x":135.33,"h":11.480000000000018,"y":607.755,"p":4,"w":15.159999999999997}]}],"type":"software","software-name":{"offsetStart":290,"normalizedForm":"R package Partiallyoverlapping","offsetEnd":321,"rawForm":"R package \nPartiallyoverlapping","boundingBoxes":[{"x":249.122,"h":11.480000000000018,"y":595.255,"p":4,"w":39.990999999999985},{"x":51.025,"h":11.48,"y":607.755,"p":4,"w":81.83}]}},
  {"_key":"60c20ad67723bebd86645394","_id":"annotations/60c20ad67723bebd86645394","_rev":"_cfFmUOm---","document":{"$oid":"60c20ad67723bebd86645393"},"publisher":{"offsetStart":252,"normalizedForm":"Cochrane Collaboration","offsetEnd":274,"rawForm":"Cochrane Collaboration","boundingBoxes":[{"x":37.2845,"h":9.925600000000003,"y":43.3133,"p":31,"w":105.3434}]},"context":"The relevant odds  ratios (OR) were used to construct a forest plot for visualization purposes using Revman 5.3 software  [30].","type":"software","software-name":{"offsetStart":102,"normalizedForm":"Revman","offsetEnd":108,"rawForm":"Revman","boundingBoxes":[{"x":438.873,"h":10.5367,"y":378.455,"p":8,"w":39.9928}]},"version":{"offsetStart":109,"normalizedForm":"5.3","offsetEnd":112,"rawForm":"5.3","boundingBoxes":[{"x":481.986,"h":10.536699999999996,"y":378.455,"p":8,"w":15.000900000000001}]}},
  {"_key":"60c20ad67723bebd86645395","_id":"annotations/60c20ad67723bebd86645395","_rev":"_cfFmUOy---","document":{"$oid":"60c20ad67723bebd86645393"},"publisher":{"offsetStart":252,"normalizedForm":"Cochrane Collaboration","offsetEnd":274,"rawForm":"Cochrane Collaboration","boundingBoxes":[{"x":37.2845,"h":9.925600000000003,"y":43.3133,"p":31,"w":105.3434}]},"context":"is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) relevant odds ratios (OR) were used to construct a forest plot for visualization purposes using Revman 5.3 software from  the Cochrane Collaboration [30].","type":"software","software-name":{"offsetStart":221,"normalizedForm":"Revman","offsetEnd":227,"rawForm":"Revman","boundingBoxes":[{"x":440.154,"h":9.9256,"y":23.1533,"p":31,"w":36.3737}]},"version":{"offsetStart":228,"normalizedForm":"5.3","offsetEnd":231,"rawForm":"5.3","boundingBoxes":[{"x":478.961,"h":9.925600000000003,"y":23.1533,"p":31,"w":13.969600000000014}]}},
  {"_key":"60c20ad67723bebd86645397","_id":"annotations/60c20ad67723bebd86645397","_rev":"_cfFmUO6---","wikipediaExternalRef":9651444,"document":{"$oid":"60c20ad67723bebd86645396"},"context":"In wake of impending restrictions, we explored available options for online classes and adopted G Suite for Education using Google Classroom coupled with Google Meet for Video-conferencing (https:// edu.google.com/products/gsuite-for-education/","wikidataId":"Q509284","type":"software","confidence":0.5486,"software-name":{"wikipediaExternalRef":9651444,"normalizedForm":"G Suite for Education","offsetStart":97,"wikidataId":"Q509284","offsetEnd":119,"lang":"en","confidence":0.5486,"rawForm":"G Suite \nfor Education","boundingBoxes":[{"x":266.623,"h":11.069999999999993,"y":425.13,"p":1,"w":30.422000000000025},{"x":72,"h":11.069999999999993,"y":437.13,"p":1,"w":57.137}]},"lang":"en"},
  {"_key":"60c20ad67723bebd86645398","_id":"annotations/60c20ad67723bebd86645398","_rev":"_cfFmUPG---","wikipediaExternalRef":1092923,"document":{"$oid":"60c20ad67723bebd86645396"},"context":"In wake of impending restrictions, we explored available options for online classes and adopted G Suite for Education using Google Classroom coupled with Google Meet for Video-conferencing (https:// edu.google.com/products/gsuite-for-education/","wikidataId":"Q95","type":"software","confidence":0.3335,"software-name":{"wikipediaExternalRef":1092923,"normalizedForm":"Google","offsetStart":157,"wikidataId":"Q95","offsetEnd":163,"lang":"en","confidence":0.3335,"rawForm":"Google","boundingBoxes":[{"x":72,"h":11.07,"y":449.13,"p":1,"w":29.475}]},"lang":"en"},
  {"_key":"60c20ae07723bebd8664539a","_id":"annotations/60c20ae07723bebd8664539a","_rev":"_cfFmUPS---","wikipediaExternalRef":20412,"document":{"$oid":"60c20ae07723bebd86645399"},"context":"Statistical analysis was performed using Matlab R2018a and Statview 5.0 (SAS institute).","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7276,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"Matlab","offsetStart":42,"wikidataId":"Q169478","offsetEnd":48,"lang":"en","confidence":0.7276,"rawForm":"Matlab","boundingBoxes":[{"x":39.6869,"h":8.854,"y":589.474,"p":2,"w":26.562}]},"version":{"offsetStart":49,"normalizedForm":"R2018a","offsetEnd":55,"rawForm":"R2018a","boundingBoxes":[{"x":71.72,"h":8.854000000000042,"y":589.474,"p":2,"w":28.186499999999995}]}},
  {"_key":"60c20ae07723bebd8664539b","_id":"annotations/60c20ae07723bebd8664539b","_rev":"_cfFmUPe---","document":{"$oid":"60c20ae07723bebd86645399"},"publisher":{"offsetStart":74,"normalizedForm":"SAS institute","offsetEnd":87,"rawForm":"SAS institute","boundingBoxes":[{"x":183.14525,"h":8.854000000000042,"y":589.474,"p":2,"w":49.20121363636363}]},"context":"Statistical analysis was performed using Matlab R2018a and Statview 5.0 (SAS institute).","type":"software","software-name":{"offsetStart":60,"normalizedForm":"Statview","offsetEnd":68,"rawForm":"Statview","boundingBoxes":[{"x":125.183,"h":8.854,"y":589.474,"p":2,"w":31.2075}]},"version":{"offsetStart":69,"normalizedForm":"5.0","offsetEnd":72,"rawForm":"5.0","boundingBoxes":[{"x":161.864,"h":8.854000000000042,"y":589.474,"p":2,"w":11.171999999999997}]}},
  {"_key":"60c20ae27723bebd8664539d","_id":"annotations/60c20ae27723bebd8664539d","_rev":"_cfFmUPq---","wikipediaExternalRef":34408890,"document":{"$oid":"60c20ae27723bebd8664539c"},"context":"After using WeChat to efficiently commu- nicate, the patient's son approved the use convalescent plasma therapy and authorized the clinician to sign the informed consent to ensure that the patient started treat- ment as soon as possible.","wikidataId":"Q283233","type":"software","confidence":0.7626,"software-name":{"wikipediaExternalRef":34408890,"normalizedForm":"WeChat","offsetStart":12,"wikidataId":"Q283233","offsetEnd":18,"lang":"en","confidence":0.7626,"rawForm":"WeChat","boundingBoxes":[{"x":425.71,"h":9.3201,"y":65.2346,"p":3,"w":33.3903}]},"lang":"en"},
  {"_key":"60c20ae57723bebd866453a6","_id":"annotations/60c20ae57723bebd866453a6","_rev":"_cfFmUPy---","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"ABGD was carried out using the online version of ABGD software [64]; https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html).","references":[{"offsetStart":15972,"normalizedForm":"[64]","refKey":62,"label":"[64]","reference_id":{"$oid":"60c20ae57723bebd8664539f"},"offsetEnd":15976,"boundingBoxes":[{"x":265.209,"h":8.5,"y":233.903,"p":5,"w":14.855999999999995}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"ABGD","offsetEnd":4,"rawForm":"ABGD","boundingBoxes":[{"x":358.355,"h":8.5,"y":220.921,"p":5,"w":27.15}]},"url":{"offsetStart":-34,"normalizedForm":"https://species.h-its.org/gmyc","offsetEnd":-4,"rawForm":"https://species.h-its.org/gmyc","boundingBoxes":[{"x":230.0826176470588,"h":8.5,"y":220.921,"p":5,"w":114.64852941176477}]}},
  {"_key":"60c20ae57723bebd866453a7","_id":"annotations/60c20ae57723bebd866453a7","_rev":"_cfFmUQ----","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"We used Tracer v. 1.6 [53] to ensure that effective sample size (ESS) values for all parameters were above 200 and to determine the burn-in.","references":[{"offsetStart":13353,"normalizedForm":"[53]","refKey":52,"label":"[53]","reference_id":{"$oid":"60c20ae57723bebd866453a0"},"offsetEnd":13358,"boundingBoxes":[{"x":411.932,"h":8.5,"y":494.294,"p":4,"w":15.839999999999975}]}],"type":"software","software-name":{"offsetStart":8,"normalizedForm":"Tracer","offsetEnd":14,"rawForm":"Tracer","boundingBoxes":[{"x":362.156,"h":8.5,"y":494.294,"p":4,"w":25.55}]},"version":{"offsetStart":18,"normalizedForm":"1.6","offsetEnd":21,"rawForm":"1.6","boundingBoxes":[{"x":398.439,"h":8.5,"y":494.294,"p":4,"w":11.46999999999997}]}},
  {"_key":"60c20ae57723bebd866453a8","_id":"annotations/60c20ae57723bebd866453a8","_rev":"_cfFmUQK---","wikipediaExternalRef":52292152,"document":{"$oid":"60c20ae57723bebd8664539e"},"context":"Sequences were aligned in Geneious V7.03 [44], using the MAFFT 7.313 [45] tool and the L-INS-i algorithm.","wikidataId":"Q4915084","type":"software","lang":"en","confidence":0.2365,"software-name":{"wikipediaExternalRef":52292152,"normalizedForm":"Geneious","offsetStart":27,"wikidataId":"Q4915084","offsetEnd":35,"lang":"en","confidence":0.2365,"rawForm":"Geneious","boundingBoxes":[{"x":200.012,"h":8.5,"y":181.916,"p":4,"w":37.71}]},"version":{"offsetStart":37,"normalizedForm":"7.03","offsetEnd":41,"rawForm":"7.03","boundingBoxes":[{"x":239.923,"h":8.5,"y":181.916,"p":4,"w":23.46999999999997}]}},
  {"_key":"60c20ae57723bebd866453a9","_id":"annotations/60c20ae57723bebd866453a9","_rev":"_cfFmUQW---","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"ABGD was carried out using the online version of ABGD software [64]; https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html).","references":[{"offsetStart":15972,"normalizedForm":"[64]","refKey":62,"label":"[64]","reference_id":{"$oid":"60c20ae57723bebd8664539f"},"offsetEnd":15976,"boundingBoxes":[{"x":265.209,"h":8.5,"y":233.903,"p":5,"w":14.855999999999995}]}],"type":"software","software-name":{"offsetStart":50,"normalizedForm":"ABGD","offsetEnd":54,"rawForm":"ABGD","boundingBoxes":[{"x":200.013,"h":8.5,"y":233.903,"p":5,"w":27.15}]},"url":{"offsetStart":70,"normalizedForm":"https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html","offsetEnd":122,"rawForm":"https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html","boundingBoxes":[{"x":286.015,"h":8.5,"y":233.903,"p":5,"w":216.65029629629635}]}},
  {"_key":"60c20ae57723bebd866453aa","_id":"annotations/60c20ae57723bebd866453aa","_rev":"_cfFmUQi---","wikipediaExternalRef":52292152,"document":{"$oid":"60c20ae57723bebd8664539e"},"context":"Sequence alignments were also inspected by eye in Geneious to confirm overall sequence quality.","wikidataId":"Q4915084","type":"software","lang":"en","confidence":0.2365,"software-name":{"wikipediaExternalRef":52292152,"normalizedForm":"Geneious","offsetStart":51,"wikidataId":"Q4915084","offsetEnd":59,"lang":"en","confidence":0.2365,"rawForm":"Geneious","boundingBoxes":[{"x":362.719,"h":8.5,"y":194.899,"p":4,"w":37.71}]},"version":{"offsetStart":37,"normalizedForm":"7.03","offsetEnd":41,"rawForm":"7.03","boundingBoxes":[{"x":239.923,"h":8.5,"y":181.916,"p":4,"w":23.46999999999997}]}},
  {"_key":"60c20ae57723bebd866453ab","_id":"annotations/60c20ae57723bebd866453ab","_rev":"_cfFmUQu---","wikipediaExternalRef":6793476,"document":{"$oid":"60c20ae57723bebd8664539e"},"context":"Sequences were aligned in Geneious V7.03 [44], using the MAFFT 7.313 [45] tool and the L-INS-i algorithm.","wikidataId":"Q6714151","references":[{"offsetStart":17646,"normalizedForm":"[45]","refKey":44,"label":"[45]","reference_id":{"$oid":"60c20ae57723bebd866453a1"},"offsetEnd":17651,"boundingBoxes":[{"x":258.122,"h":8.5,"y":467.874,"p":5,"w":16.319999999999993}]}],"type":"software","lang":"en","confidence":0.8157,"software-name":{"wikipediaExternalRef":6793476,"normalizedForm":"MAFFT","offsetStart":58,"wikidataId":"Q6714151","offsetEnd":63,"lang":"en","confidence":0.8157,"rawForm":"MAFFT","boundingBoxes":[{"x":324.962,"h":8.5,"y":181.916,"p":4,"w":32.42}]},"version":{"offsetStart":64,"normalizedForm":"7.313","offsetEnd":69,"rawForm":"7.313","boundingBoxes":[{"x":359.601,"h":8.5,"y":181.916,"p":4,"w":21.29000000000002}]}},
  {"_key":"60c20ae57723bebd866453ac","_id":"annotations/60c20ae57723bebd866453ac","_rev":"_cfFmUQ2---","document":{"$oid":"60c20ae57723bebd8664539e"},"type":"software","software-name":{"offsetStart":63,"normalizedForm":"GMYC","offsetEnd":67,"rawForm":"GMYC","boundingBoxes":[{"x":517.888,"h":8.5,"y":207.882,"p":5,"w":29.02}]},"context":"GMYC was performed using the single threshold parameter at the GMYC web- server (https://species.h-its.org/gmyc/)."},
  {"_key":"60c20ae57723bebd866453ad","_id":"annotations/60c20ae57723bebd866453ad","_rev":"_cfFmURC---","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"Trace logs and species trees for the two runs were combined using LogCombiner v 2.4.8 [52].","references":[{"offsetStart":13325,"normalizedForm":"[52]","refKey":51,"label":"[52]","reference_id":{"$oid":"60c20ae57723bebd866453a2"},"offsetEnd":13329,"boundingBoxes":[{"x":306.484,"h":8.5,"y":494.294,"p":4,"w":14.343999999999994}]}],"type":"software","software-name":{"offsetStart":67,"normalizedForm":"LogCombiner","offsetEnd":78,"rawForm":"LogCombiner","boundingBoxes":[{"x":223.089,"h":8.5,"y":494.294,"p":4,"w":54.51}]},"version":{"offsetStart":81,"normalizedForm":"2.4.8","offsetEnd":86,"rawForm":"2.4.8","boundingBoxes":[{"x":286.301,"h":8.5,"y":494.294,"p":4,"w":18.149999999999977}]}},
  {"_key":"60c20ae57723bebd866453ae","_id":"annotations/60c20ae57723bebd866453ae","_rev":"_cfFmURO---","wikipediaExternalRef":363695,"document":{"$oid":"60c20ae57723bebd8664539e"},"context":"However, we were not able to identify our specimens to species level from our BLAST search, given that only around 50% of our sequences matched existing data in the pub- lic databases, and most of these matches corresponded to genus and family level only.","wikidataId":"Q286820","type":"software","confidence":0.2888,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":79,"wikidataId":"Q286820","offsetEnd":84,"lang":"en","confidence":0.2888,"rawForm":"BLAST","boundingBoxes":[{"x":200.012,"h":8.5,"y":330.224,"p":6,"w":28.88}]},"lang":"en"},
  {"_key":"60c20ae57723bebd866453af","_id":"annotations/60c20ae57723bebd866453af","_rev":"_cfFmURa---","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"The best-fit model of nucleotide substitution for the dataset, selected using jModelTest 2.0 [49] based on the Bayesian Information Criterion, was GTR+I+G.","references":[{"offsetStart":12755,"normalizedForm":"[49]","refKey":48,"label":"[49]","reference_id":{"$oid":"60c20ae57723bebd866453a3"},"offsetEnd":12760,"boundingBoxes":[{"x":314.871,"h":8.5,"y":416.284,"p":4,"w":15.839999999999975}]}],"type":"software","software-name":{"offsetStart":79,"normalizedForm":"jModelTest","offsetEnd":89,"rawForm":"jModelTest","boundingBoxes":[{"x":255.287,"h":8.5,"y":416.284,"p":4,"w":44}]},"version":{"offsetStart":90,"normalizedForm":"2.0","offsetEnd":93,"rawForm":"2.0","boundingBoxes":[{"x":301.378,"h":8.5,"y":416.284,"p":4,"w":11.46999999999997}]}},
  {"_key":"60c20ae57723bebd866453b0","_id":"annotations/60c20ae57723bebd866453b0","_rev":"_cfFmURm---","document":{"$oid":"60c20ae57723bebd8664539e"},"type":"software","software-name":{"offsetStart":88,"normalizedForm":"L-INS-i","offsetEnd":95,"rawForm":"L-INS-i","boundingBoxes":[{"x":451.386,"h":8.5,"y":181.916,"p":4,"w":30.560000000000002}]},"context":"Sequences were aligned in Geneious V7.03 [44], using the MAFFT 7.313 [45] tool and the L-INS-i algorithm."},
  {"_key":"60c20ae57723bebd866453b1","_id":"annotations/60c20ae57723bebd866453b1","_rev":"_cfFmURu---","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"Default settings were used, however, distance matrices based on K2P distance calculated in MEGA7 were used as input.","references":[{"offsetStart":13798,"normalizedForm":"[56]","refKey":54,"label":"[56]","reference_id":{"$oid":"60c20ae57723bebd866453a4"},"offsetEnd":13803,"boundingBoxes":[{"x":401.33,"h":8.5,"y":559.321,"p":4,"w":16.319999999999993}]}],"type":"software","software-name":{"offsetStart":92,"normalizedForm":"MEGA","offsetEnd":96,"rawForm":"MEGA","boundingBoxes":[{"x":497.875,"h":8.5,"y":246.886,"p":5,"w":33.35}]},"version":{"offsetStart":134,"normalizedForm":"7.0","offsetEnd":137,"rawForm":"7.0","boundingBoxes":[{"x":387.327,"h":8.5,"y":559.321,"p":4,"w":11.79000000000002}]}},
  {"_key":"60c20ae57723bebd866453b2","_id":"annotations/60c20ae57723bebd866453b2","_rev":"_cfFmUR6---","wikipediaExternalRef":6793476,"document":{"$oid":"60c20ae57723bebd8664539e"},"context":"After adding these sequences to our dataset, we generated multiple sequence alignments with MAFFT 7.313 [45] using the L-INS-i algorithm in Geneious V7.03.","wikidataId":"Q6714151","references":[{"offsetStart":17646,"normalizedForm":"[45]","refKey":44,"label":"[45]","reference_id":{"$oid":"60c20ae57723bebd866453a1"},"offsetEnd":17651,"boundingBoxes":[{"x":258.122,"h":8.5,"y":467.874,"p":5,"w":16.319999999999993}]}],"type":"software","lang":"en","confidence":0.8157,"software-name":{"wikipediaExternalRef":6793476,"normalizedForm":"MAFFT","offsetStart":93,"wikidataId":"Q6714151","offsetEnd":98,"lang":"en","confidence":0.8157,"rawForm":"MAFFT","boundingBoxes":[{"x":200.013,"h":8.5,"y":467.874,"p":5,"w":32.42}]},"version":{"offsetStart":153,"normalizedForm":"03","offsetEnd":155,"rawForm":"03","boundingBoxes":[{"x":452.73900000000003,"h":8.5,"y":467.874,"p":5,"w":8.573333333333332}]}},
  {"_key":"60c20ae57723bebd866453b3","_id":"annotations/60c20ae57723bebd866453b3","_rev":"_cfFmUSG---","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"Sequence divergence was estimated using the Kimura-2-Parameter (K2P) model with 1000 bootstrap estimates in MEGA7.","references":[{"offsetStart":13798,"normalizedForm":"[56]","refKey":54,"label":"[56]","reference_id":{"$oid":"60c20ae57723bebd866453a4"},"offsetEnd":13803,"boundingBoxes":[{"x":401.33,"h":8.5,"y":559.321,"p":4,"w":16.319999999999993}]}],"type":"software","software-name":{"offsetStart":109,"normalizedForm":"MEGA","offsetEnd":113,"rawForm":"MEGA","boundingBoxes":[{"x":289.646,"h":8.5,"y":585.286,"p":4,"w":29.666666666666668}]},"version":{"offsetStart":113,"normalizedForm":"7","offsetEnd":114,"rawForm":"7","boundingBoxes":[{"x":289.646,"h":8.5,"y":585.286,"p":4,"w":29.666666666666668}]}},
  {"_key":"60c20ae57723bebd866453b4","_id":"annotations/60c20ae57723bebd866453b4","_rev":"_cfFmUSS---","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"We then assessed the diversity of \"molecular species\" by estimating molecular operational units (MOTUs; [55] using the software MEGA 7.0 [56] and the BOLD analyses tools [57].","references":[{"offsetStart":13798,"normalizedForm":"[56]","refKey":54,"label":"[56]","reference_id":{"$oid":"60c20ae57723bebd866453a4"},"offsetEnd":13803,"boundingBoxes":[{"x":401.33,"h":8.5,"y":559.321,"p":4,"w":16.319999999999993}]}],"type":"software","software-name":{"offsetStart":129,"normalizedForm":"MEGA","offsetEnd":133,"rawForm":"MEGA","boundingBoxes":[{"x":356.543,"h":8.5,"y":559.321,"p":4,"w":28.6}]},"version":{"offsetStart":134,"normalizedForm":"7.0","offsetEnd":137,"rawForm":"7.0","boundingBoxes":[{"x":387.327,"h":8.5,"y":559.321,"p":4,"w":11.79000000000002}]}},
  {"_key":"60c20ae57723bebd866453b5","_id":"annotations/60c20ae57723bebd866453b5","_rev":"_cfFmUSe---","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"Given that these analyses might be affected by variation in sampling size, we also used rarefaction and extrapolation methods [65,66] as implemented in the R package iNEXT [67].","references":[{"offsetStart":16743,"normalizedForm":"[67]","refKey":65,"label":"[67]","reference_id":{"$oid":"60c20ae57723bebd866453a5"},"offsetEnd":16747,"boundingBoxes":[{"x":391.69,"h":8.5,"y":337.878,"p":5,"w":14.663999999999987}]}],"type":"software","software-name":{"offsetStart":158,"normalizedForm":"R package iNEXT","offsetEnd":173,"rawForm":"R package iNEXT","boundingBoxes":[{"x":319.35,"h":8.5,"y":337.878,"p":5,"w":70.17599999999999}]}},
  {"_key":"60c20ae57723bebd866453b6","_id":"annotations/60c20ae57723bebd866453b6","_rev":"_cfFmUSq---","document":{"$oid":"60c20ae57723bebd8664539e"},"context":"Finally, output trees were summarized as maximum clade credibility (MCC) trees using mean node heights after dis- carding 25% of generations as burn-in using TreeAnnotator v1.8.4 [54].","type":"software","software-name":{"offsetStart":159,"normalizedForm":"TreeAnnotator","offsetEnd":172,"rawForm":"TreeAnnotator","boundingBoxes":[{"x":372.247,"h":8.5,"y":533.299,"p":4,"w":58.3}]},"version":{"offsetStart":174,"normalizedForm":"1.8.4","offsetEnd":179,"rawForm":"1.8.4","boundingBoxes":[{"x":432.624,"h":8.5,"y":533.299,"p":4,"w":22.529999999999973}]}},
  {"_key":"60c20ae77723bebd866453b8","_id":"annotations/60c20ae77723bebd866453b8","_rev":"_cfFmUSy---","document":{"$oid":"60c20ae77723bebd866453b7"},"context":"Statistical analysis was conducted using Graph Pad Prism 5 and SAS software version 9.3.","type":"software","software-name":{"offsetStart":41,"normalizedForm":"Graph Pad Prism","offsetEnd":57,"rawForm":"Graph \nPad Prism","boundingBoxes":[{"x":522.741,"h":7.5565,"y":696.7,"p":2,"w":21.811},{"x":298.498,"h":7.556500000000028,"y":706.836,"p":2,"w":34.807000000000016}]},"version":{"offsetStart":58,"normalizedForm":"5","offsetEnd":59,"rawForm":"5","boundingBoxes":[{"x":335.029,"h":7.5565,"y":706.836,"p":2,"w":4.08}]}},
  {"_key":"60c20ae77723bebd866453b9","_id":"annotations/60c20ae77723bebd866453b9","_rev":"_cfFmUT----","wikipediaExternalRef":990677,"document":{"$oid":"60c20ae77723bebd866453b7"},"context":"Statistical analysis was conducted using Graph Pad Prism 5 and SAS software version 9.3.","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4599,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":64,"wikidataId":"Q2003932","offsetEnd":67,"lang":"en","confidence":0.4599,"rawForm":"SAS","boundingBoxes":[{"x":355.393,"h":7.5565,"y":706.836,"p":2,"w":13.5745}]},"version":{"offsetStart":85,"normalizedForm":"9.3","offsetEnd":88,"rawForm":"9.3","boundingBoxes":[{"x":427.734,"h":7.556500000000028,"y":706.836,"p":2,"w":9.180000000000007}]}},
  {"_key":"60c20aeb7723bebd866453bb","_id":"annotations/60c20aeb7723bebd866453bb","_rev":"_cfFmUTK---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20aeb7723bebd866453ba"},"context":"Data were analyzed using Stata ver.11.0. 90) can increase the risk of COVID19 mortality.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":25,"wikidataId":"Q1204300","offsetEnd":30,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":448.519,"h":9.6835,"y":417.243,"p":1,"w":19.7472}]},"version":{"offsetStart":35,"normalizedForm":"11.0. 90","offsetEnd":44,"rawForm":"11.0. \n90","boundingBoxes":[{"x":486.1954222222222,"h":9.683499999999981,"y":417.243,"p":1,"w":19.0842777777778},{"x":229.79809999999998,"h":9.6835,"y":464.523,"p":1,"w":8.093133333333332}]}},
  {"_key":"60c20aeb7723bebd866453bc","_id":"annotations/60c20aeb7723bebd866453bc","_rev":"_cfFmUTW---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20aeb7723bebd866453ba"},"context":"The data were analyzed using Stata version 11.0.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":29,"wikidataId":"Q1204300","offsetEnd":34,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":468.418,"h":11.004,"y":695.208,"p":2,"w":22.5}]},"version":{"offsetStart":43,"normalizedForm":"11.0","offsetEnd":47,"rawForm":"11.0","boundingBoxes":[{"x":533.05,"h":11.004000000000019,"y":695.208,"p":2,"w":17.740800000000036}]}},
  {"_key":"60c20aed7723bebd866453be","_id":"annotations/60c20aed7723bebd866453be","_rev":"_cfFmUTi---","document":{"$oid":"60c20aed7723bebd866453bd"},"publisher":{"offsetStart":87,"normalizedForm":"The Mathworks Inc","offsetEnd":104,"rawForm":"The Mathworks Inc","boundingBoxes":[{"x":140.3863,"h":7.539799999999985,"y":234.131,"p":3,"w":69.28775999999999}]},"context":"Raw electromyographic signals were processed through custom MatLabÔ Ver 7.1 programs (The Mathworks Inc., Natick, MA, USA).","type":"software","software-name":{"offsetStart":61,"normalizedForm":"MatLabÔ","offsetEnd":68,"rawForm":"MatLabÔ","boundingBoxes":[{"x":32.8144,"h":7.5398,"y":234.131,"p":3,"w":35.2854}]},"version":{"offsetStart":73,"normalizedForm":"7.1","offsetEnd":76,"rawForm":"7.1","boundingBoxes":[{"x":85.5974,"h":7.539799999999985,"y":234.131,"p":3,"w":10.062600000000003}]}},
  {"_key":"60c20aed7723bebd866453bf","_id":"annotations/60c20aed7723bebd866453bf","_rev":"_cfFmUTu---","document":{"$oid":"60c20aed7723bebd866453bd"},"publisher":{"offsetStart":155,"normalizedForm":"The Mathworks Inc","offsetEnd":172,"rawForm":"The Mathworks Inc","boundingBoxes":[{"x":203.76330000000002,"h":7.539800000000014,"y":673.507,"p":3,"w":74.04476}]},"context":"Principal component analysis (PCA) was used to capture amplitude and temporal electromyographic waveform features using custom MatLabÔ Ver.7.1 programs (The Mathworks Inc., Natick, Massachusetts, USA).","type":"software","software-name":{"offsetStart":129,"normalizedForm":"MatLabÔ","offsetEnd":136,"rawForm":"MatLabÔ","boundingBoxes":[{"x":89.95,"h":7.5398,"y":673.507,"p":3,"w":35.2357}]},"version":{"offsetStart":141,"normalizedForm":"7.1","offsetEnd":144,"rawForm":"7.1","boundingBoxes":[{"x":143.82874285714286,"h":7.539800000000014,"y":673.507,"p":3,"w":10.557557142857178}]}},
  {"_key":"60c20af57723bebd866453c1","_id":"annotations/60c20af57723bebd866453c1","_rev":"_cfFmUT6---","document":{"$oid":"60c20af57723bebd866453c0"},"context":"CGenFF 16 software  was used to assist in the production of the needed topology files.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"CGenFF","offsetEnd":6,"rawForm":"CGenFF","boundingBoxes":[{"x":438.73,"h":10.4847,"y":484.823,"p":6,"w":44.6252}]},"version":{"offsetStart":7,"normalizedForm":"16","offsetEnd":9,"rawForm":"16","boundingBoxes":[{"x":484.351,"h":6.9898,"y":483.207,"p":6,"w":8.469}]}},
  {"_key":"60c20af57723bebd866453c2","_id":"annotations/60c20af57723bebd866453c2","_rev":"_cfFmUUG---","wikipediaExternalRef":306767,"document":{"$oid":"60c20af57723bebd866453c0"},"context":"We used NAMD 2 version 2.13 with CHARMM Force Field 3 version 36 for lipids, and TIP3P 4  for water molecules.","wikidataId":"Q2078655","type":"software","lang":"en","confidence":0.8178,"software-name":{"wikipediaExternalRef":306767,"normalizedForm":"NAMD","offsetStart":8,"wikidataId":"Q2078655","offsetEnd":12,"lang":"en","confidence":0.8178,"rawForm":"NAMD","boundingBoxes":[{"x":116.803,"h":10.4847,"y":481.356,"p":4,"w":37.2165}]},"version":{"offsetStart":23,"normalizedForm":"2.13","offsetEnd":27,"rawForm":"2.13","boundingBoxes":[{"x":201.3,"h":10.484699999999975,"y":481.356,"p":4,"w":20.8116}]}},
  {"_key":"60c20af57723bebd866453c3","_id":"annotations/60c20af57723bebd866453c3","_rev":"_cfFmUUS---","document":{"$oid":"60c20af57723bebd866453c0"},"context":"We used NAMD 2 version 2.13 with CHARMM Force Field 3 version 36 for lipids, and TIP3P 4  for water molecules.","type":"software","software-name":{"offsetStart":33,"normalizedForm":"CHARMM Force","offsetEnd":45,"rawForm":"CHARMM Force","boundingBoxes":[{"x":250.589,"h":10.484699999999975,"y":481.356,"p":4,"w":86.41159999999996}]},"version":{"offsetStart":52,"normalizedForm":"3","offsetEnd":53,"rawForm":"3","boundingBoxes":[{"x":366.701,"h":6.9898,"y":479.74,"p":4,"w":4.2345}]}},
  {"_key":"60c20af57723bebd866453c4","_id":"annotations/60c20af57723bebd866453c4","_rev":"_cfFmUUi---","document":{"$oid":"60c20af57723bebd866453c0"},"type":"software","software-name":{"offsetStart":76,"normalizedForm":"CHARMM-GUI","offsetEnd":88,"rawForm":"CHARMM-GUI","boundingBoxes":[{"x":457.839,"h":10.484699999999975,"y":379.412,"p":5,"w":82.15730000000002}]},"context":"The lipids, protein, water molecules, and ions were initially placed by the CHARMM-GUI  membrane builder. 12"},
  {"_key":"60c20af57723bebd866453c5","_id":"annotations/60c20af57723bebd866453c5","_rev":"_cfFmUU6---","document":{"$oid":"60c20af57723bebd866453c0"},"type":"software","software-name":{"offsetStart":256,"normalizedForm":"TASSER","offsetEnd":262,"rawForm":"TASSER","boundingBoxes":[{"x":451.41116,"h":10.4847,"y":624.803,"p":5,"w":39.79073999999999}]},"context":"The main structure (residues 27 to 1146) of the spike protein can be found in the protein data  bank #6VSB, based on the cryo-EM structure of Wrapp et al. 13 The secondary structure  of residue 1146 to 1273 was instead based on the prediction of the C-I-TASSER model. 14"},
  {"_key":"60c20b017723bebd866453c7","_id":"annotations/60c20b017723bebd866453c7","_rev":"_cfFmUVS---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20b017723bebd866453c6"},"context":"Our empirical analysis was performed using Stata 16.1 software.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":43,"wikidataId":"Q1204300","offsetEnd":48,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":317.204,"h":10.908,"y":239.504,"p":8,"w":24.036}]},"version":{"offsetStart":49,"normalizedForm":"16.1","offsetEnd":53,"rawForm":"16.1","boundingBoxes":[{"x":344.192,"h":10.907999999999987,"y":239.504,"p":8,"w":21}]}},
  {"_key":"60c20b047723bebd866453c9","_id":"annotations/60c20b047723bebd866453c9","_rev":"_cfFmUVm---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b047723bebd866453c8"},"publisher":{"offsetStart":53,"normalizedForm":"IBM Corp","offsetEnd":61,"rawForm":"IBM Corp","boundingBoxes":[{"x":139.108,"h":10.593000000000018,"y":340.673,"p":3,"w":41.6438}]},"context":"Data analysis was performed using SPSS (Version 22, IBM Corp, New York, U.S.A.).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":35,"wikidataId":"Q181596","offsetEnd":39,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":53.8583,"h":10.593,"y":340.673,"p":3,"w":23.87}]},"version":{"offsetStart":49,"normalizedForm":"22","offsetEnd":51,"rawForm":"22","boundingBoxes":[{"x":121.772,"h":10.593,"y":340.673,"p":3,"w":9.379333333333333}]}},
  {"_key":"60c20b057723bebd866453cb","_id":"annotations/60c20b057723bebd866453cb","_rev":"_cfFmUV6---","wikipediaExternalRef":23862,"document":{"$oid":"60c20b057723bebd866453ca"},"context":"Python library 2 was used to run the Apriori algorithm, and PSO-GES was exe- cuted with the author's proprietary code 3 .","wikidataId":"Q28865","type":"software","confidence":0.6138,"software-name":{"wikipediaExternalRef":23862,"normalizedForm":"Python","offsetStart":0,"wikidataId":"Q28865","offsetEnd":6,"lang":"en","confidence":0.6138,"rawForm":"Python","boundingBoxes":[{"x":39.4016,"h":8.9365,"y":457.717,"p":6,"w":31.975}]},"lang":"en"},
  {"_key":"60c20b067723bebd866453cd","_id":"annotations/60c20b067723bebd866453cd","_rev":"_cfFmUWa---","wikipediaExternalRef":2079997,"document":{"$oid":"60c20b067723bebd866453cc"},"publisher":{"offsetStart":33,"normalizedForm":"StatSoft Inc","offsetEnd":45,"rawForm":"StatSoft Inc","boundingBoxes":[{"x":482.9530888888889,"h":8.976699999999994,"y":160.753,"p":3,"w":48.62163111111107}]},"context":"STATISTICA program version 13.1 (StatSoft Inc., Tolusa, USA) was used for statistical analyses.","wikidataId":"Q1788435","type":"software","lang":"en","confidence":0.372,"software-name":{"wikipediaExternalRef":2079997,"normalizedForm":"STATISTICA","offsetStart":0,"wikidataId":"Q1788435","offsetEnd":10,"lang":"en","confidence":0.372,"rawForm":"STATISTICA","boundingBoxes":[{"x":312.718,"h":8.9767,"y":160.753,"p":3,"w":56.7718}]},"version":{"offsetStart":27,"normalizedForm":"13.1","offsetEnd":31,"rawForm":"13.1","boundingBoxes":[{"x":455.131,"h":8.976699999999994,"y":160.753,"p":3,"w":16.83620000000002}]}},
  {"_key":"60c20b0b7723bebd866453cf","_id":"annotations/60c20b0b7723bebd866453cf","_rev":"_cfFmUW6---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b0b7723bebd866453ce"},"publisher":{"offsetStart":34,"normalizedForm":"IBM Corporation","offsetEnd":49,"rawForm":"IBM Corporation","boundingBoxes":[{"x":334.43,"h":8.5,"y":173.357,"p":4,"w":68.12866666666662}]},"context":"Data was exported to SPSS (v. 26, IBM Corporation, Armonk, USA) and cleared of all incom- plete data sets; Data from emailed or mailed questionnaires were added manually to the data file, which was then analyzed in SPSS or exported for analysis to GraphPad Prism 8.2.1 (GraphPad Software, San Diego, CA, USA) and STATA v 16 (StataCorp, College Station, TX, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7466,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":21,"wikidataId":"Q181596","offsetEnd":25,"lang":"en","confidence":0.7466,"rawForm":"SPSS","boundingBoxes":[{"x":286.014,"h":8.5,"y":173.357,"p":4,"w":19.87}]},"version":{"offsetStart":30,"normalizedForm":"26","offsetEnd":32,"rawForm":"26","boundingBoxes":[{"x":320.483,"h":8.5,"y":173.357,"p":4,"w":7.859999999999999}]}},
  {"_key":"60c20b0b7723bebd866453d0","_id":"annotations/60c20b0b7723bebd866453d0","_rev":"_cfFmUXO---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b0b7723bebd866453ce"},"publisher":{"offsetStart":34,"normalizedForm":"IBM Corporation","offsetEnd":49,"rawForm":"IBM Corporation","boundingBoxes":[{"x":334.43,"h":8.5,"y":173.357,"p":4,"w":68.12866666666662}]},"context":"Data was exported to SPSS (v. 26, IBM Corporation, Armonk, USA) and cleared of all incom- plete data sets; Data from emailed or mailed questionnaires were added manually to the data file, which was then analyzed in SPSS or exported for analysis to GraphPad Prism 8.2.1 (GraphPad Software, San Diego, CA, USA) and STATA v 16 (StataCorp, College Station, TX, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7466,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":216,"wikidataId":"Q181596","offsetEnd":220,"lang":"en","confidence":0.7466,"rawForm":"SPSS","boundingBoxes":[{"x":327.74,"h":8.5,"y":199.378,"p":4,"w":19.87}]},"version":{"offsetStart":30,"normalizedForm":"26","offsetEnd":32,"rawForm":"26","boundingBoxes":[{"x":320.483,"h":8.5,"y":173.357,"p":4,"w":7.859999999999999}]}},
  {"_key":"60c20b0b7723bebd866453d1","_id":"annotations/60c20b0b7723bebd866453d1","_rev":"_cfFmUXe---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b0b7723bebd866453ce"},"publisher":{"offsetStart":34,"normalizedForm":"IBM Corporation","offsetEnd":49,"rawForm":"IBM Corporation","boundingBoxes":[{"x":334.43,"h":8.5,"y":173.357,"p":4,"w":68.12866666666662}]},"context":"Additionally, we performed a factor analysis including Kaiser-Meyer-Olkin's criteria (KMO) for sampling adequacy, to confirm the validity of our indices, and tested for co-linearity among the profile variables (both SPSS).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":218,"wikidataId":"Q181596","offsetEnd":222,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":334.203,"h":8.5,"y":437.828,"p":4,"w":17.006666666666668}]},"version":{"offsetStart":30,"normalizedForm":"26","offsetEnd":32,"rawForm":"26","boundingBoxes":[{"x":320.483,"h":8.5,"y":173.357,"p":4,"w":7.859999999999999}]}},
  {"_key":"60c20b0b7723bebd866453d2","_id":"annotations/60c20b0b7723bebd866453d2","_rev":"_cfFmUXy---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20b0b7723bebd866453ce"},"publisher":{"offsetStart":272,"normalizedForm":"GraphPad Software","offsetEnd":289,"rawForm":"GraphPad Software","boundingBoxes":[{"x":204.92533333333333,"h":8.5,"y":212.361,"p":4,"w":74.451}]},"context":"We conducted a correlation matrix analysis cal- culating Spearman's R, first among the index questions and the result of the calculated indices, then with the profile questions against each other and the indices (all in GraphPad Prism).","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":221,"wikidataId":"Q5597066","offsetEnd":235,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":485.118,"h":8.5,"y":398.823,"p":4,"w":64.09414285714291}]},"version":{"offsetStart":264,"normalizedForm":"8.2.1","offsetEnd":269,"rawForm":"8.2.1","boundingBoxes":[{"x":524.746,"h":8.5,"y":199.378,"p":4,"w":18.790000000000077}]}},
  {"_key":"60c20b0b7723bebd866453d3","_id":"annotations/60c20b0b7723bebd866453d3","_rev":"_cfFmUYC---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20b0b7723bebd866453ce"},"publisher":{"offsetStart":272,"normalizedForm":"GraphPad Software","offsetEnd":289,"rawForm":"GraphPad Software","boundingBoxes":[{"x":204.92533333333333,"h":8.5,"y":212.361,"p":4,"w":74.451}]},"context":"Data was exported to SPSS (v. 26, IBM Corporation, Armonk, USA) and cleared of all incom- plete data sets; Data from emailed or mailed questionnaires were added manually to the data file, which was then analyzed in SPSS or exported for analysis to GraphPad Prism 8.2.1 (GraphPad Software, San Diego, CA, USA) and STATA v 16 (StataCorp, College Station, TX, USA).","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":249,"wikidataId":"Q5597066","offsetEnd":263,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":455.695,"h":8.5,"y":199.378,"p":4,"w":66.85600000000005}]},"version":{"offsetStart":264,"normalizedForm":"8.2.1","offsetEnd":269,"rawForm":"8.2.1","boundingBoxes":[{"x":524.746,"h":8.5,"y":199.378,"p":4,"w":18.790000000000077}]}},
  {"_key":"60c20b0b7723bebd866453d4","_id":"annotations/60c20b0b7723bebd866453d4","_rev":"_cfFmUYW---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20b0b7723bebd866453ce"},"publisher":{"offsetStart":327,"normalizedForm":"StataCorp","offsetEnd":336,"rawForm":"StataCorp","boundingBoxes":[{"x":446.2344545454545,"h":8.5,"y":212.361,"p":4,"w":37.30909090909091}]},"context":"Data was exported to SPSS (v. 26, IBM Corporation, Armonk, USA) and cleared of all incom- plete data sets; Data from emailed or mailed questionnaires were added manually to the data file, which was then analyzed in SPSS or exported for analysis to GraphPad Prism 8.2.1 (GraphPad Software, San Diego, CA, USA) and STATA v 16 (StataCorp, College Station, TX, USA).","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7652,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"STATA","offsetStart":315,"wikidataId":"Q1204300","offsetEnd":320,"lang":"en","confidence":0.7652,"rawForm":"STATA","boundingBoxes":[{"x":390.725,"h":8.5,"y":212.361,"p":4,"w":30.65}]},"version":{"offsetStart":323,"normalizedForm":"16","offsetEnd":325,"rawForm":"16","boundingBoxes":[{"x":430.353,"h":8.5,"y":212.361,"p":4,"w":9.54}]}},
  {"_key":"60c20b127723bebd866453d6","_id":"annotations/60c20b127723bebd866453d6","_rev":"_cfFmUYy---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20b127723bebd866453d5"},"publisher":{"offsetStart":41,"normalizedForm":"StataCorp","offsetEnd":50,"rawForm":"StataCorp","boundingBoxes":[{"x":311.01835,"h":8.5499,"y":635.933,"p":6,"w":34.76115}]},"context":"Analysis was performed using STATA 13.1 (StataCorp), and R v 3.5.1 (R Core Team (2017).","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7652,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"STATA","offsetStart":29,"wikidataId":"Q1204300","offsetEnd":34,"lang":"en","confidence":0.7652,"rawForm":"STATA","boundingBoxes":[{"x":255.496,"h":8.5499,"y":635.933,"p":6,"w":30.2595}]},"version":{"offsetStart":35,"normalizedForm":"13.1","offsetEnd":39,"rawForm":"13.1","boundingBoxes":[{"x":287.896,"h":8.54989999999998,"y":635.933,"p":6,"w":16.629899999999964}]}},
  {"_key":"60c20b167723bebd866453d8","_id":"annotations/60c20b167723bebd866453d8","_rev":"_cfFmUZK---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b167723bebd866453d7"},"publisher":{"offsetStart":80,"normalizedForm":"SPSS","offsetEnd":84,"rawForm":"SPSS","boundingBoxes":[{"x":536.802,"h":9.584,"y":173.996,"p":4,"w":18.97216}]},"context":"Statistical analyses were performed using SPSS (SPSS for Windows, version 26.0, SPSS, Chicago, IL, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7435,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":42,"wikidataId":"Q181596","offsetEnd":46,"lang":"en","confidence":0.7435,"rawForm":"SPSS","boundingBoxes":[{"x":369.37,"h":9.584,"y":173.996,"p":4,"w":21.2743}]},"version":{"offsetStart":74,"normalizedForm":"26.0","offsetEnd":78,"rawForm":"26.0","boundingBoxes":[{"x":514.942,"h":9.584000000000003,"y":173.996,"p":4,"w":15.621359999999981}]}},
  {"_key":"60c20b167723bebd866453d9","_id":"annotations/60c20b167723bebd866453d9","_rev":"_cfFmUZe---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b167723bebd866453d7"},"publisher":{"offsetStart":80,"normalizedForm":"SPSS","offsetEnd":84,"rawForm":"SPSS","boundingBoxes":[{"x":536.802,"h":9.584,"y":173.996,"p":4,"w":18.97216}]},"context":"Statistical analyses were performed using SPSS (SPSS for Windows, version 26.0, SPSS, Chicago, IL, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7435,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":48,"wikidataId":"Q181596","offsetEnd":52,"lang":"en","confidence":0.7435,"rawForm":"SPSS","boundingBoxes":[{"x":397.8541,"h":9.584,"y":173.996,"p":4,"w":19.620400000000004}]},"version":{"offsetStart":74,"normalizedForm":"26.0","offsetEnd":78,"rawForm":"26.0","boundingBoxes":[{"x":514.942,"h":9.584000000000003,"y":173.996,"p":4,"w":15.621359999999981}]}},
  {"_key":"60c20b1e7723bebd866453db","_id":"annotations/60c20b1e7723bebd866453db","_rev":"_cfFmUZu---","wikipediaExternalRef":990677,"document":{"$oid":"60c20b1e7723bebd866453da"},"publisher":{"offsetStart":54,"normalizedForm":"SAS Institute Inc","offsetEnd":71,"rawForm":"SAS Institute Inc","boundingBoxes":[{"x":392.74725,"h":9.099000000000046,"y":569.64,"p":3,"w":55.81482999999997}]},"context":"Statistical analyses were performed using SAS v. 9.4 (SAS Institute Inc., Cary, NC, USA) and R 3.3.1 (R Foundation for Statistical Computing, Vienna, Austria).","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":42,"wikidataId":"Q2003932","offsetEnd":45,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":352.414,"h":9.099,"y":569.64,"p":3,"w":14.6709}]},"version":{"offsetStart":49,"normalizedForm":"9.4","offsetEnd":52,"rawForm":"9.4","boundingBoxes":[{"x":375.987,"h":9.099000000000046,"y":569.64,"p":3,"w":10.637999999999977}]}},
  {"_key":"60c20b207723bebd866453dd","_id":"annotations/60c20b207723bebd866453dd","_rev":"_cfFmUa----","document":{"$oid":"60c20b207723bebd866453dc"},"context":"The analyses were conducted using DISMO package version Rv3.4.0.","type":"software","software-name":{"offsetStart":34,"normalizedForm":"DISMO","offsetEnd":39,"rawForm":"DISMO","boundingBoxes":[{"x":377.685,"h":9.24,"y":641.658,"p":6,"w":31.88}]},"version":{"offsetStart":57,"normalizedForm":"Rv","offsetEnd":59,"rawForm":"Rv","boundingBoxes":[{"x":81.6368,"h":9.24,"y":653.677,"p":6,"w":12.03}]}},
  {"_key":"60c20b257723bebd866453df","_id":"annotations/60c20b257723bebd866453df","_rev":"_cfFmUaK---","wikipediaExternalRef":990677,"document":{"$oid":"60c20b257723bebd866453de"},"publisher":{"offsetStart":18,"normalizedForm":"SAS Institute","offsetEnd":31,"rawForm":"SAS Institute","boundingBoxes":[{"x":230.171,"h":8.519999999999982,"y":313.361,"p":3,"w":51.15300000000002}]},"context":"SAS 9.4 software (SAS Institute, Cary, NC) was used for all analyses.","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":0,"wikidataId":"Q2003932","offsetEnd":3,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":150.812,"h":8.52,"y":313.361,"p":3,"w":16}]},"version":{"offsetStart":4,"normalizedForm":"9.4","offsetEnd":7,"rawForm":"9.4","boundingBoxes":[{"x":169.965,"h":8.519999999999982,"y":313.361,"p":3,"w":12.599999999999994}]}},
  {"_key":"60c20b287723bebd866453e7","_id":"annotations/60c20b287723bebd866453e7","_rev":"_cfFmUaa---","document":{"$oid":"60c20b287723bebd866453e0"},"context":", X!Tandem Vengeance (2015.12.15.2) 34 and MS-GF+ release  (v2018.04.09) 35 .","references":[{"offsetStart":22108,"normalizedForm":"34","refKey":35,"label":"34","reference_id":{"$oid":"60c20b287723bebd866453e1"},"offsetEnd":22111,"boundingBoxes":[{"x":403.39,"h":7.668,"y":266.75,"p":10,"w":8.58}]}],"type":"software","software-name":{"offsetStart":2,"normalizedForm":"X!Tandem Vengeance","offsetEnd":20,"rawForm":"X!Tandem Vengeance","boundingBoxes":[{"x":186.89,"h":11.663999999999987,"y":268.278,"p":10,"w":126.65200000000004}]},"version":{"offsetStart":22,"normalizedForm":"2015.12.15.2","offsetEnd":34,"rawForm":"2015.12.15.2","boundingBoxes":[{"x":331.98685714285716,"h":11.663999999999987,"y":268.278,"p":10,"w":65.81828571428571}]}},
  {"_key":"60c20b287723bebd866453e8","_id":"annotations/60c20b287723bebd866453e8","_rev":"_cfFmUam---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The SearchGUI package yielded no gain in determining the missing protein  HSBP1L1 and other proteins listed in Table 1.","references":[{"offsetStart":58604,"normalizedForm":"30","refKey":31,"label":"30","reference_id":{"$oid":"60c20b287723bebd866453e2"},"offsetEnd":58607,"boundingBoxes":[{"x":143.42,"h":7.668,"y":483.61,"p":25,"w":8.58}]}],"type":"software","software-name":{"offsetStart":4,"normalizedForm":"SearchGUI","offsetEnd":13,"rawForm":"SearchGUI","boundingBoxes":[{"x":147.609,"h":11.664,"y":290.718,"p":27,"w":58.4107}]}},
  {"_key":"60c20b287723bebd866453e9","_id":"annotations/60c20b287723bebd866453e9","_rev":"_cfFmUa2---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":5,"normalizedForm":"identyPROT","offsetEnd":15,"rawForm":"identyPROT","boundingBoxes":[{"x":153.233,"h":11.664,"y":470.138,"p":27,"w":65.6165}]},"context":"With identyPROT search engine 37 the two hits were observed in the APMS  dataset 54 obtained after fishing of proteins with the protein of coronavirus."},
  {"_key":"60c20b287723bebd866453ea","_id":"annotations/60c20b287723bebd866453ea","_rev":"_cfFmUbC---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The  MaxQuant search engine identified this peptide in the LNCaP cell line only by merging  several spectra (\"matching between runs\" option in MaxQuant) 32 .","type":"software","software-name":{"offsetStart":6,"normalizedForm":"MaxQuant","offsetEnd":14,"rawForm":"MaxQuant","boundingBoxes":[{"x":85.104,"h":11.664,"y":88.8483,"p":26,"w":55.4199}]},"version":{"offsetStart":106,"normalizedForm":"1.5.3.31","offsetEnd":114,"rawForm":"1.5.3.31","boundingBoxes":[{"x":467.452,"h":11.663999999999987,"y":597.248,"p":25,"w":42.11999999999995}]}},
  {"_key":"60c20b287723bebd866453eb","_id":"annotations/60c20b287723bebd866453eb","_rev":"_cfFmUbS---","wikipediaExternalRef":2039930,"document":{"$oid":"60c20b287723bebd866453e0"},"context":"assembly (Ensembl release  97) was used as a reference.","wikidataId":"Q1344256","type":"software","lang":"en","confidence":0.7496,"software-name":{"wikipediaExternalRef":2039930,"normalizedForm":"Ensembl","offsetStart":10,"wikidataId":"Q1344256","offsetEnd":17,"lang":"en","confidence":0.7496,"rawForm":"Ensembl","boundingBoxes":[{"x":468.9060375,"h":11.664,"y":537.458,"p":8,"w":43.568262499999996}]},"version":{"offsetStart":28,"normalizedForm":"97","offsetEnd":30,"rawForm":"97","boundingBoxes":[{"x":85.104,"h":11.664,"y":559.778,"p":8,"w":11.517133333333334}]}},
  {"_key":"60c20b287723bebd866453ec","_id":"annotations/60c20b287723bebd866453ec","_rev":"_cfFmUbe---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":13,"normalizedForm":"LAST","offsetEnd":17,"rawForm":"LAST","boundingBoxes":[{"x":157.22,"h":11.664,"y":178.608,"p":17,"w":32.5037}]},"context":"Although the LAST and BWA algorithms (originally developed for the mapping of short  reads 49,50 ) were also employed for ONT data processing 23 , the minimap2 tool 51 is  nowadays widely used for long noisy read mapping."},
  {"_key":"60c20b287723bebd866453ed","_id":"annotations/60c20b287723bebd866453ed","_rev":"_cfFmUbq---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":22,"normalizedForm":"BWA","offsetEnd":25,"rawForm":"BWA","boundingBoxes":[{"x":215.838,"h":11.664,"y":178.608,"p":17,"w":30.2228}]},"context":"Although the LAST and BWA algorithms (originally developed for the mapping of short  reads 49,50 ) were also employed for ONT data processing 23 , the minimap2 tool 51 is  nowadays widely used for long noisy read mapping."},
  {"_key":"60c20b287723bebd866453ee","_id":"annotations/60c20b287723bebd866453ee","_rev":"_cfFmUb6---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":28,"normalizedForm":"NextProt","offsetEnd":36,"rawForm":"NextProt","boundingBoxes":[{"x":324.975,"h":11.664,"y":739.204,"p":12,"w":44.47875555555556}]},"context":"In the July 2020 version of NextProt, this protein was transferred from  the PE2 (e.g."},
  {"_key":"60c20b287723bebd866453ef","_id":"annotations/60c20b287723bebd866453ef","_rev":"_cfFmUcG---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The search was conducted using SearchGUI.","references":[{"offsetStart":58604,"normalizedForm":"30","refKey":31,"label":"30","reference_id":{"$oid":"60c20b287723bebd866453e2"},"offsetEnd":58607,"boundingBoxes":[{"x":143.42,"h":7.668,"y":483.61,"p":25,"w":8.58}]}],"type":"software","software-name":{"offsetStart":31,"normalizedForm":"SearchGUI","offsetEnd":40,"rawForm":"SearchGUI","boundingBoxes":[{"x":350.948,"h":11.664,"y":290.718,"p":10,"w":55.48563}]}},
  {"_key":"60c20b287723bebd866453f0","_id":"annotations/60c20b287723bebd866453f0","_rev":"_cfFmUcS---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"In summary with other data from MaxQuant, the  evidence of only the peptides of the first half of HSBP1L1 sequence were visible in  several datasets and absent from the second half of the sequence, could indicate, that not  the full-length protein, but the nonsense mediated decay product of HSBP1L1 (K7ENV5)  was expressed, comprising only 45 a.a.r.","type":"software","software-name":{"offsetStart":32,"normalizedForm":"MaxQuant","offsetEnd":40,"rawForm":"MaxQuant","boundingBoxes":[{"x":469.932,"h":11.664,"y":649.568,"p":27,"w":52.25724444444444}]},"version":{"offsetStart":106,"normalizedForm":"1.5.3.31","offsetEnd":114,"rawForm":"1.5.3.31","boundingBoxes":[{"x":467.452,"h":11.663999999999987,"y":597.248,"p":25,"w":42.11999999999995}]}},
  {"_key":"60c20b287723bebd866453f1","_id":"annotations/60c20b287723bebd866453f1","_rev":"_cfFmUci---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":41,"normalizedForm":"FastQC","offsetEnd":47,"rawForm":"FastQC","boundingBoxes":[{"x":352.691,"h":11.664,"y":447.698,"p":8,"w":39.7094}]},"context":"The derived fastq files were analyzed by FastQC and then were processed by  Trimmomatic."},
  {"_key":"60c20b287723bebd866453f2","_id":"annotations/60c20b287723bebd866453f2","_rev":"_cfFmUcu---","document":{"$oid":"60c20b287723bebd866453e0"},"context":", X!Tandem Vengeance (2015.12.15.2) 34 and MS-GF+ release  (v2018.04.09) 35 .","references":[{"offsetStart":22146,"normalizedForm":"35","refKey":36,"label":"35","reference_id":{"$oid":"60c20b287723bebd866453e3"},"offsetEnd":22149,"boundingBoxes":[{"x":158.66,"h":7.668,"y":289.19,"p":10,"w":8.58}]}],"type":"software","software-name":{"offsetStart":43,"normalizedForm":"MS-GF","offsetEnd":48,"rawForm":"MS-GF","boundingBoxes":[{"x":456.444,"h":11.663999999999987,"y":268.278,"p":10,"w":47.03139999999996}]},"version":{"offsetStart":62,"normalizedForm":"2018.04.09","offsetEnd":72,"rawForm":"2018.04.09","boundingBoxes":[{"x":90.76153846153846,"h":11.663999999999987,"y":290.718,"p":10,"w":62.2329230769231}]}},
  {"_key":"60c20b287723bebd866453f3","_id":"annotations/60c20b287723bebd866453f3","_rev":"_cfFmUc6---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":47,"normalizedForm":"STAR- RSEM","offsetEnd":58,"rawForm":"STAR-\n\nRSEM","boundingBoxes":[{"x":514.676,"h":11.663999999999987,"y":559.778,"p":8,"w":37.91949999999997},{"x":85.104,"h":11.664,"y":582.248,"p":8,"w":30.82408}]},"context":"Finally, we compared the results obtained with STAR- RSEM, bowtie2-RSEM and Salmon, calculated the Spearman/Pearson correlation  coefficients and created clustering dendrograms."},
  {"_key":"60c20b287723bebd866453f4","_id":"annotations/60c20b287723bebd866453f4","_rev":"_cfFmUdK---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"Quite similar results were observed  when using MaxQuant of the version 1.6.12.0 (as compared to version 1.5.3.31","type":"software","software-name":{"offsetStart":49,"normalizedForm":"MaxQuant","offsetEnd":57,"rawForm":"MaxQuant","boundingBoxes":[{"x":150.111,"h":11.664,"y":597.248,"p":25,"w":55.5465}]},"version":{"offsetStart":106,"normalizedForm":"1.5.3.31","offsetEnd":114,"rawForm":"1.5.3.31","boundingBoxes":[{"x":467.452,"h":11.663999999999987,"y":597.248,"p":25,"w":42.11999999999995}]}},
  {"_key":"60c20b287723bebd866453f5","_id":"annotations/60c20b287723bebd866453f5","_rev":"_cfFmUdW---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":54,"normalizedForm":"MinIONqc.R script","offsetEnd":71,"rawForm":"MinIONqc.R script","boundingBoxes":[{"x":445.18,"h":11.663999999999987,"y":694.448,"p":9,"w":102.6399428571429}]},"context":"Further pipelines included the quality control by the MinIONqc.R script,  followed by mapping the reads onto the gencode.v32.transcriptome using minimap2 v."},
  {"_key":"60c20b287723bebd866453f6","_id":"annotations/60c20b287723bebd866453f6","_rev":"_cfFmUdi---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":56,"normalizedForm":"NextProt","offsetEnd":64,"rawForm":"NextProt","boundingBoxes":[{"x":258.576,"h":12.636,"y":176.55,"p":2,"w":48.109511111111104}]},"context":"Within half a year, since  the January 2020 version of NextProt, the number of entries in the MP+uPE1  datasets has changed, mainly due to the achievements of antibody-based  proteomics."},
  {"_key":"60c20b287723bebd866453f7","_id":"annotations/60c20b287723bebd866453f7","_rev":"_cfFmUdu---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":56,"normalizedForm":"NextProt","offsetEnd":64,"rawForm":"NextProt","boundingBoxes":[{"x":402.776,"h":11.664,"y":133.728,"p":13,"w":46.7986}]},"context":"So, at the time of this writing, the updated version of NextProt included 9 missing  genes and 11 genes characterized as uPE1 from Chr18."},
  {"_key":"60c20b287723bebd866453f8","_id":"annotations/60c20b287723bebd866453f8","_rev":"_cfFmUd6---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":60,"normalizedForm":"bowtie2-RSEM","offsetEnd":72,"rawForm":"bowtie2-RSEM","boundingBoxes":[{"x":132.732,"h":11.663999999999987,"y":582.248,"p":8,"w":81.7355}]},"context":"Finally, we compared the results obtained with STAR- RSEM, bowtie2-RSEM and Salmon, calculated the Spearman/Pearson correlation  coefficients and created clustering dendrograms."},
  {"_key":"60c20b287723bebd866453f9","_id":"annotations/60c20b287723bebd866453f9","_rev":"_cfFmUeG---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The peak lists obtained from MS/MS spectra were identified using OMSSA  version 2.1.9 33","references":[{"offsetStart":22069,"normalizedForm":"33","refKey":34,"label":"33","reference_id":{"$oid":"60c20b287723bebd866453e4"},"offsetEnd":22072,"boundingBoxes":[{"x":162.14,"h":7.668,"y":266.75,"p":10,"w":8.58}]}],"type":"software","software-name":{"offsetStart":65,"normalizedForm":"OMSSA","offsetEnd":72,"rawForm":"OMSSA","boundingBoxes":[{"x":507.7,"h":11.664,"y":245.838,"p":10,"w":44.7509}]},"version":{"offsetStart":81,"normalizedForm":"2.1.9","offsetEnd":86,"rawForm":"2.1.9","boundingBoxes":[{"x":136.088,"h":11.663999999999987,"y":268.278,"p":10,"w":26.02369999999999}]}},
  {"_key":"60c20b287723bebd866453fa","_id":"annotations/60c20b287723bebd866453fa","_rev":"_cfFmUeW---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The overall statistics of alignment mapping was produced using the \"samtools  stats\" command, and the quantitative data were further collected by executing the program Salmon. 0.12/1.1.0","type":"software","software-name":{"offsetStart":68,"normalizedForm":"samtools stats","offsetEnd":84,"rawForm":"samtools \n\nstats","boundingBoxes":[{"x":506.3795111111111,"h":11.7806,"y":739.074,"p":9,"w":46.17208888888889},{"x":85.104,"h":11.7806,"y":761.538,"p":9,"w":23.997583333333335}]},"version":{"offsetStart":170,"normalizedForm":"Salmon. 0.12/1.1.0","offsetEnd":188,"rawForm":"Salmon. 0.12/1.1.0","boundingBoxes":[{"x":132.86,"h":11.664000000000001,"y":66.3883,"p":10,"w":99.14999999999998}]}},
  {"_key":"60c20b287723bebd866453fb","_id":"annotations/60c20b287723bebd866453fb","_rev":"_cfFmUei---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"With a modified sequence database, the search was implemented using  SearchGUI 30 with a parent mass tolerance of 7 ppm and a fragment mass tolerance of 20  ppm.","references":[{"offsetStart":58604,"normalizedForm":"30","refKey":31,"label":"30","reference_id":{"$oid":"60c20b287723bebd866453e2"},"offsetEnd":58607,"boundingBoxes":[{"x":143.42,"h":7.668,"y":483.61,"p":25,"w":8.58}]}],"type":"software","software-name":{"offsetStart":70,"normalizedForm":"SearchGUI","offsetEnd":79,"rawForm":"SearchGUI","boundingBoxes":[{"x":85.104,"h":11.664,"y":485.138,"p":25,"w":58.2941}]}},
  {"_key":"60c20b287723bebd866453fc","_id":"annotations/60c20b287723bebd866453fc","_rev":"_cfFmUeu---","wikipediaExternalRef":31179919,"document":{"$oid":"60c20b287723bebd866453e0"},"context":"Our choice was further confirmed, because in the  July 2020 version of NeXtProt HSBP1L1 has left the pool of missing proteins and gained  the respectful PE1 status.","wikidataId":"Q6983890","type":"software","confidence":0.5129,"software-name":{"wikipediaExternalRef":31179919,"normalizedForm":"NeXtProt","offsetStart":72,"wikidataId":"Q6983890","offsetEnd":80,"lang":"en","confidence":0.5129,"rawForm":"NeXtProt","boundingBoxes":[{"x":195.386,"h":11.664,"y":507.458,"p":30,"w":49.6757}]},"lang":"en"},
  {"_key":"60c20b287723bebd866453fd","_id":"annotations/60c20b287723bebd866453fd","_rev":"_cfFmUf----","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The decoy sequences  were created by reversing the target sequences in SearchGUI.","references":[{"offsetStart":58604,"normalizedForm":"30","refKey":31,"label":"30","reference_id":{"$oid":"60c20b287723bebd866453e2"},"offsetEnd":58607,"boundingBoxes":[{"x":143.42,"h":7.668,"y":483.61,"p":25,"w":8.58}]}],"type":"software","software-name":{"offsetStart":72,"normalizedForm":"SearchGUI","offsetEnd":81,"rawForm":"SearchGUI","boundingBoxes":[{"x":349.267,"h":11.664,"y":358.038,"p":10,"w":55.59057}]}},
  {"_key":"60c20b287723bebd866453fe","_id":"annotations/60c20b287723bebd866453fe","_rev":"_cfFmUfO---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The read mapping and expression quantification were carried out  employing STAR 2.7 (splice-aware mapping to genome), bowtie2 (mapping to  transcripts), RSEM 1.3 (quantifications of the reads), and Salmon (quasi-mapping and  quantification) software packages.","type":"software","software-name":{"offsetStart":76,"normalizedForm":"STAR","offsetEnd":80,"rawForm":"STAR","boundingBoxes":[{"x":150.124,"h":11.664,"y":492.578,"p":8,"w":33.2295}]},"version":{"offsetStart":81,"normalizedForm":"2.7","offsetEnd":84,"rawForm":"2.7","boundingBoxes":[{"x":192.944,"h":11.663999999999987,"y":492.578,"p":8,"w":16.303699999999992}]}},
  {"_key":"60c20b287723bebd866453ff","_id":"annotations/60c20b287723bebd866453ff","_rev":"_cfFmUfe---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":77,"normalizedForm":"Trimmomatic","offsetEnd":88,"rawForm":"Trimmomatic","boundingBoxes":[{"x":85.104,"h":11.664,"y":470.138,"p":8,"w":68.38131666666666}]},"context":"The derived fastq files were analyzed by FastQC and then were processed by  Trimmomatic."},
  {"_key":"60c20b287723bebd86645400","_id":"annotations/60c20b287723bebd86645400","_rev":"_cfFmUfq---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The peptides and proteins  were inferred from the spectrum identification results using PeptideShaker 36 version  1.16.45.","type":"software","software-name":{"offsetStart":89,"normalizedForm":"PeptideShaker","offsetEnd":102,"rawForm":"PeptideShaker","boundingBoxes":[{"x":423.93,"h":11.664,"y":537.458,"p":10,"w":74.9736}]},"version":{"offsetStart":116,"normalizedForm":"1.16","offsetEnd":121,"rawForm":"1.16.","boundingBoxes":[{"x":85.104,"h":11.663999999999987,"y":559.778,"p":10,"w":26.322500000000005}]}},
  {"_key":"60c20b287723bebd86645401","_id":"annotations/60c20b287723bebd86645401","_rev":"_cfFmUf6---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":110,"normalizedForm":"Mascot","offsetEnd":116,"rawForm":"Mascot","boundingBoxes":[{"x":262.344,"h":11.664,"y":627.128,"p":10,"w":38.2709}]},"context":"The same modifications and m/z tolerance settings (10 ppm for MS1 and 0.01 Da  for MS2) were used to perform Mascot (version of the 2010 year) and identyPROT 37  MS/MS searches."},
  {"_key":"60c20b287723bebd86645402","_id":"annotations/60c20b287723bebd86645402","_rev":"_cfFmUgK---","wikipediaExternalRef":41223765,"document":{"$oid":"60c20b287723bebd866453e0"},"context":"The read mapping and expression quantification were carried out  employing STAR 2.7 (splice-aware mapping to genome), bowtie2 (mapping to  transcripts), RSEM 1.3 (quantifications of the reads), and Salmon (quasi-mapping and  quantification) software packages.","wikidataId":"Q16335221","type":"software","confidence":0.7224,"software-name":{"wikipediaExternalRef":41223765,"normalizedForm":"bowtie2","offsetStart":119,"wikidataId":"Q16335221","offsetEnd":126,"lang":"en","confidence":0.7224,"rawForm":"bowtie2","boundingBoxes":[{"x":431.61,"h":11.663999999999987,"y":492.578,"p":8,"w":41.86079999999998}]},"lang":"en"},
  {"_key":"60c20b287723bebd86645403","_id":"annotations/60c20b287723bebd86645403","_rev":"_cfFmUgW---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The  MaxQuant search engine identified this peptide in the LNCaP cell line only by merging  several spectra (\"matching between runs\" option in MaxQuant) 32 .","type":"software","software-name":{"offsetStart":145,"normalizedForm":"MaxQuant","offsetEnd":153,"rawForm":"MaxQuant","boundingBoxes":[{"x":354.625,"h":11.7806,"y":111.158,"p":26,"w":53.2008}]},"version":{"offsetStart":106,"normalizedForm":"1.5.3.31","offsetEnd":114,"rawForm":"1.5.3.31","boundingBoxes":[{"x":467.452,"h":11.663999999999987,"y":597.248,"p":25,"w":42.11999999999995}]}},
  {"_key":"60c20b287723bebd86645404","_id":"annotations/60c20b287723bebd86645404","_rev":"_cfFmUgi---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":146,"normalizedForm":"minimap2","offsetEnd":154,"rawForm":"minimap2","boundingBoxes":[{"x":485.372,"h":11.663999999999987,"y":716.768,"p":9,"w":52.55279999999999}]},"context":"Further pipelines included the quality control by the MinIONqc.R script,  followed by mapping the reads onto the gencode.v32.transcriptome using minimap2 v."},
  {"_key":"60c20b287723bebd86645405","_id":"annotations/60c20b287723bebd86645405","_rev":"_cfFmUgu---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":152,"normalizedForm":"minimap2","offsetEnd":160,"rawForm":"minimap2","boundingBoxes":[{"x":447.572,"h":11.663999999999987,"y":201.048,"p":17,"w":52.53989999999999}]},"context":"Although the LAST and BWA algorithms (originally developed for the mapping of short  reads 49,50 ) were also employed for ONT data processing 23 , the minimap2 tool 51 is  nowadays widely used for long noisy read mapping."},
  {"_key":"60c20b287723bebd86645406","_id":"annotations/60c20b287723bebd86645406","_rev":"_cfFmUh----","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The read mapping and expression quantification were carried out  employing STAR 2.7 (splice-aware mapping to genome), bowtie2 (mapping to  transcripts), RSEM 1.3 (quantifications of the reads), and Salmon (quasi-mapping and  quantification) software packages.","type":"software","software-name":{"offsetStart":155,"normalizedForm":"RSEM","offsetEnd":159,"rawForm":"RSEM","boundingBoxes":[{"x":151.908,"h":11.664,"y":515.018,"p":8,"w":35.3938}]},"version":{"offsetStart":160,"normalizedForm":"1.3","offsetEnd":163,"rawForm":"1.3","boundingBoxes":[{"x":192.447,"h":11.663999999999987,"y":515.018,"p":8,"w":16.303699999999992}]}},
  {"_key":"60c20b287723bebd86645407","_id":"annotations/60c20b287723bebd86645407","_rev":"_cfFmUhK---","document":{"$oid":"60c20b287723bebd866453e0"},"type":"software","software-name":{"offsetStart":166,"normalizedForm":"SearchGUI/PeptideShaker","offsetEnd":189,"rawForm":"SearchGUI/PeptideShaker","boundingBoxes":[{"x":137.645,"h":11.663999999999987,"y":201.048,"p":10,"w":137.116}]},"context":"The MS/MS dataset from the Mann's group was downloaded from the PRIDE  databank (project accession number PXD005141) and searched by the engines embedded  into the SearchGUI/PeptideShaker platform 30 and by MaxQuant 31 using the same  parameters, as previously specified 32 ."},
  {"_key":"60c20b287723bebd86645408","_id":"annotations/60c20b287723bebd86645408","_rev":"_cfFmUhW---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"Nonetheless, we did not observe a perfect match between the results  obtained using various genome annotations (RefSeq/Ensembl/Gencode) and data  processing protocols (STAR+RSEM, bowtie2+RSEM, Salmon), as well as between  technical replications: the Spearman correlation coefficient between various data  processing pipelines or technical replicates ranging from 60% to 97%.","type":"software","software-name":{"offsetStart":170,"normalizedForm":"STAR","offsetEnd":174,"rawForm":"STAR","boundingBoxes":[{"x":210.86402727272727,"h":11.664,"y":470.138,"p":19,"w":68.31924545454545}]},"version":{"offsetStart":81,"normalizedForm":"2.7","offsetEnd":84,"rawForm":"2.7","boundingBoxes":[{"x":192.944,"h":11.663999999999987,"y":492.578,"p":8,"w":16.303699999999992}]}},
  {"_key":"60c20b287723bebd86645409","_id":"annotations/60c20b287723bebd86645409","_rev":"_cfFmUhi---","wikipediaExternalRef":41223765,"document":{"$oid":"60c20b287723bebd866453e0"},"context":"Nonetheless, we did not observe a perfect match between the results  obtained using various genome annotations (RefSeq/Ensembl/Gencode) and data  processing protocols (STAR+RSEM, bowtie2+RSEM, Salmon), as well as between  technical replications: the Spearman correlation coefficient between various data  processing pipelines or technical replicates ranging from 60% to 97%.","wikidataId":"Q16335221","type":"software","confidence":0.7224,"software-name":{"wikipediaExternalRef":41223765,"normalizedForm":"bowtie2","offsetStart":181,"wikidataId":"Q16335221","offsetEnd":188,"lang":"en","confidence":0.7224,"rawForm":"bowtie2","boundingBoxes":[{"x":293.954,"h":11.663999999999987,"y":470.138,"p":19,"w":81.19883076923077}]},"lang":"en"},
  {"_key":"60c20b287723bebd8664540a","_id":"annotations/60c20b287723bebd8664540a","_rev":"_cfFmUhu---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"Nonetheless, we did not observe a perfect match between the results  obtained using various genome annotations (RefSeq/Ensembl/Gencode) and data  processing protocols (STAR+RSEM, bowtie2+RSEM, Salmon), as well as between  technical replications: the Spearman correlation coefficient between various data  processing pipelines or technical replicates ranging from 60% to 97%.","type":"software","software-name":{"offsetStart":189,"normalizedForm":"RSEM","offsetEnd":193,"rawForm":"RSEM","boundingBoxes":[{"x":293.954,"h":11.664,"y":470.138,"p":19,"w":81.19883076923078}]},"version":{"offsetStart":160,"normalizedForm":"1.3","offsetEnd":163,"rawForm":"1.3","boundingBoxes":[{"x":192.447,"h":11.663999999999987,"y":515.018,"p":8,"w":16.303699999999992}]}},
  {"_key":"60c20b287723bebd8664540b","_id":"annotations/60c20b287723bebd8664540b","_rev":"_cfFmUh6---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The MS/MS dataset from the Mann's group was downloaded from the PRIDE  databank (project accession number PXD005141) and searched by the engines embedded  into the SearchGUI/PeptideShaker platform 30 and by MaxQuant 31 using the same  parameters, as previously specified 32 .","type":"software","software-name":{"offsetStart":209,"normalizedForm":"MaxQuant","offsetEnd":217,"rawForm":"MaxQuant","boundingBoxes":[{"x":392.782,"h":11.664,"y":201.048,"p":10,"w":55.5465}]},"version":{"offsetStart":106,"normalizedForm":"1.5.3.31","offsetEnd":114,"rawForm":"1.5.3.31","boundingBoxes":[{"x":467.452,"h":11.663999999999987,"y":597.248,"p":25,"w":42.11999999999995}]}},
  {"_key":"60c20b287723bebd8664540c","_id":"annotations/60c20b287723bebd8664540c","_rev":"_cfFmUiG---","document":{"$oid":"60c20b287723bebd866453e0"},"publisher":{"offsetStart":212,"normalizedForm":"ONT","offsetEnd":215,"rawForm":"ONT","boundingBoxes":[{"x":413.38,"h":11.664,"y":649.568,"p":9,"w":19.34815}]},"context":"The fast5 files produced by MinION were uploaded onto the Amazon Web  Services ElasticCloud2 and processed using the GPU-powered (Nvidia Tesla V100)  virtual instance p3.2xlarge (8x2.7 GHz vCPUs, 1 GPU) by the ONT-provided basecalling  software guppy_basecaller 27 with parameters \"-flowcell FLO-MIN107 -kit SQK- RNA002\".","references":[{"offsetStart":20833,"normalizedForm":"27","refKey":28,"label":"27","reference_id":{"$oid":"60c20b287723bebd866453e5"},"offsetEnd":20836,"boundingBoxes":[{"x":237.89,"h":7.668,"y":670.48,"p":9,"w":8.58}]}],"type":"software","software-name":{"offsetStart":248,"normalizedForm":"guppy_basecaller","offsetEnd":264,"rawForm":"guppy_basecaller","boundingBoxes":[{"x":138.356,"h":11.664,"y":672.008,"p":9,"w":90.9144}]}},
  {"_key":"60c20b287723bebd8664540d","_id":"annotations/60c20b287723bebd8664540d","_rev":"_cfFmUiS---","document":{"$oid":"60c20b287723bebd866453e0"},"context":"The sequence of Pept-24 is split between exons 1 and 2 of the HSBP1L1 gene  (Fig. 3), with the first two amino acids encoded at the tail of exon 1, while the rest of the  peptide occupies the whole length of exon 2. The inspection of the splice region in  Integrated Genome Viewer 53 has shown no abnormalities that can course the variations in  the sequence of this proteotypic peptide.","references":[{"offsetStart":55295,"normalizedForm":"53","refKey":56,"label":"53","reference_id":{"$oid":"60c20b287723bebd866453e6"},"offsetEnd":55298,"boundingBoxes":[{"x":226.73,"h":7.668,"y":132.2,"p":23,"w":8.58}]}],"type":"software","software-name":{"offsetStart":259,"normalizedForm":"Integrated Genome Viewer","offsetEnd":283,"rawForm":"Integrated Genome Viewer","boundingBoxes":[{"x":85.104,"h":11.663999999999987,"y":133.728,"p":23,"w":141.53160000000003}]}},
  {"_key":"60c20b2f7723bebd8664540f","_id":"annotations/60c20b2f7723bebd8664540f","_rev":"_cfFmUie---","document":{"$oid":"60c20b2f7723bebd8664540e"},"publisher":{"offsetStart":40,"normalizedForm":"European Directorate for","offsetEnd":65,"rawForm":"European \nDirectorate for","boundingBoxes":[{"x":257.886,"h":7.5238,"y":56.5606,"p":4,"w":36.3915},{"x":42.7322,"h":7.523799999999994,"y":67.0214,"p":4,"w":57.6073}]},"context":"CombiStats software (distributed by the European Directorate for the Quality of Medicines) was used to calculate individual SN titres.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"CombiStats","offsetEnd":10,"rawForm":"CombiStats","boundingBoxes":[{"x":93.0067,"h":7.5238,"y":56.5606,"p":4,"w":43.1979}]}},
  {"_key":"60c20b307723bebd86645411","_id":"annotations/60c20b307723bebd86645411","_rev":"_cfFmUiq---","document":{"$oid":"60c20b307723bebd86645410"},"type":"software","software-name":{"offsetStart":563,"normalizedForm":"ResApp","offsetEnd":571,"rawForm":"ResApp","boundingBoxes":[{"x":339.619,"h":6.873,"y":764.054,"p":1,"w":23.0623}]}},
  {"_key":"60c20b347723bebd86645413","_id":"annotations/60c20b347723bebd86645413","_rev":"_cfFmUi2---","document":{"$oid":"60c20b347723bebd86645412"},"context":"The British Association of Head and Neck Oncologists recommends prioritising cases that are likely to represent malignancy and deferring cases with a lower likelihood. 2 A risk calculator (the head and neck cancer risk calculator, version 2; 'HaNC-RC v.2') has been generated in order to establish the probability of head and neck cancer in indi- vidual patients. 3","type":"software","software-name":{"offsetStart":246,"normalizedForm":"HaNC-RC","offsetEnd":253,"rawForm":"HaNC-RC","boundingBoxes":[{"x":496.67742499999997,"h":10.000099999999975,"y":477.564,"p":1,"w":38.824974999999995}]},"version":{"offsetStart":256,"normalizedForm":"2","offsetEnd":257,"rawForm":"2","boundingBoxes":[{"x":545.27488,"h":9.3201,"y":478.314,"p":1,"w":3.4294400000000005}]}},
  {"_key":"60c20b3d7723bebd86645415","_id":"annotations/60c20b3d7723bebd86645415","_rev":"_cfFmUjC---","document":{"$oid":"60c20b3d7723bebd86645414"},"type":"software","software-name":{"offsetStart":37,"normalizedForm":"clingo","offsetEnd":43,"rawForm":"clingo","boundingBoxes":[{"x":309.286,"h":7.6114,"y":185.498,"p":6,"w":32.8417}]},"context":"In addition to standard definitions, clingo allows to define constraints, i.e., rules with the empty head, for instance"},
  {"_key":"60c20b3d7723bebd86645416","_id":"annotations/60c20b3d7723bebd86645416","_rev":"_cfFmUjO---","document":{"$oid":"60c20b3d7723bebd86645414"},"type":"software","software-name":{"offsetStart":39,"normalizedForm":"clingo","offsetEnd":45,"rawForm":"clingo","boundingBoxes":[{"x":51.7788,"h":7.6114,"y":173.546,"p":6,"w":34.652519999999996}]},"context":"For experiments we took advantages of clingo-one of the most efficient and widely used answer set programming system available 5 today."},
  {"_key":"60c20b3d7723bebd86645417","_id":"annotations/60c20b3d7723bebd86645417","_rev":"_cfFmUja---","wikipediaExternalRef":990298,"document":{"$oid":"60c20b3d7723bebd86645414"},"context":"In all experiments, we used Intel Xeon CPU E5-2650 v2, 2.6 GHz (single-core out of eight), under Ubuntu 18.04 operating system with 60 GB available RAM. Algorithm 1 shows the process for synthesizing a grammar (the set of production rules with v 0 being always the start symbol) from positive and negative words.","wikidataId":"Q381","type":"software","lang":"en","confidence":0.6643,"software-name":{"wikipediaExternalRef":990298,"normalizedForm":"Ubuntu","offsetStart":98,"wikidataId":"Q381","offsetEnd":104,"lang":"en","confidence":0.6643,"rawForm":"Ubuntu","boundingBoxes":[{"x":141.06,"h":8.9365,"y":537.871,"p":9,"w":33.2173}]},"version":{"offsetStart":105,"normalizedForm":"18.04","offsetEnd":110,"rawForm":"18.04","boundingBoxes":[{"x":177.329,"h":8.936500000000024,"y":537.871,"p":9,"w":22.686800000000005}]}},
  {"_key":"60c20b3d7723bebd86645418","_id":"annotations/60c20b3d7723bebd86645418","_rev":"_cfFmUjm---","document":{"$oid":"60c20b3d7723bebd86645414"},"type":"software","software-name":{"offsetStart":107,"normalizedForm":"Synapse","offsetEnd":114,"rawForm":"Synapse","boundingBoxes":[{"x":212.794,"h":8.9365,"y":247.837,"p":3,"w":35.2028}]},"context":"Nakamura et al. have been working on another approach for incremental learning of CFGs implemented in the Synapse system [15]."},
  {"_key":"60c20b3d7723bebd86645419","_id":"annotations/60c20b3d7723bebd86645419","_rev":"_cfFmUjy---","wikipediaExternalRef":23862,"document":{"$oid":"60c20b3d7723bebd86645414"},"context":"In this section, we describe some experiments comparing the performance of our approaches implemented 6 in Python, using clingo (ASP) and using Gurobi Optimizer, with our implementation of Imada et al. algorithm [11] using the PicoSAT solver (SAT), when positive and negative words are given.","wikidataId":"Q28865","type":"software","confidence":0.6138,"software-name":{"wikipediaExternalRef":23862,"normalizedForm":"Python","offsetStart":108,"wikidataId":"Q28865","offsetEnd":114,"lang":"en","confidence":0.6138,"rawForm":"Python","boundingBoxes":[{"x":217.502,"h":8.9365,"y":191.173,"p":9,"w":29.775085714285712}]},"lang":"en"},
  {"_key":"60c20b3d7723bebd8664541a","_id":"annotations/60c20b3d7723bebd8664541a","_rev":"_cfFmUk----","wikipediaExternalRef":44209778,"document":{"$oid":"60c20b3d7723bebd86645414"},"context":"Because of the possibility of future comparisons with other methods, the Python implementation 3 of our winning method is given via GitLab.","wikidataId":"Q16639197","type":"software","confidence":0.7933,"software-name":{"wikipediaExternalRef":44209778,"normalizedForm":"GitLab","offsetStart":133,"wikidataId":"Q16639197","offsetEnd":139,"lang":"en","confidence":0.7933,"rawForm":"GitLab","boundingBoxes":[{"x":284.545,"h":8.9365,"y":405.247,"p":3,"w":29.121857142857138}]},"lang":"en"},
  {"_key":"60c20b3d7723bebd8664541b","_id":"annotations/60c20b3d7723bebd8664541b","_rev":"_cfFmUkK---","document":{"$oid":"60c20b3d7723bebd86645414"},"type":"software","software-name":{"offsetStart":16370,"normalizedForm":"clingo","offsetEnd":16376,"rawForm":"clingo","boundingBoxes":[{"x":68.5187,"h":7.6114,"y":258.416,"p":7,"w":32.8417}]}},
  {"_key":"60c20b3d7723bebd8664541c","_id":"annotations/60c20b3d7723bebd8664541c","_rev":"_cfFmUkS---","document":{"$oid":"60c20b3d7723bebd86645414"},"type":"software","software-name":{"offsetStart":20082,"normalizedForm":"clingo","offsetEnd":20088,"rawForm":"clingo","boundingBoxes":[{"x":285.156,"h":7.6114,"y":190.556,"p":9,"w":32.8417}]}},
  {"_key":"60c20b3f7723bebd86645420","_id":"annotations/60c20b3f7723bebd86645420","_rev":"_cfFmUke---","document":{"$oid":"60c20b3f7723bebd8664541d"},"type":"software","software-name":{"offsetStart":29,"normalizedForm":"cpptraj","offsetEnd":36,"rawForm":"cpptraj","boundingBoxes":[{"x":486.424,"h":6.9562,"y":238.572,"p":10,"w":20.5325}]},"context":"A cluster analysis using the cpptraj module of AmberTools14 identified the most populated states sampled during the simulation of each system with a fixed clustering radius of 3.5 Å."},
  {"_key":"60c20b3f7723bebd86645421","_id":"annotations/60c20b3f7723bebd86645421","_rev":"_cfFmUkq---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20b3f7723bebd8664541d"},"publisher":{"offsetStart":90,"normalizedForm":"Health","offsetEnd":96,"rawForm":"Health","boundingBoxes":[{"x":113.373,"h":6.9637,"y":278.25,"p":10,"w":19.373314285714283}]},"context":"The images were analyzed with ImageJ (Rasband, W.S., ImageJ, U.S. National Institutes of Health, Bethesda, Maryland, USA, http://imagej.nih.gov/ ij/).","wikidataId":"Q1659584","type":"software","confidence":0.8009,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":30,"wikidataId":"Q1659584","offsetEnd":36,"lang":"en","confidence":0.8009,"rawForm":"ImageJ","boundingBoxes":[{"x":155.084,"h":6.9637,"y":269.746,"p":10,"w":21.4635}]},"url":{"offsetStart":123,"normalizedForm":"http://imagej.nih.gov/ ij","offsetEnd":149,"rawForm":"http://imagej.nih.gov/ \nij","boundingBoxes":[{"x":223.879,"h":6.963700000000017,"y":278.25,"p":10,"w":67.77670000000003},{"x":43.5973,"h":6.9637,"y":286.697,"p":10,"w":4.38384}]},"lang":"en"},
  {"_key":"60c20b3f7723bebd86645422","_id":"annotations/60c20b3f7723bebd86645422","_rev":"_cfFmUk2---","document":{"$oid":"60c20b3f7723bebd8664541d"},"type":"software","software-name":{"offsetStart":48,"normalizedForm":"AmberTools","offsetEnd":58,"rawForm":"AmberTools","boundingBoxes":[{"x":303.59,"h":6.9637,"y":247.012,"p":10,"w":44.6821}]},"context":"A cluster analysis using the cpptraj module of AmberTools14 identified the most populated states sampled during the simulation of each system with a fixed clustering radius of 3.5 Å."},
  {"_key":"60c20b3f7723bebd86645423","_id":"annotations/60c20b3f7723bebd86645423","_rev":"_cfFmUlC---","document":{"$oid":"60c20b3f7723bebd8664541d"},"context":"Molecular docking was performed with the program Auto- dock VINA 43 .","references":[{"offsetStart":44394,"normalizedForm":"43","refKey":42,"label":"43","reference_id":{"$oid":"60c20b3f7723bebd8664541e"},"offsetEnd":44397,"boundingBoxes":[{"x":78.8598,"h":5.5709,"y":409.823,"p":10,"w":5.7263}]}],"type":"software","software-name":{"offsetStart":49,"normalizedForm":"Auto- dock VINA","offsetEnd":64,"rawForm":"Auto-\ndock VINA","boundingBoxes":[{"x":269.691,"h":6.963700000000017,"y":402.573,"p":10,"w":17.65590000000003},{"x":43.5973,"h":6.963700000000017,"y":411.077,"p":10,"w":35.245200000000004}]}},
  {"_key":"60c20b3f7723bebd86645424","_id":"annotations/60c20b3f7723bebd86645424","_rev":"_cfFmUlK---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20b3f7723bebd8664541d"},"publisher":{"offsetStart":90,"normalizedForm":"Health","offsetEnd":96,"rawForm":"Health","boundingBoxes":[{"x":113.373,"h":6.9637,"y":278.25,"p":10,"w":19.373314285714283}]},"context":"The images were analyzed with ImageJ (Rasband, W.S., ImageJ, U.S. National Institutes of Health, Bethesda, Maryland, USA, http://imagej.nih.gov/ ij/).","wikidataId":"Q1659584","type":"software","confidence":0.8009,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":53,"wikidataId":"Q1659584","offsetEnd":59,"lang":"en","confidence":0.8009,"rawForm":"ImageJ","boundingBoxes":[{"x":231.599,"h":6.9637,"y":269.746,"p":10,"w":19.926}]},"url":{"offsetStart":123,"normalizedForm":"http://imagej.nih.gov/ ij","offsetEnd":149,"rawForm":"http://imagej.nih.gov/ \nij","boundingBoxes":[{"x":223.879,"h":6.963700000000017,"y":278.25,"p":10,"w":67.77670000000003},{"x":43.5973,"h":6.9637,"y":286.697,"p":10,"w":4.38384}]},"lang":"en"},
  {"_key":"60c20b3f7723bebd86645425","_id":"annotations/60c20b3f7723bebd86645425","_rev":"_cfFmUlW---","document":{"$oid":"60c20b3f7723bebd8664541d"},"type":"software","software-name":{"offsetStart":128,"normalizedForm":"Autodock VINA","offsetEnd":141,"rawForm":"Autodock VINA","boundingBoxes":[{"x":100.629,"h":8.821000000000026,"y":540.697,"p":6,"w":67.5502}]},"context":"Due to the intrinsic limitations of the docking scoring function employed, the ranked average binding affinities predicted by Autodock VINA failed to replicate the trend observed by spectrofluorimetry quantification of drug accumu- lation (reported in Fig. 4a)."},
  {"_key":"60c20b3f7723bebd86645426","_id":"annotations/60c20b3f7723bebd86645426","_rev":"_cfFmUli---","document":{"$oid":"60c20b3f7723bebd8664541d"},"context":"Two docking poses of the AcrB-FQ complex located inside the DP T were selected and used as starting points for 100-ns-long MD simulations for each compound, performed using Amber18 46 .","references":[{"offsetStart":45779,"normalizedForm":"46","refKey":45,"label":"46","reference_id":{"$oid":"60c20b3f7723bebd8664541f"},"offsetEnd":45782,"boundingBoxes":[{"x":281.65,"h":5.5709,"y":559.549,"p":10,"w":5.7263}]}],"type":"software","software-name":{"offsetStart":175,"normalizedForm":"Amber","offsetEnd":180,"rawForm":"Amber","boundingBoxes":[{"x":254.496,"h":6.9637,"y":560.808,"p":10,"w":27.2766}]}},
  {"_key":"60c20b3f7723bebd86645427","_id":"annotations/60c20b3f7723bebd86645427","_rev":"_cfFmUlu---","wikipediaExternalRef":21490336,"document":{"$oid":"60c20b3f7723bebd8664541d"},"context":"Hydrogen bonds (cut-off distance of 3.5 Å and angle of 120˚between donor and acceptor atoms) and hydrophobic contacts (distance of <2.5 Å between the centers of mass of the molecule and of the residues of the binding region) were analyzed using a customized tcl script for VMD 53 .","wikidataId":"Q187432","type":"software","confidence":0.2792,"software-name":{"wikipediaExternalRef":21490336,"normalizedForm":"script","offsetStart":265,"wikidataId":"Q187432","offsetEnd":271,"lang":"en","confidence":0.2792,"rawForm":"script","boundingBoxes":[{"x":374.06,"h":6.9637,"y":221.613,"p":10,"w":16.6322}]},"lang":"en"},
  {"_key":"60c20b437723bebd86645429","_id":"annotations/60c20b437723bebd86645429","_rev":"_cfFmUl2---","wikipediaExternalRef":1520204,"document":{"$oid":"60c20b437723bebd86645428"},"context":"org/) preprint platforms and Google Scholar for studies not indexed in the aforementioned databases.","wikidataId":"Q494817","type":"software","confidence":0.9596,"software-name":{"wikipediaExternalRef":1520204,"normalizedForm":"Google Scholar","offsetStart":29,"wikidataId":"Q494817","offsetEnd":43,"lang":"en","confidence":0.9596,"rawForm":"Google Scholar","boundingBoxes":[{"x":434.786,"h":9.357500000000016,"y":489.478,"p":3,"w":66.69369999999998}]},"lang":"en"},
  {"_key":"60c20b467723bebd8664542c","_id":"annotations/60c20b467723bebd8664542c","_rev":"_cfFmUmC---","document":{"$oid":"60c20b467723bebd8664542a"},"context":"RePro [14] was proposed to predict concept models for future drifts using historical trends of concept change.","references":[{"offsetStart":5389,"normalizedForm":"[14]","refKey":13,"label":"[14]","reference_id":{"$oid":"60c20b467723bebd8664542b"},"offsetEnd":5394,"boundingBoxes":[{"x":221.617,"h":8.936500000000024,"y":519.061,"p":2,"w":15.475899999999996}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"RePro","offsetEnd":5,"rawForm":"RePro","boundingBoxes":[{"x":190.067,"h":8.9365,"y":519.061,"p":2,"w":27.4231}]}},
  {"_key":"60c20b467723bebd8664542d","_id":"annotations/60c20b467723bebd8664542d","_rev":"_cfFmUmO---","document":{"$oid":"60c20b467723bebd8664542a"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"ProChange","offsetEnd":9,"rawForm":"ProChange","boundingBoxes":[{"x":123.703,"h":8.9365,"y":68.7469,"p":3,"w":48.3126}]},"context":"ProChange [9] finds both real and virtual drifts in unlabelled transactional data streams using the Hellinger distance, and models the volatil- ity of drifts using a probabilistic network to predict the location of future drifts."},
  {"_key":"60c20b467723bebd8664542e","_id":"annotations/60c20b467723bebd8664542e","_rev":"_cfFmUma---","document":{"$oid":"60c20b467723bebd8664542a"},"type":"software","software-name":{"offsetStart":4,"normalizedForm":"GraphPool","offsetEnd":13,"rawForm":"GraphPool","boundingBoxes":[{"x":73.3886,"h":8.9365,"y":104.612,"p":3,"w":47.2945}]},"context":"The GraphPool framework [1] refines the pool of concepts by applying a merging mechanism whenever necessary by considering the correlation among features."},
  {"_key":"60c20b467723bebd8664542f","_id":"annotations/60c20b467723bebd8664542f","_rev":"_cfFmUmm---","document":{"$oid":"60c20b467723bebd8664542a"},"type":"software","software-name":{"offsetStart":11,"normalizedForm":"scikit-multiflow","offsetEnd":27,"rawForm":"scikit-multiflow","boundingBoxes":[{"x":263.204,"h":8.936500000000002,"y":56.7948,"p":10,"w":66.70860000000005}]},"context":"Similar to scikit-multiflow [13] we esti- mate memory consumption, by adding up the key data structures used by PEARL and PEARL (PO) (Table 2)."},
  {"_key":"60c20b467723bebd86645430","_id":"annotations/60c20b467723bebd86645430","_rev":"_cfFmUmu---","wikipediaExternalRef":990298,"document":{"$oid":"60c20b467723bebd8664542a"},"context":"The experimentation is performed on the following machine and architecture: Dell PowerEdge R740 with 40 CPUs, 125.42 GiB (Swap 976.00 MiB) and Ubuntu 18.04 with AMD64 4.15.0-46-generic.","wikidataId":"Q381","type":"software","lang":"en","confidence":0.6643,"software-name":{"wikipediaExternalRef":990298,"normalizedForm":"Ubuntu","offsetStart":144,"wikidataId":"Q381","offsetEnd":150,"lang":"en","confidence":0.6643,"rawForm":"Ubuntu","boundingBoxes":[{"x":352.075,"h":8.9365,"y":176.342,"p":8,"w":33.2173}]},"version":{"offsetStart":152,"normalizedForm":"18.04","offsetEnd":157,"rawForm":"18.04","boundingBoxes":[{"x":39.402,"h":8.936499999999995,"y":188.294,"p":8,"w":22.686800000000005}]}},
  {"_key":"60c20b477723bebd86645432","_id":"annotations/60c20b477723bebd86645432","_rev":"_cfFmUm6---","document":{"$oid":"60c20b477723bebd86645431"},"type":"software","software-name":{"offsetStart":139,"normalizedForm":"REDCap (","offsetEnd":147,"rawForm":"REDCap (","boundingBoxes":[{"x":295.729,"h":9.163700000000006,"y":328.154,"p":1,"w":44.58472222222224}]},"context":"Each site requires a designated principal investigator who is responsible for: all team members having GCP; data qual- ity and entry via REDCap (Research Electronic Data Capture), and obtain- ing local ethical/audit approval (it can be registered as a service evalu- ation or clinical audit)."},
  {"_key":"60c20b477723bebd86645433","_id":"annotations/60c20b477723bebd86645433","_rev":"_cfFmUnG---","document":{"$oid":"60c20b477723bebd86645431"},"type":"software","software-name":{"offsetStart":147,"normalizedForm":"Research Electronic Data Capture)","offsetEnd":181,"rawForm":"Research \nElectronic Data Capture)","boundingBoxes":[{"x":340.3137222222222,"h":9.1637,"y":328.154,"p":1,"w":33.053777777777775},{"x":221.919,"h":9.163700000000006,"y":339.206,"p":1,"w":98.10246666666663}]},"context":"Each site requires a designated principal investigator who is responsible for: all team members having GCP; data qual- ity and entry via REDCap (Research Electronic Data Capture), and obtain- ing local ethical/audit approval (it can be registered as a service evalu- ation or clinical audit)."},
  {"_key":"60c20b4e7723bebd86645437","_id":"annotations/60c20b4e7723bebd86645437","_rev":"_cfFmUnS---","document":{"$oid":"60c20b4e7723bebd86645435"},"context":"We employed the Pushshift API (Baumgartner et al. 2020) to scrape data from posts in the five meme subreddits.","references":[{"offsetStart":12307,"normalizedForm":"Baumgartner et al. 2020","refKey":2,"label":"(Baumgartner et al. 2020)","reference_id":{"$oid":"60c20b4e7723bebd86645436"},"offsetEnd":12333,"boundingBoxes":[{"x":261.923,"h":11.681600000000003,"y":674.31,"p":4,"w":106.3682}]}],"type":"software","software-name":{"offsetStart":16,"normalizedForm":"Pushshift API","offsetEnd":29,"rawForm":"Pushshift API","boundingBoxes":[{"x":201.653,"h":11.681600000000003,"y":674.31,"p":4,"w":57.16319999999999}]}},
  {"_key":"60c20b4e7723bebd86645438","_id":"annotations/60c20b4e7723bebd86645438","_rev":"_cfFmUna---","document":{"$oid":"60c20b4e7723bebd86645435"},"publisher":{"offsetStart":60,"normalizedForm":"Keras","offsetEnd":65,"rawForm":"Keras","boundingBoxes":[{"x":386.902,"h":11.5052,"y":342.088,"p":19,"w":22.7066}]},"context":"• All networks include ReduceLROnPlateau functionality from Keras that reduces the current learning rate by 25% whenever the validation accuracy does not increase in the span of 3 epochs.","type":"software","software-name":{"offsetStart":23,"normalizedForm":"ReduceLROnPlateau","offsetEnd":40,"rawForm":"ReduceLROnPlateau","boundingBoxes":[{"x":224.555,"h":11.5052,"y":342.088,"p":19,"w":83.0942}]}},
  {"_key":"60c20b4e7723bebd86645439","_id":"annotations/60c20b4e7723bebd86645439","_rev":"_cfFmUnm---","wikipediaExternalRef":1661566,"document":{"$oid":"60c20b4e7723bebd86645435"},"context":"This was done using the NLTK and gensim Python libraries (Rehurek and Sojka 2011; Loper and Bird 2002).","wikidataId":"Q1635410","type":"software","confidence":0.8155,"software-name":{"wikipediaExternalRef":1661566,"normalizedForm":"NLTK","offsetStart":25,"wikidataId":"Q1635410","offsetEnd":29,"lang":"en","confidence":0.8155,"rawForm":"NLTK","boundingBoxes":[{"x":133.406,"h":11.6816,"y":505.051,"p":7,"w":25.431}]},"lang":"en"},
  {"_key":"60c20b4e7723bebd8664543a","_id":"annotations/60c20b4e7723bebd8664543a","_rev":"_cfFmUny---","wikipediaExternalRef":36473068,"document":{"$oid":"60c20b4e7723bebd86645435"},"context":"This was done using the NLTK and gensim Python libraries (Rehurek and Sojka 2011; Loper and Bird 2002).","wikidataId":"Q5533567","type":"software","confidence":0.6707,"software-name":{"wikipediaExternalRef":36473068,"normalizedForm":"gensim","offsetStart":34,"wikidataId":"Q5533567","offsetEnd":40,"lang":"en","confidence":0.6707,"rawForm":"gensim","boundingBoxes":[{"x":179.485,"h":11.6816,"y":505.051,"p":7,"w":29.2726}]},"lang":"en"},
  {"_key":"60c20b4e7723bebd8664543b","_id":"annotations/60c20b4e7723bebd8664543b","_rev":"_cfFmUo----","document":{"$oid":"60c20b4e7723bebd86645435"},"type":"software","software-name":{"offsetStart":70,"normalizedForm":"GridSearchCV","offsetEnd":82,"rawForm":"GridSearchCV","boundingBoxes":[{"x":281.169,"h":11.6816,"y":145.932,"p":16,"w":57.08935384615385}]},"context":"All of the modifications and fine-tuning, including class-weight and GridSearchCV, efforts used in those models are the same here."},
  {"_key":"60c20b567723bebd8664543d","_id":"annotations/60c20b567723bebd8664543d","_rev":"_cfFmUoG---","document":{"$oid":"60c20b567723bebd8664543c"},"context":"Análise estatística foi feita por meio do programa Statistical Package for the Social Sciences (SPSS) versão 22.0","type":"software","software-name":{"offsetStart":52,"normalizedForm":"Statistical Package for the Social Sciences (SPSS)","offsetEnd":103,"rawForm":"Statistical Package for the Social \nSciences (SPSS)","boundingBoxes":[{"x":163.861,"h":7.579599999999999,"y":193.163,"p":2,"w":122.6171},{"x":47.375,"h":7.579599999999999,"y":204.621,"p":2,"w":59.64030000000001}]},"version":{"offsetStart":111,"normalizedForm":"22.0","offsetEnd":115,"rawForm":"22.0","boundingBoxes":[{"x":137.046,"h":7.579599999999999,"y":204.621,"p":2,"w":15.509800000000013}]}},
  {"_key":"60c20b577723bebd8664543f","_id":"annotations/60c20b577723bebd8664543f","_rev":"_cfFmUoS---","document":{"$oid":"60c20b577723bebd8664543e"},"type":"software","software-name":{"offsetStart":48,"normalizedForm":"DENZO","offsetEnd":53,"rawForm":"DENZO","boundingBoxes":[{"x":96.4926,"h":8.966,"y":146.007,"p":3,"w":32.2866}]},"context":"Data were indexed, integrated and scaled using DENZO and SCALEPACK (Otwinowski & Minor, 1997)."},
  {"_key":"60c20b577723bebd86645440","_id":"annotations/60c20b577723bebd86645440","_rev":"_cfFmUoe---","document":{"$oid":"60c20b577723bebd8664543e"},"type":"software","software-name":{"offsetStart":58,"normalizedForm":"SCALEPACK","offsetEnd":67,"rawForm":"SCALEPACK","boundingBoxes":[{"x":152.448,"h":8.966,"y":146.007,"p":3,"w":53.7601}]},"context":"Data were indexed, integrated and scaled using DENZO and SCALEPACK (Otwinowski & Minor, 1997)."},
  {"_key":"60c20b587723bebd86645442","_id":"annotations/60c20b587723bebd86645442","_rev":"_cfFmUoq---","wikipediaExternalRef":20412,"document":{"$oid":"60c20b587723bebd86645441"},"publisher":{"offsetStart":107,"normalizedForm":"The MathWorks Inc","offsetEnd":124,"rawForm":"The MathWorks Inc","boundingBoxes":[{"x":425.88,"h":11.480000000000018,"y":409.223,"p":10,"w":79.69400000000002}]},"context":"The MATLAB ® function 'corrcoef' returns a matrix of cor- relation coefficients calculated from an input matrix whose rows are observations (countries) and whose columns are variables (e.g., deaths per million, BCG rates).","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7687,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":4,"wikidataId":"Q169478","offsetEnd":10,"lang":"en","confidence":0.7687,"rawForm":"MATLAB","boundingBoxes":[{"x":324.028,"h":11.48,"y":309.223,"p":10,"w":41.774}]},"version":{"offsetStart":99,"normalizedForm":"R2020a","offsetEnd":105,"rawForm":"R2020a","boundingBoxes":[{"x":390.53225000000003,"h":11.480000000000018,"y":409.223,"p":10,"w":28.17750000000001}]}},
  {"_key":"60c20b587723bebd86645443","_id":"annotations/60c20b587723bebd86645443","_rev":"_cfFmUoy---","wikipediaExternalRef":20412,"document":{"$oid":"60c20b587723bebd86645441"},"publisher":{"offsetStart":107,"normalizedForm":"The MathWorks Inc","offsetEnd":124,"rawForm":"The MathWorks Inc","boundingBoxes":[{"x":425.88,"h":11.480000000000018,"y":409.223,"p":10,"w":79.69400000000002}]},"context":"For statistical analyses, The MATLAB ® function 'cor- rcoef' was used for Pearson's correlation coefficients for statistical relationships between independent variables.","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7687,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":30,"wikidataId":"Q169478","offsetEnd":36,"lang":"en","confidence":0.7687,"rawForm":"MATLAB","boundingBoxes":[{"x":436.201,"h":11.48,"y":234.223,"p":10,"w":42.373}]},"version":{"offsetStart":99,"normalizedForm":"R2020a","offsetEnd":105,"rawForm":"R2020a","boundingBoxes":[{"x":390.53225000000003,"h":11.480000000000018,"y":409.223,"p":10,"w":28.17750000000001}]}},
  {"_key":"60c20b587723bebd86645444","_id":"annotations/60c20b587723bebd86645444","_rev":"_cfFmUp----","wikipediaExternalRef":20412,"document":{"$oid":"60c20b587723bebd86645441"},"publisher":{"offsetStart":107,"normalizedForm":"The MathWorks Inc","offsetEnd":124,"rawForm":"The MathWorks Inc","boundingBoxes":[{"x":425.88,"h":11.480000000000018,"y":409.223,"p":10,"w":79.69400000000002}]},"context":"A general- ized linear model regression with the MATLAB ® function 'glmfit' was used for multivariate analysis.","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7687,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":49,"wikidataId":"Q169478","offsetEnd":55,"lang":"en","confidence":0.7687,"rawForm":"MATLAB","boundingBoxes":[{"x":460.4,"h":11.48,"y":359.223,"p":10,"w":41.926}]},"version":{"offsetStart":99,"normalizedForm":"R2020a","offsetEnd":105,"rawForm":"R2020a","boundingBoxes":[{"x":390.53225000000003,"h":11.480000000000018,"y":409.223,"p":10,"w":28.17750000000001}]}},
  {"_key":"60c20b587723bebd86645445","_id":"annotations/60c20b587723bebd86645445","_rev":"_cfFmUpK---","wikipediaExternalRef":20412,"document":{"$oid":"60c20b587723bebd86645441"},"publisher":{"offsetStart":107,"normalizedForm":"The MathWorks Inc","offsetEnd":124,"rawForm":"The MathWorks Inc","boundingBoxes":[{"x":425.88,"h":11.480000000000018,"y":409.223,"p":10,"w":79.69400000000002}]},"context":"Data processing, visualization, and statistical analyses were carried out using MATLAB ® Online (R2020a; The MathWorks Inc. 2020).","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7687,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":82,"wikidataId":"Q169478","offsetEnd":88,"lang":"en","confidence":0.7687,"rawForm":"MATLAB","boundingBoxes":[{"x":306.128,"h":11.48,"y":409.223,"p":10,"w":41.92}]},"version":{"offsetStart":99,"normalizedForm":"R2020a","offsetEnd":105,"rawForm":"R2020a","boundingBoxes":[{"x":390.53225000000003,"h":11.480000000000018,"y":409.223,"p":10,"w":28.17750000000001}]}},
  {"_key":"60c20b607723bebd86645447","_id":"annotations/60c20b607723bebd86645447","_rev":"_cfFmUpW---","document":{"$oid":"60c20b607723bebd86645446"},"context":"We employed Mplus 7.0 to conduct regression analysis with latent variables.","type":"software","software-name":{"offsetStart":12,"normalizedForm":"Mplus","offsetEnd":17,"rawForm":"Mplus","boundingBoxes":[{"x":197.688,"h":8.9767,"y":136.722,"p":7,"w":25.9972}]},"version":{"offsetStart":18,"normalizedForm":"7.0","offsetEnd":21,"rawForm":"7.0","boundingBoxes":[{"x":228.189,"h":8.976699999999994,"y":136.722,"p":7,"w":11.936300000000017}]}},
  {"_key":"60c20b607723bebd86645448","_id":"annotations/60c20b607723bebd86645448","_rev":"_cfFmUpi---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b607723bebd86645446"},"context":"We analysed the data in SPSS and Mplus 7.0, with .05 as the significant level across all analyses.","wikidataId":"Q181596","type":"software","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":24,"wikidataId":"Q181596","offsetEnd":28,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":406.714,"h":8.9767,"y":412.762,"p":6,"w":20.5886}]},"lang":"en"},
  {"_key":"60c20b607723bebd86645449","_id":"annotations/60c20b607723bebd86645449","_rev":"_cfFmUpq---","document":{"$oid":"60c20b607723bebd86645446"},"context":"We analysed the data in SPSS and Mplus 7.0, with .05 as the significant level across all analyses.","type":"software","software-name":{"offsetStart":33,"normalizedForm":"Mplus","offsetEnd":38,"rawForm":"Mplus","boundingBoxes":[{"x":448.384,"h":8.9767,"y":412.762,"p":6,"w":25.9109}]},"version":{"offsetStart":39,"normalizedForm":"7.0","offsetEnd":42,"rawForm":"7.0","boundingBoxes":[{"x":477.354,"h":8.976699999999994,"y":412.762,"p":6,"w":10.554525000000012}]}},
  {"_key":"60c20b607723bebd8664544a","_id":"annotations/60c20b607723bebd8664544a","_rev":"_cfFmUp2---","wikipediaExternalRef":34408890,"document":{"$oid":"60c20b607723bebd86645446"},"context":"Over 200 student helpers who majored in psychology voluntar- ily distributed the online survey link on various inter- net platforms, including WeChat (the most popular APP for instant message in mainland China), Weibo, QQ, etc.","wikidataId":"Q283233","type":"software","confidence":0.7626,"software-name":{"wikipediaExternalRef":34408890,"normalizedForm":"WeChat","offsetStart":144,"wikidataId":"Q283233","offsetEnd":150,"lang":"en","confidence":0.7626,"rawForm":"WeChat","boundingBoxes":[{"x":168.999,"h":8.9767,"y":436.737,"p":4,"w":34.2791}]},"lang":"en"},
  {"_key":"60c20b637723bebd8664544d","_id":"annotations/60c20b637723bebd8664544d","_rev":"_cfFmUqC---","document":{"$oid":"60c20b637723bebd8664544b"},"context":"In order to determine the interaction between AHNPA deriva- tives and APN, compound 13b was docked into the active sites of APN (PDB entry: 2DQM) using SYBYL 7.0. 12","references":[{"offsetStart":9859,"normalizedForm":"12","refKey":10,"label":"12","reference_id":{"$oid":"60c20b637723bebd8664544c"},"offsetEnd":9862,"boundingBoxes":[{"x":194.456,"h":5.0205,"y":693.361,"p":4,"w":6.9696}]}],"type":"software","software-name":{"offsetStart":153,"normalizedForm":"SYBYL","offsetEnd":158,"rawForm":"SYBYL","boundingBoxes":[{"x":160.27,"h":5.2721,"y":696.68,"p":4,"w":16.3402}]},"version":{"offsetStart":159,"normalizedForm":"7.0","offsetEnd":162,"rawForm":"7.0","boundingBoxes":[{"x":181.077,"h":7.531799999999976,"y":694.923,"p":4,"w":10.02494999999999}]}},
  {"_key":"60c20b6c7723bebd8664544f","_id":"annotations/60c20b6c7723bebd8664544f","_rev":"_cfFmUqO---","wikipediaExternalRef":34408890,"document":{"$oid":"60c20b6c7723bebd8664544e"},"context":"By WeChat and  online document editing all patients were treated with medical observation scale.","wikidataId":"Q283233","type":"software","confidence":0.7626,"software-name":{"wikipediaExternalRef":34408890,"normalizedForm":"WeChat","offsetStart":3,"wikidataId":"Q283233","offsetEnd":9,"lang":"en","confidence":0.7626,"rawForm":"WeChat","boundingBoxes":[{"x":453.78,"h":8.5272,"y":580.69,"p":1,"w":30.8937}]},"lang":"en"},
  {"_key":"60c20b6c7723bebd86645450","_id":"annotations/60c20b6c7723bebd86645450","_rev":"_cfFmUqa---","wikipediaExternalRef":34408890,"document":{"$oid":"60c20b6c7723bebd8664544e"},"context":"This system uses  WeChat and online document editing means to maintain continuous and interactive monitoring of the  patients' conditions in order to minimize the risk of cross-infection.","wikidataId":"Q283233","type":"software","confidence":0.7626,"software-name":{"wikipediaExternalRef":34408890,"normalizedForm":"WeChat","offsetStart":19,"wikidataId":"Q283233","offsetEnd":25,"lang":"en","confidence":0.7626,"rawForm":"WeChat","boundingBoxes":[{"x":111.06,"h":8.5272,"y":520.927,"p":7,"w":30.8591}]},"lang":"en"},
  {"_key":"60c20b6c7723bebd86645451","_id":"annotations/60c20b6c7723bebd86645451","_rev":"_cfFmUqi---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b6c7723bebd8664544e"},"context":"Statistical analysis was performed using SPSS26•0.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":41,"wikidataId":"Q181596","offsetEnd":45,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":288.897,"h":8.5272,"y":690.129,"p":5,"w":26.599399999999996}]},"version":{"offsetStart":45,"normalizedForm":"26•0","offsetEnd":49,"rawForm":"26•0","boundingBoxes":[{"x":288.897,"h":8.527199999999993,"y":690.129,"p":5,"w":35.465866666666614}]}},
  {"_key":"60c20b6d7723bebd86645458","_id":"annotations/60c20b6d7723bebd86645458","_rev":"_cfFmUqu---","document":{"$oid":"60c20b6d7723bebd86645452"},"publisher":{"offsetStart":62,"normalizedForm":"Fluidigm","offsetEnd":70,"rawForm":"Fluidigm","boundingBoxes":[{"x":387.7523111111111,"h":8.6524,"y":190.328,"p":11,"w":33.346488888888885}]},"context":"The data were analysed with Real-Time PCR Analysis Software (Fluidigm Corporation, CA, USA).","type":"software","software-name":{"offsetStart":29,"normalizedForm":"Real-Time PCR Analysis","offsetEnd":51,"rawForm":"Real-Time PCR Analysis","boundingBoxes":[{"x":247.975,"h":8.6524,"y":190.328,"p":11,"w":94.72979999999998}]}},
  {"_key":"60c20b6d7723bebd86645459","_id":"annotations/60c20b6d7723bebd86645459","_rev":"_cfFmUq6---","document":{"$oid":"60c20b6d7723bebd86645452"},"context":"The maps were created within R using ggplot2 (Wickham, 2016) and ggmap (Kahle and Wickham, 2013).","references":[{"offsetStart":40524,"normalizedForm":"Wickham, 2016","refKey":38,"label":"(Wickham, 2016)","reference_id":{"$oid":"60c20b6d7723bebd86645453"},"offsetEnd":40540,"boundingBoxes":[{"x":362.551,"h":8.652399999999943,"y":579.241,"p":10,"w":70.49380000000002}]}],"type":"software","software-name":{"offsetStart":37,"normalizedForm":"ggplot","offsetEnd":43,"rawForm":"ggplot","boundingBoxes":[{"x":327.458,"h":8.6524,"y":579.241,"p":10,"w":32.0992}]},"version":{"offsetStart":43,"normalizedForm":"2","offsetEnd":44,"rawForm":"2","boundingBoxes":[{"x":327.458,"h":8.6524,"y":579.241,"p":10,"w":32.0992}]}},
  {"_key":"60c20b6d7723bebd8664545a","_id":"annotations/60c20b6d7723bebd8664545a","_rev":"_cfFmUrG---","document":{"$oid":"60c20b6d7723bebd86645452"},"context":"The unmapped reads were then balanced using Trimmomatic and assembled into contigs using SPAdes (v3.9.1) genome assembler (Bankevich et al., 2012).","references":[{"offsetStart":37467,"normalizedForm":"Bankevich et al., 2012","refKey":1,"label":"(Bankevich et al., 2012)","reference_id":{"$oid":"60c20b6d7723bebd86645454"},"offsetEnd":37491,"boundingBoxes":[{"x":282.67,"h":8.6524,"y":139.248,"p":10,"w":101.36199999999997}]}],"type":"software","software-name":{"offsetStart":45,"normalizedForm":"Trimmomatic","offsetEnd":56,"rawForm":"Trimmomatic","boundingBoxes":[{"x":277.568,"h":8.6524,"y":163.682,"p":10,"w":53.0085}]},"version":{"offsetStart":84,"normalizedForm":"0.36","offsetEnd":88,"rawForm":"0.36","boundingBoxes":[{"x":255.41750000000002,"h":8.6524,"y":139.248,"p":10,"w":19.07249999999999}]}},
  {"_key":"60c20b6d7723bebd8664545b","_id":"annotations/60c20b6d7723bebd8664545b","_rev":"_cfFmUrS---","document":{"$oid":"60c20b6d7723bebd86645452"},"context":"The quality of the raw reads was checked using FASTQC (v0.11.7) (https://www.bioinformatics.bab- raham.ac.uk/projects/fastqc/).","type":"software","software-name":{"offsetStart":47,"normalizedForm":"FASTQC","offsetEnd":53,"rawForm":"FASTQC","boundingBoxes":[{"x":366.235,"h":8.6524,"y":114.813,"p":10,"w":35.1926}]},"url":{"offsetStart":65,"normalizedForm":"https://www.bioinformatics.bab- raham.ac.uk/projects/fastqc","offsetEnd":124,"rawForm":"https://www.bioinformatics.bab-\nraham.ac.uk/projects/fastqc","boundingBoxes":[{"x":445.9656875,"h":8.6524,"y":114.813,"p":10,"w":128.95031250000005},{"x":168.548,"h":8.6524,"y":127.059,"p":10,"w":108.3168}]},"version":{"offsetStart":56,"normalizedForm":"0.11.7","offsetEnd":62,"rawForm":"0.11.7","boundingBoxes":[{"x":408.2987111111111,"h":8.6524,"y":114.813,"p":10,"w":26.576977777777756}]}},
  {"_key":"60c20b6d7723bebd8664545c","_id":"annotations/60c20b6d7723bebd8664545c","_rev":"_cfFmUre---","document":{"$oid":"60c20b6d7723bebd86645452"},"context":"Reads were aligned to the Atlantic Salmon genome using bwa mem (v0.7.17-r1188) and unmapped reads were retained.","type":"software","software-name":{"offsetStart":56,"normalizedForm":"bwa mem","offsetEnd":63,"rawForm":"bwa mem","boundingBoxes":[{"x":229.436,"h":8.6524,"y":151.493,"p":10,"w":40.105699999999985}]},"version":{"offsetStart":66,"normalizedForm":"0.7.17-r","offsetEnd":74,"rawForm":"0.7.17-r","boundingBoxes":[{"x":276.64451333333335,"h":8.6524,"y":151.493,"p":10,"w":52.11067333333335}]}},
  {"_key":"60c20b6d7723bebd8664545d","_id":"annotations/60c20b6d7723bebd8664545d","_rev":"_cfFmUrq---","document":{"$oid":"60c20b6d7723bebd86645452"},"context":"The maps were created within R using ggplot2 (Wickham, 2016) and ggmap (Kahle and Wickham, 2013).","references":[{"offsetStart":40550,"normalizedForm":"Kahle and Wickham, 2013","refKey":19,"label":"(Kahle and Wickham, 2013)","reference_id":{"$oid":"60c20b6d7723bebd86645455"},"offsetEnd":40576,"boundingBoxes":[{"x":485.971,"h":8.652399999999943,"y":579.241,"p":10,"w":88.99580000000003},{"x":168.548,"h":8.652400000000057,"y":591.487,"p":10,"w":22.057500000000005}]}],"type":"software","software-name":{"offsetStart":65,"normalizedForm":"ggmap","offsetEnd":70,"rawForm":"ggmap","boundingBoxes":[{"x":454.167,"h":8.6524,"y":579.241,"p":10,"w":28.8355}]}},
  {"_key":"60c20b6d7723bebd8664545e","_id":"annotations/60c20b6d7723bebd8664545e","_rev":"_cfFmUry---","document":{"$oid":"60c20b6d7723bebd86645452"},"context":"Low quality reads or regions of adapter sequences were removed using Trimmomatic (v0.36) (Bankevich et al., 2012).","references":[{"offsetStart":37467,"normalizedForm":"Bankevich et al., 2012","refKey":1,"label":"(Bankevich et al., 2012)","reference_id":{"$oid":"60c20b6d7723bebd86645454"},"offsetEnd":37491,"boundingBoxes":[{"x":282.67,"h":8.6524,"y":139.248,"p":10,"w":101.36199999999997}]}],"type":"software","software-name":{"offsetStart":70,"normalizedForm":"Trimmomatic","offsetEnd":81,"rawForm":"Trimmomatic","boundingBoxes":[{"x":194.229,"h":8.6524,"y":139.248,"p":10,"w":53.0085}]},"version":{"offsetStart":84,"normalizedForm":"0.36","offsetEnd":88,"rawForm":"0.36","boundingBoxes":[{"x":255.41750000000002,"h":8.6524,"y":139.248,"p":10,"w":19.07249999999999}]}},
  {"_key":"60c20b6d7723bebd8664545f","_id":"annotations/60c20b6d7723bebd8664545f","_rev":"_cfFmUs----","document":{"$oid":"60c20b6d7723bebd86645452"},"context":"The multiple protein alignments were then used as to build phylogenies using PhyML 3.0 (Guindon et al., 2010) plugin within Geneious with 100 boot- straps to generate branch support values.","references":[{"offsetStart":39148,"normalizedForm":"Guindon et al., 2010","refKey":15,"label":"(Guindon et al., 2010)","reference_id":{"$oid":"60c20b6d7723bebd86645456"},"offsetEnd":39171,"boundingBoxes":[{"x":316.799,"h":8.6524,"y":383.651,"p":10,"w":94.64630000000005}]}],"type":"software","software-name":{"offsetStart":78,"normalizedForm":"PhyML","offsetEnd":83,"rawForm":"PhyML","boundingBoxes":[{"x":269.801,"h":8.6524,"y":383.651,"p":10,"w":27.1678}]},"version":{"offsetStart":84,"normalizedForm":"3.0","offsetEnd":87,"rawForm":"3.0","boundingBoxes":[{"x":300.699,"h":8.6524,"y":383.651,"p":10,"w":12.418299999999988}]}},
  {"_key":"60c20b6d7723bebd86645460","_id":"annotations/60c20b6d7723bebd86645460","_rev":"_cfFmUsK---","document":{"$oid":"60c20b6d7723bebd86645452"},"context":"Putative viral contigs were identified by aligning translated con- tigs using DIAMOND (v0.9.16.117) (Buchfink et al., 2015) to the nr database.","references":[{"offsetStart":37857,"normalizedForm":"Buchfink et al., 2015","refKey":5,"label":"(Buchfink et al., 2015)","reference_id":{"$oid":"60c20b6d7723bebd86645457"},"offsetEnd":37881,"boundingBoxes":[{"x":311.98,"h":8.6524,"y":188.117,"p":10,"w":92.32089999999994}]}],"type":"software","software-name":{"offsetStart":78,"normalizedForm":"DIAMOND","offsetEnd":85,"rawForm":"DIAMOND","boundingBoxes":[{"x":210.217,"h":8.6524,"y":188.117,"p":10,"w":44.5264}]},"version":{"offsetStart":88,"normalizedForm":"0.9.16.117","offsetEnd":98,"rawForm":"0.9.16.117","boundingBoxes":[{"x":261.57646923076925,"h":8.6524,"y":188.117,"p":10,"w":43.609161538461535}]}},
  {"_key":"60c20b6d7723bebd86645461","_id":"annotations/60c20b6d7723bebd86645461","_rev":"_cfFmUsW---","document":{"$oid":"60c20b6d7723bebd86645452"},"publisher":{"offsetStart":113,"normalizedForm":"Thermo Fisher Scientific","offsetEnd":137,"rawForm":"Thermo Fisher Scientific","boundingBoxes":[{"x":237.7646,"h":8.6524,"y":457.182,"p":10,"w":93.4390363636364}]},"context":"Assembled viral sequence contigs from the appropriate sample were imported into Primer Express v3.0.1 software (Thermo Fisher Scientific, Waltham, MA) where qPCR Taqman assays were designed using default parameters (Supplementary file 1).","type":"software","software-name":{"offsetStart":80,"normalizedForm":"Primer Express","offsetEnd":94,"rawForm":"Primer Express","boundingBoxes":[{"x":514.204,"h":8.6524,"y":444.936,"p":10,"w":60.736000000000104}]},"version":{"offsetStart":97,"normalizedForm":"3.0.1","offsetEnd":102,"rawForm":"3.0.1","boundingBoxes":[{"x":168.548,"h":8.6524,"y":457.182,"p":10,"w":24.182000000000016}]}},
  {"_key":"60c20b6d7723bebd86645462","_id":"annotations/60c20b6d7723bebd86645462","_rev":"_cfFmUsi---","wikipediaExternalRef":40693593,"document":{"$oid":"60c20b6d7723bebd86645452"},"context":"The unmapped reads were then balanced using Trimmomatic and assembled into contigs using SPAdes (v3.9.1) genome assembler (Bankevich et al., 2012).","wikidataId":"Q16335200","type":"software","lang":"en","confidence":0.7275,"software-name":{"wikipediaExternalRef":40693593,"normalizedForm":"SPAdes","offsetStart":90,"wikidataId":"Q16335200","offsetEnd":96,"lang":"en","confidence":0.7275,"rawForm":"SPAdes","boundingBoxes":[{"x":474.859,"h":8.6524,"y":163.682,"p":10,"w":30.8977}]},"version":{"offsetStart":99,"normalizedForm":"3.9.1","offsetEnd":104,"rawForm":"3.9.1","boundingBoxes":[{"x":512.7546249999999,"h":8.6524,"y":163.682,"p":10,"w":21.915750000000003}]}},
  {"_key":"60c20b6d7723bebd86645463","_id":"annotations/60c20b6d7723bebd86645463","_rev":"_cfFmUsu---","document":{"$oid":"60c20b6d7723bebd86645452"},"context":"The novel salmon viruses were aligned with other viral genomes with shared amino acid similarity as detected by DIAMOND (Buchfink et al., 2015).","references":[{"offsetStart":38938,"normalizedForm":"Buchfink et al., 2015","refKey":5,"label":"(Buchfink et al., 2015)","reference_id":{"$oid":"60c20b6d7723bebd86645457"},"offsetEnd":38961,"boundingBoxes":[{"x":269.688,"h":8.6524,"y":359.273,"p":10,"w":92.18574999999998}]}],"type":"software","software-name":{"offsetStart":114,"normalizedForm":"DIAMOND","offsetEnd":121,"rawForm":"DIAMOND","boundingBoxes":[{"x":221.725,"h":8.6524,"y":359.273,"p":10,"w":44.5264}]},"version":{"offsetStart":88,"normalizedForm":"0.9.16.117","offsetEnd":98,"rawForm":"0.9.16.117","boundingBoxes":[{"x":261.57646923076925,"h":8.6524,"y":188.117,"p":10,"w":43.609161538461535}]}},
  {"_key":"60c20b6d7723bebd86645464","_id":"annotations/60c20b6d7723bebd86645464","_rev":"_cfFmUs6---","wikipediaExternalRef":52292152,"document":{"$oid":"60c20b6d7723bebd86645452"},"context":"The multiple protein alignments were then used as to build phylogenies using PhyML 3.0 (Guindon et al., 2010) plugin within Geneious with 100 boot- straps to generate branch support values.","wikidataId":"Q4915084","type":"software","lang":"en","confidence":0.2365,"software-name":{"wikipediaExternalRef":52292152,"normalizedForm":"Geneious","offsetStart":125,"wikidataId":"Q4915084","offsetEnd":133,"lang":"en","confidence":0.2365,"rawForm":"Geneious","boundingBoxes":[{"x":471.741,"h":8.6524,"y":383.651,"p":10,"w":38.0887}]},"version":{"offsetStart":177,"normalizedForm":"10.1.3","offsetEnd":183,"rawForm":"10.1.3","boundingBoxes":[{"x":391.22904,"h":8.6524,"y":212.495,"p":10,"w":26.530280000000005}]}},
  {"_key":"60c20b6d7723bebd86645465","_id":"annotations/60c20b6d7723bebd86645465","_rev":"_cfFmUtG---","wikipediaExternalRef":52292152,"document":{"$oid":"60c20b6d7723bebd86645452"},"context":"Reference alignments of all the reads to the viral contigs were used to ensure that no assembly artefacts occurred and the contigs were trimmed appropriately using Geneious (V10.1.3).","wikidataId":"Q4915084","type":"software","lang":"en","confidence":0.4424,"software-name":{"wikipediaExternalRef":52292152,"normalizedForm":"Geneious","offsetStart":166,"wikidataId":"Q4915084","offsetEnd":174,"lang":"en","confidence":0.4424,"rawForm":"Geneious","boundingBoxes":[{"x":345.713,"h":8.6524,"y":212.495,"p":10,"w":38.0887}]},"version":{"offsetStart":177,"normalizedForm":"10.1.3","offsetEnd":183,"rawForm":"10.1.3","boundingBoxes":[{"x":391.22904,"h":8.6524,"y":212.495,"p":10,"w":26.530280000000005}]}},
  {"_key":"60c20b8b7723bebd86645467","_id":"annotations/60c20b8b7723bebd86645467","_rev":"_cfFmUtS---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b8b7723bebd86645466"},"publisher":{"offsetStart":47,"normalizedForm":"SPSS Inc","offsetEnd":55,"rawForm":"SPSS Inc","boundingBoxes":[{"x":97.11945999999999,"h":8.986999999999966,"y":590.347,"p":3,"w":29.53326}]},"context":"All analyses were done in PASW ver- sion 18.0 (SPSS Inc., Chicago, IL, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.5336,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"PASW","offsetStart":26,"wikidataId":"Q181596","offsetEnd":30,"lang":"en","confidence":0.5336,"rawForm":"PASW","boundingBoxes":[{"x":247.558,"h":8.987,"y":577.817,"p":3,"w":24.7249}]},"version":{"offsetStart":41,"normalizedForm":"18.0","offsetEnd":45,"rawForm":"18.0","boundingBoxes":[{"x":73.9036,"h":8.986999999999966,"y":590.347,"p":3,"w":16.7504}]}},
  {"_key":"60c20b8f7723bebd8664546b","_id":"annotations/60c20b8f7723bebd8664546b","_rev":"_cfFmUte---","document":{"$oid":"60c20b8f7723bebd86645468"},"publisher":{"offsetStart":24,"normalizedForm":"Illumina, Inc","offsetEnd":37,"rawForm":"Illumina, Inc","boundingBoxes":[{"x":457.12758,"h":9.584000000000003,"y":241.849,"p":3,"w":55.287319999999966}]},"context":"The BaseSpace pipeline (Illumina, Inc., San Diego, CA, USA) and the TGex software (LifeMap Sciences, Inc., Alameda, CA, USA) were used for the variant calling and annotating variants, respectively.","type":"software","software-name":{"offsetStart":4,"normalizedForm":"BaseSpace pipeline","offsetEnd":22,"rawForm":"BaseSpace pipeline","boundingBoxes":[{"x":362.113,"h":9.584000000000003,"y":241.849,"p":3,"w":86.84309999999999}]}},
  {"_key":"60c20b8f7723bebd8664546c","_id":"annotations/60c20b8f7723bebd8664546c","_rev":"_cfFmUtq---","document":{"$oid":"60c20b8f7723bebd86645468"},"publisher":{"offsetStart":84,"normalizedForm":"LifeMap Sciences, Inc","offsetEnd":105,"rawForm":"LifeMap Sciences, Inc","boundingBoxes":[{"x":280.60865,"h":9.584000000000003,"y":255.358,"p":3,"w":91.08195}]},"context":"The BaseSpace pipeline (Illumina, Inc., San Diego, CA, USA) and the TGex software (LifeMap Sciences, Inc., Alameda, CA, USA) were used for the variant calling and annotating variants, respectively.","type":"software","software-name":{"offsetStart":69,"normalizedForm":"TGex","offsetEnd":73,"rawForm":"TGex","boundingBoxes":[{"x":208.675,"h":9.584,"y":255.358,"p":3,"w":23.6922}]}},
  {"_key":"60c20b8f7723bebd8664546d","_id":"annotations/60c20b8f7723bebd8664546d","_rev":"_cfFmUty---","document":{"$oid":"60c20b8f7723bebd86645468"},"type":"software","software-name":{"offsetStart":82,"normalizedForm":"GnomAD","offsetEnd":88,"rawForm":"GnomAD","boundingBoxes":[{"x":380.261,"h":9.584,"y":239.677,"p":6,"w":43.9602}]},"context":"This variant was predicted benign by in silico tools and it was not found in the GnomAD database."},
  {"_key":"60c20b8f7723bebd8664546e","_id":"annotations/60c20b8f7723bebd8664546e","_rev":"_cfFmUu----","document":{"$oid":"60c20b8f7723bebd86645468"},"type":"software","software-name":{"offsetStart":96,"normalizedForm":"Integrative Genome Viewer (IGV)","offsetEnd":128,"rawForm":"Integrative \nGenome Viewer (IGV)","boundingBoxes":[{"x":469.595,"h":9.584,"y":309.396,"p":3,"w":49.1427},{"x":76.535,"h":9.584000000000003,"y":322.905,"p":3,"w":96.22533333333334}]},"context":"Variants were examined for coverage and Qscore (minimum threshold of 30) and visualized by the Integrative Genome Viewer (IGV)."},
  {"_key":"60c20b8f7723bebd8664546f","_id":"annotations/60c20b8f7723bebd8664546f","_rev":"_cfFmUuK---","document":{"$oid":"60c20b8f7723bebd86645468"},"type":"software","software-name":{"offsetStart":155,"normalizedForm":"PolyPhen2","offsetEnd":164,"rawForm":"PolyPhen2","boundingBoxes":[{"x":331.3041090909091,"h":9.584000000000003,"y":131.602,"p":5,"w":44.28998181818184}]},"context":"To predict the potential impact on proteins of the rare identified variants (two in the PCSK3 gene and one in the TMPRSS2 gene), we used different tools (PolyPhen2, Mutation Taster, SIFT) [17-19], and two ensemble score (MetaLR_pred, MetaSVM_pred.)."},
  {"_key":"60c20b8f7723bebd86645470","_id":"annotations/60c20b8f7723bebd86645470","_rev":"_cfFmUuW---","document":{"$oid":"60c20b8f7723bebd86645468"},"context":"To predict the potential impact on proteins of the rare identified variants (two in the PCSK3 gene and one in the TMPRSS2 gene), we used different tools (PolyPhen2, Mutation Taster, SIFT) [17-19], and two ensemble score (MetaLR_pred, MetaSVM_pred.).","references":[{"offsetStart":15923,"normalizedForm":"[17]","refKey":16,"label":"[17]","reference_id":{"$oid":"60c20b8f7723bebd86645469"},"offsetEnd":15930,"boundingBoxes":[{"x":485.671,"h":9.584000000000003,"y":131.602,"p":5,"w":30.02510000000001}]},{"offsetStart":15923,"normalizedForm":"[19]","refKey":17,"label":"[19]","reference_id":{"$oid":"60c20b8f7723bebd8664546a"},"offsetEnd":15930,"boundingBoxes":[{"x":485.671,"h":9.584000000000003,"y":131.602,"p":5,"w":30.02510000000001}]}],"type":"software","software-name":{"offsetStart":166,"normalizedForm":"Mutation Taster, SIFT","offsetEnd":187,"rawForm":"Mutation Taster, SIFT","boundingBoxes":[{"x":383.178,"h":9.584000000000003,"y":131.602,"p":5,"w":95.06608}]}},
  {"_key":"60c20b8f7723bebd86645471","_id":"annotations/60c20b8f7723bebd86645471","_rev":"_cfFmUui---","document":{"$oid":"60c20b8f7723bebd86645468"},"type":"software","software-name":{"offsetStart":223,"normalizedForm":"MetaLR_pred","offsetEnd":234,"rawForm":"MetaLR_pred","boundingBoxes":[{"x":191.43005384615387,"h":9.584,"y":145.111,"p":5,"w":57.2775923076923}]},"context":"To predict the potential impact on proteins of the rare identified variants (two in the PCSK3 gene and one in the TMPRSS2 gene), we used different tools (PolyPhen2, Mutation Taster, SIFT) [17-19], and two ensemble score (MetaLR_pred, MetaSVM_pred.)."},
  {"_key":"60c20b8f7723bebd86645472","_id":"annotations/60c20b8f7723bebd86645472","_rev":"_cfFmUuu---","document":{"$oid":"60c20b8f7723bebd86645468"},"type":"software","software-name":{"offsetStart":236,"normalizedForm":"MetaSVM_pred","offsetEnd":248,"rawForm":"MetaSVM_pred","boundingBoxes":[{"x":256.417,"h":9.584,"y":145.111,"p":5,"w":63.58824}]},"context":"To predict the potential impact on proteins of the rare identified variants (two in the PCSK3 gene and one in the TMPRSS2 gene), we used different tools (PolyPhen2, Mutation Taster, SIFT) [17-19], and two ensemble score (MetaLR_pred, MetaSVM_pred.)."},
  {"_key":"60c20b8f7723bebd86645474","_id":"annotations/60c20b8f7723bebd86645474","_rev":"_cfFmUu6---","wikipediaExternalRef":20412,"document":{"$oid":"60c20b8f7723bebd86645473"},"context":"Using a custom MATLAB script based on edge detection, we seg- mented the retracting ends of the ablated myofibril and fit the trajec- tories to a standard Kelvin-Voigt viscoelastic solid model widely used  for retracting stress fibers and cell-cell junctions in nonmuscle  cells (Fernandez-Gonzalez et al., 2009; Kumar et al., 2006; Lee  et al., 2018).","wikidataId":"Q169478","type":"software","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":15,"wikidataId":"Q169478","offsetEnd":21,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":376.554,"h":7.1839,"y":521.22,"p":2,"w":31.9756}]},"lang":"en"},
  {"_key":"60c20b8f7723bebd86645475","_id":"annotations/60c20b8f7723bebd86645475","_rev":"_cfFmUvG---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20b8f7723bebd86645473"},"context":"Statistical analysis was performed in GraphPad and Excel.","wikidataId":"Q5597066","type":"software","confidence":0.2942,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad","offsetStart":38,"wikidataId":"Q5597066","offsetEnd":46,"lang":"en","confidence":0.2942,"rawForm":"GraphPad","boundingBoxes":[{"x":177.052,"h":7.1839,"y":352.231,"p":8,"w":34.4796}]},"lang":"en"},
  {"_key":"60c20b8f7723bebd86645476","_id":"annotations/60c20b8f7723bebd86645476","_rev":"_cfFmUvS---","document":{"$oid":"60c20b8f7723bebd86645473"},"context":"The Axion instrument was controlled using Maestro  Pro firmware version 1.5.3.4.","type":"software","software-name":{"offsetStart":42,"normalizedForm":"Maestro Pro","offsetEnd":55,"rawForm":"Maestro \n\nPro","boundingBoxes":[{"x":258.577,"h":7.1839,"y":222.233,"p":8,"w":29.0636},{"x":44.7883,"h":7.1839,"y":235.215,"p":8,"w":12.0718}]},"version":{"offsetStart":73,"normalizedForm":"1.5.3.4","offsetEnd":80,"rawForm":"1.5.3.4","boundingBoxes":[{"x":125.802,"h":7.183899999999994,"y":235.215,"p":8,"w":22.427737499999992}]}},
  {"_key":"60c20b8f7723bebd86645477","_id":"annotations/60c20b8f7723bebd86645477","_rev":"_cfFmUvi---","wikipediaExternalRef":20268,"document":{"$oid":"60c20b8f7723bebd86645473"},"context":"Statistical analysis was performed in GraphPad and Excel.","wikidataId":"Q11272","type":"software","confidence":0.378,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Excel","offsetStart":51,"wikidataId":"Q11272","offsetEnd":56,"lang":"en","confidence":0.378,"rawForm":"Excel","boundingBoxes":[{"x":230.457,"h":7.1839,"y":352.231,"p":8,"w":16.713083333333337}]},"lang":"en"},
  {"_key":"60c20b927723bebd86645479","_id":"annotations/60c20b927723bebd86645479","_rev":"_cfFmUvu---","document":{"$oid":"60c20b927723bebd86645478"},"publisher":{"offsetStart":55,"normalizedForm":"Scivis","offsetEnd":61,"rawForm":"Scivis","boundingBoxes":[{"x":96.63036249999999,"h":8.7472,"y":595.194,"p":4,"w":21.921975}]},"context":"Radionuclide images were reconstructed using HiSPECT (Scivis, Göttingen, Germany) iterative reconstruc- tion software and fused with CT images using proprietary InVivoScope (Bioscan) software.","type":"software","software-name":{"offsetStart":46,"normalizedForm":"HiSPECT","offsetEnd":53,"rawForm":"HiSPECT","boundingBoxes":[{"x":51.0242,"h":8.7472,"y":595.194,"p":4,"w":39.0713}]}},
  {"_key":"60c20b927723bebd8664547a","_id":"annotations/60c20b927723bebd8664547a","_rev":"_cfFmUv6---","wikipediaExternalRef":179088,"document":{"$oid":"60c20b927723bebd86645478"},"publisher":{"offsetStart":79,"normalizedForm":"IBM","offsetEnd":82,"rawForm":"IBM","boundingBoxes":[{"x":139.33576,"h":8.7472,"y":346.311,"p":5,"w":14.420279999999998}]},"context":"An independent samples t test was performed with SPSS Statistics 21 software (IBM, Armonk, NY) to compare normal liver uptake between the different radiolabelled G3 DARPins (p values <0.05 were considered statistically significant).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.4856,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS Statistics","offsetStart":49,"wikidataId":"Q181596","offsetEnd":65,"lang":"en","confidence":0.4856,"rawForm":"SPSS \nStatistics","boundingBoxes":[{"x":267.135,"h":8.7472,"y":333.839,"p":5,"w":21.9974},{"x":51.0226,"h":8.7472,"y":346.311,"p":5,"w":34.6071}]},"version":{"offsetStart":66,"normalizedForm":"21","offsetEnd":68,"rawForm":"21","boundingBoxes":[{"x":87.5316,"h":8.7472,"y":346.311,"p":5,"w":9.9626}]}},
  {"_key":"60c20b927723bebd8664547b","_id":"annotations/60c20b927723bebd8664547b","_rev":"_cfFmUwG---","wikipediaExternalRef":24666773,"document":{"$oid":"60c20b927723bebd86645478"},"publisher":{"offsetStart":102,"normalizedForm":"Tree Star","offsetEnd":112,"rawForm":"Tree \nStar","boundingBoxes":[{"x":272.71119999999996,"h":8.7472,"y":271.421,"p":5,"w":16.4088},{"x":51.0236,"h":8.7472,"y":283.894,"p":5,"w":14.056000000000001}]},"context":"A total of 10,000 cell events were recorded per sample and data were analysed using FlowJo software (Tree Star, Ashland, OR).","wikidataId":"Q5462055","type":"software","confidence":0.4725,"software-name":{"wikipediaExternalRef":24666773,"normalizedForm":"FlowJo","offsetStart":85,"wikidataId":"Q5462055","offsetEnd":91,"lang":"en","confidence":0.4725,"rawForm":"FlowJo","boundingBoxes":[{"x":200.692,"h":8.7472,"y":271.421,"p":5,"w":28.8298}]},"lang":"en"},
  {"_key":"60c20b927723bebd8664547c","_id":"annotations/60c20b927723bebd8664547c","_rev":"_cfFmUwS---","document":{"$oid":"60c20b927723bebd86645478"},"publisher":{"offsetStart":176,"normalizedForm":"Bioscan","offsetEnd":183,"rawForm":"Bioscan","boundingBoxes":[{"x":108.59546666666667,"h":8.7472,"y":620.081,"p":4,"w":29.172266666666665}]},"context":"Radionuclide images were reconstructed using HiSPECT (Scivis, Göttingen, Germany) iterative reconstruc- tion software and fused with CT images using proprietary InVivoScope (Bioscan) software.","type":"software","software-name":{"offsetStart":163,"normalizedForm":"InVivoScope","offsetEnd":174,"rawForm":"InVivoScope","boundingBoxes":[{"x":51.0242,"h":8.7472,"y":620.081,"p":4,"w":50.891}]}},
  {"_key":"60c20b947723bebd8664547e","_id":"annotations/60c20b947723bebd8664547e","_rev":"_cfFmUwe---","wikipediaExternalRef":20268,"document":{"$oid":"60c20b947723bebd8664547d"},"publisher":{"offsetStart":77,"normalizedForm":"Microsoft","offsetEnd":86,"rawForm":"Microsoft","boundingBoxes":[{"x":504.693,"h":8.7472,"y":483.117,"p":2,"w":39.5216}]},"context":"Descriptive statistics and unpaired, 2 tailed t-tests were calculated using Microsoft Excel (Redmond, WA) to compare the pre-intervention and post-intervention time periods.","wikidataId":"Q11272","type":"software","confidence":0.378,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Excel","offsetStart":88,"wikidataId":"Q11272","offsetEnd":93,"lang":"en","confidence":0.378,"rawForm":"Excel","boundingBoxes":[{"x":306.141,"h":8.7472,"y":495.589,"p":2,"w":22.0223}]},"lang":"en"},
  {"_key":"60c20b957723bebd86645480","_id":"annotations/60c20b957723bebd86645480","_rev":"_cfFmUwq---","document":{"$oid":"60c20b957723bebd8664547f"},"context":"The raw sequences were aligned with the Bur- rows-Wheeler Alignment tool (BWA) (v.0.7.10), duplicates were marked and removed with Picard, and indels were aligned with GATKLite v.2.3.9.","type":"software","software-name":{"offsetStart":40,"normalizedForm":"Bur- rows-Wheeler Alignment tool (BWA)","offsetEnd":78,"rawForm":"Bur-\nrows-Wheeler Alignment tool (BWA)","boundingBoxes":[{"x":529.392,"h":8.509,"y":107.903,"p":2,"w":17.17050000000006},{"x":307.501,"h":8.509,"y":119.808,"p":2,"w":151.21330000000006}]},"version":{"offsetStart":82,"normalizedForm":"0.7.10","offsetEnd":88,"rawForm":"0.7.10","boundingBoxes":[{"x":472.4964,"h":8.509,"y":119.808,"p":2,"w":22.384799999999984}]}},
  {"_key":"60c20b957723bebd86645481","_id":"annotations/60c20b957723bebd86645481","_rev":"_cfFmUw2---","document":{"$oid":"60c20b957723bebd8664547f"},"context":"Of note, during routine splicing analyses (Human Splicing Finder 3.1), the variants c.3410C>T and c.4382G>A were predicted to potentially alter splicing by generating an exonic splicing silencer (ESS) or an exonic splicing enhancer (ESE), respectively.","type":"software","software-name":{"offsetStart":43,"normalizedForm":"Human Splicing Finder","offsetEnd":65,"rawForm":"Human \nSplicing Finder","boundingBoxes":[{"x":518.3220166666666,"h":8.509,"y":430.643,"p":6,"w":28.240083333333335},{"x":307.504,"h":8.509000000000015,"y":442.605,"p":6,"w":67.53879999999998}]},"version":{"offsetStart":66,"normalizedForm":"3.1","offsetEnd":69,"rawForm":"3.1","boundingBoxes":[{"x":384.55,"h":8.509000000000015,"y":442.605,"p":6,"w":10.797779999999989}]}},
  {"_key":"60c20b957723bebd86645482","_id":"annotations/60c20b957723bebd86645482","_rev":"_cfFmUxC---","document":{"$oid":"60c20b957723bebd8664547f"},"type":"software","software-name":{"offsetStart":72,"normalizedForm":"GENESIS","offsetEnd":79,"rawForm":"GENESIS","boundingBoxes":[{"x":422.529,"h":8.509,"y":550.215,"p":2,"w":36.0185}]},"context":"Exome sequencing (ES) of the index individual was performed within the GENESIS (GEM.app)"},
  {"_key":"60c20b957723bebd86645483","_id":"annotations/60c20b957723bebd86645483","_rev":"_cfFmUxO---","document":{"$oid":"60c20b957723bebd8664547f"},"type":"software","software-name":{"offsetStart":84,"normalizedForm":".","offsetEnd":85,"rawForm":".","boundingBoxes":[{"x":482.422,"h":8.509,"y":550.215,"p":2,"w":4.896}]},"context":"Exome sequencing (ES) of the index individual was performed within the GENESIS (GEM.app)"},
  {"_key":"60c20b957723bebd86645484","_id":"annotations/60c20b957723bebd86645484","_rev":"_cfFmUxa---","document":{"$oid":"60c20b957723bebd8664547f"},"context":"It is relatively intolerant to missense variation, having a positive Z score of 2.41 (observed/expected ratio: 0.79, gnomAD v.2.1.1,","type":"software","software-name":{"offsetStart":119,"normalizedForm":"gnomAD","offsetEnd":125,"rawForm":"gnomAD","boundingBoxes":[{"x":307.504,"h":8.509,"y":418.681,"p":6,"w":37.3446}]},"version":{"offsetStart":128,"normalizedForm":"2.1.1","offsetEnd":133,"rawForm":"2.1.1","boundingBoxes":[{"x":354.97115,"h":8.509000000000015,"y":418.681,"p":6,"w":18.60787499999998}]}},
  {"_key":"60c20b957723bebd86645485","_id":"annotations/60c20b957723bebd86645485","_rev":"_cfFmUxm---","document":{"$oid":"60c20b957723bebd8664547f"},"type":"software","software-name":{"offsetStart":132,"normalizedForm":"Picard","offsetEnd":138,"rawForm":"Picard","boundingBoxes":[{"x":447.586,"h":8.509,"y":131.77,"p":2,"w":23.840142857142858}]},"context":"The raw sequences were aligned with the Bur- rows-Wheeler Alignment tool (BWA) (v.0.7.10), duplicates were marked and removed with Picard, and indels were aligned with GATKLite v.2.3.9."},
  {"_key":"60c20b957723bebd86645486","_id":"annotations/60c20b957723bebd86645486","_rev":"_cfFmUxy---","document":{"$oid":"60c20b957723bebd8664547f"},"context":"The raw sequences were aligned with the Bur- rows-Wheeler Alignment tool (BWA) (v.0.7.10), duplicates were marked and removed with Picard, and indels were aligned with GATKLite v.2.3.9.","type":"software","software-name":{"offsetStart":170,"normalizedForm":"GATKLite","offsetEnd":178,"rawForm":"GATKLite","boundingBoxes":[{"x":362.039,"h":8.509,"y":143.732,"p":2,"w":39.7978}]},"version":{"offsetStart":181,"normalizedForm":"2.3.9","offsetEnd":186,"rawForm":"2.3.9","boundingBoxes":[{"x":411.98602500000004,"h":8.508999999999986,"y":143.732,"p":2,"w":18.572562500000004}]}},
  {"_key":"60c20b957723bebd86645487","_id":"annotations/60c20b957723bebd86645487","_rev":"_cfFmUyC---","document":{"$oid":"60c20b957723bebd8664547f"},"context":"The variant was absent from our in-house database composed of 3,550 sequenced samples (RD-Con- nect's integrated platform for rare diseases) but present in the heterozygous state with a minor allele frequency of 2 in 282,866 (MAF ¼ 7 3 10 À6 ) in two individuals of African ancestry in gnomAD v.2.1.1.","type":"software","software-name":{"offsetStart":290,"normalizedForm":"gnomAD","offsetEnd":296,"rawForm":"gnomAD","boundingBoxes":[{"x":355.179,"h":8.509,"y":275.26,"p":2,"w":37.1779}]},"version":{"offsetStart":299,"normalizedForm":"2.1.1","offsetEnd":304,"rawForm":"2.1.1","boundingBoxes":[{"x":402.237775,"h":8.509000000000015,"y":275.26,"p":2,"w":18.4369375}]}},
  {"_key":"60c20b9d7723bebd8664548b","_id":"annotations/60c20b9d7723bebd8664548b","_rev":"_cfFmUyO---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":4,"normalizedForm":"MatureBayes","offsetEnd":15,"rawForm":"MatureBayes","boundingBoxes":[{"x":304.706,"h":10.8,"y":679.264,"p":5,"w":63.804}]},"context":"The MatureBayes prediction revealed 22-nucleotide  long 8 mature miRNAs from the pre-miRNA sequences on their 5' and 3' stem locations (Table"},
  {"_key":"60c20b9d7723bebd8664548c","_id":"annotations/60c20b9d7723bebd8664548c","_rev":"_cfFmUya---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":4,"normalizedForm":"MatureBayes","offsetEnd":15,"rawForm":"MatureBayes","boundingBoxes":[{"x":97.572,"h":10.8,"y":74.624,"p":17,"w":63.804}]},"context":"The MatureBayes tool was used at default parameters to predict mature miRNAs (13)."},
  {"_key":"60c20b9d7723bebd8664548d","_id":"annotations/60c20b9d7723bebd8664548d","_rev":"_cfFmUym---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":12,"normalizedForm":"MFold","offsetEnd":17,"rawForm":"MFold","boundingBoxes":[{"x":132.468,"h":10.8,"y":336.014,"p":5,"w":32.616}]},"context":"Next, using MFold web server the Minimal Folding Free Energy (MFE) of each sequence was  calculated because MFE of the pre-miRNA folding is inversely proportional to the  thermodynamic stability of the molecule (11)."},
  {"_key":"60c20b9d7723bebd8664548e","_id":"annotations/60c20b9d7723bebd8664548e","_rev":"_cfFmUyy---","wikipediaExternalRef":36691501,"document":{"$oid":"60c20b9d7723bebd86645488"},"context":"Software packages R and R Studio were used to visualize the top  GO terms and KEGG pathways.","wikidataId":"Q4798119","type":"software","confidence":0.3467,"software-name":{"wikipediaExternalRef":36691501,"normalizedForm":"R Studio","offsetStart":24,"wikidataId":"Q4798119","offsetEnd":32,"lang":"en","confidence":0.3467,"rawForm":"R Studio","boundingBoxes":[{"x":348.18,"h":10.799999999999955,"y":595.504,"p":17,"w":43.30599999999998}]},"lang":"en"},
  {"_key":"60c20b9d7723bebd8664548f","_id":"annotations/60c20b9d7723bebd8664548f","_rev":"_cfFmUz----","document":{"$oid":"60c20b9d7723bebd86645488"},"context":"Genes were mapped onto the KEGG pathways using the PaintOmics3  (60) using default parameters.","type":"software","software-name":{"offsetStart":51,"normalizedForm":"PaintOmics","offsetEnd":61,"rawForm":"PaintOmics","boundingBoxes":[{"x":478.06,"h":10.8,"y":567.874,"p":17,"w":62.028}]},"version":{"offsetStart":61,"normalizedForm":"3","offsetEnd":64,"rawForm":"3","boundingBoxes":[{"x":478.06,"h":10.8,"y":567.874,"p":17,"w":62.028}]}},
  {"_key":"60c20b9d7723bebd86645490","_id":"annotations/60c20b9d7723bebd86645490","_rev":"_cfFmUzK---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":59,"normalizedForm":"MFold","offsetEnd":64,"rawForm":"MFold","boundingBoxes":[{"x":397.87,"h":10.8,"y":404.794,"p":16,"w":32.616}]},"context":"The VMir-derived pre-miRNA sequences were submitted to the MFold (11) web-server with  default parameters for secondary structure prediction and MFE (ΔG in kcal/mol) calculation."},
  {"_key":"60c20b9d7723bebd86645491","_id":"annotations/60c20b9d7723bebd86645491","_rev":"_cfFmUzW---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":68,"normalizedForm":"ClueGO","offsetEnd":74,"rawForm":"ClueGO","boundingBoxes":[{"x":166.436,"h":10.8,"y":512.674,"p":17,"w":39.972}]},"context":"To conduct GO and KEGG pathway analysis for the  target mRNAs, the ClueGO (26), CluePedia (58), CytoKEGG, and KEGGParser (59) plugins on  Cytoscape (27) were used."},
  {"_key":"60c20b9d7723bebd86645492","_id":"annotations/60c20b9d7723bebd86645492","_rev":"_cfFmUzi---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":70,"normalizedForm":"MFold","offsetEnd":75,"rawForm":"MFold","boundingBoxes":[{"x":172.908,"h":10.8,"y":418.834,"p":5,"w":29.77}]},"context":"The secondary structure of these sequences was  also predicted using MFold."},
  {"_key":"60c20b9d7723bebd86645493","_id":"annotations/60c20b9d7723bebd86645493","_rev":"_cfFmUzu---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":71,"normalizedForm":"Molecular COmplex DEtection (MCODE)","offsetEnd":106,"rawForm":"Molecular COmplex DEtection (MCODE)","boundingBoxes":[{"x":209.184,"h":10.799999999999955,"y":555.874,"p":9,"w":206.568}]},"context":"To identify the significant interactions  within the PPI network, the Molecular COmplex DEtection (MCODE) plugin (31) in Cytoscape  was utilized, which predicted 16 significant interaction modules."},
  {"_key":"60c20b9d7723bebd86645494","_id":"annotations/60c20b9d7723bebd86645494","_rev":"_cfFmUz6---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":77,"normalizedForm":"ReactomeFI","offsetEnd":87,"rawForm":"ReactomeFI","boundingBoxes":[{"x":432.946,"h":10.8,"y":102.224,"p":36,"w":58.68}]},"context":"(A) PPI  network of the target genes of SARS-CoV-2 miRNAs constructed using ReactomeFI plugin in  Cytoscape."},
  {"_key":"60c20b9d7723bebd86645495","_id":"annotations/60c20b9d7723bebd86645495","_rev":"_cfFmU0G---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":81,"normalizedForm":"CluePedia","offsetEnd":90,"rawForm":"CluePedia","boundingBoxes":[{"x":236.186,"h":10.8,"y":512.674,"p":17,"w":49.356}]},"context":"To conduct GO and KEGG pathway analysis for the  target mRNAs, the ClueGO (26), CluePedia (58), CytoKEGG, and KEGGParser (59) plugins on  Cytoscape (27) were used."},
  {"_key":"60c20b9d7723bebd86645496","_id":"annotations/60c20b9d7723bebd86645496","_rev":"_cfFmU0S---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20b9d7723bebd86645488"},"context":"A PPI network of the 1121 targets  was constructed using the ReactomeFI plugin in Cytoscape (Figure 5A) (27).","wikidataId":"Q3699942","type":"software","confidence":0.8058,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":83,"wikidataId":"Q3699942","offsetEnd":92,"lang":"en","confidence":0.8058,"rawForm":"Cytoscape","boundingBoxes":[{"x":324.348,"h":10.8,"y":500.674,"p":9,"w":49.824}]},"lang":"en"},
  {"_key":"60c20b9d7723bebd86645497","_id":"annotations/60c20b9d7723bebd86645497","_rev":"_cfFmU0e---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":84,"normalizedForm":"VMir","offsetEnd":88,"rawForm":"VMir","boundingBoxes":[{"x":200.34,"h":10.908,"y":268.694,"p":5,"w":26.664}]},"context":"The length of these sequences ranged between 70 and 148  nucleotides, and they had VMir score ≥115, hairpin size ≥ 70, and window count ≥ 35 (Figure  1A, Supplementary Material -Sheet 1)."},
  {"_key":"60c20b9d7723bebd86645498","_id":"annotations/60c20b9d7723bebd86645498","_rev":"_cfFmU0q---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20b9d7723bebd86645488"},"context":"The GO analysis of the 1121 potential targets of the SARS-CoV-2 miRNAs was executed using  the Cytoscape plugin, ClueGo (26,27) 3D, Figure 4A-D, Supplementary Material-Sheet  6).","wikidataId":"Q3699942","type":"software","confidence":0.8039,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":96,"wikidataId":"Q3699942","offsetEnd":105,"lang":"en","confidence":0.8039,"rawForm":"Cytoscape","boundingBoxes":[{"x":94.212,"h":10.8,"y":429.874,"p":8,"w":49.944}]},"lang":"en"},
  {"_key":"60c20b9d7723bebd86645499","_id":"annotations/60c20b9d7723bebd86645499","_rev":"_cfFmU02---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":97,"normalizedForm":"CytoKEGG","offsetEnd":105,"rawForm":"CytoKEGG","boundingBoxes":[{"x":315.418,"h":10.8,"y":512.674,"p":17,"w":53.024}]},"context":"To conduct GO and KEGG pathway analysis for the  target mRNAs, the ClueGO (26), CluePedia (58), CytoKEGG, and KEGGParser (59) plugins on  Cytoscape (27) were used."},
  {"_key":"60c20b9d7723bebd8664549a","_id":"annotations/60c20b9d7723bebd8664549a","_rev":"_cfFmU1C---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20b9d7723bebd86645488"},"context":"(A) PPI  network of the target genes of SARS-CoV-2 miRNAs constructed using ReactomeFI plugin in  Cytoscape.","wikidataId":"Q3699942","type":"software","confidence":0.8039,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":100,"wikidataId":"Q3699942","offsetEnd":109,"lang":"en","confidence":0.8039,"rawForm":"Cytoscape","boundingBoxes":[{"x":72.024,"h":10.8,"y":129.824,"p":36,"w":47.595600000000005}]},"lang":"en"},
  {"_key":"60c20b9d7723bebd8664549b","_id":"annotations/60c20b9d7723bebd8664549b","_rev":"_cfFmU1K---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":109,"normalizedForm":"MFold","offsetEnd":114,"rawForm":"MFold","boundingBoxes":[{"x":394.51,"h":10.8,"y":102.224,"p":30,"w":29.825}]},"context":"(B) Secondary structures of the predicated  stem-loops of most likely pre-miRNAs candidates generated using MFold."},
  {"_key":"60c20b9d7723bebd8664549c","_id":"annotations/60c20b9d7723bebd8664549c","_rev":"_cfFmU1a---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":111,"normalizedForm":"KEGGParser","offsetEnd":121,"rawForm":"KEGGParser","boundingBoxes":[{"x":399.166,"h":10.8,"y":512.674,"p":17,"w":63.264}]},"context":"To conduct GO and KEGG pathway analysis for the  target mRNAs, the ClueGO (26), CluePedia (58), CytoKEGG, and KEGGParser (59) plugins on  Cytoscape (27) were used."},
  {"_key":"60c20b9d7723bebd8664549d","_id":"annotations/60c20b9d7723bebd8664549d","_rev":"_cfFmU1m---","document":{"$oid":"60c20b9d7723bebd86645488"},"context":"The GO analysis of the 1121 potential targets of the SARS-CoV-2 miRNAs was executed using  the Cytoscape plugin, ClueGo (26,27) 3D, Figure 4A-D, Supplementary Material-Sheet  6).","references":[{"offsetStart":15622,"normalizedForm":"(26","refKey":29,"label":"(26,","reference_id":{"$oid":"60c20b9d7723bebd86645489"},"offsetEnd":15630,"boundingBoxes":[{"x":237.89,"h":10.800000000000011,"y":429.874,"p":8,"w":34.95600000000002}]},{"offsetStart":15622,"normalizedForm":"27)","refKey":30,"label":"27)","reference_id":{"$oid":"60c20b9d7723bebd8664548a"},"offsetEnd":15630,"boundingBoxes":[{"x":237.89,"h":10.800000000000011,"y":429.874,"p":8,"w":34.95600000000002}]}],"type":"software","software-name":{"offsetStart":114,"normalizedForm":"ClueGo","offsetEnd":120,"rawForm":"ClueGo","boundingBoxes":[{"x":192.912,"h":10.8,"y":429.874,"p":8,"w":37.308}]}},
  {"_key":"60c20b9d7723bebd8664549e","_id":"annotations/60c20b9d7723bebd8664549e","_rev":"_cfFmU12---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20b9d7723bebd86645488"},"context":"To identify the significant interactions  within the PPI network, the Molecular COmplex DEtection (MCODE) plugin (31) in Cytoscape  was utilized, which predicted 16 significant interaction modules.","wikidataId":"Q3699942","type":"software","confidence":0.8058,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":122,"wikidataId":"Q3699942","offsetEnd":133,"lang":"en","confidence":0.8058,"rawForm":"Cytoscape","boundingBoxes":[{"x":490.156,"h":10.8,"y":555.874,"p":9,"w":49.944}]},"lang":"en"},
  {"_key":"60c20b9d7723bebd8664549f","_id":"annotations/60c20b9d7723bebd8664549f","_rev":"_cfFmU2C---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20b9d7723bebd86645488"},"context":"To conduct GO and KEGG pathway analysis for the  target mRNAs, the ClueGO (26), CluePedia (58), CytoKEGG, and KEGGParser (59) plugins on  Cytoscape (27) were used.","wikidataId":"Q3699942","type":"software","confidence":0.8039,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":140,"wikidataId":"Q3699942","offsetEnd":149,"lang":"en","confidence":0.8039,"rawForm":"Cytoscape","boundingBoxes":[{"x":72.024,"h":10.8,"y":540.274,"p":17,"w":49.932}]},"lang":"en"},
  {"_key":"60c20b9d7723bebd866454a0","_id":"annotations/60c20b9d7723bebd866454a0","_rev":"_cfFmU2O---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":156,"normalizedForm":"VMir","offsetEnd":160,"rawForm":"VMir","boundingBoxes":[{"x":378.794,"h":10.8,"y":185.984,"p":5,"w":26.664}]},"context":"As pre-miRNAs form hair-pin loop structures during their biogenesis, we first searched for such  arrangements in the SARS-CoV-2 genomic sequence using the VMir software (10)."},
  {"_key":"60c20b9d7723bebd866454a1","_id":"annotations/60c20b9d7723bebd866454a1","_rev":"_cfFmU2a---","document":{"$oid":"60c20b9d7723bebd86645488"},"type":"software","software-name":{"offsetStart":197,"normalizedForm":"MatureBayes","offsetEnd":208,"rawForm":"MatureBayes","boundingBoxes":[{"x":92.064,"h":10.8,"y":679.264,"p":5,"w":63.804}]},"context":"The  pre-miRNAs MD50, MD62, and MD86 on the direct strand and MR5 on the reverse strand, with  MFEI ≤ -0.85 kcal/mol, were chosen as the best candidates for the prediction of mature miRNAs  via MatureBayes tool (Figure 1B) (13)."},
  {"_key":"60c20ba07723bebd866454a3","_id":"annotations/60c20ba07723bebd866454a3","_rev":"_cfFmU2q---","wikipediaExternalRef":48508507,"document":{"$oid":"60c20ba07723bebd866454a2"},"context":"The training process has been done using the TensorFlow library.","wikidataId":"Q21447895","type":"software","confidence":0.7843,"software-name":{"wikipediaExternalRef":48508507,"normalizedForm":"TensorFlow","offsetStart":46,"wikidataId":"Q21447895","offsetEnd":56,"lang":"en","confidence":0.7843,"rawForm":"TensorFlow","boundingBoxes":[{"x":221.329,"h":8.9365,"y":368.637,"p":6,"w":50.2952}]},"lang":"en"},
  {"_key":"60c20ba67723bebd866454a6","_id":"annotations/60c20ba67723bebd866454a6","_rev":"_cfFmU22---","wikipediaExternalRef":1979375,"document":{"$oid":"60c20ba67723bebd866454a5"},"publisher":{"offsetStart":12,"normalizedForm":"SAS Institute Inc","offsetEnd":29,"rawForm":"SAS Institute Inc","boundingBoxes":[{"x":110.513,"h":11.480000000000018,"y":620.162,"p":4,"w":72.7305}]},"context":"JMP®14.0.0,","wikidataId":"Q1161680","type":"software","lang":"en","confidence":0.3648,"software-name":{"wikipediaExternalRef":1979375,"normalizedForm":"JMP","offsetStart":0,"wikidataId":"Q1161680","offsetEnd":3,"lang":"en","confidence":0.3648,"rawForm":"JMP","boundingBoxes":[{"x":51.0236,"h":11.48,"y":620.162,"p":4,"w":30.37636363636363}]},"version":{"offsetStart":4,"normalizedForm":"14.0.0","offsetEnd":10,"rawForm":"14.0.0","boundingBoxes":[{"x":51.0236,"h":11.480000000000018,"y":620.162,"p":4,"w":50.627272727272725}]}},
  {"_key":"60c20ba67723bebd866454a7","_id":"annotations/60c20ba67723bebd866454a7","_rev":"_cfFmU3C---","document":{"$oid":"60c20ba67723bebd866454a5"},"publisher":{"offsetStart":87,"normalizedForm":"GraphPad Software, Inc","offsetEnd":110,"rawForm":"GraphPad \nSoftware, Inc","boundingBoxes":[{"x":247.398,"h":11.48,"y":632.662,"p":4,"w":41.701},{"x":51.0236,"h":11.480000000000018,"y":645.162,"p":4,"w":52.8}]},"context":"SAS Institute Inc. was used for statistical analysis and GraphPadPrism® Version 5.02, GraphPad Software, Inc., USA was used for Bland-Altmann analysis and graph preparation.","type":"software","software-name":{"offsetStart":58,"normalizedForm":"GraphPadPrism","offsetEnd":71,"rawForm":"GraphPadPrism","boundingBoxes":[{"x":107.585,"h":11.48,"y":632.662,"p":4,"w":74.403}]},"version":{"offsetStart":81,"normalizedForm":"5.02","offsetEnd":85,"rawForm":"5.02","boundingBoxes":[{"x":222.408,"h":11.480000000000018,"y":632.662,"p":4,"w":16.831999999999994}]}},
  {"_key":"60c20ba67723bebd866454a8","_id":"annotations/60c20ba67723bebd866454a8","_rev":"_cfFmU3O---","document":{"$oid":"60c20ba67723bebd866454a5"},"type":"software","software-name":{"offsetStart":90,"normalizedForm":"IDEA","offsetEnd":94,"rawForm":"IDEA","boundingBoxes":[{"x":431.9166666666667,"h":11.48,"y":245.255,"p":3,"w":20.526666666666664}]},"context":"During the experiment, ventilation parameters were recorded by means of custom software (IDEA) and stored for offline analysis."},
  {"_key":"60c20ba77723bebd866454aa","_id":"annotations/60c20ba77723bebd866454aa","_rev":"_cfFmU3a---","wikipediaExternalRef":4294204,"document":{"$oid":"60c20ba77723bebd866454a9"},"context":"The data for each category were compared to the control group using a commercial statistics package (Medcalc, version 12.7.2).","wikidataId":"Q4272521","type":"software","lang":"en","confidence":0.2533,"software-name":{"wikipediaExternalRef":4294204,"normalizedForm":"Medcalc","offsetStart":103,"wikidataId":"Q4272521","offsetEnd":110,"lang":"en","confidence":0.2533,"rawForm":"Medcalc","boundingBoxes":[{"x":314.75197777777777,"h":6.0253,"y":101.839,"p":3,"w":22.581844444444446}]},"version":{"offsetStart":120,"normalizedForm":"12.7.2","offsetEnd":126,"rawForm":"12.7.2","boundingBoxes":[{"x":366.123,"h":6.025300000000001,"y":101.839,"p":3,"w":16.761225000000024}]}},
  {"_key":"60c20bab7723bebd866454ac","_id":"annotations/60c20bab7723bebd866454ac","_rev":"_cfFmU3q---","wikipediaExternalRef":990677,"document":{"$oid":"60c20bab7723bebd866454ab"},"publisher":{"offsetStart":75,"normalizedForm":"SAS Institute","offsetEnd":88,"rawForm":"SAS Institute","boundingBoxes":[{"x":215.00775,"h":8.000999999999976,"y":662.333,"p":3,"w":45.04625000000004}]},"context":"All statistical analyses were performed with the use of SAS, version 9.2 (SAS Institute, Cary, North Carolina).","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":57,"wikidataId":"Q2003932","offsetEnd":60,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":149.799,"h":8.001,"y":662.333,"p":3,"w":12.399750000000001}]},"version":{"offsetStart":70,"normalizedForm":"9.2","offsetEnd":73,"rawForm":"9.2","boundingBoxes":[{"x":197.416,"h":8.000999999999976,"y":662.333,"p":3,"w":10.799999999999983}]}},
  {"_key":"60c20bb17723bebd866454ae","_id":"annotations/60c20bb17723bebd866454ae","_rev":"_cfFmU32---","wikipediaExternalRef":363695,"document":{"$oid":"60c20bb17723bebd866454ad"},"context":"Although BLAST will identify similar genes, it is also necessary to compile and evaluate the similarities in sets of the related sequences.","wikidataId":"Q286820","type":"software","confidence":0.2835,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":9,"wikidataId":"Q286820","offsetEnd":14,"lang":"en","confidence":0.2835,"rawForm":"BLAST","boundingBoxes":[{"x":419.187,"h":9.1656,"y":579.509,"p":7,"w":30.8542}]},"lang":"en"},
  {"_key":"60c20bb17723bebd866454af","_id":"annotations/60c20bb17723bebd866454af","_rev":"_cfFmU4C---","wikipediaExternalRef":363695,"document":{"$oid":"60c20bb17723bebd866454ad"},"context":"Various versions of BLAST are the most used tool in bioinformatics to trace evolution.","wikidataId":"Q286820","type":"software","confidence":0.2835,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":21,"wikidataId":"Q286820","offsetEnd":26,"lang":"en","confidence":0.2835,"rawForm":"BLAST","boundingBoxes":[{"x":346.903,"h":9.1656,"y":567.546,"p":7,"w":30.7765}]},"lang":"en"},
  {"_key":"60c20bb17723bebd866454b0","_id":"annotations/60c20bb17723bebd866454b0","_rev":"_cfFmU4O---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20bb17723bebd866454ad"},"context":"Multiple sequence alignment software, such as ClustalW, is used for this purpose.","wikidataId":"Q866737","type":"software","confidence":0.7823,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"ClustalW","offsetStart":47,"wikidataId":"Q866737","offsetEnd":55,"lang":"en","confidence":0.7823,"rawForm":"ClustalW","boundingBoxes":[{"x":450.024,"h":9.1656,"y":615.395,"p":7,"w":33.79137777777778}]},"lang":"en"},
  {"_key":"60c20bb17723bebd866454b1","_id":"annotations/60c20bb17723bebd866454b1","_rev":"_cfFmU4a---","wikipediaExternalRef":363695,"document":{"$oid":"60c20bb17723bebd866454ad"},"publisher":{"offsetStart":101,"normalizedForm":"National Centers for Biotechnology Information (NCBI)","offsetEnd":154,"rawForm":"National Centers for Biotechnology Information (NCBI)","boundingBoxes":[{"x":303.59,"h":9.16560000000004,"y":531.66,"p":7,"w":222.45740000000006}]},"context":"The most popular tool for finding similarity is BLAST (Basic Local Alignment Search Tool) from the National Centers for Biotechnology Information (NCBI), which calculates similarity between query sequences and infers a probability based on a matrix database.","wikidataId":"Q286820","type":"software","confidence":0.9398,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST (Basic Local Alignment Search Tool)","offsetStart":49,"wikidataId":"Q286820","offsetEnd":90,"lang":"en","confidence":0.9398,"rawForm":"BLAST (Basic Local Alignment Search Tool)","boundingBoxes":[{"x":312.718,"h":9.16560000000004,"y":519.755,"p":7,"w":180.75019999999995}]},"lang":"en"},
  {"_key":"60c20bb87723bebd866454b3","_id":"annotations/60c20bb87723bebd866454b3","_rev":"_cfFmU4m---","wikipediaExternalRef":42738050,"document":{"$oid":"60c20bb87723bebd866454b2"},"context":"Today, the computerisation of human resource management is a reality, with the ap- pointment of human resource focal points at the district, medical region and hospital levels, and the use of the iHRIS software, although challenges persist in terms of its implementation in Dakar [2,22].","wikidataId":"Q17514273","type":"software","confidence":0.4751,"software-name":{"wikipediaExternalRef":42738050,"normalizedForm":"iHRIS","offsetStart":198,"wikidataId":"Q17514273","offsetEnd":203,"lang":"en","confidence":0.4751,"rawForm":"iHRIS","boundingBoxes":[{"x":166.728,"h":7.1652,"y":410.837,"p":5,"w":19.735}]},"lang":"en"},
  {"_key":"60c20bba7723bebd866454b5","_id":"annotations/60c20bba7723bebd866454b5","_rev":"_cfFmU4y---","wikipediaExternalRef":990677,"document":{"$oid":"60c20bba7723bebd866454b4"},"publisher":{"offsetStart":58,"normalizedForm":"SAS Institute","offsetEnd":71,"rawForm":"SAS Institute","boundingBoxes":[{"x":94.8963,"h":7.165200000000027,"y":426.485,"p":3,"w":42.56226000000001}]},"context":"All statistical analysis was done using SAS 9.4 version, SAS Institute, Cary, NC.","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":41,"wikidataId":"Q2003932","offsetEnd":44,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":37.581,"h":7.1652,"y":426.485,"p":3,"w":13.4776}]},"version":{"offsetStart":45,"normalizedForm":"9.4","offsetEnd":48,"rawForm":"9.4","boundingBoxes":[{"x":53.001,"h":7.165200000000027,"y":426.485,"p":3,"w":10.8857}]}},
  {"_key":"60c20bc57723bebd866454b7","_id":"annotations/60c20bc57723bebd866454b7","_rev":"_cfFmU5----","wikipediaExternalRef":34408890,"document":{"$oid":"60c20bc57723bebd866454b6"},"context":"Data were gathered by semistructured interviews mostly through phone or internet communication tools such as WeChat and QQ due to social distancing measures.","wikidataId":"Q283233","type":"software","confidence":0.7626,"software-name":{"wikipediaExternalRef":34408890,"normalizedForm":"WeChat","offsetStart":111,"wikidataId":"Q283233","offsetEnd":117,"lang":"en","confidence":0.7626,"rawForm":"WeChat","boundingBoxes":[{"x":254.16,"h":9.32,"y":169.04,"p":3,"w":34.21}]},"lang":"en"},
  {"_key":"60c20bcd7723bebd866454b9","_id":"annotations/60c20bcd7723bebd866454b9","_rev":"_cfFmU5K---","document":{"$oid":"60c20bcd7723bebd866454b8"},"type":"software","software-name":{"offsetStart":143,"normalizedForm":"NIS-Elements D","offsetEnd":157,"rawForm":"NIS-Elements D","boundingBoxes":[{"x":414.027,"h":8.5,"y":161.224,"p":4,"w":65.5}]},"context":"The visualized gene expression pattern of the zebrafish embryos and larvae were recorded by the Nikon DS-Fi3 microscope camera system and the NIS-Elements D software."},
  {"_key":"60c20bcd7723bebd866454ba","_id":"annotations/60c20bcd7723bebd866454ba","_rev":"_cfFmU5W---","document":{"$oid":"60c20bcd7723bebd866454b8"},"type":"software","software-name":{"offsetStart":167,"normalizedForm":"NIS-Ele- ments D","offsetEnd":183,"rawForm":"NIS-Ele-\nments D","boundingBoxes":[{"x":540.564,"h":8.5,"y":286.232,"p":4,"w":34.89999999999998},{"x":200.012,"h":8.5,"y":299.271,"p":4,"w":34.091999999999985}]},"context":"For image recording, the sections were thawed and incubated in 1x PBS for 5 min prior to the image documentation by the Nikon DS-Fi3 microscope camera system and the NIS-Ele- ments D software."},
  {"_key":"60c20bcf7723bebd866454bc","_id":"annotations/60c20bcf7723bebd866454bc","_rev":"_cfFmU5m---","wikipediaExternalRef":179088,"document":{"$oid":"60c20bcf7723bebd866454bb"},"publisher":{"offsetStart":40,"normalizedForm":"IBM","offsetEnd":43,"rawForm":"IBM","boundingBoxes":[{"x":475.086,"h":7.6673,"y":353.23,"p":4,"w":15.0238}]},"context":"Statistical analysis was performed with IBM SPSS Statistics v24.0.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.4875,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS Statistics","offsetStart":44,"wikidataId":"Q181596","offsetEnd":59,"lang":"en","confidence":0.4875,"rawForm":"SPSS Statistics","boundingBoxes":[{"x":491.924,"h":7.6673000000000116,"y":353.23,"p":4,"w":56.158000000000015}]},"version":{"offsetStart":62,"normalizedForm":"24.0","offsetEnd":66,"rawForm":"24.0","boundingBoxes":[{"x":308.918,"h":7.6673000000000116,"y":364.739,"p":4,"w":18.530749999999955}]}},
  {"_key":"60c20bd07723bebd866454be","_id":"annotations/60c20bd07723bebd866454be","_rev":"_cfFmU5y---","wikipediaExternalRef":179088,"document":{"$oid":"60c20bd07723bebd866454bd"},"context":"SPSS 17.0 software was used for statistical description and analysis of test data.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":0,"wikidataId":"Q181596","offsetEnd":4,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":410.397,"h":9.2054,"y":463.457,"p":2,"w":19.7758}]},"version":{"offsetStart":5,"normalizedForm":"17.0","offsetEnd":9,"rawForm":"17.0","boundingBoxes":[{"x":434.888,"h":9.205399999999997,"y":463.457,"p":2,"w":16.61759999999998}]}},
  {"_key":"60c20bd07723bebd866454bf","_id":"annotations/60c20bd07723bebd866454bf","_rev":"_cfFmU6----","wikipediaExternalRef":179088,"document":{"$oid":"60c20bd07723bebd866454bd"},"context":"ere was no statistical sig- nificance in the SPSS 17.0 software analysis in severe and nonsevere patients (P > 0.05).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":45,"wikidataId":"Q181596","offsetEnd":49,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":377.015,"h":9.2054,"y":108.063,"p":4,"w":19.7758}]},"version":{"offsetStart":50,"normalizedForm":"17.0","offsetEnd":54,"rawForm":"17.0","boundingBoxes":[{"x":400.542,"h":9.205399999999997,"y":108.063,"p":4,"w":16.61759999999998}]}},
  {"_key":"60c20bd37723bebd866454c1","_id":"annotations/60c20bd37723bebd866454c1","_rev":"_cfFmU6K---","wikipediaExternalRef":424589,"document":{"$oid":"60c20bd37723bebd866454c0"},"context":"Backup imaging platforms to account for unforeseen technology issues included Apple Facetime, Facebook Messenger, Google Hangouts video, WhatsApp video chat, and Skype.","wikidataId":"Q40984","type":"software","confidence":0.7288,"software-name":{"wikipediaExternalRef":424589,"normalizedForm":"Skype","offsetStart":164,"wikidataId":"Q40984","offsetEnd":169,"lang":"en","confidence":0.7288,"rawForm":"Skype","boundingBoxes":[{"x":473.835,"h":7.5398,"y":537.484,"p":4,"w":20.41116666666667}]},"lang":"en"},
  {"_key":"60c20bd77723bebd866454c3","_id":"annotations/60c20bd77723bebd866454c3","_rev":"_cfFmU6W---","wikipediaExternalRef":179088,"document":{"$oid":"60c20bd77723bebd866454c2"},"context":"All the data collected in the data- base were analyzed using SPSS version 12.0.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":61,"wikidataId":"Q181596","offsetEnd":65,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":411.341,"h":9.68,"y":361.91,"p":2,"w":22.8243}]},"version":{"offsetStart":74,"normalizedForm":"12.0","offsetEnd":78,"rawForm":"12.0","boundingBoxes":[{"x":471.826,"h":9.680000000000007,"y":361.91,"p":2,"w":16.43392}]}},
  {"_key":"60c20bda7723bebd866454c5","_id":"annotations/60c20bda7723bebd866454c5","_rev":"_cfFmU6i---","document":{"$oid":"60c20bda7723bebd866454c4"},"type":"software","software-name":{"offsetStart":35,"normalizedForm":"EpiModel","offsetEnd":43,"rawForm":"EpiModel","boundingBoxes":[{"x":244.1,"h":12.177,"y":519.899,"p":4,"w":43.318}]},"context":"The Epidemic Model was built using EpiModel package [10] in R Language for Statistical Computing."},
  {"_key":"60c20bda7723bebd866454c6","_id":"annotations/60c20bda7723bebd866454c6","_rev":"_cfFmU6u---","document":{"$oid":"60c20bda7723bebd866454c4"},"type":"software","software-name":{"offsetStart":60,"normalizedForm":"R Language for Statistical Computing","offsetEnd":96,"rawForm":"R Language for Statistical Computing","boundingBoxes":[{"x":365.457,"h":12.177000000000021,"y":519.899,"p":4,"w":168.9171}]},"context":"The Epidemic Model was built using EpiModel package [10] in R Language for Statistical Computing."},
  {"_key":"60c20bda7723bebd866454c7","_id":"annotations/60c20bda7723bebd866454c7","_rev":"_cfFmU7----","document":{"$oid":"60c20bda7723bebd866454c4"},"type":"software","software-name":{"offsetStart":81,"normalizedForm":"EpiModel","offsetEnd":89,"rawForm":"EpiModel","boundingBoxes":[{"x":457.8,"h":12.177,"y":205.899,"p":3,"w":43.318}]},"context":"Research Design and Methods: The Stochastic Simulation Model was built using the EpiModel package  in R. As a proof of concept study, we ran the simulation on Kasaragod, the most affected district in  Kerala."},
  {"_key":"60c20bde7723bebd866454c9","_id":"annotations/60c20bde7723bebd866454c9","_rev":"_cfFmU7K---","document":{"$oid":"60c20bde7723bebd866454c8"},"publisher":{"offsetStart":47,"normalizedForm":"Sven Mostböck","offsetEnd":60,"rawForm":"Sven Mostböck","boundingBoxes":[{"x":154.636,"h":9,"y":261.57,"p":5,"w":58.82177777777778}]},"context":"Data was analyzed using FCSalyzer-α freeware (Sven Mostböck, Vienna, Austria).","type":"software","software-name":{"offsetStart":24,"normalizedForm":"FCSalyzer-α","offsetEnd":35,"rawForm":"FCSalyzer-α","boundingBoxes":[{"x":409.74,"h":9,"y":247.57,"p":5,"w":52.03000000000003}]}},
  {"_key":"60c20bde7723bebd866454ca","_id":"annotations/60c20bde7723bebd866454ca","_rev":"_cfFmU7W---","document":{"$oid":"60c20bde7723bebd866454c8"},"publisher":{"offsetStart":151,"normalizedForm":"Tecan Group Ltd","offsetEnd":166,"rawForm":"Tecan Group Ltd","boundingBoxes":[{"x":231.60999999999999,"h":9,"y":219.57,"p":6,"w":64.434}]},"context":"The sample volume was then increased to 50 μl and the sample's fluorescence was recorded using an Infinite M1000 plate reader and Magellan software (Tecan Group Ltd., Männedorf, Switzerland).","type":"software","software-name":{"offsetStart":132,"normalizedForm":"Magellan","offsetEnd":140,"rawForm":"Magellan","boundingBoxes":[{"x":150,"h":9,"y":219.57,"p":6,"w":37.77}]}},
  {"_key":"60c20bde7723bebd866454cb","_id":"annotations/60c20bde7723bebd866454cb","_rev":"_cfFmU7i---","document":{"$oid":"60c20bde7723bebd866454c8"},"type":"software","software-name":{"offsetStart":162,"normalizedForm":"RZ","offsetEnd":164,"rawForm":"RZ","boundingBoxes":[{"x":286.11,"h":9,"y":149.57,"p":7,"w":17.78}]},"context":"Auditory brainstem responses (ABRs) were recorded in response to clicks and tones (4, 8, 16, 24 and 32 kHz) between 100 dB and 20 dB in 5 dB increments using a RZ6 signal processor and BioSig software (TDT, Alachua FL)."},
  {"_key":"60c20bde7723bebd866454cc","_id":"annotations/60c20bde7723bebd866454cc","_rev":"_cfFmU7u---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20bde7723bebd866454c8"},"publisher":{"offsetStart":177,"normalizedForm":"National Institute of Health","offsetEnd":205,"rawForm":"National Institute of Health","boundingBoxes":[{"x":293.05566666666664,"h":9,"y":553.57,"p":6,"w":107.17761904761903}]},"context":"Fluorescence microscopy images were captured using an Axio Observer.Z1 motorized microscope system and Zen 2.3 software (Zeiss, Thornwood NY, USA), and analyzed using ImageJ (National Institute of Health, Bethesda, MD, USA).","wikidataId":"Q1659584","type":"software","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":169,"wikidataId":"Q1659584","offsetEnd":175,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":257.479,"h":9,"y":553.57,"p":6,"w":28.88}]},"lang":"en"},
  {"_key":"60c20bde7723bebd866454cd","_id":"annotations/60c20bde7723bebd866454cd","_rev":"_cfFmU76---","document":{"$oid":"60c20bde7723bebd866454c8"},"publisher":{"offsetStart":193,"normalizedForm":"BD Biosciences","offsetEnd":207,"rawForm":"BD Biosciences","boundingBoxes":[{"x":238.12,"h":9,"y":247.57,"p":5,"w":59.33384615384614}]},"context":"Flow cytometry was performed in the University of Pennsylvania Flow Cytometry Core using a LSRII flow cytometer (BD Biosciences, San Jose CA, USA) and data recorded with DiVa 6.1.3","type":"software","software-name":{"offsetStart":172,"normalizedForm":"DiVa","offsetEnd":176,"rawForm":"DiVa","boundingBoxes":[{"x":150,"h":9,"y":247.57,"p":5,"w":20.55}]},"version":{"offsetStart":177,"normalizedForm":"6.1.3","offsetEnd":182,"rawForm":"6.1.3","boundingBoxes":[{"x":173.05,"h":9,"y":247.57,"p":5,"w":20}]}},
  {"_key":"60c20bde7723bebd866454ce","_id":"annotations/60c20bde7723bebd866454ce","_rev":"_cfFmU8G---","document":{"$oid":"60c20bde7723bebd866454c8"},"publisher":{"offsetStart":204,"normalizedForm":"TDT","offsetEnd":207,"rawForm":"TDT","boundingBoxes":[{"x":462.56600000000003,"h":9,"y":149.57,"p":7,"w":14.718}]},"context":"Auditory brainstem responses (ABRs) were recorded in response to clicks and tones (4, 8, 16, 24 and 32 kHz) between 100 dB and 20 dB in 5 dB increments using a RZ6 signal processor and BioSig software (TDT, Alachua FL).","type":"software","software-name":{"offsetStart":187,"normalizedForm":"BioSig","offsetEnd":193,"rawForm":"BioSig","boundingBoxes":[{"x":390.54,"h":9,"y":149.57,"p":7,"w":27.79}]}},
  {"_key":"60c20bdf7723bebd866454d0","_id":"annotations/60c20bdf7723bebd866454d0","_rev":"_cfFmU8S---","document":{"$oid":"60c20bdf7723bebd866454cf"},"publisher":{"offsetStart":86,"normalizedForm":"BD","offsetEnd":88,"rawForm":"BD","boundingBoxes":[{"x":368.494075,"h":9.099,"y":179.231,"p":8,"w":8.40015}]},"context":"Flow cytometry was performed on an LSRII flow cytometer using the FACSDiva software (BD, USA); 1 × 10 4 events were collected per sample, and analyzed using the Flowjo software version 10 (Treestar, Ashland, USA).","type":"software","software-name":{"offsetStart":67,"normalizedForm":"FACSDiva","offsetEnd":75,"rawForm":"FACSDiva","boundingBoxes":[{"x":292.25,"h":9.099,"y":179.231,"p":8,"w":37.5426}]}},
  {"_key":"60c20bdf7723bebd866454d1","_id":"annotations/60c20bdf7723bebd866454d1","_rev":"_cfFmU8e---","document":{"$oid":"60c20bdf7723bebd866454cf"},"publisher":{"offsetStart":191,"normalizedForm":"Treestar","offsetEnd":199,"rawForm":"Treestar","boundingBoxes":[{"x":342.80899,"h":9.099,"y":189.234,"p":8,"w":27.22392}]},"context":"Flow cytometry was performed on an LSRII flow cytometer using the FACSDiva software (BD, USA); 1 × 10 4 events were collected per sample, and analyzed using the Flowjo software version 10 (Treestar, Ashland, USA).","type":"software","software-name":{"offsetStart":163,"normalizedForm":"Flowjo","offsetEnd":169,"rawForm":"Flowjo","boundingBoxes":[{"x":240.54,"h":9.099,"y":189.234,"p":8,"w":24.8337}]},"version":{"offsetStart":187,"normalizedForm":"10","offsetEnd":189,"rawForm":"10","boundingBoxes":[{"x":328.66,"h":9.099,"y":189.234,"p":8,"w":8.6895}]}},
  {"_key":"60c20be47723bebd866454d3","_id":"annotations/60c20be47723bebd866454d3","_rev":"_cfFmU8q---","document":{"$oid":"60c20be47723bebd866454d2"},"context":"Sequence identity was visualized using EvolView (http://www. evolgenius.info/) and SARS-CoV Co-V-2 WA1 served as the reference sequence.","type":"software","software-name":{"offsetStart":39,"normalizedForm":"EvolView","offsetEnd":47,"rawForm":"EvolView","boundingBoxes":[{"x":213.241,"h":8.217,"y":361.309,"p":9,"w":33.5255}]},"url":{"offsetStart":49,"normalizedForm":"http://www. evolgenius.info","offsetEnd":77,"rawForm":"http://www. \nevolgenius.info","boundingBoxes":[{"x":251.71939166666667,"h":8.216999999999985,"y":361.309,"p":9,"w":43.04730833333335},{"x":39.685,"h":8.216999999999985,"y":372.059,"p":9,"w":57.78520588235294}]}},
  {"_key":"60c20be47723bebd866454d4","_id":"annotations/60c20be47723bebd866454d4","_rev":"_cfFmU82---","document":{"$oid":"60c20be47723bebd866454d2"},"context":"Homology models were visualized and manipulated in MacPyMol (version 1.3).","type":"software","software-name":{"offsetStart":52,"normalizedForm":"MacPyMol","offsetEnd":60,"rawForm":"MacPyMol","boundingBoxes":[{"x":113.382,"h":8.217,"y":425.809,"p":9,"w":39.9465}]},"version":{"offsetStart":70,"normalizedForm":"1.3","offsetEnd":73,"rawForm":"1.3","boundingBoxes":[{"x":186.807,"h":8.216999999999985,"y":425.809,"p":9,"w":9.271320000000003}]}},
  {"_key":"60c20be47723bebd866454d5","_id":"annotations/60c20be47723bebd866454d5","_rev":"_cfFmU9C---","document":{"$oid":"60c20be47723bebd866454d2"},"publisher":{"offsetStart":128,"normalizedForm":"GraphPad","offsetEnd":136,"rawForm":"GraphPad","boundingBoxes":[{"x":246.05768181818183,"h":8.217,"y":221.559,"p":9,"w":33.357454545454544}]},"context":"The curves of the relative infection rates versus the serum dilutions (log 10 -transformed values) were plotted using Prism 8 (GraphPad).","type":"software","software-name":{"offsetStart":119,"normalizedForm":"Prism","offsetEnd":124,"rawForm":"Prism","boundingBoxes":[{"x":212.276,"h":8.217,"y":221.559,"p":9,"w":21.8302}]},"version":{"offsetStart":125,"normalizedForm":"8","offsetEnd":126,"rawForm":"8","boundingBoxes":[{"x":235.562,"h":8.217,"y":221.559,"p":9,"w":4.8704}]}},
  {"_key":"60c20be47723bebd866454d6","_id":"annotations/60c20be47723bebd866454d6","_rev":"_cfFmU9O---","document":{"$oid":"60c20be47723bebd866454d2"},"type":"software","software-name":{"offsetStart":140,"normalizedForm":"Flexivent","offsetEnd":149,"rawForm":"Flexivent","boundingBoxes":[{"x":319.524,"h":8.217,"y":501.059,"p":9,"w":34.2757}]},"context":"Respiratory mechanics were assessed using the forced oscil- lation technique, as previously described 42 , using the latest version of the Flexivent operating software (FlexiWare v.8.1.3)."},
  {"_key":"60c20be47723bebd866454d7","_id":"annotations/60c20be47723bebd866454d7","_rev":"_cfFmU9a---","wikipediaExternalRef":52292152,"document":{"$oid":"60c20be47723bebd866454d2"},"context":"Heat maps were constructed from a set of representative group-2B coro- naviruses using alignment data paired with neighbour-joining phyloge- netic trees built in Geneious (v.9.1.5),","wikidataId":"Q4915084","type":"software","lang":"en","confidence":0.2365,"software-name":{"wikipediaExternalRef":52292152,"normalizedForm":"Geneious","offsetStart":162,"wikidataId":"Q4915084","offsetEnd":170,"lang":"en","confidence":0.2365,"rawForm":"Geneious","boundingBoxes":[{"x":106.25,"h":8.217,"y":318.309,"p":9,"w":35.1688}]},"version":{"offsetStart":174,"normalizedForm":"9.1.5","offsetEnd":179,"rawForm":"9.1.5","boundingBoxes":[{"x":151.50331,"h":8.216999999999985,"y":318.309,"p":9,"w":15.053850000000011}]}},
  {"_key":"60c20be47723bebd866454d8","_id":"annotations/60c20be47723bebd866454d8","_rev":"_cfFmU9m---","document":{"$oid":"60c20be47723bebd866454d2"},"context":"Respiratory mechanics were assessed using the forced oscil- lation technique, as previously described 42 , using the latest version of the Flexivent operating software (FlexiWare v.8.1.3).","type":"software","software-name":{"offsetStart":170,"normalizedForm":"FlexiWare","offsetEnd":179,"rawForm":"FlexiWare","boundingBoxes":[{"x":430.38244999999995,"h":8.217,"y":501.059,"p":9,"w":35.95005}]},"version":{"offsetStart":182,"normalizedForm":"8.1.3","offsetEnd":187,"rawForm":"8.1.3","boundingBoxes":[{"x":473.6577555555555,"h":8.216999999999985,"y":501.059,"p":9,"w":15.68188888888892}]}},
  {"_key":"60c20bef7723bebd866454db","_id":"annotations/60c20bef7723bebd866454db","_rev":"_cfFmU9y---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20bef7723bebd866454da"},"publisher":{"offsetStart":48,"normalizedForm":"NIH","offsetEnd":51,"rawForm":"NIH","boundingBoxes":[{"x":349.27058,"h":9.1806,"y":108.804,"p":4,"w":13.76874}]},"context":"Data were analyzed using the Image J software (NIH, Bethesda, MD, USA, RRID: SCR_003070).","wikidataId":"Q1659584","type":"software","confidence":0.8344,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":29,"wikidataId":"Q1659584","offsetEnd":37,"lang":"en","confidence":0.8344,"rawForm":"Image \nJ","boundingBoxes":[{"x":526.913,"h":9.1806,"y":97.3475,"p":4,"w":23.5343},{"x":305.109,"h":9.1806,"y":108.804,"p":4,"w":3.1138}]},"lang":"en"},
  {"_key":"60c20bef7723bebd866454dc","_id":"annotations/60c20bef7723bebd866454dc","_rev":"_cfFmV-----","wikipediaExternalRef":179088,"document":{"$oid":"60c20bef7723bebd866454da"},"context":"Statistical analysis was performed using SPSS and GraphPad PRISM 6.0 software (RRID: SCR_002798) for both parametric and non-parametric comparisons.","wikidataId":"Q181596","type":"software","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":42,"wikidataId":"Q181596","offsetEnd":46,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":378.126,"h":9.1806,"y":161.193,"p":5,"w":18.7782}]},"lang":"en"},
  {"_key":"60c20bef7723bebd866454dd","_id":"annotations/60c20bef7723bebd866454dd","_rev":"_cfFmV-G---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20bef7723bebd866454da"},"publisher":{"offsetStart":61,"normalizedForm":"NIH","offsetEnd":64,"rawForm":"NIH","boundingBoxes":[{"x":452.21258,"h":9.1806,"y":97.3474,"p":5,"w":13.76874}]},"context":"The final bands were quantified using the Image J software (NIH, Bethesda, MD, USA, RRID: SCR_003070).","wikidataId":"Q1659584","type":"software","confidence":0.9507,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":43,"wikidataId":"Q1659584","offsetEnd":50,"lang":"en","confidence":0.9507,"rawForm":"Image J","boundingBoxes":[{"x":382.634,"h":9.180599999999998,"y":97.3474,"p":5,"w":28.70980000000003}]},"lang":"en"},
  {"_key":"60c20bef7723bebd866454de","_id":"annotations/60c20bef7723bebd866454de","_rev":"_cfFmV-S---","wikipediaExternalRef":20412,"document":{"$oid":"60c20bef7723bebd866454da"},"context":"Image processing was carried out offline using MatLab software.","wikidataId":"Q169478","type":"software","confidence":0.7769,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MatLab","offsetStart":48,"wikidataId":"Q169478","offsetEnd":54,"lang":"en","confidence":0.7769,"rawForm":"MatLab","boundingBoxes":[{"x":355.509,"h":9.1806,"y":385.977,"p":3,"w":29.45}]},"lang":"en"},
  {"_key":"60c20bef7723bebd866454df","_id":"annotations/60c20bef7723bebd866454df","_rev":"_cfFmV-e---","document":{"$oid":"60c20bef7723bebd866454da"},"context":"Statistical analysis was performed using SPSS and GraphPad PRISM 6.0 software (RRID: SCR_002798) for both parametric and non-parametric comparisons.","type":"software","software-name":{"offsetStart":51,"normalizedForm":"GraphPad PRISM","offsetEnd":65,"rawForm":"GraphPad PRISM","boundingBoxes":[{"x":423.171,"h":9.180599999999998,"y":161.193,"p":5,"w":71.9384}]},"version":{"offsetStart":66,"normalizedForm":"6.0","offsetEnd":69,"rawForm":"6.0","boundingBoxes":[{"x":501.076,"h":9.180599999999998,"y":161.193,"p":5,"w":11.247899999999959}]}},
  {"_key":"60c20bef7723bebd866454e0","_id":"annotations/60c20bef7723bebd866454e0","_rev":"_cfFmV-q---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20bef7723bebd866454da"},"publisher":{"offsetStart":105,"normalizedForm":"NIH","offsetEnd":108,"rawForm":"NIH","boundingBoxes":[{"x":131.23658,"h":9.1806,"y":363.45,"p":4,"w":13.76874}]},"context":"We randomly chose four fields from the area of interest in each section and used the Image J software (NIH, Bethesda, MD, RRID: SCR_003070) for mean integrated optical density (IOD) analysis.","wikidataId":"Q1659584","type":"software","confidence":0.9507,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":87,"wikidataId":"Q1659584","offsetEnd":94,"lang":"en","confidence":0.9507,"rawForm":"Image J","boundingBoxes":[{"x":59.5891,"h":9.180600000000027,"y":363.45,"p":4,"w":29.3938}]},"lang":"en"},
  {"_key":"60c20bef7723bebd866454e1","_id":"annotations/60c20bef7723bebd866454e1","_rev":"_cfFmV-2---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20bef7723bebd866454da"},"publisher":{"offsetStart":184,"normalizedForm":"NIH","offsetEnd":187,"rawForm":"NIH","boundingBoxes":[{"x":345.29358,"h":9.1806,"y":626.672,"p":3,"w":13.76874}]},"context":"Infarct volume was determined by subtracting the area stained with cresyl violet in the ipsilateral hemisphere from that of the contralateral hemisphere using the Image J software (NIH, Bethesda, MD, USA, RRID: SCR_003070), and then multiplying by section interval thickness.","wikidataId":"Q1659584","type":"software","confidence":0.9507,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":165,"wikidataId":"Q1659584","offsetEnd":172,"lang":"en","confidence":0.9507,"rawForm":"Image J","boundingBoxes":[{"x":519.353,"h":9.180600000000027,"y":615.215,"p":3,"w":31.085800000000063}]},"lang":"en"},
  {"_key":"60c20bf57723bebd866454e3","_id":"annotations/60c20bf57723bebd866454e3","_rev":"_cfFmV_C---","document":{"$oid":"60c20bf47723bebd866454e2"},"publisher":{"offsetStart":24,"normalizedForm":"Swiss Institute of Bioinformatics","offsetEnd":57,"rawForm":"Swiss Institute of Bioinformatics","boundingBoxes":[{"x":147.83175,"h":6.3974999999999795,"y":409.458,"p":13,"w":98.20425}]},"context":"PeptideCutter software (Swiss Institute of Bioinformatics) was used to identify sites in enterocin A with a high susceptibility to trypsin, chymotrypsin, and pepsin (45).","type":"software","software-name":{"offsetStart":0,"normalizedForm":"PeptideCutter","offsetEnd":13,"rawForm":"PeptideCutter","boundingBoxes":[{"x":69.6734,"h":6.3975,"y":409.458,"p":13,"w":43.8975}]}},
  {"_key":"60c20bf57723bebd866454e4","_id":"annotations/60c20bf57723bebd866454e4","_rev":"_cfFmV_O---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20bf47723bebd866454e2"},"context":"To quantify activity of all tested samples, ImageJ software was used to analyze images of the agar diffusion plates.","wikidataId":"Q1659584","type":"software","confidence":0.8009,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":44,"wikidataId":"Q1659584","offsetEnd":50,"lang":"en","confidence":0.8009,"rawForm":"ImageJ","boundingBoxes":[{"x":187.904,"h":6.3975,"y":443.314,"p":15,"w":22.3875}]},"lang":"en"},
  {"_key":"60c20bf57723bebd866454e5","_id":"annotations/60c20bf57723bebd866454e5","_rev":"_cfFmV_a---","wikipediaExternalRef":20412,"document":{"$oid":"60c20bf47723bebd866454e2"},"context":"Sequence-activity data were modeled using the lassoglm function in MATLAB with 5-fold cross- validation and lambda values ranging from 10 Ϫ3 to 10 3 and assuming that activity scores were drawn from a binary distribution.","wikidataId":"Q169478","type":"software","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":67,"wikidataId":"Q169478","offsetEnd":73,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":283.718,"h":6.3975,"y":676.613,"p":15,"w":26.5425}]},"lang":"en"},
  {"_key":"60c20bf57723bebd866454e6","_id":"annotations/60c20bf57723bebd866454e6","_rev":"_cfFmV_m---","wikipediaExternalRef":20412,"document":{"$oid":"60c20bf47723bebd866454e2"},"context":"Unique sequences with reads above this threshold were isolated and analyzed via a custom MATLAB script.","wikidataId":"Q169478","type":"software","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":90,"wikidataId":"Q169478","offsetEnd":96,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":204.987,"h":6.3975,"y":293.208,"p":14,"w":26.5425}]},"lang":"en"},
  {"_key":"60c20bf57723bebd866454e7","_id":"annotations/60c20bf57723bebd866454e7","_rev":"_cfFmV_y---","wikipediaExternalRef":20412,"document":{"$oid":"60c20bf47723bebd866454e2"},"context":"Independently, class IIa bacteriocin and manPTS sequences were aligned using the multialign function in MATLAB with default settings.","wikidataId":"Q169478","type":"software","confidence":0.7679,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":105,"wikidataId":"Q169478","offsetEnd":111,"lang":"en","confidence":0.7679,"rawForm":"MATLAB","boundingBoxes":[{"x":169.552,"h":6.3975,"y":638.612,"p":15,"w":26.5425}]},"lang":"en"},
  {"_key":"60c20bf57723bebd866454e8","_id":"annotations/60c20bf57723bebd866454e8","_rev":"_cfFmVA----","wikipediaExternalRef":3793613,"document":{"$oid":"60c20bf47723bebd866454e2"},"context":"The average brightness of each halo, excluding the interior point made by the pipette tip, was measured using ImageJ.","wikidataId":"Q1659584","type":"software","confidence":0.8009,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":111,"wikidataId":"Q1659584","offsetEnd":117,"lang":"en","confidence":0.8009,"rawForm":"ImageJ","boundingBoxes":[{"x":122.556,"h":6.3975,"y":462.314,"p":15,"w":20.52}]},"lang":"en"},
  {"_key":"60c20bf57723bebd866454e9","_id":"annotations/60c20bf57723bebd866454e9","_rev":"_cfFmVAK---","document":{"$oid":"60c20bf47723bebd866454e2"},"type":"software","software-name":{"offsetStart":128,"normalizedForm":"Usearch","offsetEnd":135,"rawForm":"Usearch","boundingBoxes":[{"x":149.853,"h":6.3975,"y":216.482,"p":14,"w":25.17}]},"context":"Illumina iSeq sequencing generated approximately 7 million reads specific to libraries 1 and 2. Sequences were processed using Usearch by filtering for a maximum error rate of 0.001 and denoised using the unoise3 command to correct single-base pair errors which may have occurred during sequencing (71, 72)."},
  {"_key":"60c20bf57723bebd866454ea","_id":"annotations/60c20bf57723bebd866454ea","_rev":"_cfFmVAW---","document":{"$oid":"60c20bf47723bebd866454e2"},"publisher":{"offsetStart":24,"normalizedForm":"Swiss Institute of Bioinformatics","offsetEnd":57,"rawForm":"Swiss Institute of Bioinformatics","boundingBoxes":[{"x":147.83175,"h":6.3974999999999795,"y":409.458,"p":13,"w":98.20425}]},"context":"Rationally designed AMPs were used to evaluate the utility of domain swapping for identifying compelling class IIa bacteriocins and our ability to design active and proteolytically stable variants using PeptideCutter software to identify protease cleavage sites (45).","type":"software","software-name":{"offsetStart":206,"normalizedForm":"PeptideCutter","offsetEnd":219,"rawForm":"PeptideCutter","boundingBoxes":[{"x":64.2427,"h":7.677,"y":588.632,"p":3,"w":52.677}]}},
  {"_key":"60c20bf57723bebd866454eb","_id":"annotations/60c20bf57723bebd866454eb","_rev":"_cfFmVAi---","wikipediaExternalRef":20412,"document":{"$oid":"60c20bf47723bebd866454e2"},"context":"The inverse of locally normalized brightness values was then globally fit to the equation below, which is derived from the Michaelis-Menten equation assuming a low substrate concentration (supplemental derivation [see equations S1 and S2 in the supplemental material]), using the fitnlm function on MATLAB.","wikidataId":"Q169478","type":"software","confidence":0.7679,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":302,"wikidataId":"Q169478","offsetEnd":308,"lang":"en","confidence":0.7679,"rawForm":"MATLAB","boundingBoxes":[{"x":167.877,"h":6.3975,"y":500.315,"p":15,"w":24.081428571428567}]},"lang":"en"},
  {"_key":"60c20bf67723bebd866454ed","_id":"annotations/60c20bf67723bebd866454ed","_rev":"_cfFmVAu---","wikipediaExternalRef":179088,"document":{"$oid":"60c20bf67723bebd866454ec"},"publisher":{"offsetStart":53,"normalizedForm":"IBM Corporation","offsetEnd":69,"rawForm":"IBM \nCorporation","boundingBoxes":[{"x":527.7185000000001,"h":11.48,"y":557.662,"p":5,"w":16.552500000000002},{"x":306.142,"h":11.48,"y":570.162,"p":5,"w":48.12225}]},"context":"The analyses were performed using SPSS version 16.0 (IBM Corporation, Chicago, IL, USA) for Windows 3 (CTCAE v3.0, Microsoft Corporation, Redmond, WA, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":34,"wikidataId":"Q181596","offsetEnd":38,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":447.401,"h":11.48,"y":557.662,"p":5,"w":22.1}]},"version":{"offsetStart":47,"normalizedForm":"16.0","offsetEnd":51,"rawForm":"16.0","boundingBoxes":[{"x":502.701,"h":11.480000000000018,"y":557.662,"p":5,"w":17.350000000000023}]}},
  {"_key":"60c20bf67723bebd866454ee","_id":"annotations/60c20bf67723bebd866454ee","_rev":"_cfFmVB----","document":{"$oid":"60c20bf67723bebd866454ec"},"publisher":{"offsetStart":117,"normalizedForm":"Microsoft Corporation","offsetEnd":138,"rawForm":"Microsoft Corporation","boundingBoxes":[{"x":328.817,"h":11.480000000000018,"y":582.662,"p":5,"w":89.66325}]},"context":"The analyses were performed using SPSS version 16.0 (IBM Corporation, Chicago, IL, USA) for Windows 3 (CTCAE v3.0, Microsoft Corporation, Redmond, WA, USA).","type":"software","software-name":{"offsetStart":104,"normalizedForm":"CTCAE","offsetEnd":109,"rawForm":"CTCAE","boundingBoxes":[{"x":513.6648333333334,"h":11.48,"y":570.162,"p":5,"w":30.48916666666667}]},"version":{"offsetStart":112,"normalizedForm":"3.0","offsetEnd":115,"rawForm":"3.0","boundingBoxes":[{"x":306.142,"h":11.480000000000018,"y":582.662,"p":5,"w":16.160000000000025}]}},
  {"_key":"60c20bf67723bebd866454ef","_id":"annotations/60c20bf67723bebd866454ef","_rev":"_cfFmVBK---","document":{"$oid":"60c20bf67723bebd866454ec"},"publisher":{"offsetStart":181,"normalizedForm":"Hokai Company","offsetEnd":194,"rawForm":"Hokai Company","boundingBoxes":[{"x":188.2645,"h":11.480000000000018,"y":707.662,"p":3,"w":61.890874999999994}]},"context":"A series of CT data (slice thickness, 0.625 mm) or MRI data (slice thickness, 2.5 mm) related to HCC before MWA were converted to DICOM format and then imported into the 3DVAPS (Hokai Company, Zhuhai,  China).","type":"software","software-name":{"offsetStart":173,"normalizedForm":"3DVAPS","offsetEnd":179,"rawForm":"3DVAPS","boundingBoxes":[{"x":144.063,"h":11.480000000000018,"y":707.662,"p":3,"w":36.81999999999999}]}},
  {"_key":"60c20bf77723bebd866454f2","_id":"annotations/60c20bf77723bebd866454f2","_rev":"_cfFmVBW---","wikipediaExternalRef":8855979,"document":{"$oid":"60c20bf77723bebd866454f0"},"context":"Spectra were processed by NmrPipe and visualized with NmrDraw [21].","wikidataId":"Q7042688","type":"software","confidence":0.4317,"software-name":{"wikipediaExternalRef":8855979,"normalizedForm":"NmrPipe","offsetStart":27,"wikidataId":"Q7042688","offsetEnd":34,"lang":"en","confidence":0.4317,"rawForm":"NmrPipe","boundingBoxes":[{"x":356.649,"h":7.5318,"y":679.336,"p":2,"w":33.1423}]},"lang":"en"},
  {"_key":"60c20bf77723bebd866454f3","_id":"annotations/60c20bf77723bebd866454f3","_rev":"_cfFmVBi---","document":{"$oid":"60c20bf77723bebd866454f0"},"context":"Spectra were processed by NmrPipe and visualized with NmrDraw [21].","references":[{"offsetStart":5447,"normalizedForm":"[21]","refKey":20,"label":"[21]","reference_id":{"$oid":"60c20bf77723bebd866454f1"},"offsetEnd":5451,"boundingBoxes":[{"x":517.318,"h":7.531799999999976,"y":679.336,"p":2,"w":13.993599999999901}]}],"type":"software","software-name":{"offsetStart":55,"normalizedForm":"NmrDraw","offsetEnd":62,"rawForm":"NmrDraw","boundingBoxes":[{"x":475.81,"h":7.5318,"y":679.336,"p":2,"w":37.4068}]}},
  {"_key":"60c20bf77723bebd866454f4","_id":"annotations/60c20bf77723bebd866454f4","_rev":"_cfFmVBu---","document":{"$oid":"60c20bf77723bebd866454f0"},"publisher":{"offsetStart":218,"normalizedForm":"Synergy Software","offsetEnd":234,"rawForm":"Synergy Software","boundingBoxes":[{"x":129.25,"h":7.531800000000004,"y":162.068,"p":3,"w":62.98988}]},"context":"The decays of cross-peak intensities with time in the 15 N R z and R xy experiments were fit to a single exponential by a  non-linear least-squares fit with fitting errors typically less than 5% (Kaleidagraph 3.08, Synergy Software).","type":"software","software-name":{"offsetStart":199,"normalizedForm":"Kaleidagraph","offsetEnd":211,"rawForm":"Kaleidagraph","boundingBoxes":[{"x":58.4763,"h":7.5318,"y":162.068,"p":3,"w":48.666000000000004}]},"version":{"offsetStart":212,"normalizedForm":"3.08","offsetEnd":216,"rawForm":"3.08","boundingBoxes":[{"x":109.123,"h":7.531800000000004,"y":162.068,"p":3,"w":14.44543999999999}]}},
  {"_key":"60c20bf87723bebd866454f7","_id":"annotations/60c20bf87723bebd866454f7","_rev":"_cfFmVB6---","document":{"$oid":"60c20bf87723bebd866454f5"},"context":"The free software used was Orange (Demsar et al. 2013).","references":[{"offsetStart":8324,"normalizedForm":"(Demsar et al. 2013","refKey":25,"label":"(Demsar et al. 2013","reference_id":{"$oid":"60c20bf87723bebd866454f6"},"offsetEnd":8343,"boundingBoxes":[{"x":260.551,"h":8.757100000000037,"y":538.356,"p":3,"w":75.80326666666667}]}],"type":"software","software-name":{"offsetStart":27,"normalizedForm":"Orange","offsetEnd":33,"rawForm":"Orange","boundingBoxes":[{"x":228.739,"h":8.7571,"y":538.356,"p":3,"w":29.3149}]}},
  {"_key":"60c20bf97723bebd866454f9","_id":"annotations/60c20bf97723bebd866454f9","_rev":"_cfFmVCG---","document":{"$oid":"60c20bf97723bebd866454f8"},"type":"software","software-name":{"offsetStart":34,"normalizedForm":"Immuno","offsetEnd":40,"rawForm":"Immuno","boundingBoxes":[{"x":224.986,"h":9.947,"y":75.5027,"p":1,"w":30.0195}]},"context":"Table S1: Extracted data from the Immuno-analytics tool."},
  {"_key":"60c20bfd7723bebd866454fb","_id":"annotations/60c20bfd7723bebd866454fb","_rev":"_cfFmVCS---","document":{"$oid":"60c20bfd7723bebd866454fa"},"type":"software","software-name":{"offsetStart":167,"normalizedForm":"APT","offsetEnd":170,"rawForm":"APT","boundingBoxes":[{"x":283.635,"h":8.9365,"y":486.322,"p":14,"w":21.4455}]},"context":"It has a (non-choice-free) Petri net solution, but not a choice-free one: the numerical construction of the proper synthesis phase (for instance with the use of the APT tool [14]) finds an unsolvable ESSP problem."},
  {"_key":"60c20c027723bebd866454ff","_id":"annotations/60c20c027723bebd866454ff","_rev":"_cfFmVCe---","document":{"$oid":"60c20c027723bebd866454fc"},"context":"For example, the PhiPack was designed to work for low-divergence genomes, it still requires 1~5% of variants to perform statistical analysis.","type":"software","software-name":{"offsetStart":17,"normalizedForm":"PhiPack","offsetEnd":24,"rawForm":"PhiPack","boundingBoxes":[{"x":267.6,"h":11.628,"y":523.896,"p":5,"w":39.36}]},"version":{"offsetStart":70,"normalizedForm":"17","offsetEnd":72,"rawForm":"17","boundingBoxes":[{"x":396.36,"h":7.7908,"y":476.357,"p":5,"w":8.1003}]}},
  {"_key":"60c20c027723bebd86645500","_id":"annotations/60c20c027723bebd86645500","_rev":"_cfFmVCu---","wikipediaExternalRef":23939,"document":{"$oid":"60c20c027723bebd866454fc"},"context":"Custom scripts in Perl, Python, and R were used for various calculations and graphics.","wikidataId":"Q42478","type":"software","confidence":0.6985,"software-name":{"wikipediaExternalRef":23939,"normalizedForm":"Perl","offsetStart":18,"wikidataId":"Q42478","offsetEnd":22,"lang":"en","confidence":0.6985,"rawForm":"Perl","boundingBoxes":[{"x":285.48,"h":11.628,"y":501.096,"p":11,"w":17.856}]},"lang":"en"},
  {"_key":"60c20c027723bebd86645501","_id":"annotations/60c20c027723bebd86645501","_rev":"_cfFmVC6---","wikipediaExternalRef":23862,"document":{"$oid":"60c20c027723bebd866454fc"},"context":"Custom scripts in Perl, Python, and R were used for various calculations and graphics.","wikidataId":"Q28865","type":"software","confidence":0.6138,"software-name":{"wikipediaExternalRef":23862,"normalizedForm":"Python","offsetStart":24,"wikidataId":"Q28865","offsetEnd":30,"lang":"en","confidence":0.6138,"rawForm":"Python","boundingBoxes":[{"x":310.68,"h":11.628,"y":501.096,"p":11,"w":31.57714285714286}]},"lang":"en"},
  {"_key":"60c20c027723bebd86645502","_id":"annotations/60c20c027723bebd86645502","_rev":"_cfFmVDG---","document":{"$oid":"60c20c027723bebd866454fc"},"type":"software","software-name":{"offsetStart":39,"normalizedForm":"SNP-sites","offsetEnd":48,"rawForm":"SNP-sites","boundingBoxes":[{"x":89.64,"h":11.628000000000043,"y":501.096,"p":11,"w":47.38800000000002}]},"context":"Variants of SNPs were named using the SNP-sites software 34 ."},
  {"_key":"60c20c027723bebd86645503","_id":"annotations/60c20c027723bebd86645503","_rev":"_cfFmVDS---","document":{"$oid":"60c20c027723bebd866454fc"},"publisher":{"offsetStart":40,"normalizedForm":"ONT","offsetEnd":43,"rawForm":"ONT","boundingBoxes":[{"x":452.16,"h":11.628,"y":149.376,"p":11,"w":20.008799999999997}]},"context":"Raw sequencing data were acquired using ONT's MinKnow software (3.6.5)","type":"software","software-name":{"offsetStart":46,"normalizedForm":"MinKnow","offsetEnd":53,"rawForm":"MinKnow","boundingBoxes":[{"x":488.52,"h":11.628,"y":149.376,"p":11,"w":49.344}]},"version":{"offsetStart":65,"normalizedForm":"3.6.5","offsetEnd":70,"rawForm":"3.6.5","boundingBoxes":[{"x":120.84514285714286,"h":11.628000000000014,"y":164.376,"p":11,"w":22.82571428571427}]}},
  {"_key":"60c20c027723bebd86645504","_id":"annotations/60c20c027723bebd86645504","_rev":"_cfFmVDe---","document":{"$oid":"60c20c027723bebd866454fc"},"context":"There are several tools, including Simplot 15 , RDP4 16 , and PhiPack 17 , that are specifically designed for detecting homologous recombination.","references":[{"offsetStart":11768,"normalizedForm":"16","refKey":15,"label":"16","reference_id":{"$oid":"60c20c027723bebd866454fd"},"offsetEnd":11771,"boundingBoxes":[{"x":319.68,"h":7.7908,"y":476.357,"p":5,"w":8.1003}]}],"type":"software","software-name":{"offsetStart":48,"normalizedForm":"RDP4","offsetEnd":52,"rawForm":"RDP4","boundingBoxes":[{"x":287.4,"h":11.627999999999986,"y":479.256,"p":5,"w":29.279999999999973}]}},
  {"_key":"60c20c027723bebd86645505","_id":"annotations/60c20c027723bebd86645505","_rev":"_cfFmVDu---","document":{"$oid":"60c20c027723bebd866454fc"},"type":"software","software-name":{"offsetStart":51,"normalizedForm":"ARTIC COVID-19","offsetEnd":65,"rawForm":"ARTIC COVID-19","boundingBoxes":[{"x":193.32,"h":11.628000000000014,"y":246.816,"p":11,"w":92.87919999999997}]},"context":"Automatic genome analyses were performed with the ARTIC COVID-19 nextflow software package for read-quality score filtering, reference alignment, and consensus sequence generation."},
  {"_key":"60c20c027723bebd86645506","_id":"annotations/60c20c027723bebd86645506","_rev":"_cfFmVD6---","document":{"$oid":"60c20c027723bebd866454fc"},"type":"software","software-name":{"offsetStart":61,"normalizedForm":"RAMPART","offsetEnd":68,"rawForm":"RAMPART","boundingBoxes":[{"x":300.12,"h":11.628,"y":494.136,"p":8,"w":58.212}]},"context":"The feature of live-basecalling is necessary when using the RAMPART tool 22 to monitor the on-going progress during sampling and to check whether all amplicons have been sampled."},
  {"_key":"60c20c027723bebd86645507","_id":"annotations/60c20c027723bebd86645507","_rev":"_cfFmVEG---","document":{"$oid":"60c20c027723bebd866454fc"},"context":"There are several tools, including Simplot 15 , RDP4 16 , and PhiPack 17 , that are specifically designed for detecting homologous recombination.","type":"software","software-name":{"offsetStart":62,"normalizedForm":"PhiPack","offsetEnd":69,"rawForm":"PhiPack","boundingBoxes":[{"x":354.12,"h":11.628,"y":479.256,"p":5,"w":39.24}]},"version":{"offsetStart":70,"normalizedForm":"17","offsetEnd":72,"rawForm":"17","boundingBoxes":[{"x":396.36,"h":7.7908,"y":476.357,"p":5,"w":8.1003}]}},
  {"_key":"60c20c027723bebd86645508","_id":"annotations/60c20c027723bebd86645508","_rev":"_cfFmVES---","document":{"$oid":"60c20c027723bebd866454fc"},"context":"High-accuracy basecalling of nanopore reads was later performed using Guppy v3.4.5 on an HP Prodesk830 computer equipped with an NVIDIA RTX 2060 GPU.","type":"software","software-name":{"offsetStart":70,"normalizedForm":"Guppy","offsetEnd":75,"rawForm":"Guppy","boundingBoxes":[{"x":419.4,"h":11.628,"y":217.056,"p":11,"w":32.88}]},"version":{"offsetStart":77,"normalizedForm":"3.4.5","offsetEnd":82,"rawForm":"3.4.5","boundingBoxes":[{"x":455.04,"h":11.628000000000014,"y":217.056,"p":11,"w":30}]}},
  {"_key":"60c20c027723bebd86645509","_id":"annotations/60c20c027723bebd86645509","_rev":"_cfFmVEe---","document":{"$oid":"60c20c027723bebd866454fc"},"type":"software","software-name":{"offsetStart":73,"normalizedForm":"COVID","offsetEnd":78,"rawForm":"COVID","boundingBoxes":[{"x":372.24,"h":11.628,"y":523.896,"p":8,"w":33.675000000000004}]},"context":"The final stage for bioinformatics analysis was handled by the nextflow COVID-19 workflow that includes read-quality score filtering, reference alignment, and consensus sequence generation, which only takes about twenty minutes."},
  {"_key":"60c20c027723bebd8664550a","_id":"annotations/60c20c027723bebd8664550a","_rev":"_cfFmVEq---","document":{"$oid":"60c20c027723bebd866454fc"},"type":"software","software-name":{"offsetStart":131,"normalizedForm":"NEEDLE","offsetEnd":137,"rawForm":"NEEDLE","boundingBoxes":[{"x":385.44,"h":11.628,"y":456.336,"p":11,"w":46.692}]},"context":"Each of the remaining 17,500 genome sequences was individually aligned to the reference SARS-CoV-2 genome (NC_045512.2) using the NEEDLE tool (Needleman- Wunsch global alignment of two sequences) from the EMBOSS package v6.6.0.0 33 ."},
  {"_key":"60c20c027723bebd8664550b","_id":"annotations/60c20c027723bebd8664550b","_rev":"_cfFmVE2---","document":{"$oid":"60c20c027723bebd866454fc"},"type":"software","software-name":{"offsetStart":153,"normalizedForm":"Wunsch","offsetEnd":161,"rawForm":"-\nWunsch","boundingBoxes":[{"x":513.8290909090908,"h":11.628,"y":456.336,"p":11,"w":5.686909090909091},{"x":72,"h":11.628,"y":471.216,"p":11,"w":39.36}]},"context":"Each of the remaining 17,500 genome sequences was individually aligned to the reference SARS-CoV-2 genome (NC_045512.2) using the NEEDLE tool (Needleman- Wunsch global alignment of two sequences) from the EMBOSS package v6.6.0.0 33 ."},
  {"_key":"60c20c027723bebd8664550c","_id":"annotations/60c20c027723bebd8664550c","_rev":"_cfFmVFG---","wikipediaExternalRef":1527385,"document":{"$oid":"60c20c027723bebd866454fc"},"context":"The evolutionary history of SARS-CoV-2 was inferred using a Bayesian approach, implemented through the Markov chain Monte Carlo framework available in BEAST 1.10.4 31 , utilizing the BEAGLE library v3 32 to increase computational performance.","wikidataId":"Q791633","references":[{"offsetStart":31654,"normalizedForm":"32","refKey":32,"label":"32","reference_id":{"$oid":"60c20c027723bebd866454fe"},"offsetEnd":31657,"boundingBoxes":[{"x":499.08,"h":7.7908,"y":288.557,"p":11,"w":8.1003}]}],"type":"software","lang":"en","confidence":0.3766,"software-name":{"wikipediaExternalRef":1527385,"normalizedForm":"BEAGLE","offsetStart":185,"wikidataId":"Q791633","offsetEnd":191,"lang":"en","confidence":0.3766,"rawForm":"BEAGLE","boundingBoxes":[{"x":398.88,"h":11.628,"y":291.456,"p":11,"w":47.172}]},"version":{"offsetStart":201,"normalizedForm":"3","offsetEnd":202,"rawForm":"3","boundingBoxes":[{"x":484.08,"h":11.628,"y":291.456,"p":11,"w":12}]}},
  {"_key":"60c20c027723bebd8664550d","_id":"annotations/60c20c027723bebd8664550d","_rev":"_cfFmVFS---","wikipediaExternalRef":3678414,"document":{"$oid":"60c20c027723bebd866454fc"},"context":"Each of the remaining 17,500 genome sequences was individually aligned to the reference SARS-CoV-2 genome (NC_045512.2) using the NEEDLE tool (Needleman- Wunsch global alignment of two sequences) from the EMBOSS package v6.6.0.0 33 .","wikidataId":"Q690201","type":"software","lang":"en","confidence":0.8057,"software-name":{"wikipediaExternalRef":3678414,"normalizedForm":"EMBOSS","offsetStart":206,"wikidataId":"Q690201","offsetEnd":212,"lang":"en","confidence":0.8057,"rawForm":"EMBOSS","boundingBoxes":[{"x":331.92,"h":11.628,"y":471.216,"p":11,"w":47.952}]},"version":{"offsetStart":222,"normalizedForm":"6.6.0.0","offsetEnd":229,"rawForm":"6.6.0.0","boundingBoxes":[{"x":425.16,"h":11.627999999999986,"y":471.216,"p":11,"w":39.120000000000005}]}},
  {"_key":"60c20c027723bebd8664550f","_id":"annotations/60c20c027723bebd8664550f","_rev":"_cfFmVFe---","document":{"$oid":"60c20c027723bebd8664550e"},"type":"software","software-name":{"offsetStart":10,"normalizedForm":"FlexAEAD","offsetEnd":18,"rawForm":"FlexAEAD","boundingBoxes":[{"x":333.263,"h":9.9626,"y":275.912,"p":4,"w":55.7407}]},"context":"Although, FlexAEAD is out of NIST lightweight cryptography competition, this particular vulnerability has a far-reaching impact on designing ciphers using AES S-box."},
  {"_key":"60c20c027723bebd86645510","_id":"annotations/60c20c027723bebd86645510","_rev":"_cfFmVFu---","document":{"$oid":"60c20c027723bebd8664550e"},"type":"software","software-name":{"offsetStart":88,"normalizedForm":"FlexAEAD","offsetEnd":96,"rawForm":"FlexAEAD","boundingBoxes":[{"x":88.9309,"h":9.9626,"y":520.398,"p":3,"w":55.7407}]},"context":"Further, we have used the iterated truncated differentials to mount forgery attacks on FlexAEAD similar to the ones reported by Eichlseder et al. [12,13]."},
  {"_key":"60c20c047723bebd86645512","_id":"annotations/60c20c047723bebd86645512","_rev":"_cfFmVF6---","wikipediaExternalRef":21845564,"document":{"$oid":"60c20c047723bebd86645511"},"context":"JAGS v 4.3.0 is used (via rjags) to implement Gibbs sampling.","wikidataId":"Q6316598","type":"software","lang":"en","confidence":0.3297,"software-name":{"wikipediaExternalRef":21845564,"normalizedForm":"JAGS","offsetStart":0,"wikidataId":"Q6316598","offsetEnd":4,"lang":"en","confidence":0.3297,"rawForm":"JAGS","boundingBoxes":[{"x":393.699,"h":10.536,"y":486.696,"p":4,"w":28.6788}]},"version":{"offsetStart":7,"normalizedForm":"4.3.0","offsetEnd":12,"rawForm":"4.3.0","boundingBoxes":[{"x":434.369,"h":10.536000000000001,"y":486.696,"p":4,"w":24}]}},
  {"_key":"60c20c1b7723bebd86645515","_id":"annotations/60c20c1b7723bebd86645515","_rev":"_cfFmVGG---","wikipediaExternalRef":2324407,"document":{"$oid":"60c20c1b7723bebd86645514"},"publisher":{"offsetStart":25,"normalizedForm":"Schro ¨dinger","offsetEnd":38,"rawForm":"Schro ¨dinger","boundingBoxes":[{"x":44.8462,"h":8.458999999999975,"y":167.622,"p":3,"w":48.7950875}]},"context":"PyMOL (version 1.5.0.3;","wikidataId":"Q1373457","type":"software","lang":"en","confidence":0.8093,"software-name":{"wikipediaExternalRef":2324407,"normalizedForm":"PyMOL","offsetStart":0,"wikidataId":"Q1373457","offsetEnd":5,"lang":"en","confidence":0.8093,"rawForm":"PyMOL","boundingBoxes":[{"x":190.094,"h":8.1993,"y":155.887,"p":3,"w":33.909}]},"version":{"offsetStart":15,"normalizedForm":"1.5.0.3","offsetEnd":22,"rawForm":"1.5.0.3","boundingBoxes":[{"x":268.044,"h":8.288999999999987,"y":155.887,"p":3,"w":24.297874999999976}]}},
  {"_key":"60c20c1b7723bebd86645516","_id":"annotations/60c20c1b7723bebd86645516","_rev":"_cfFmVGS---","document":{"$oid":"60c20c1b7723bebd86645514"},"type":"software","software-name":{"offsetStart":5,"normalizedForm":"MolProbity","offsetEnd":15,"rawForm":"MolProbity","boundingBoxes":[{"x":197.746,"h":8.1993,"y":131.963,"p":3,"w":46.6533}]},"context":"Both MolProbity (Chen et al., 2010) and the wwPDB validation server (Gore et al., 2017) were used for model validation."},
  {"_key":"60c20c1b7723bebd86645517","_id":"annotations/60c20c1b7723bebd86645517","_rev":"_cfFmVGe---","document":{"$oid":"60c20c1b7723bebd86645514"},"type":"software","software-name":{"offsetStart":42,"normalizedForm":"LabDB","offsetEnd":47,"rawForm":"LabDB","boundingBoxes":[{"x":265.43,"h":8.289,"y":179.755,"p":3,"w":30.3723}]},"context":"All experimental steps were tracked using LabDB (Zimmerman et al., 2014)."},
  {"_key":"60c20c1b7723bebd86645518","_id":"annotations/60c20c1b7723bebd86645518","_rev":"_cfFmVGq---","document":{"$oid":"60c20c1b7723bebd86645514"},"type":"software","software-name":{"offsetStart":45,"normalizedForm":"wwPDB validation","offsetEnd":61,"rawForm":"wwPDB validation","boundingBoxes":[{"x":107.319,"h":8.288999999999987,"y":143.925,"p":3,"w":77.9224}]},"context":"Both MolProbity (Chen et al., 2010) and the wwPDB validation server (Gore et al., 2017) were used for model validation."},
  {"_key":"60c20c1b7723bebd86645519","_id":"annotations/60c20c1b7723bebd86645519","_rev":"_cfFmVG2---","document":{"$oid":"60c20c1b7723bebd86645514"},"type":"software","software-name":{"offsetStart":72,"normalizedForm":"TLS Motion Deter- mination","offsetEnd":98,"rawForm":"TLS Motion Deter-\nmination","boundingBoxes":[{"x":484.102,"h":8.199299999999994,"y":717.771,"p":2,"w":80.77300000000002},{"x":313.795,"h":8.1993,"y":729.733,"p":2,"w":35.7392}]},"context":"TLS groups were determined and set up with a standalone version of the TLS Motion Deter- mination server (Painter & Merritt, 2006)."},
  {"_key":"60c20c1b7723bebd8664551a","_id":"annotations/60c20c1b7723bebd8664551a","_rev":"_cfFmVHC---","document":{"$oid":"60c20c1b7723bebd86645514"},"type":"software","software-name":{"offsetStart":86,"normalizedForm":"ACHESYM","offsetEnd":93,"rawForm":"ACHESYM","boundingBoxes":[{"x":516.02,"h":8.1993,"y":693.903,"p":2,"w":48.8212}]},"context":"The protein model was placed in the standardized position in the unit cell using the ACHESYM server (Kowiel et al., 2014)."},
  {"_key":"60c20c1b7723bebd8664551b","_id":"annotations/60c20c1b7723bebd8664551b","_rev":"_cfFmVHO---","document":{"$oid":"60c20c1b7723bebd86645514"},"type":"software","software-name":{"offsetStart":97,"normalizedForm":"REFMAC","offsetEnd":103,"rawForm":"REFMAC","boundingBoxes":[{"x":506.042,"h":8.1993,"y":634.092,"p":2,"w":41.672}]},"context":"The structure was refined with H atoms in riding positions using HKL-3000, which interacts with REFMAC and other programs from the CCP4 package (Vagin & Teplyakov, 2010; Murshudov et al., 2011; Winn et al., 2011)."},
  {"_key":"60c20c207723bebd8664551d","_id":"annotations/60c20c207723bebd8664551d","_rev":"_cfFmVHe---","wikipediaExternalRef":6964154,"document":{"$oid":"60c20c207723bebd8664551c"},"context":"The software HAPLOVIEW (version 2.05) was used to construct haplotypes from the genotype data.","wikidataId":"Q5652128","type":"software","lang":"en","confidence":0.7604,"software-name":{"wikipediaExternalRef":6964154,"normalizedForm":"HAPLOVIEW","offsetStart":14,"wikidataId":"Q5652128","offsetEnd":23,"lang":"en","confidence":0.7604,"rawForm":"HAPLOVIEW","boundingBoxes":[{"x":315.099,"h":8.1324,"y":511.39,"p":2,"w":54.8917}]},"version":{"offsetStart":33,"normalizedForm":"2.05","offsetEnd":37,"rawForm":"2.05","boundingBoxes":[{"x":406.542,"h":8.132399999999961,"y":511.39,"p":2,"w":14.267200000000003}]}},
  {"_key":"60c20c207723bebd8664551e","_id":"annotations/60c20c207723bebd8664551e","_rev":"_cfFmVHu---","wikipediaExternalRef":179088,"document":{"$oid":"60c20c207723bebd8664551c"},"publisher":{"offsetStart":59,"normalizedForm":"SPSS Inc","offsetEnd":67,"rawForm":"SPSS Inc","boundingBoxes":[{"x":400.361,"h":8.132400000000018,"y":437.234,"p":2,"w":33.23705000000001}]},"context":"Data were analyzed using the SPSS software (version 10.0, SPSS Inc, Chicago, IL, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7466,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":29,"wikidataId":"Q181596","offsetEnd":33,"lang":"en","confidence":0.7466,"rawForm":"SPSS","boundingBoxes":[{"x":534.607,"h":8.1324,"y":426.633,"p":2,"w":19.5914}]},"version":{"offsetStart":53,"normalizedForm":"10.0","offsetEnd":57,"rawForm":"10.0","boundingBoxes":[{"x":379.272,"h":8.132400000000018,"y":437.234,"p":2,"w":14.346080000000029}]}},
  {"_key":"60c20c287723bebd86645521","_id":"annotations/60c20c287723bebd86645521","_rev":"_cfFmVH6---","document":{"$oid":"60c20c287723bebd8664551f"},"context":"One of such reasoner is Ticker [6], while a more recent distributed implementation is presented in [14].","references":[{"offsetStart":3959,"normalizedForm":"[6]","refKey":5,"label":"[6]","reference_id":{"$oid":"60c20c287723bebd86645520"},"offsetEnd":3962,"boundingBoxes":[{"x":371.946,"h":8.936499999999995,"y":200.256,"p":2,"w":9.960825}]}],"type":"software","software-name":{"offsetStart":24,"normalizedForm":"Ticker","offsetEnd":30,"rawForm":"Ticker","boundingBoxes":[{"x":339.798,"h":8.9265,"y":200.256,"p":2,"w":28.1344}]}},
  {"_key":"60c20c287723bebd86645522","_id":"annotations/60c20c287723bebd86645522","_rev":"_cfFmVIG---","wikipediaExternalRef":2564605,"document":{"$oid":"60c20c287723bebd8664551f"},"context":"We used Golang 1.13 to compile and run our system and Pypy 7.2.0 to run Laser1.","wikidataId":"Q1143023","type":"software","lang":"en","confidence":0.2942,"software-name":{"wikipediaExternalRef":2564605,"normalizedForm":"Pypy","offsetStart":55,"wikidataId":"Q1143023","offsetEnd":59,"lang":"en","confidence":0.2942,"rawForm":"Pypy","boundingBoxes":[{"x":205.167,"h":8.9365,"y":470.237,"p":9,"w":22.5613}]},"version":{"offsetStart":60,"normalizedForm":"7.2.0","offsetEnd":65,"rawForm":"7.2.0","boundingBoxes":[{"x":232.263,"h":8.936500000000024,"y":470.237,"p":9,"w":20.475099999999998}]}},
  {"_key":"60c20c287723bebd86645523","_id":"annotations/60c20c287723bebd86645523","_rev":"_cfFmVIS---","document":{"$oid":"60c20c287723bebd8664551f"},"type":"software","software-name":{"offsetStart":61,"normalizedForm":"ASP","offsetEnd":64,"rawForm":"ASP","boundingBoxes":[{"x":106.6817,"h":8.9365,"y":80.699,"p":2,"w":15.1521}]},"context":"First, its semantics is grounded on Answer Set Programming (ASP); thus it provides an AI that is explainable by design, which means that it can be used also by non experts or audited by regulators."},
  {"_key":"60c20c287723bebd86645524","_id":"annotations/60c20c287723bebd86645524","_rev":"_cfFmVIe---","wikipediaExternalRef":23862,"document":{"$oid":"60c20c287723bebd8664551f"},"context":"The reason behind this difference is purely technical and due to the fact that the new implementation does not have the overhead introduced by the interpretation layer of Python.","wikidataId":"Q28865","type":"software","confidence":0.6138,"software-name":{"wikipediaExternalRef":23862,"normalizedForm":"Python","offsetStart":173,"wikidataId":"Q28865","offsetEnd":179,"lang":"en","confidence":0.6138,"rawForm":"Python","boundingBoxes":[{"x":278.152,"h":8.9365,"y":558.466,"p":10,"w":29.778514285714284}]},"lang":"en"},
  {"_key":"60c20c2a7723bebd86645526","_id":"annotations/60c20c2a7723bebd86645526","_rev":"_cfFmVIq---","document":{"$oid":"60c20c2a7723bebd86645525"},"publisher":{"offsetStart":40,"normalizedForm":"Affymetrix","offsetEnd":50,"rawForm":"Affymetrix","boundingBoxes":[{"x":229.50823076923078,"h":7.0058,"y":549.068,"p":4,"w":33.0923076923077}]},"context":"Raw image data were analyzed with AGCC (Affymetrix), and gene expression intensities were normalized and summarized with RMA algorithm (49).","type":"software","software-name":{"offsetStart":34,"normalizedForm":"AGCC","offsetEnd":38,"rawForm":"AGCC","boundingBoxes":[{"x":200.971,"h":7.0058,"y":549.068,"p":4,"w":21.7818}]}},
  {"_key":"60c20c2a7723bebd86645527","_id":"annotations/60c20c2a7723bebd86645527","_rev":"_cfFmVI2---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20c2a7723bebd86645525"},"publisher":{"offsetStart":120,"normalizedForm":"GraphPad Software","offsetEnd":137,"rawForm":"GraphPad Software","boundingBoxes":[{"x":332.5790777777778,"h":7.005799999999994,"y":162.535,"p":4,"w":59.31952222222219}]},"context":"Intergroup differences were tested by ANOVA, followed by Tukey's or Bonferroni post hoc tests using GraphPad Prism 5 (GraphPad Software), if not stated otherwise.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.8862,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":101,"wikidataId":"Q5597066","offsetEnd":116,"lang":"en","confidence":0.8862,"rawForm":"GraphPad \nPrism","boundingBoxes":[{"x":509.434,"h":7.0058,"y":153.578,"p":4,"w":31.7549},{"x":302.059,"h":7.0058,"y":162.535,"p":4,"w":18.5865}]},"version":{"offsetStart":117,"normalizedForm":"5","offsetEnd":118,"rawForm":"5","boundingBoxes":[{"x":322.695,"h":7.0058,"y":162.535,"p":4,"w":3.9851}]}},
  {"_key":"60c20c2a7723bebd86645528","_id":"annotations/60c20c2a7723bebd86645528","_rev":"_cfFmVJC---","wikipediaExternalRef":24666773,"document":{"$oid":"60c20c2a7723bebd86645525"},"publisher":{"offsetStart":134,"normalizedForm":"Tree Star","offsetEnd":143,"rawForm":"Tree Star","boundingBoxes":[{"x":114.75026,"h":7.005800000000022,"y":270.14,"p":4,"w":28.670140000000004}]},"context":"Flow cytometry was performed using the BD LSRFortessa cell analyzer (BD Biosciences), and results were analyzed using FlowJo 7.6.5 (Tree Star).","wikidataId":"Q5462055","type":"software","lang":"en","confidence":0.4725,"software-name":{"wikipediaExternalRef":24666773,"normalizedForm":"FlowJo","offsetStart":120,"wikidataId":"Q5462055","offsetEnd":126,"lang":"en","confidence":0.4725,"rawForm":"FlowJo","boundingBoxes":[{"x":65.5925,"h":7.0058,"y":270.14,"p":4,"w":23.2076}]},"version":{"offsetStart":127,"normalizedForm":"7.6.5","offsetEnd":132,"rawForm":"7.6.5","boundingBoxes":[{"x":92.1245,"h":7.005800000000022,"y":270.14,"p":4,"w":15.940399999999997}]}},
  {"_key":"60c20c357723bebd8664552a","_id":"annotations/60c20c357723bebd8664552a","_rev":"_cfFmVJO---","wikipediaExternalRef":179088,"document":{"$oid":"60c20c357723bebd86645529"},"publisher":{"offsetStart":79,"normalizedForm":"SPSS IBM","offsetEnd":87,"rawForm":"SPSS IBM","boundingBoxes":[{"x":315.212,"h":8.729499999999973,"y":281.002,"p":2,"w":33.63074999999998}]},"context":"All the analyses were performed with commercial software (SPSS version 22.0; SPSS IBM, Armonk, New York, United States).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7466,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":59,"wikidataId":"Q181596","offsetEnd":63,"lang":"en","confidence":0.7466,"rawForm":"SPSS","boundingBoxes":[{"x":476.8485,"h":8.7295,"y":269,"p":2,"w":17.102}]},"version":{"offsetStart":72,"normalizedForm":"22.0","offsetEnd":76,"rawForm":"22.0","boundingBoxes":[{"x":531.308,"h":8.729499999999973,"y":269,"p":2,"w":15.789600000000064}]}},
  {"_key":"60c20c397723bebd8664552d","_id":"annotations/60c20c397723bebd8664552d","_rev":"_cfFmVJe---","document":{"$oid":"60c20c397723bebd8664552b"},"context":"In Phase 2, the remaining 848 studies underwent a second review in which study authors double-coded each project description using Covidence [15] software.","references":[{"offsetStart":7964,"normalizedForm":"[15]","refKey":14,"label":"[15]","reference_id":{"$oid":"60c20c397723bebd8664552c"},"offsetEnd":7969,"boundingBoxes":[{"x":466.347,"h":11.480000000000018,"y":421.135,"p":2,"w":17.619999999999948}]}],"type":"software","software-name":{"offsetStart":133,"normalizedForm":"Covidence","offsetEnd":142,"rawForm":"Covidence","boundingBoxes":[{"x":417.565,"h":11.48,"y":421.135,"p":2,"w":45.112}]}},
  {"_key":"60c20c457723bebd86645530","_id":"annotations/60c20c457723bebd86645530","_rev":"_cfFmVJq---","document":{"$oid":"60c20c457723bebd8664552e"},"publisher":{"offsetStart":95,"normalizedForm":"Laser- Gene, DNAStar","offsetEnd":115,"rawForm":"Laser-\nGene, DNAStar","boundingBoxes":[{"x":502.22670000000005,"h":9.962600000000009,"y":140.439,"p":4,"w":26.50619999999992},{"x":301.586,"h":9.962600000000009,"y":152.394,"p":4,"w":62.98882500000002}]},"context":"The resulting chromatograms were analyzed using the SeqMan multiple sequence alignment tool (Laser- Gene, DNAStar, Madison, WI).","type":"software","software-name":{"offsetStart":54,"normalizedForm":"SeqMan","offsetEnd":60,"rawForm":"SeqMan","boundingBoxes":[{"x":301.586,"h":9.9626,"y":140.439,"p":4,"w":33.5042}]}},
  {"_key":"60c20c457723bebd86645531","_id":"annotations/60c20c457723bebd86645531","_rev":"_cfFmVJ6---","document":{"$oid":"60c20c457723bebd8664552e"},"context":"Consensus sequences were compared with a reference APN sequence in GenBank (accession number AJ421875) using BLAST (Basic Local Alignment Search Tool). 23","references":[{"offsetStart":11654,"normalizedForm":"23","refKey":22,"label":"23","reference_id":{"$oid":"60c20c457723bebd8664552f"},"offsetEnd":11658,"boundingBoxes":[{"x":463.741,"h":7.5716,"y":186.434,"p":4,"w":7.935}]}],"type":"software","software-name":{"offsetStart":111,"normalizedForm":"BLAST (Basic Local Alignment Search Tool","offsetEnd":152,"rawForm":"BLAST \n(Basic Local Alignment Search Tool","boundingBoxes":[{"x":501.595,"h":9.9626,"y":176.304,"p":4,"w":27.1381},{"x":301.586,"h":9.962600000000009,"y":188.259,"p":4,"w":153.65319999999997}]}},
  {"_key":"60c20c477723bebd86645533","_id":"annotations/60c20c477723bebd86645533","_rev":"_cfFmVKG---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20c477723bebd86645532"},"context":"Data management and statistical analyses were performed using Stata 16 MP.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":63,"wikidataId":"Q1204300","offsetEnd":68,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":223.879,"h":8.5,"y":226.194,"p":6,"w":19.41}]},"version":{"offsetStart":69,"normalizedForm":"16 MP","offsetEnd":74,"rawForm":"16 MP","boundingBoxes":[{"x":245.479,"h":8.5,"y":226.194,"p":6,"w":22.921666666666653}]}},
  {"_key":"60c20c527723bebd86645535","_id":"annotations/60c20c527723bebd86645535","_rev":"_cfFmVKS---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20c527723bebd86645534"},"context":"Initial velocity rates were fitted using GraphPad Prism 6 to the Michealis-Menten curve, determining V max and K m .","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":41,"wikidataId":"Q5597066","offsetEnd":55,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":385.264,"h":9,"y":245.57,"p":5,"w":65.82999999999998}]},"version":{"offsetStart":56,"normalizedForm":"6","offsetEnd":57,"rawForm":"6","boundingBoxes":[{"x":453.594,"h":9,"y":245.57,"p":5,"w":5}]}},
  {"_key":"60c20c527723bebd86645536","_id":"annotations/60c20c527723bebd86645536","_rev":"_cfFmVKe---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20c527723bebd86645534"},"context":"Gels were imaged on BioRad Gel-Doc imagers, quantified using ImageJ, and cropped where indicated.","wikidataId":"Q1659584","type":"software","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":61,"wikidataId":"Q1659584","offsetEnd":67,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":447.74,"h":9,"y":151.57,"p":4,"w":26.897142857142853}]},"lang":"en"},
  {"_key":"60c20c527723bebd86645537","_id":"annotations/60c20c527723bebd86645537","_rev":"_cfFmVKu---","document":{"$oid":"60c20c527723bebd86645534"},"publisher":{"offsetStart":105,"normalizedForm":"GraphPad","offsetEnd":113,"rawForm":"GraphPad","boundingBoxes":[{"x":278.541,"h":9,"y":335.57,"p":4,"w":37.32}]},"context":"Initial linear cleavage rates (V i ) were fitted by the Michealis-Menten equation using Prism software (GraphPad) based on a free AMC standard curve.","type":"software","software-name":{"offsetStart":89,"normalizedForm":"Prism","offsetEnd":94,"rawForm":"Prism","boundingBoxes":[{"x":211.106,"h":9,"y":335.57,"p":4,"w":23.34}]}},
  {"_key":"60c20c527723bebd86645538","_id":"annotations/60c20c527723bebd86645538","_rev":"_cfFmVL----","document":{"$oid":"60c20c527723bebd86645534"},"publisher":{"offsetStart":184,"normalizedForm":"Molecular Devices","offsetEnd":201,"rawForm":"Molecular Devices","boundingBoxes":[{"x":191.375,"h":9,"y":293.57,"p":4,"w":73.58449999999999}]},"context":"Substrates and DUBs were pre-incubated at 37°C for 5, min and cleavage of Ubl-AMCs was performed at 37°C using a Spectramax fluorescence plate reader running SoftMax Pro 5 software (Molecular Devices) operated in kinetic mode, in black, flat-bottom 384-well plates (Corning #3575), where free AMC fluorescence was monitored by excitation at 355 nm and emission at 460 nm.","type":"software","software-name":{"offsetStart":159,"normalizedForm":"SoftMax Pro","offsetEnd":170,"rawForm":"SoftMax Pro","boundingBoxes":[{"x":461.972,"h":9,"y":279.57,"p":4,"w":51.389999999999986}]},"version":{"offsetStart":171,"normalizedForm":"5","offsetEnd":172,"rawForm":"5","boundingBoxes":[{"x":515.862,"h":9,"y":279.57,"p":4,"w":5}]}},
  {"_key":"60c20c537723bebd8664553a","_id":"annotations/60c20c537723bebd8664553a","_rev":"_cfFmVLK---","wikipediaExternalRef":990677,"document":{"$oid":"60c20c537723bebd86645539"},"context":"The schedules were generated through the Statistical Analysis System (SAS) software, version  9.3.","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.9516,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"Statistical Analysis System (SAS)","offsetStart":41,"wikidataId":"Q2003932","offsetEnd":74,"lang":"en","confidence":0.9516,"rawForm":"Statistical Analysis System (SAS)","boundingBoxes":[{"x":288.227,"h":6.844800000000021,"y":274.375,"p":3,"w":167.8107}]},"version":{"offsetStart":95,"normalizedForm":"9.3","offsetEnd":98,"rawForm":"9.3","boundingBoxes":[{"x":66.24,"h":6.844800000000021,"y":293.335,"p":3,"w":13.772099999999995}]}},
  {"_key":"60c20c537723bebd8664553b","_id":"annotations/60c20c537723bebd8664553b","_rev":"_cfFmVLW---","document":{"$oid":"60c20c537723bebd86645539"},"publisher":{"offsetStart":252,"normalizedForm":"Phoenix","offsetEnd":259,"rawForm":"Phoenix","boundingBoxes":[{"x":269.892,"h":6.8448,"y":634.855,"p":3,"w":39.7639}]},"context":"The AEs of special  interest included neurological and infusion-site-related AEs.The PK parameters of the RJX  components were calculated, whenever possible, from the concentrations versus time profiles using  non-compartmental analysis (NCA), with Phoenix ® WinNonlin ® version 8.0.","type":"software","software-name":{"offsetStart":263,"normalizedForm":"WinNonlin","offsetEnd":272,"rawForm":"WinNonlin","boundingBoxes":[{"x":318.785,"h":6.8448,"y":634.855,"p":3,"w":50.1569}]},"version":{"offsetStart":284,"normalizedForm":"8.0","offsetEnd":287,"rawForm":"8.0","boundingBoxes":[{"x":417.516,"h":6.844799999999964,"y":634.855,"p":3,"w":13.77457499999997}]}},
  {"_key":"60c20c567723bebd8664553d","_id":"annotations/60c20c567723bebd8664553d","_rev":"_cfFmVLi---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20c567723bebd8664553c"},"publisher":{"offsetStart":52,"normalizedForm":"GraphPad Software","offsetEnd":69,"rawForm":"GraphPad Software","boundingBoxes":[{"x":174.2743222222222,"h":9.584000000000003,"y":358.073,"p":5,"w":84.16145555555559}]},"context":"All analyses were performed on GraphPad Prism v.7 (GraphPad Software, San Diego, CA, USA).","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":32,"wikidataId":"Q5597066","offsetEnd":46,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":76.535,"h":9.584000000000003,"y":358.073,"p":5,"w":75.02959999999999}]},"version":{"offsetStart":49,"normalizedForm":"7","offsetEnd":50,"rawForm":"7","boundingBoxes":[{"x":162.20313333333334,"h":9.584,"y":358.073,"p":5,"w":4.077066666666666}]}},
  {"_key":"60c20c567723bebd8664553e","_id":"annotations/60c20c567723bebd8664553e","_rev":"_cfFmVLy---","document":{"$oid":"60c20c567723bebd8664553c"},"publisher":{"offsetStart":103,"normalizedForm":"Systat Software Inc","offsetEnd":122,"rawForm":"Systat Software Inc","boundingBoxes":[{"x":80.46245714285713,"h":9.584000000000003,"y":490.995,"p":4,"w":80.70272285714286}]},"context":"These data were plotted and Hill 4 parameter sigmoidal regression was performed on Sigma Plot v.12.0 (Systat Software Inc., San Jose, CA, USA).","type":"software","software-name":{"offsetStart":83,"normalizedForm":"Sigma Plot","offsetEnd":93,"rawForm":"Sigma Plot","boundingBoxes":[{"x":446.1,"h":9.584000000000003,"y":477.486,"p":4,"w":46.424800000000005}]},"version":{"offsetStart":96,"normalizedForm":"12.0","offsetEnd":100,"rawForm":"12.0","boundingBoxes":[{"x":502.7799,"h":9.584000000000003,"y":477.486,"p":4,"w":15.959800000000087}]}},
  {"_key":"60c20c567723bebd8664553f","_id":"annotations/60c20c567723bebd8664553f","_rev":"_cfFmVMC---","document":{"$oid":"60c20c567723bebd8664553c"},"publisher":{"offsetStart":103,"normalizedForm":"Systat Software Inc","offsetEnd":122,"rawForm":"Systat Software Inc","boundingBoxes":[{"x":80.46245714285713,"h":9.583999999999946,"y":601.242,"p":4,"w":80.50549285714287}]},"context":"These data were plotted and Hill 4 parameter sigmoidal regression was performed on Sigma Plot v.12.0 (Systat Software Inc.).","type":"software","software-name":{"offsetStart":83,"normalizedForm":"Sigma Plot","offsetEnd":93,"rawForm":"Sigma Plot","boundingBoxes":[{"x":446.1,"h":9.583999999999946,"y":587.733,"p":4,"w":46.424800000000005}]},"version":{"offsetStart":96,"normalizedForm":"12.0","offsetEnd":100,"rawForm":"12.0","boundingBoxes":[{"x":502.7799,"h":9.583999999999946,"y":587.733,"p":4,"w":15.959800000000087}]}},
  {"_key":"60c20c5a7723bebd86645541","_id":"annotations/60c20c5a7723bebd86645541","_rev":"_cfFmVMO---","wikipediaExternalRef":23862,"document":{"$oid":"60c20c5a7723bebd86645540"},"context":"To this end, we have developed an open source python toolkit PyLipID (https://github.com/wlsong/PyLipID)","wikidataId":"Q28865","type":"software","confidence":0.5769,"software-name":{"wikipediaExternalRef":23862,"normalizedForm":"python","offsetStart":46,"wikidataId":"Q28865","offsetEnd":52,"lang":"en","confidence":0.5769,"rawForm":"python","boundingBoxes":[{"x":239.347,"h":6.9899,"y":505.755,"p":2,"w":22.4664}]},"lang":"en"},
  {"_key":"60c20c607723bebd86645543","_id":"annotations/60c20c607723bebd86645543","_rev":"_cfFmVMa---","document":{"$oid":"60c20c607723bebd86645542"},"type":"software","software-name":{"offsetStart":18,"normalizedForm":"HTH","offsetEnd":21,"rawForm":"HTH","boundingBoxes":[{"x":392.528,"h":8.931,"y":575.783,"p":4,"w":21.567}]},"context":"Using the program HTH (34) and searching the Pfam Data- base of protein families (35), we identified a putative helix-turn- helix motif within the first 34 amino acids and a tetratricopep- tide repeat spanning amino acids 71-104 of OatC."},
  {"_key":"60c20c607723bebd86645544","_id":"annotations/60c20c607723bebd86645544","_rev":"_cfFmVMm---","document":{"$oid":"60c20c607723bebd86645542"},"type":"software","software-name":{"offsetStart":66,"normalizedForm":"MyHits","offsetEnd":72,"rawForm":"MyHits","boundingBoxes":[{"x":344.558,"h":8.931,"y":540.507,"p":5,"w":30.7125}]},"context":"OatC Contains a Nucleophile Elbow Motif-Motif scanning using the MyHits web server (45) revealed a putative nucleo- phile elbow motif (GXS 286 XGG) in the primary sequence of OatC (Fig. 3A)."},
  {"_key":"60c20c607723bebd86645545","_id":"annotations/60c20c607723bebd86645545","_rev":"_cfFmVM2---","document":{"$oid":"60c20c607723bebd86645542"},"type":"software","software-name":{"offsetStart":69,"normalizedForm":"OatC","offsetEnd":73,"rawForm":"OatC","boundingBoxes":[{"x":184.268,"h":8.931,"y":188.051,"p":8,"w":22.0252}]},"context":"As shown in supplemental Fig. S2, we propose a topology diagram for OatC that is based on sec- ondary structure prediction (52)."},
  {"_key":"60c20c647723bebd86645547","_id":"annotations/60c20c647723bebd86645547","_rev":"_cfFmVNC---","wikipediaExternalRef":2783580,"document":{"$oid":"60c20c647723bebd86645546"},"publisher":{"offsetStart":52,"normalizedForm":"ESRI","offsetEnd":56,"rawForm":"ESRI","boundingBoxes":[{"x":112.96571666666667,"h":8.9801,"y":691.947,"p":3,"w":19.626866666666665}]},"context":"All likely matches were plotted in ArcGIS v. 10.1 (ESRI, USA) and the distance between the actual geolocated compound and the matched com- pound from the community survey was calculated.","wikidataId":"Q513297","type":"software","lang":"en","confidence":0.7383,"software-name":{"wikipediaExternalRef":2783580,"normalizedForm":"ArcGIS","offsetStart":35,"wikidataId":"Q513297","offsetEnd":41,"lang":"en","confidence":0.7383,"rawForm":"ArcGIS","boundingBoxes":[{"x":267.941,"h":8.9801,"y":678.964,"p":3,"w":33.0893}]},"version":{"offsetStart":46,"normalizedForm":"10.1","offsetEnd":50,"rawForm":"10.1","boundingBoxes":[{"x":85.5512,"h":8.980099999999993,"y":691.947,"p":3,"w":17.700199999999995}]}},
  {"_key":"60c20c647723bebd86645548","_id":"annotations/60c20c647723bebd86645548","_rev":"_cfFmVNS---","wikipediaExternalRef":2783580,"document":{"$oid":"60c20c647723bebd86645546"},"publisher":{"offsetStart":52,"normalizedForm":"ESRI","offsetEnd":56,"rawForm":"ESRI","boundingBoxes":[{"x":112.96571666666667,"h":8.9801,"y":691.947,"p":3,"w":19.626866666666665}]},"context":"Locations of compounds were plotted using ArcGIS and a compound was con- sidered to be correctly located if it fell within the  catchment area or intersecting catchment areas that matched the response provided at the facility.","wikidataId":"Q513297","type":"software","lang":"en","confidence":0.7383,"software-name":{"wikipediaExternalRef":2783580,"normalizedForm":"ArcGIS","offsetStart":43,"wikidataId":"Q513297","offsetEnd":49,"lang":"en","confidence":0.7383,"rawForm":"ArcGIS","boundingBoxes":[{"x":358.472,"h":8.9801,"y":705.102,"p":4,"w":33.0893}]},"version":{"offsetStart":46,"normalizedForm":"10.1","offsetEnd":50,"rawForm":"10.1","boundingBoxes":[{"x":85.5512,"h":8.980099999999993,"y":691.947,"p":3,"w":17.700199999999995}]}},
  {"_key":"60c20c647723bebd86645549","_id":"annotations/60c20c647723bebd86645549","_rev":"_cfFmVNm---","wikipediaExternalRef":2783580,"document":{"$oid":"60c20c647723bebd86645546"},"publisher":{"offsetStart":52,"normalizedForm":"ESRI","offsetEnd":56,"rawForm":"ESRI","boundingBoxes":[{"x":112.96571666666667,"h":8.9801,"y":691.947,"p":3,"w":19.626866666666665}]},"context":"Euclidian distances were calculated using the ArcGIS Euclidian distance tool in the spatial analyst package to delineate catchment areas for both health facilities (Fig. 3a) and primary schools (Fig. 3b).","wikidataId":"Q513297","type":"software","lang":"en","confidence":0.7383,"software-name":{"wikipediaExternalRef":2783580,"normalizedForm":"ArcGIS","offsetStart":47,"wikidataId":"Q513297","offsetEnd":53,"lang":"en","confidence":0.7383,"rawForm":"ArcGIS","boundingBoxes":[{"x":113.218,"h":8.9801,"y":184.997,"p":5,"w":33.2003}]},"version":{"offsetStart":46,"normalizedForm":"10.1","offsetEnd":50,"rawForm":"10.1","boundingBoxes":[{"x":85.5512,"h":8.980099999999993,"y":691.947,"p":3,"w":17.700199999999995}]}},
  {"_key":"60c20c647723bebd8664554a","_id":"annotations/60c20c647723bebd8664554a","_rev":"_cfFmVN2---","wikipediaExternalRef":2783580,"document":{"$oid":"60c20c647723bebd86645546"},"publisher":{"offsetStart":52,"normalizedForm":"ESRI","offsetEnd":56,"rawForm":"ESRI","boundingBoxes":[{"x":112.96571666666667,"h":8.9801,"y":691.947,"p":3,"w":19.626866666666665}]},"context":"Locations of participants followed to their com- pounds were plotted in ArcGIS and were classified as correctly located based on the participatory map- ping exercise if they fell within the reported cell.","wikidataId":"Q513297","type":"software","lang":"en","confidence":0.7383,"software-name":{"wikipediaExternalRef":2783580,"normalizedForm":"ArcGIS","offsetStart":72,"wikidataId":"Q513297","offsetEnd":78,"lang":"en","confidence":0.7383,"rawForm":"ArcGIS","boundingBoxes":[{"x":155.74,"h":8.9801,"y":626.918,"p":4,"w":33.0893}]},"version":{"offsetStart":46,"normalizedForm":"10.1","offsetEnd":50,"rawForm":"10.1","boundingBoxes":[{"x":85.5512,"h":8.980099999999993,"y":691.947,"p":3,"w":17.700199999999995}]}},
  {"_key":"60c20c647723bebd8664554b","_id":"annotations/60c20c647723bebd8664554b","_rev":"_cfFmVOK---","wikipediaExternalRef":2783580,"document":{"$oid":"60c20c647723bebd86645546"},"publisher":{"offsetStart":52,"normalizedForm":"ESRI","offsetEnd":56,"rawForm":"ESRI","boundingBoxes":[{"x":112.96571666666667,"h":8.9801,"y":691.947,"p":3,"w":19.626866666666665}]},"context":"The distance between the edge of the cell/buffer and the incorrectly located compounds was calculated in ArcGIS to determine the mean error associated with the approach.","wikidataId":"Q513297","type":"software","lang":"en","confidence":0.7383,"software-name":{"wikipediaExternalRef":2783580,"normalizedForm":"ArcGIS","offsetStart":107,"wikidataId":"Q513297","offsetEnd":113,"lang":"en","confidence":0.7383,"rawForm":"ArcGIS","boundingBoxes":[{"x":294.178,"h":8.9801,"y":483.939,"p":4,"w":33.2003}]},"version":{"offsetStart":46,"normalizedForm":"10.1","offsetEnd":50,"rawForm":"10.1","boundingBoxes":[{"x":85.5512,"h":8.980099999999993,"y":691.947,"p":3,"w":17.700199999999995}]}},
  {"_key":"60c20c647723bebd8664554c","_id":"annotations/60c20c647723bebd8664554c","_rev":"_cfFmVOa---","wikipediaExternalRef":11944583,"document":{"$oid":"60c20c647723bebd86645546"},"publisher":{"offsetStart":130,"normalizedForm":"Clark Laboratories","offsetEnd":148,"rawForm":"Clark Laboratories","boundingBoxes":[{"x":216.75238333333334,"h":8.980099999999993,"y":562.012,"p":5,"w":79.96970897435898}]},"context":"The cost-distance models for both health facilities (Fig. 3c) and primary schools (Fig. 3d) were created using IDRISI software (Clark Laboratories, USA) and imported into ArcGIS for analysis.","wikidataId":"Q5970081","type":"software","confidence":0.3782,"software-name":{"wikipediaExternalRef":11944583,"normalizedForm":"IDRISI","offsetStart":113,"wikidataId":"Q5970081","offsetEnd":119,"lang":"en","confidence":0.3782,"rawForm":"IDRISI","boundingBoxes":[{"x":134.762,"h":8.9801,"y":562.012,"p":5,"w":32.6653}]},"lang":"en"},
  {"_key":"60c20c647723bebd8664554d","_id":"annotations/60c20c647723bebd8664554d","_rev":"_cfFmVOm---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20c647723bebd86645546"},"publisher":{"offsetStart":131,"normalizedForm":"StataCorp","offsetEnd":140,"rawForm":"StataCorp","boundingBoxes":[{"x":112.94331818181819,"h":8.9801,"y":574.987,"p":3,"w":40.38586363636364}]},"context":"Names from the two databases were matched using Levenshtein's dis- tance algorithm [28] for string matching using Stata v. 12.1 (StataCorp, USA).","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7154,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":115,"wikidataId":"Q1204300","offsetEnd":120,"lang":"en","confidence":0.7154,"rawForm":"Stata","boundingBoxes":[{"x":279.278,"h":8.9801,"y":561.948,"p":3,"w":21.8502}]},"version":{"offsetStart":125,"normalizedForm":"12.1","offsetEnd":129,"rawForm":"12.1","boundingBoxes":[{"x":85.7782,"h":8.980099999999993,"y":574.987,"p":3,"w":17.700199999999995}]}},
  {"_key":"60c20c647723bebd8664554e","_id":"annotations/60c20c647723bebd8664554e","_rev":"_cfFmVO2---","wikipediaExternalRef":2783580,"document":{"$oid":"60c20c647723bebd86645546"},"publisher":{"offsetStart":52,"normalizedForm":"ESRI","offsetEnd":56,"rawForm":"ESRI","boundingBoxes":[{"x":112.96571666666667,"h":8.9801,"y":691.947,"p":3,"w":19.626866666666665}]},"context":"The cost-distance models for both health facilities (Fig. 3c) and primary schools (Fig. 3d) were created using IDRISI software (Clark Laboratories, USA) and imported into ArcGIS for analysis.","wikidataId":"Q513297","type":"software","lang":"en","confidence":0.7383,"software-name":{"wikipediaExternalRef":2783580,"normalizedForm":"ArcGIS","offsetStart":174,"wikidataId":"Q513297","offsetEnd":180,"lang":"en","confidence":0.7383,"rawForm":"ArcGIS","boundingBoxes":[{"x":182.218,"h":8.9801,"y":575.051,"p":5,"w":33.1453}]},"version":{"offsetStart":46,"normalizedForm":"10.1","offsetEnd":50,"rawForm":"10.1","boundingBoxes":[{"x":85.5512,"h":8.980099999999993,"y":691.947,"p":3,"w":17.700199999999995}]}},
  {"_key":"60c20c647723bebd86645550","_id":"annotations/60c20c647723bebd86645550","_rev":"_cfFmVPC---","document":{"$oid":"60c20c647723bebd8664554f"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"SOAPsnp","offsetEnd":7,"rawForm":"SOAPsnp","boundingBoxes":[{"x":460.911,"h":8.854,"y":612.9,"p":3,"w":36.8695}]},"context":"SOAPsnp software was used to detect SNPs by comparing healthy volunteer and patient files with CCDS, dbSNP, and the Human Genome Database."},
  {"_key":"60c20c647723bebd86645551","_id":"annotations/60c20c647723bebd86645551","_rev":"_cfFmVPS---","wikipediaExternalRef":179088,"document":{"$oid":"60c20c647723bebd8664554f"},"context":"All statistical analyses were performed using SPSS version 22.0 software.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":46,"wikidataId":"Q181596","offsetEnd":50,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":220.591,"h":8.854,"y":693.178,"p":3,"w":18.677}]},"version":{"offsetStart":59,"normalizedForm":"22.0","offsetEnd":63,"rawForm":"22.0","boundingBoxes":[{"x":273.429,"h":8.854000000000042,"y":693.178,"p":3,"w":15.722500000000025}]}},
  {"_key":"60c20c647723bebd86645552","_id":"annotations/60c20c647723bebd86645552","_rev":"_cfFmVPi---","document":{"$oid":"60c20c647723bebd8664554f"},"type":"software","software-name":{"offsetStart":51,"normalizedForm":"MOE","offsetEnd":54,"rawForm":"MOE","boundingBoxes":[{"x":72.4312,"h":8.854,"y":441.177,"p":3,"w":21.4766}]},"context":"The structure of the Y395H mutant was built using MOE software (Molecular Operating Environment 2013.08;"},
  {"_key":"60c20c647723bebd86645553","_id":"annotations/60c20c647723bebd86645553","_rev":"_cfFmVPu---","wikipediaExternalRef":51708210,"publisher":{"offsetStart":107,"normalizedForm":"Chemical Computing Group Inc","offsetEnd":135,"rawForm":"Chemical Computing Group Inc","boundingBoxes":[{"x":81.9796,"h":8.853999999999985,"y":452.63,"p":3,"w":129.5585}]},"context":"The structure of the Y395H mutant was built using MOE software (Molecular Operating Environment 2013.08;","confidence":0.6533,"url":{"offsetStart":138,"normalizedForm":"www.chemcomp. com","offsetEnd":156,"rawForm":"www.chemcomp. \ncom","boundingBoxes":[{"x":223.09,"h":8.853999999999985,"y":452.63,"p":3,"w":65.9718},{"x":45.3543,"h":8.854,"y":464.138,"p":3,"w":14.755875}]},"version":{"offsetStart":98,"normalizedForm":"2013.08","offsetEnd":105,"rawForm":"2013.08","boundingBoxes":[{"x":45.3543,"h":8.853999999999985,"y":452.63,"p":3,"w":27.806975}]},"document":{"$oid":"60c20c647723bebd8664554f"},"wikidataId":"Q28447694","type":"software","software-name":{"wikipediaExternalRef":51708210,"normalizedForm":"Molecular Operating Environment","offsetStart":65,"wikidataId":"Q28447694","offsetEnd":96,"lang":"en","confidence":0.6533,"rawForm":"Molecular Operating Environment","boundingBoxes":[{"x":143.40448,"h":8.853999999999985,"y":441.177,"p":3,"w":145.67012000000003}]},"lang":"en"},
  {"_key":"60c20c647723bebd86645554","_id":"annotations/60c20c647723bebd86645554","_rev":"_cfFmVP6---","document":{"$oid":"60c20c647723bebd8664554f"},"type":"software","software-name":{"offsetStart":88,"normalizedForm":"GATK","offsetEnd":92,"rawForm":"GATK","boundingBoxes":[{"x":357.561,"h":8.854,"y":670.385,"p":3,"w":25.4125}]},"context":"Insertions and deletions (indels) were detected using the Burrows-Wheeler Aligner and GATK software, and were defined using CCDS, dbSNP, and the Human Genome Database."},
  {"_key":"60c20c647723bebd86645555","_id":"annotations/60c20c647723bebd86645555","_rev":"_cfFmVQG---","wikipediaExternalRef":2324407,"document":{"$oid":"60c20c647723bebd8664554f"},"context":"Chemical Computing Group Inc., www.chemcomp. com) and structural figures prepared using PyMOL 2.2.","wikidataId":"Q1373457","type":"software","lang":"en","confidence":0.8093,"software-name":{"wikipediaExternalRef":2324407,"normalizedForm":"PyMOL","offsetStart":89,"wikidataId":"Q1373457","offsetEnd":94,"lang":"en","confidence":0.8093,"rawForm":"PyMOL","boundingBoxes":[{"x":212.371,"h":8.854,"y":464.138,"p":3,"w":30.1625}]},"version":{"offsetStart":95,"normalizedForm":"2.2","offsetEnd":98,"rawForm":"2.2","boundingBoxes":[{"x":245.424,"h":8.853999999999985,"y":464.138,"p":3,"w":9.93225000000001}]}},
  {"_key":"60c20c697723bebd86645558","_id":"annotations/60c20c697723bebd86645558","_rev":"_cfFmVQS---","document":{"$oid":"60c20c697723bebd86645556"},"context":"Following the NPPTL protocol, the N95 respirator was placed on the head form and adjusted using the training feature in the Fit Proþ soft- ware (v3.3). 32","references":[{"offsetStart":15367,"normalizedForm":"32","refKey":32,"label":"32","reference_id":{"$oid":"60c20c697723bebd86645557"},"offsetEnd":15370,"boundingBoxes":[{"x":353.707,"h":6.1553,"y":160.43,"p":3,"w":7.1249}]}],"type":"software","software-name":{"offsetStart":126,"normalizedForm":"Fit Proþ","offsetEnd":134,"rawForm":"Fit Proþ","boundingBoxes":[{"x":496.181,"h":9.234000000000009,"y":150.927,"p":3,"w":35.25849999999997}]},"version":{"offsetStart":148,"normalizedForm":"3.3","offsetEnd":151,"rawForm":"3.3","boundingBoxes":[{"x":331.4553285714286,"h":9.234000000000009,"y":162.492,"p":3,"w":14.849314285714286}]}},
  {"_key":"60c20c737723bebd8664555a","_id":"annotations/60c20c737723bebd8664555a","_rev":"_cfFmVQe---","wikipediaExternalRef":179088,"document":{"$oid":"60c20c737723bebd86645559"},"publisher":{"offsetStart":40,"normalizedForm":"SPSS Inc","offsetEnd":48,"rawForm":"SPSS Inc","boundingBoxes":[{"x":491.37908,"h":7.782299999999964,"y":590.865,"p":2,"w":29.373800000000017}]},"context":"Data was analyzed with SPSS version 23 (SPSS Inc., Chi- cago, IL, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7466,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":23,"wikidataId":"Q181596","offsetEnd":27,"lang":"en","confidence":0.7466,"rawForm":"SPSS","boundingBoxes":[{"x":425.981,"h":7.7823,"y":590.865,"p":2,"w":16.9279}]},"version":{"offsetStart":36,"normalizedForm":"23","offsetEnd":38,"rawForm":"23","boundingBoxes":[{"x":475.699,"h":7.7823,"y":590.865,"p":2,"w":8.8069}]}},
  {"_key":"60c20c737723bebd8664555b","_id":"annotations/60c20c737723bebd8664555b","_rev":"_cfFmVQq---","wikipediaExternalRef":179088,"document":{"$oid":"60c20c737723bebd86645559"},"publisher":{"offsetStart":58,"normalizedForm":"SPSS Inc","offsetEnd":66,"rawForm":"SPSS Inc","boundingBoxes":[{"x":310.83348,"h":8.240000000000009,"y":624.457,"p":3,"w":31.792059999999992}]},"context":"Statistical analysis was performed with SPSS version 23 (SPSS Inc., Chicago, IL, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7466,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":40,"wikidataId":"Q181596","offsetEnd":44,"lang":"en","confidence":0.7466,"rawForm":"SPSS","boundingBoxes":[{"x":482.567,"h":8.24,"y":613.459,"p":3,"w":17.9236}]},"version":{"offsetStart":53,"normalizedForm":"23","offsetEnd":55,"rawForm":"23","boundingBoxes":[{"x":536.31,"h":8.24,"y":613.459,"p":3,"w":9.325}]}},
  {"_key":"60c20c747723bebd8664555d","_id":"annotations/60c20c747723bebd8664555d","_rev":"_cfFmVQ2---","document":{"$oid":"60c20c747723bebd8664555c"},"publisher":{"offsetStart":180,"normalizedForm":"Muthén","offsetEnd":186,"rawForm":"Muthén","boundingBoxes":[{"x":209.3986857142857,"h":9.584,"y":403.961,"p":4,"w":33.46011428571428}]},"context":"To test the proposed model, structural equation models (SEM) were performed to test the causal assumptions derived from the proposed model (Figure 1) by using Mplus Version 7.4 (Muthén and Muthén, Version 7.4, Los Angeles, CA, USA).","type":"software","software-name":{"offsetStart":161,"normalizedForm":"Mplus","offsetEnd":166,"rawForm":"Mplus","boundingBoxes":[{"x":118.92,"h":9.584,"y":403.961,"p":4,"w":29.1137}]},"version":{"offsetStart":175,"normalizedForm":"7.4","offsetEnd":178,"rawForm":"7.4","boundingBoxes":[{"x":188.041,"h":9.584000000000003,"y":403.961,"p":4,"w":12.702300000000008}]}},
  {"_key":"60c20c777723bebd8664555f","_id":"annotations/60c20c777723bebd8664555f","_rev":"_cfFmVRC---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20c777723bebd8664555e"},"context":"The STATA 15.0 software package was used for CFA.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7367,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"STATA","offsetStart":4,"wikidataId":"Q1204300","offsetEnd":9,"lang":"en","confidence":0.7367,"rawForm":"STATA","boundingBoxes":[{"x":82.4287,"h":8.7472,"y":513.274,"p":7,"w":31.9361}]},"version":{"offsetStart":10,"normalizedForm":"15.0","offsetEnd":14,"rawForm":"15.0","boundingBoxes":[{"x":118.995,"h":8.74720000000002,"y":513.274,"p":7,"w":17.499299999999977}]}},
  {"_key":"60c20c777723bebd86645560","_id":"annotations/60c20c777723bebd86645560","_rev":"_cfFmVRO---","document":{"$oid":"60c20c777723bebd8664555e"},"type":"software","software-name":{"offsetStart":35,"normalizedForm":"EnjoySurvey","offsetEnd":46,"rawForm":"EnjoySurvey","boundingBoxes":[{"x":261.942,"h":8.7472,"y":202.487,"p":5,"w":52.7848}]},"context":"The survey was programmed with the EnjoySurvey software."},
  {"_key":"60c20c817723bebd86645562","_id":"annotations/60c20c817723bebd86645562","_rev":"_cfFmVRa---","document":{"$oid":"60c20c817723bebd86645561"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"PlasmidFinder","offsetEnd":13,"rawForm":"PlasmidFinder","boundingBoxes":[{"x":54.777,"h":7.6593,"y":645.784,"p":37,"w":52.5102}]},"context":"PlasmidFinder showed that pXXB210 had 100% identity with the IncA/C2 replicon."},
  {"_key":"60c20c817723bebd86645563","_id":"annotations/60c20c817723bebd86645563","_rev":"_cfFmVRm---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20c817723bebd86645561"},"context":"Data were analyzed using GraphPad Prism v8.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":25,"wikidataId":"Q5597066","offsetEnd":39,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":132.819,"h":7.65930000000003,"y":526.273,"p":6,"w":59.87270000000004}]},"version":{"offsetStart":41,"normalizedForm":"8","offsetEnd":42,"rawForm":"8","boundingBoxes":[{"x":195.707,"h":7.6593,"y":526.273,"p":6,"w":7.207066666666667}]}},
  {"_key":"60c20c817723bebd86645564","_id":"annotations/60c20c817723bebd86645564","_rev":"_cfFmVRy---","document":{"$oid":"60c20c817723bebd86645561"},"context":"Phylogenetic trees were constructed by MEGA5.1, and the re- sults suggested that the HA gene of JM/19 belonged to clade 2.3.4.4 ( Fig. 1 A).","type":"software","software-name":{"offsetStart":39,"normalizedForm":"MEGA","offsetEnd":43,"rawForm":"MEGA","boundingBoxes":[{"x":484.642,"h":7.6593,"y":386.071,"p":17,"w":21.4051875}]},"version":{"offsetStart":43,"normalizedForm":"5.1","offsetEnd":46,"rawForm":"5.1","boundingBoxes":[{"x":484.642,"h":7.659299999999973,"y":386.071,"p":17,"w":29.967262500000004}]}},
  {"_key":"60c20c817723bebd86645565","_id":"annotations/60c20c817723bebd86645565","_rev":"_cfFmVS----","document":{"$oid":"60c20c817723bebd86645561"},"type":"software","software-name":{"offsetStart":43,"normalizedForm":"ISfinder","offsetEnd":51,"rawForm":"ISfinder","boundingBoxes":[{"x":212.564,"h":7.6593,"y":365.254,"p":38,"w":26.752622222222218}]},"context":"In addition, IS elements were annotated by ISfinder, and align- ments were performed against published mcr-3.1 -carrying plasmid genomes (KY924928, CP032937, CP045953, AP018939, MN647787, MN6 47788 and MN6 47789)."},
  {"_key":"60c20c867723bebd86645567","_id":"annotations/60c20c867723bebd86645567","_rev":"_cfFmVSK---","document":{"$oid":"60c20c867723bebd86645566"},"publisher":{"offsetStart":110,"normalizedForm":"MBF Bioscience","offsetEnd":124,"rawForm":"MBF Bioscience","boundingBoxes":[{"x":400.28875,"h":8.341000000000008,"y":278.932,"p":6,"w":58.88915909090912}]},"context":"Neurolucida software was used to create morphological reconstruction using ten cells per layer in each brain.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"Neurolucida","offsetEnd":11,"rawForm":"Neurolucida","boundingBoxes":[{"x":320.484,"h":7.463,"y":378.871,"p":13,"w":41.4375}]},"version":{"offsetStart":127,"normalizedForm":"11.02.1","offsetEnd":134,"rawForm":"11.02.1","boundingBoxes":[{"x":466.018,"h":8.341000000000008,"y":278.932,"p":6,"w":30.381760000000043}]}},
  {"_key":"60c20c867723bebd86645568","_id":"annotations/60c20c867723bebd86645568","_rev":"_cfFmVSW---","wikipediaExternalRef":20412,"document":{"$oid":"60c20c867723bebd86645566"},"publisher":{"offsetStart":22,"normalizedForm":"MathWorks","offsetEnd":31,"rawForm":"MathWorks","boundingBoxes":[{"x":256.78448333333336,"h":7.463,"y":138.885,"p":14,"w":33.83535}]},"context":"and MATLAB toolboxes (MathWorks).","wikidataId":"Q169478","type":"software","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":4,"wikidataId":"Q169478","offsetEnd":10,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":183.251,"h":7.463,"y":138.885,"p":14,"w":34.2095}]},"url":{"offsetStart":-28,"normalizedForm":"cartoolcommunity.unige.ch","offsetEnd":-3,"rawForm":"cartoolcommunity.unige.ch","boundingBoxes":[{"x":75.88088571428571,"h":7.462999999999994,"y":138.885,"p":14,"w":84.48214285714286}]},"lang":"en"},
  {"_key":"60c20c867723bebd86645569","_id":"annotations/60c20c867723bebd86645569","_rev":"_cfFmVSi---","document":{"$oid":"60c20c867723bebd86645566"},"type":"software","software-name":{"offsetStart":6,"normalizedForm":"MetaMorph","offsetEnd":15,"rawForm":"MetaMorph","boundingBoxes":[{"x":126.992,"h":7.463,"y":650.2,"p":13,"w":39.6278}]},"context":"Using MetaMorph software, cell coordinates were projected on the closest curve following the path of radial glia fiber to estimate the relative percentage of migration progress."},
  {"_key":"60c20c867723bebd8664556a","_id":"annotations/60c20c867723bebd8664556a","_rev":"_cfFmVSu---","document":{"$oid":"60c20c867723bebd86645566"},"publisher":{"offsetStart":50,"normalizedForm":"Denis Brunet","offsetEnd":63,"rawForm":"Denis \nBrunet","boundingBoxes":[{"x":281.156,"h":7.463,"y":128.85,"p":14,"w":18.8697},{"x":48.0186,"h":7.463,"y":138.885,"p":14,"w":21.8454}]},"context":"Analyses were performed using Cartool software by Denis Brunet (cartoolcommunity.unige.ch),","type":"software","software-name":{"offsetStart":30,"normalizedForm":"Cartool","offsetEnd":37,"rawForm":"Cartool","boundingBoxes":[{"x":213.498,"h":7.463,"y":128.85,"p":14,"w":24.0409}]}},
  {"_key":"60c20c867723bebd8664556b","_id":"annotations/60c20c867723bebd8664556b","_rev":"_cfFmVS2---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20c867723bebd86645566"},"context":"Statistical analysis was conducted using GraphPad Prism 7. The normality of sample distributions was assessed with the Shapiro-Wilk criterion.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":41,"wikidataId":"Q5597066","offsetEnd":55,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":449.35,"h":7.462999999999994,"y":251.362,"p":14,"w":55.315499999999986}]},"version":{"offsetStart":56,"normalizedForm":"7","offsetEnd":57,"rawForm":"7","boundingBoxes":[{"x":507.064,"h":7.463,"y":251.362,"p":14,"w":3.1875}]}},
  {"_key":"60c20c867723bebd8664556c","_id":"annotations/60c20c867723bebd8664556c","_rev":"_cfFmVTG---","wikipediaExternalRef":24893,"document":{"$oid":"60c20c867723bebd86645566"},"publisher":{"offsetStart":40,"normalizedForm":"Adobe","offsetEnd":45,"rawForm":"Adobe","boundingBoxes":[{"x":201.092,"h":7.463,"y":320.187,"p":13,"w":22.5675}]},"context":"Large-field images were assembled using Adobe Photoshop.","wikidataId":"Q129793","type":"software","confidence":0.646,"software-name":{"wikipediaExternalRef":24893,"normalizedForm":"Photoshop","offsetStart":46,"wikidataId":"Q129793","offsetEnd":55,"lang":"en","confidence":0.646,"rawForm":"Photoshop","boundingBoxes":[{"x":228.135,"h":7.463,"y":320.187,"p":13,"w":34.096050000000005}]},"lang":"en"},
  {"_key":"60c20c867723bebd8664556d","_id":"annotations/60c20c867723bebd8664556d","_rev":"_cfFmVTS---","document":{"$oid":"60c20c867723bebd86645566"},"publisher":{"offsetStart":110,"normalizedForm":"MBF Bioscience","offsetEnd":124,"rawForm":"MBF Bioscience","boundingBoxes":[{"x":400.28875,"h":8.341000000000008,"y":278.932,"p":6,"w":58.88915909090912}]},"context":"We also performed dendritic arborization reconstruction of electroporated cells using Neurolucida software (MBF Bioscience, v11.02.1), separating cells that reached layer IV and misplaced cells.","type":"software","software-name":{"offsetStart":88,"normalizedForm":"Neurolucida","offsetEnd":99,"rawForm":"Neurolucida","boundingBoxes":[{"x":311.981,"h":8.341,"y":278.932,"p":6,"w":45.4252}]},"version":{"offsetStart":127,"normalizedForm":"11.02.1","offsetEnd":134,"rawForm":"11.02.1","boundingBoxes":[{"x":466.018,"h":8.341000000000008,"y":278.932,"p":6,"w":30.381760000000043}]}},
  {"_key":"60c20c867723bebd8664556e","_id":"annotations/60c20c867723bebd8664556e","_rev":"_cfFmVTe---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20c867723bebd86645566"},"context":"For video time-lapse analyses, slight drifts correction of the slices and single cell tracking were performed with ImageJ64 Software (v1.48).","wikidataId":"Q1659584","type":"software","lang":"en","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":116,"wikidataId":"Q1659584","offsetEnd":122,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":425.768,"h":7.463,"y":228.861,"p":13,"w":30.7822}]},"version":{"offsetStart":122,"normalizedForm":"64","offsetEnd":124,"rawForm":"64","boundingBoxes":[{"x":425.768,"h":7.463,"y":228.861,"p":13,"w":30.7822}]}},
  {"_key":"60c20c867723bebd8664556f","_id":"annotations/60c20c867723bebd8664556f","_rev":"_cfFmVTq---","document":{"$oid":"60c20c867723bebd86645566"},"type":"software","software-name":{"offsetStart":116,"normalizedForm":"MetaMorph","offsetEnd":125,"rawForm":"MetaMorph","boundingBoxes":[{"x":489.602,"h":7.463,"y":138.889,"p":13,"w":40.256}]},"context":"The distance between GFP-labeled cells leading process and nestin- labeled radial glia in the CP was measured using MetaMorph software, starting at the base of the leading process."},
  {"_key":"60c20c867723bebd86645570","_id":"annotations/60c20c867723bebd86645570","_rev":"_cfFmVT2---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20c867723bebd86645566"},"context":"The pixel intensity threshold for RFP and GFP was adjusted such that the tissue background corresponded to level 0. The ratio of RFP-intensity over GFP- intensity of each cell was then measured using the ImageJ64 software (v1.48).","wikidataId":"Q1659584","type":"software","lang":"en","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":206,"wikidataId":"Q1659584","offsetEnd":212,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":233.971,"h":7.463,"y":410.16,"p":13,"w":33.3344}]},"version":{"offsetStart":212,"normalizedForm":"64","offsetEnd":214,"rawForm":"64","boundingBoxes":[{"x":233.971,"h":7.463,"y":410.16,"p":13,"w":33.3344}]}},
  {"_key":"60c20c867723bebd86645571","_id":"annotations/60c20c867723bebd86645571","_rev":"_cfFmVUC---","document":{"$oid":"60c20c867723bebd86645566"},"context":"Long-term imaging was performed by time-lapse sequence recordings with a Nikon A1R Resonant Scanner Upright Microscope maintained in a thermoregulated chamber (37°C, 5% CO 2 ) for 12 to 14 h (one large image/ 10 min) using a 488 nm laser illumination diode, 20× Plan Fluor ELWD DIC L objective and NIS-Elements AR software (v4.30.02).","type":"software","software-name":{"offsetStart":302,"normalizedForm":"NIS-Elements AR","offsetEnd":317,"rawForm":"NIS-Elements AR","boundingBoxes":[{"x":368.106,"h":7.463000000000022,"y":427.903,"p":12,"w":61.37100000000004}]},"version":{"offsetStart":329,"normalizedForm":"4.30.02","offsetEnd":336,"rawForm":"4.30.02","boundingBoxes":[{"x":466.61054545454544,"h":7.463000000000022,"y":427.903,"p":12,"w":26.53236363636364}]}},
  {"_key":"60c20c887723bebd86645573","_id":"annotations/60c20c887723bebd86645573","_rev":"_cfFmVUO---","wikipediaExternalRef":4294204,"document":{"$oid":"60c20c887723bebd86645572"},"publisher":{"offsetStart":85,"normalizedForm":"MedCalc Software","offsetEnd":101,"rawForm":"MedCalc Software","boundingBoxes":[{"x":395.4169375,"h":7.480000000000018,"y":285.787,"p":2,"w":60.411951388888895}]},"context":"All statistical analyses were performed using MedCalc for Windows, version 9.3.9.0 (MedCalc Software, Mariakerke, Belgium).","wikidataId":"Q4272521","type":"software","lang":"en","confidence":0.7594,"software-name":{"wikipediaExternalRef":4294204,"normalizedForm":"MedCalc","offsetStart":46,"wikidataId":"Q4272521","offsetEnd":53,"lang":"en","confidence":0.7594,"rawForm":"MedCalc","boundingBoxes":[{"x":490.873,"h":7.48,"y":276.275,"p":2,"w":31.161}]},"version":{"offsetStart":76,"normalizedForm":"9.3.9.0","offsetEnd":83,"rawForm":"9.3.9.0","boundingBoxes":[{"x":366.212,"h":7.480000000000018,"y":285.787,"p":2,"w":23.375}]}},
  {"_key":"60c20c987723bebd86645576","_id":"annotations/60c20c987723bebd86645576","_rev":"_cfFmVUa---","wikipediaExternalRef":179088,"document":{"$oid":"60c20c987723bebd86645575"},"context":"Statistical analyses were done using SPSS software (ver- sion 13) unless otherwise indicated.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":37,"wikidataId":"Q181596","offsetEnd":41,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":480.41,"h":8.3885,"y":734.516,"p":2,"w":19.1045}]},"version":{"offsetStart":62,"normalizedForm":"13","offsetEnd":64,"rawForm":"13","boundingBoxes":[{"x":332.56,"h":8.3885,"y":746.649,"p":2,"w":8.296666666666667}]}},
  {"_key":"60c20c987723bebd86645577","_id":"annotations/60c20c987723bebd86645577","_rev":"_cfFmVUu---","document":{"$oid":"60c20c987723bebd86645575"},"type":"software","software-name":{"offsetStart":55,"normalizedForm":"R software package rms","offsetEnd":78,"rawForm":"R software \npackage rms","boundingBoxes":[{"x":252.902,"h":8.388500000000022,"y":442.038,"p":3,"w":45.841000000000065},{"x":47.8488,"h":8.388500000000022,"y":454.17,"p":3,"w":51.3}]},"context":"The bias- corrected c-statistic was computed using the R software package rms 8 ."},
  {"_key":"60c20c9a7723bebd86645579","_id":"annotations/60c20c9a7723bebd86645579","_rev":"_cfFmVU6---","document":{"$oid":"60c20c9a7723bebd86645578"},"type":"software","software-name":{"offsetStart":127,"normalizedForm":"R stats","offsetEnd":134,"rawForm":"R stats","boundingBoxes":[{"x":71.9732,"h":11.967099999999988,"y":176.892,"p":7,"w":36.34849999999999}]},"context":"In our case, the spline correlogram routines from a dedicated R package [11], and the related spline fitting routines in the R stats library [12], were adapted and rewritten in C++, in order to be integrated efficiently with our simulation code."},
  {"_key":"60c20c9b7723bebd8664557b","_id":"annotations/60c20c9b7723bebd8664557b","_rev":"_cfFmVVG---","document":{"$oid":"60c20c9b7723bebd8664557a"},"publisher":{"offsetStart":116,"normalizedForm":"SPSS Inc","offsetEnd":124,"rawForm":"SPSS Inc","boundingBoxes":[{"x":229.75519999999997,"h":7.539800000000014,"y":517.412,"p":3,"w":28.96986000000001}]},"context":"Statistical analysis was performed using the Statistical Package for Social Sciences (SPSS) 23.0 software program (SPSS Inc., Chi- cago, IL, USA).","type":"software","software-name":{"offsetStart":45,"normalizedForm":"Statistical Package for Social Sciences (SPSS)","offsetEnd":92,"rawForm":"Statistical Package \nfor Social Sciences (SPSS)","boundingBoxes":[{"x":214.693,"h":7.539800000000014,"y":506.924,"p":3,"w":69.16489999999996},{"x":32.8267,"h":7.539800000000014,"y":517.412,"p":3,"w":98.05739999999999}]},"version":{"offsetStart":93,"normalizedForm":"23.0","offsetEnd":97,"rawForm":"23.0","boundingBoxes":[{"x":134.246,"h":7.539800000000014,"y":517.412,"p":3,"w":16.121700000000004}]}},
  {"_key":"60c20ca67723bebd86645584","_id":"annotations/60c20ca67723bebd86645584","_rev":"_cfFmVVO---","document":{"$oid":"60c20ca67723bebd8664557c"},"context":"and the DICHROWEB server (www.cryst.bbk.ac.uk/cdweb/html/home.html) (1, 40, 62).","references":[{"offsetStart":15868,"normalizedForm":"(1","refKey":0,"label":"(1,","reference_id":{"$oid":"60c20ca67723bebd8664557d"},"offsetEnd":15879,"boundingBoxes":[{"x":181.63,"h":6.489000000000033,"y":638.569,"p":3,"w":29.913250000000005}]},{"offsetStart":15868,"normalizedForm":"40","refKey":41,"label":"40,","reference_id":{"$oid":"60c20ca67723bebd8664557e"},"offsetEnd":15879,"boundingBoxes":[{"x":181.63,"h":6.489000000000033,"y":638.569,"p":3,"w":29.913250000000005}]},{"offsetStart":15868,"normalizedForm":"62)","refKey":64,"label":"62)","reference_id":{"$oid":"60c20ca67723bebd8664557f"},"offsetEnd":15879,"boundingBoxes":[{"x":181.63,"h":6.489000000000033,"y":638.569,"p":3,"w":29.913250000000005}]}],"type":"software","software-name":{"offsetStart":8,"normalizedForm":"DICHROWEB","offsetEnd":17,"rawForm":"DICHROWEB","boundingBoxes":[{"x":216.075,"h":6.489,"y":629.546,"p":3,"w":46.613}]},"url":{"offsetStart":27,"normalizedForm":"www.cryst.bbk.ac.uk/cdweb/html/home.html","offsetEnd":67,"rawForm":"www.cryst.bbk.ac.uk/cdweb/html/home.html","boundingBoxes":[{"x":46.40593333333333,"h":6.489000000000033,"y":638.569,"p":3,"w":129.65333333333328}]}},
  {"_key":"60c20ca67723bebd86645585","_id":"annotations/60c20ca67723bebd86645585","_rev":"_cfFmVVa---","wikipediaExternalRef":8109474,"document":{"$oid":"60c20ca67723bebd8664557c"},"context":"The data were analyzed using Origin 7.0.","wikidataId":"Q31708","type":"software","lang":"en","confidence":0.297,"software-name":{"wikipediaExternalRef":8109474,"normalizedForm":"Origin","offsetStart":29,"wikidataId":"Q31708","offsetEnd":35,"lang":"en","confidence":0.297,"rawForm":"Origin","boundingBoxes":[{"x":162.336,"h":6.489,"y":674.661,"p":3,"w":19.439}]},"version":{"offsetStart":36,"normalizedForm":"7.0","offsetEnd":39,"rawForm":"7.0","boundingBoxes":[{"x":184.105,"h":6.489000000000033,"y":674.661,"p":3,"w":7.875}]}},
  {"_key":"60c20ca67723bebd86645586","_id":"annotations/60c20ca67723bebd86645586","_rev":"_cfFmVVm---","document":{"$oid":"60c20ca67723bebd8664557c"},"type":"software","software-name":{"offsetStart":42,"normalizedForm":"ASTRA","offsetEnd":47,"rawForm":"ASTRA","boundingBoxes":[{"x":116.379,"h":6.489,"y":548.342,"p":3,"w":24.584}]},"context":"Peak analysis was performed by using the ASTRA software provided with the system."},
  {"_key":"60c20ca67723bebd86645587","_id":"annotations/60c20ca67723bebd86645587","_rev":"_cfFmVVy---","document":{"$oid":"60c20ca67723bebd8664557c"},"context":"Secondary structure assignment was achieved through use of the K2d web server (www.embl-heidelberg.de/ϳandrade/k2d)","type":"software","software-name":{"offsetStart":63,"normalizedForm":"K2d","offsetEnd":66,"rawForm":"K2d","boundingBoxes":[{"x":256.831,"h":6.489000000000033,"y":620.523,"p":3,"w":12.509000000000015}]},"url":{"offsetStart":80,"normalizedForm":"www.embl-heidelberg.de/ϳandrade/k2d","offsetEnd":115,"rawForm":"www.embl-heidelberg.de/ϳandrade/k2d","boundingBoxes":[{"x":67.09568648648649,"h":6.489000000000033,"y":629.546,"p":3,"w":117.58202702702705}]}},
  {"_key":"60c20ca67723bebd86645588","_id":"annotations/60c20ca67723bebd86645588","_rev":"_cfFmVW----","document":{"$oid":"60c20ca67723bebd8664557c"},"context":"FA data collection was controlled by using the FA module of the Fluoressence software (version 2.1.5.0).","type":"software","software-name":{"offsetStart":65,"normalizedForm":"Fluoressence","offsetEnd":77,"rawForm":"Fluoressence","boundingBoxes":[{"x":474.39,"h":6.489,"y":322.521,"p":3,"w":39.214}]},"version":{"offsetStart":97,"normalizedForm":"2.1.5.0","offsetEnd":104,"rawForm":"2.1.5.0","boundingBoxes":[{"x":327.059,"h":6.488999999999976,"y":331.544,"p":3,"w":18.418555555555542}]}},
  {"_key":"60c20ca67723bebd86645589","_id":"annotations/60c20ca67723bebd86645589","_rev":"_cfFmVWK---","document":{"$oid":"60c20ca67723bebd8664557c"},"context":"The model was then refined using alternating cycles of manual fitting in Coot and TURBO-FRODO (8, 17) and simulated annealing in CNS 1.2 (6).","references":[{"offsetStart":29970,"normalizedForm":"(8","refKey":8,"label":"(8,","reference_id":{"$oid":"60c20ca67723bebd86645580"},"offsetEnd":29978,"boundingBoxes":[{"x":358.98,"h":6.488999999999976,"y":413.29,"p":4,"w":20.225999999999942}]},{"offsetStart":29970,"normalizedForm":"17)","refKey":18,"label":"17)","reference_id":{"$oid":"60c20ca67723bebd86645581"},"offsetEnd":29978,"boundingBoxes":[{"x":358.98,"h":6.488999999999976,"y":413.29,"p":4,"w":20.225999999999942}]}],"type":"software","software-name":{"offsetStart":84,"normalizedForm":"TURBO-FRODO","offsetEnd":95,"rawForm":"TURBO-FRODO","boundingBoxes":[{"x":301.164,"h":6.488999999999976,"y":413.29,"p":4,"w":55.20199999999994}]}},
  {"_key":"60c20ca67723bebd8664558a","_id":"annotations/60c20ca67723bebd8664558a","_rev":"_cfFmVWW---","wikipediaExternalRef":2324407,"document":{"$oid":"60c20ca67723bebd8664557c"},"context":"In all cases, a C ␣ root mean square deviation (RMSD) was calculated by using either PyMol (12) or Coot.","wikidataId":"Q1373457","references":[{"offsetStart":31169,"normalizedForm":"12","refKey":12,"label":"(12)","reference_id":{"$oid":"60c20ca67723bebd86645582"},"offsetEnd":31174,"boundingBoxes":[{"x":361.606,"h":6.489000000000033,"y":557.829,"p":4,"w":12.362000000000023}]}],"type":"software","confidence":0.799,"software-name":{"wikipediaExternalRef":2324407,"normalizedForm":"PyMol","offsetStart":86,"wikidataId":"Q1373457","offsetEnd":91,"lang":"en","confidence":0.799,"rawForm":"PyMol","boundingBoxes":[{"x":339.433,"h":6.489,"y":557.829,"p":4,"w":19.698}]},"lang":"en"},
  {"_key":"60c20ca67723bebd8664558b","_id":"annotations/60c20ca67723bebd8664558b","_rev":"_cfFmVWe---","document":{"$oid":"60c20ca67723bebd8664557c"},"type":"software","software-name":{"offsetStart":88,"normalizedForm":"ProMotif","offsetEnd":96,"rawForm":"ProMotif","boundingBoxes":[{"x":451.433,"h":6.489,"y":584.932,"p":4,"w":26.145777777777777}]},"context":"Further examination of the helix-helix dimerization interface was accomplished through ProMotif, as found within the PDBSum webserver (26, 33-35)."},
  {"_key":"60c20ca67723bebd8664558c","_id":"annotations/60c20ca67723bebd8664558c","_rev":"_cfFmVWq---","document":{"$oid":"60c20ca67723bebd8664557c"},"context":"The nsp9 G104E model was subjected to a single round of rigid body refine- ment as implemented within Refmac5 as part of the CCP4 package (3).","type":"software","software-name":{"offsetStart":102,"normalizedForm":"Refmac","offsetEnd":108,"rawForm":"Refmac","boundingBoxes":[{"x":392.338,"h":6.489,"y":395.221,"p":4,"w":26.908}]},"version":{"offsetStart":108,"normalizedForm":"5","offsetEnd":109,"rawForm":"5","boundingBoxes":[{"x":392.338,"h":6.489,"y":395.221,"p":4,"w":26.908}]}},
  {"_key":"60c20ca67723bebd8664558d","_id":"annotations/60c20ca67723bebd8664558d","_rev":"_cfFmVW2---","document":{"$oid":"60c20ca67723bebd8664557c"},"type":"software","software-name":{"offsetStart":102,"normalizedForm":"HKL2000","offsetEnd":109,"rawForm":"HKL2000","boundingBoxes":[{"x":466.395,"h":6.488999999999976,"y":322.948,"p":4,"w":29.406999999999982}]},"context":"The data were indexed, integrated, merged, and scaled to 2.6-Å resolution, as implemented within the HKL2000 package (47)."},
  {"_key":"60c20ca67723bebd8664558e","_id":"annotations/60c20ca67723bebd8664558e","_rev":"_cfFmVXC---","wikipediaExternalRef":8109474,"document":{"$oid":"60c20ca67723bebd8664557c"},"context":"Samples which showed a saturation curve were fit to a simple dissociation model using the included analysis software (Origin 7) specifically designed for dilution ITC data analysis.","wikidataId":"Q31708","type":"software","lang":"en","confidence":0.297,"software-name":{"wikipediaExternalRef":8109474,"normalizedForm":"Origin","offsetStart":120,"wikidataId":"Q31708","offsetEnd":126,"lang":"en","confidence":0.297,"rawForm":"Origin","boundingBoxes":[{"x":384.901,"h":6.489,"y":575.406,"p":3,"w":18.96}]},"version":{"offsetStart":127,"normalizedForm":"7","offsetEnd":128,"rawForm":"7","boundingBoxes":[{"x":406.017,"h":6.489,"y":575.406,"p":3,"w":3.0905}]}},
  {"_key":"60c20ca67723bebd8664558f","_id":"annotations/60c20ca67723bebd8664558f","_rev":"_cfFmVXO---","wikipediaExternalRef":5268864,"document":{"$oid":"60c20ca67723bebd8664557c"},"context":"The nsp9 G104E model was subjected to a single round of rigid body refine- ment as implemented within Refmac5 as part of the CCP4 package (3).","wikidataId":"Q5145814","type":"software","confidence":0.3545,"software-name":{"wikipediaExternalRef":5268864,"normalizedForm":"CCP4","offsetStart":125,"wikidataId":"Q5145814","offsetEnd":129,"lang":"en","confidence":0.3545,"rawForm":"CCP4","boundingBoxes":[{"x":467.974,"h":6.488999999999976,"y":395.221,"p":4,"w":17.639999999999986}]},"lang":"en"},
  {"_key":"60c20ca67723bebd86645590","_id":"annotations/60c20ca67723bebd86645590","_rev":"_cfFmVXa---","document":{"$oid":"60c20ca67723bebd8664557c"},"context":"The model was then refined using alternating cycles of manual fitting in Coot and TURBO-FRODO (8, 17) and simulated annealing in CNS 1.2 (6).","references":[{"offsetStart":30013,"normalizedForm":"6","refKey":5,"label":"(6)","reference_id":{"$oid":"60c20ca67723bebd86645583"},"offsetEnd":30016,"boundingBoxes":[{"x":495.502,"h":6.488999999999976,"y":413.29,"p":4,"w":7.959000000000003}]}],"type":"software","software-name":{"offsetStart":131,"normalizedForm":"CNS","offsetEnd":134,"rawForm":"CNS","boundingBoxes":[{"x":467.357,"h":6.489,"y":413.29,"p":4,"w":14.168}]},"version":{"offsetStart":135,"normalizedForm":"1.2","offsetEnd":138,"rawForm":"1.2","boundingBoxes":[{"x":484.138,"h":6.488999999999976,"y":413.29,"p":4,"w":8.75}]}},
  {"_key":"60c20ca67723bebd86645591","_id":"annotations/60c20ca67723bebd86645591","_rev":"_cfFmVXi---","document":{"$oid":"60c20ca67723bebd8664557c"},"type":"software","software-name":{"offsetStart":140,"normalizedForm":"Prism","offsetEnd":145,"rawForm":"Prism","boundingBoxes":[{"x":487.538,"h":6.489,"y":358.613,"p":3,"w":17.248}]},"context":"The data were analyzed using nonlinear regression fitting of the data to the following equation (42) for a single site binding model using Prism software:"},
  {"_key":"60c20ca67723bebd86645592","_id":"annotations/60c20ca67723bebd86645592","_rev":"_cfFmVXu---","document":{"$oid":"60c20ca67723bebd8664557c"},"type":"software","software-name":{"offsetStart":231,"normalizedForm":"Blue-Ice","offsetEnd":239,"rawForm":"Blue-Ice","boundingBoxes":[{"x":487.592,"h":6.488999999999976,"y":286.811,"p":4,"w":25.494000000000028}]},"context":"Protein was concentrated to 5.8 mg/ml and mixed in a 1:1 ratio with crystallization cocktail (1.7 Diffraction experiments were remotely conducted on beamline 11-1 of the Stanford Synchrotron Radiation Laboratory (SSRL) using the Blue-Ice interface and Web-Ice analysis software (21, 44)."},
  {"_key":"60c20ca67723bebd86645593","_id":"annotations/60c20ca67723bebd86645593","_rev":"_cfFmVX6---","document":{"$oid":"60c20ca67723bebd8664557c"},"type":"software","software-name":{"offsetStart":255,"normalizedForm":"Web-Ice","offsetEnd":262,"rawForm":"Web-Ice","boundingBoxes":[{"x":314.226,"h":6.488999999999976,"y":295.845,"p":4,"w":25.577999999999975}]},"context":"Protein was concentrated to 5.8 mg/ml and mixed in a 1:1 ratio with crystallization cocktail (1.7 Diffraction experiments were remotely conducted on beamline 11-1 of the Stanford Synchrotron Radiation Laboratory (SSRL) using the Blue-Ice interface and Web-Ice analysis software (21, 44)."},
  {"_key":"60c20ca67723bebd86645594","_id":"annotations/60c20ca67723bebd86645594","_rev":"_cfFmVYG---","document":{"$oid":"60c20ca67723bebd8664557c"},"type":"software","software-name":{"offsetStart":520,"normalizedForm":"ProtParam","offsetEnd":529,"rawForm":"ProtParam","boundingBoxes":[{"x":136.999,"h":6.489,"y":449.093,"p":3,"w":32.564}]},"context":"Concentrated protein was subsequently applied to a Superdex 75 HL 16/60 column pre-equilibrated in buffer C. Fractions were analyzed by SDS-PAGE with appropriate fractions pooled and dialyzed against either 1 liter of buffer D (50 mM MES [morpho- lineethanesulfonic acid; pH 5.6], 15 mM NaCl, 0.5 mM TCEP [tri(2-carboxyethyl) phosphine HCl]) or 1 liter of buffer C. Final samples were stored at 4°C and assayed for protein concentration at 280 nm using an extinction coefficient of 13,075 M Ϫ1 cm Ϫ1 calculated by ProtParam (63) using the coding sequence of the mature nsp9 product with a C-terminal tag (LEHHHHHH)."},
  {"_key":"60c20ca77723bebd86645596","_id":"annotations/60c20ca77723bebd86645596","_rev":"_cfFmVYS---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20ca77723bebd86645595"},"context":"H1N1 HA1 sequences were aligned using ClustalW multiple alignment in Bioedit version 7.1.11.","wikidataId":"Q866737","type":"software","confidence":0.7823,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"ClustalW","offsetStart":39,"wikidataId":"Q866737","offsetEnd":47,"lang":"en","confidence":0.7823,"rawForm":"ClustalW","boundingBoxes":[{"x":427.338,"h":11.48,"y":383.635,"p":2,"w":38.149}]},"lang":"en"},
  {"_key":"60c20ca77723bebd86645597","_id":"annotations/60c20ca77723bebd86645597","_rev":"_cfFmVYe---","document":{"$oid":"60c20ca77723bebd86645595"},"context":"H1N1 HA1 sequences were aligned using ClustalW multiple alignment in Bioedit version 7.1.11.","type":"software","software-name":{"offsetStart":71,"normalizedForm":"Bioedit","offsetEnd":78,"rawForm":"Bioedit","boundingBoxes":[{"x":317.156,"h":11.48,"y":396.135,"p":2,"w":30.29}]},"version":{"offsetStart":87,"normalizedForm":"7.1.11","offsetEnd":93,"rawForm":"7.1.11","boundingBoxes":[{"x":383.673,"h":11.480000000000018,"y":396.135,"p":2,"w":24.291428571428526}]}},
  {"_key":"60c20ca77723bebd86645598","_id":"annotations/60c20ca77723bebd86645598","_rev":"_cfFmVYq---","document":{"$oid":"60c20ca77723bebd86645595"},"context":"A rooted phylogenetic tree was constructed by the maximum-likelihood method with the JTT+G model in MEGA7 software.","type":"software","software-name":{"offsetStart":102,"normalizedForm":"MEGA","offsetEnd":106,"rawForm":"MEGA","boundingBoxes":[{"x":376.816,"h":11.48,"y":421.135,"p":2,"w":34.49}]},"version":{"offsetStart":106,"normalizedForm":"7","offsetEnd":107,"rawForm":"7","boundingBoxes":[{"x":376.816,"h":11.48,"y":421.135,"p":2,"w":34.49}]}},
  {"_key":"60c20ca87723bebd8664559a","_id":"annotations/60c20ca87723bebd8664559a","_rev":"_cfFmVYy---","wikipediaExternalRef":20412,"document":{"$oid":"60c20ca87723bebd86645599"},"context":"Matlab code :","wikidataId":"Q169478","type":"software","confidence":0.7276,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"Matlab","offsetStart":0,"wikidataId":"Q169478","offsetEnd":6,"lang":"en","confidence":0.7276,"rawForm":"Matlab","boundingBoxes":[{"x":306.159,"h":8.7771,"y":385.702,"p":11,"w":30.9837}]},"lang":"en"},
  {"_key":"60c20ca87723bebd8664559b","_id":"annotations/60c20ca87723bebd8664559b","_rev":"_cfFmVZ----","wikipediaExternalRef":20412,"document":{"$oid":"60c20ca87723bebd86645599"},"context":"The Matlab code for the figures has been given below.","wikidataId":"Q169478","type":"software","confidence":0.7276,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"Matlab","offsetStart":4,"wikidataId":"Q169478","offsetEnd":10,"lang":"en","confidence":0.7276,"rawForm":"Matlab","boundingBoxes":[{"x":380.299,"h":8.7571,"y":360.938,"p":11,"w":28.2111}]},"lang":"en"},
  {"_key":"60c20ca87723bebd8664559c","_id":"annotations/60c20ca87723bebd8664559c","_rev":"_cfFmVZK---","wikipediaExternalRef":49024,"document":{"$oid":"60c20ca87723bebd86645599"},"context":"The Tables are calculated using Wolfram Mathematica 9.0 and the figures have been drawn using MAT- LAB R2018a.","wikidataId":"Q81294","type":"software","lang":"en","confidence":0.8947,"software-name":{"wikipediaExternalRef":49024,"normalizedForm":"Wolfram Mathematica","offsetStart":32,"wikidataId":"Q81294","offsetEnd":52,"lang":"en","confidence":0.8947,"rawForm":"Wolfram \nMathematica","boundingBoxes":[{"x":509.115,"h":8.7571,"y":336.026,"p":11,"w":35.159},{"x":306.159,"h":8.7571,"y":348.482,"p":11,"w":51.9948}]},"version":{"offsetStart":53,"normalizedForm":"9.0","offsetEnd":56,"rawForm":"9.0","boundingBoxes":[{"x":359.589,"h":8.75709999999998,"y":348.482,"p":11,"w":12.447299999999984}]}},
  {"_key":"60c20ca87723bebd8664559d","_id":"annotations/60c20ca87723bebd8664559d","_rev":"_cfFmVZW---","wikipediaExternalRef":20412,"document":{"$oid":"60c20ca87723bebd86645599"},"context":"Also Broumi et al. [16] applied neutro- sophic set theory in some computing procedures in Matlab for operational matrices.","wikidataId":"Q169478","type":"software","confidence":0.7276,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"Matlab","offsetStart":90,"wikidataId":"Q169478","offsetEnd":96,"lang":"en","confidence":0.7276,"rawForm":"Matlab","boundingBoxes":[{"x":516.039,"h":8.7571,"y":384.221,"p":1,"w":28.2141}]},"lang":"en"},
  {"_key":"60c20ca87723bebd8664559e","_id":"annotations/60c20ca87723bebd8664559e","_rev":"_cfFmVZi---","document":{"$oid":"60c20ca87723bebd86645599"},"context":"The Tables are calculated using Wolfram Mathematica 9.0 and the figures have been drawn using MAT- LAB R2018a.","type":"software","software-name":{"offsetStart":95,"normalizedForm":"MAT- LAB","offsetEnd":103,"rawForm":"MAT-\nLAB","boundingBoxes":[{"x":520.753,"h":8.75709999999998,"y":348.482,"p":11,"w":23.422099999999887},{"x":306.159,"h":8.7571,"y":360.938,"p":11,"w":19.9192}]},"version":{"offsetStart":105,"normalizedForm":"2018a","offsetEnd":110,"rawForm":"2018a","boundingBoxes":[{"x":327.821,"h":8.75709999999998,"y":360.938,"p":11,"w":28.685485714285733}]}},
  {"_key":"60c20cae7723bebd866455a0","_id":"annotations/60c20cae7723bebd866455a0","_rev":"_cfFmVZu---","document":{"$oid":"60c20cae7723bebd8664559f"},"type":"software","software-name":{"offsetStart":2,"normalizedForm":"NatStat","offsetEnd":9,"rawForm":"NatStat","boundingBoxes":[{"x":81.694,"h":8.7372,"y":555.158,"p":16,"w":32.6906125}]},"context":"• NatStat:"},
  {"_key":"60c20cae7723bebd866455a1","_id":"annotations/60c20cae7723bebd866455a1","_rev":"_cfFmVZ6---","document":{"$oid":"60c20cae7723bebd8664559f"},"type":"software","software-name":{"offsetStart":13,"normalizedForm":"NatStat","offsetEnd":20,"rawForm":"NatStat","boundingBoxes":[{"x":334.573,"h":8.7372,"y":207.093,"p":16,"w":34.5931}]},"context":"Eurostat and NatStat offer the longest time series for many countries."},
  {"_key":"60c20cae7723bebd866455a2","_id":"annotations/60c20cae7723bebd866455a2","_rev":"_cfFmVaG---","document":{"$oid":"60c20cae7723bebd8664559f"},"type":"software","software-name":{"offsetStart":13,"normalizedForm":"NatStat","offsetEnd":20,"rawForm":"NatStat","boundingBoxes":[{"x":158.847,"h":8.7372,"y":221.518,"p":16,"w":34.5931}]},"context":"In addition, NatStat data rarely has any missing entries and therefore was most often chosen for further processing within this study, see orange circles in Table S2."},
  {"_key":"60c20cae7723bebd866455a3","_id":"annotations/60c20cae7723bebd866455a3","_rev":"_cfFmVaS---","document":{"$oid":"60c20cae7723bebd8664559f"},"type":"software","software-name":{"offsetStart":168,"normalizedForm":"NatStat","offsetEnd":175,"rawForm":"NatStat","boundingBoxes":[{"x":196.03053333333335,"h":7.0774,"y":614.21,"p":47,"w":26.162733333333332}]},"context":"Figure S31 Fits to cumulative survival probability (CSP) data for selected countries and different stock data sources: ACEA [24], UNECE [25], and national statistics (NatStat, sources see Table S1)."},
  {"_key":"60c20cae7723bebd866455a4","_id":"annotations/60c20cae7723bebd866455a4","_rev":"_cfFmVae---","wikipediaExternalRef":20268,"document":{"$oid":"60c20cae7723bebd8664559f"},"context":"• Appendix A: Background information on the effects of scrappage schemes • Appendix B: Background information on the choice of a Gaussian distribution to model the imports and exports of used car • Appendix C: Vehicle stock data • Appendix D: New registration data • Appendix E: Imports and exports data • Appendix F: Cumulative survival probabilities (CSPs) • Appendix G: Proof of concept of new CSP estimation method • Appendix H: The simplified CSP estimation method • Appendix I: Time variability of CSP fitting parameters: Case study for Latvia • Appendix J: The influence of data resolution • Appendix K: Overview of all gathered and pre-processed data which are attached as Excel sheets.","wikidataId":"Q11272","type":"software","confidence":0.378,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Excel","offsetStart":692,"wikidataId":"Q11272","offsetEnd":697,"lang":"en","confidence":0.378,"rawForm":"Excel","boundingBoxes":[{"x":445.201,"h":8.8471,"y":481.733,"p":1,"w":21.7891}]},"lang":"en"},
  {"_key":"60c20cb57723bebd866455a8","_id":"annotations/60c20cb57723bebd866455a8","_rev":"_cfFmVaq---","document":{"$oid":"60c20cb57723bebd866455a5"},"context":"Kafka proved itself to be an efficient medium for the transmission of huge message streams, as was already shown in the paper [54] (Section VI.B), also when the particular system elements were dispersed in a computing cloud [54] (Figure 6), it mirrors the real conditions very well.","references":[{"offsetStart":41329,"normalizedForm":"[56","refKey":61,"label":"[56,","reference_id":{"$oid":"60c20cb57723bebd866455a6"},"offsetEnd":41337,"boundingBoxes":[{"x":188.291,"h":9.583999999999946,"y":631.761,"p":13,"w":29.15549999999999}]},{"offsetStart":41329,"normalizedForm":"57]","refKey":62,"label":"57]","reference_id":{"$oid":"60c20cb57723bebd866455a7"},"offsetEnd":41337,"boundingBoxes":[{"x":188.291,"h":9.583999999999946,"y":631.761,"p":13,"w":29.15549999999999}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Kafka","offsetEnd":5,"rawForm":"Kafka","boundingBoxes":[{"x":414.892,"h":9.584,"y":672.289,"p":13,"w":25.8959}]}},
  {"_key":"60c20cb57723bebd866455a9","_id":"annotations/60c20cb57723bebd866455a9","_rev":"_cfFmVa2---","document":{"$oid":"60c20cb57723bebd866455a5"},"context":"We decided to use Kafka [56,57] platform.","references":[{"offsetStart":41329,"normalizedForm":"[56","refKey":61,"label":"[56,","reference_id":{"$oid":"60c20cb57723bebd866455a6"},"offsetEnd":41337,"boundingBoxes":[{"x":188.291,"h":9.583999999999946,"y":631.761,"p":13,"w":29.15549999999999}]},{"offsetStart":41329,"normalizedForm":"57]","refKey":62,"label":"57]","reference_id":{"$oid":"60c20cb57723bebd866455a7"},"offsetEnd":41337,"boundingBoxes":[{"x":188.291,"h":9.583999999999946,"y":631.761,"p":13,"w":29.15549999999999}]}],"type":"software","software-name":{"offsetStart":18,"normalizedForm":"Kafka","offsetEnd":23,"rawForm":"Kafka","boundingBoxes":[{"x":159.464,"h":9.584,"y":631.761,"p":13,"w":26.3388}]}},
  {"_key":"60c20cb87723bebd866455ab","_id":"annotations/60c20cb87723bebd866455ab","_rev":"_cfFmVbC---","document":{"$oid":"60c20cb87723bebd866455aa"},"context":"An open-sourced freeware Node XL (http://nodexl.codeplex.com/)","type":"software","software-name":{"offsetStart":26,"normalizedForm":"Node XL","offsetEnd":33,"rawForm":"Node XL","boundingBoxes":[{"x":56.6929,"h":8.976699999999994,"y":100.723,"p":4,"w":39.28289999999999}]},"url":{"offsetStart":35,"normalizedForm":"http://nodexl.codeplex.com","offsetEnd":61,"rawForm":"http://nodexl.codeplex.com","boundingBoxes":[{"x":105.05141379310345,"h":8.976699999999994,"y":100.723,"p":4,"w":109.05475862068968}]}},
  {"_key":"60c20cb87723bebd866455ac","_id":"annotations/60c20cb87723bebd866455ac","_rev":"_cfFmVbO---","wikipediaExternalRef":990677,"document":{"$oid":"60c20cb87723bebd866455aa"},"publisher":{"offsetStart":74,"normalizedForm":"SAS Institute Inc","offsetEnd":91,"rawForm":"SAS Institute Inc","boundingBoxes":[{"x":107.313525,"h":8.976699999999994,"y":232.761,"p":4,"w":63.717535}]},"context":"All statistical analyses were performed using SAS software, version 9.4 (SAS Institute Inc., Cary, NC, USA).","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":46,"wikidataId":"Q2003932","offsetEnd":49,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":235.502,"h":8.9767,"y":220.743,"p":4,"w":16.9342}]},"version":{"offsetStart":69,"normalizedForm":"9.4","offsetEnd":72,"rawForm":"9.4","boundingBoxes":[{"x":88.1006,"h":8.976699999999994,"y":232.761,"p":4,"w":11.759900000000002}]}},
  {"_key":"60c20cd87723bebd866455af","_id":"annotations/60c20cd87723bebd866455af","_rev":"_cfFmVba---","wikipediaExternalRef":179088,"document":{"$oid":"60c20cd87723bebd866455ad"},"context":"We also examined the potential interaction effect between country and each of the predictors of COVD- related concerns included in the regression equation, using the PROCESS macro for SPSS [19].","wikidataId":"Q181596","references":[{"offsetStart":16891,"normalizedForm":"[19]","refKey":18,"label":"[19]","reference_id":{"$oid":"60c20cd87723bebd866455ae"},"offsetEnd":16895,"boundingBoxes":[{"x":433.275,"h":11.480000000000018,"y":620.162,"p":4,"w":15.488}]}],"type":"software","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":186,"wikidataId":"Q181596","offsetEnd":190,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":408.4,"h":11.48,"y":620.162,"p":4,"w":22.4}]},"lang":"en"},
  {"_key":"60c20cd87723bebd866455b0","_id":"annotations/60c20cd87723bebd866455b0","_rev":"_cfFmVbq---","wikipediaExternalRef":179088,"document":{"$oid":"60c20cd87723bebd866455ad"},"context":"The complete model explained 41% and  Potential differences between the two countries in the strengths of the associations between each of the predic- tors and COVID-related concerns were tested as interac- tions effect, using the PROCESS macro for SPSS [19].","wikidataId":"Q181596","references":[{"offsetStart":16891,"normalizedForm":"[19]","refKey":18,"label":"[19]","reference_id":{"$oid":"60c20cd87723bebd866455ae"},"offsetEnd":16895,"boundingBoxes":[{"x":433.275,"h":11.480000000000018,"y":620.162,"p":4,"w":15.488}]}],"type":"software","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":251,"wikidataId":"Q181596","offsetEnd":255,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":223.628,"h":11.48,"y":120.255,"p":7,"w":22.21}]},"lang":"en"},
  {"_key":"60c20cd97723bebd866455b2","_id":"annotations/60c20cd97723bebd866455b2","_rev":"_cfFmVb2---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20cd97723bebd866455b1"},"context":"The relative intensities of protein bands were analyzed with ImageJ software.","wikidataId":"Q1659584","type":"software","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":61,"wikidataId":"Q1659584","offsetEnd":67,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":437.95,"h":8.5,"y":373.426,"p":4,"w":28.1}]},"lang":"en"},
  {"_key":"60c20cdc7723bebd866455b4","_id":"annotations/60c20cdc7723bebd866455b4","_rev":"_cfFmVcC---","document":{"$oid":"60c20cdc7723bebd866455b3"},"type":"software","software-name":{"offsetStart":53,"normalizedForm":"Zoom","offsetEnd":57,"rawForm":"Zoom","boundingBoxes":[{"x":99.3922,"h":10.906,"y":473.25,"p":10,"w":20.4896}]},"context":"For these purposes, teachers now used tools such as Zoom, Google Hangout and Microsoft Teams."},
  {"_key":"60c20cdc7723bebd866455b5","_id":"annotations/60c20cdc7723bebd866455b5","_rev":"_cfFmVcO---","wikipediaExternalRef":15441720,"document":{"$oid":"60c20cdc7723bebd866455b3"},"context":"Both authors worked closely to conduct the analysis using Nvivo (version 11.4.3) and post-it notes.","wikidataId":"Q6955723","type":"software","lang":"en","confidence":0.4816,"software-name":{"wikipediaExternalRef":15441720,"normalizedForm":"Nvivo","offsetStart":59,"wikidataId":"Q6955723","offsetEnd":64,"lang":"en","confidence":0.4816,"rawForm":"Nvivo","boundingBoxes":[{"x":218.031,"h":10.906,"y":426.694,"p":6,"w":23.4935}]},"version":{"offsetStart":74,"normalizedForm":"11.4.3","offsetEnd":80,"rawForm":"11.4.3","boundingBoxes":[{"x":277.14,"h":10.906000000000006,"y":426.694,"p":6,"w":23.068714285714293}]}},
  {"_key":"60c20cdc7723bebd866455b6","_id":"annotations/60c20cdc7723bebd866455b6","_rev":"_cfFmVcW---","wikipediaExternalRef":1092923,"document":{"$oid":"60c20cdc7723bebd866455b3"},"context":"For these purposes, teachers now used tools such as Zoom, Google Hangout and Microsoft Teams.","wikidataId":"Q95","type":"software","confidence":0.3333,"software-name":{"wikipediaExternalRef":1092923,"normalizedForm":"Google","offsetStart":59,"wikidataId":"Q95","offsetEnd":65,"lang":"en","confidence":0.3333,"rawForm":"Google","boundingBoxes":[{"x":127.645,"h":10.906,"y":473.25,"p":10,"w":28.614}]},"lang":"en"},
  {"_key":"60c20cdc7723bebd866455b7","_id":"annotations/60c20cdc7723bebd866455b7","_rev":"_cfFmVci---","wikipediaExternalRef":42694174,"document":{"$oid":"60c20cdc7723bebd866455b3"},"context":"Many teachers used The Learning Platform (a specific learning platform: Skolplattformen), and Google Classroom, (see Fig. 3) to distribute semester planning, schedule, tasks et cetera.","wikidataId":"Q16927658","type":"software","confidence":0.9768,"software-name":{"wikipediaExternalRef":42694174,"normalizedForm":"Google Classroom","offsetStart":96,"wikidataId":"Q16927658","offsetEnd":112,"lang":"en","confidence":0.9768,"rawForm":"Google Classroom","boundingBoxes":[{"x":64.2042,"h":10.906000000000006,"y":279.717,"p":11,"w":71.80209}]},"lang":"en"},
  {"_key":"60c20ce37723bebd866455bc","_id":"annotations/60c20ce37723bebd866455bc","_rev":"_cfFmVcu---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"I","offsetEnd":1,"rawForm":"I","boundingBoxes":[{"x":93.624,"h":12,"y":660.844,"p":8,"w":5.239}]},"context":"I-Tasser predicted five models, out of which model 1 was selected having a C-score of - 2.03 (Figure 9A)."},
  {"_key":"60c20ce37723bebd866455bd","_id":"annotations/60c20ce37723bebd866455bd","_rev":"_cfFmVc6---","document":{"$oid":"60c20ce37723bebd866455b8"},"context":"VaxiJen predicts protective antigens with accuracy ranging  between 79% to 89% as tested on three different datasets (Doytchinova & Flower, 2007).","type":"software","software-name":{"offsetStart":0,"normalizedForm":"VaxiJen","offsetEnd":7,"rawForm":"VaxiJen","boundingBoxes":[{"x":232.73,"h":12,"y":188.684,"p":14,"w":38.46}]},"url":{"offsetStart":97,"normalizedForm":"http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html","offsetEnd":153,"rawForm":"http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html","boundingBoxes":[{"x":114.89237288135594,"h":12,"y":160.484,"p":14,"w":310.9328813559322}]}},
  {"_key":"60c20ce37723bebd866455be","_id":"annotations/60c20ce37723bebd866455be","_rev":"_cfFmVdG---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":2,"normalizedForm":"Tasser","offsetEnd":8,"rawForm":"Tasser","boundingBoxes":[{"x":104.10199999999999,"h":12,"y":660.844,"p":8,"w":31.433999999999997}]},"context":"I-Tasser predicted five models, out of which model 1 was selected having a C-score of - 2.03 (Figure 9A)."},
  {"_key":"60c20ce37723bebd866455bf","_id":"annotations/60c20ce37723bebd866455bf","_rev":"_cfFmVdS---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":2,"normalizedForm":"Pymol script","offsetEnd":14,"rawForm":"Pymol script","boundingBoxes":[{"x":351.046,"h":12,"y":307.154,"p":9,"w":65.57999999999998}]},"context":"A Pymol script generated by PRODIGY  helped to visualize the interacting residues between the multi-epitope vaccine candidate and  the predicted HLA-B*15:03 subtype structure (Figure 10A)."},
  {"_key":"60c20ce37723bebd866455c0","_id":"annotations/60c20ce37723bebd866455c0","_rev":"_cfFmVde---","wikipediaExternalRef":41452308,"document":{"$oid":"60c20ce37723bebd866455b8"},"context":"The I-Tasser (Iterative threading assembly refinement) predicts accurate  structures by first identifying templates from PDB using multiple threading and identifies  functions through the protein functions database.","wikidataId":"Q17029600","type":"software","confidence":0.7047,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-Tasser","offsetStart":4,"wikidataId":"Q17029600","offsetEnd":12,"lang":"en","confidence":0.7047,"rawForm":"I-Tasser","boundingBoxes":[{"x":160.076,"h":12,"y":624.724,"p":15,"w":42.03599999999997}]},"lang":"en"},
  {"_key":"60c20ce37723bebd866455c1","_id":"annotations/60c20ce37723bebd866455c1","_rev":"_cfFmVdq---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":28,"normalizedForm":"CTLPred","offsetEnd":35,"rawForm":"CTLPred","boundingBoxes":[{"x":106.092,"h":12,"y":365.474,"p":14,"w":44.58}]},"context":"CTLs were predicted  using CTLPred (Bhasin & Raghava, 2004)."},
  {"_key":"60c20ce37723bebd866455c2","_id":"annotations/60c20ce37723bebd866455c2","_rev":"_cfFmVd2---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":28,"normalizedForm":"PRODIGY","offsetEnd":37,"rawForm":"PRODIGY","boundingBoxes":[{"x":491.806,"h":12,"y":307.154,"p":9,"w":48.12}]},"context":"A Pymol script generated by PRODIGY  helped to visualize the interacting residues between the multi-epitope vaccine candidate and  the predicted HLA-B*15:03 subtype structure (Figure 10A)."},
  {"_key":"60c20ce37723bebd866455c3","_id":"annotations/60c20ce37723bebd866455c3","_rev":"_cfFmVeC---","document":{"$oid":"60c20ce37723bebd866455b8"},"context":"The docking was carried out using Autodock Vina (Trott &  Olson, 2009).","references":[{"offsetStart":30707,"normalizedForm":"Trott & Olson, 2009","refKey":34,"label":"(Trott & Olson, 2009)","reference_id":{"$oid":"60c20ce37723bebd866455b9"},"offsetEnd":30732,"boundingBoxes":[{"x":496.78,"h":12,"y":662.884,"p":14,"w":43.152000000000044},{"x":72.024,"h":12,"y":691.08,"p":14,"w":62.50266666666667}]}],"type":"software","software-name":{"offsetStart":34,"normalizedForm":"Autodock Vina","offsetEnd":47,"rawForm":"Autodock Vina","boundingBoxes":[{"x":416.582,"h":12,"y":662.884,"p":14,"w":76.14000000000004}]}},
  {"_key":"60c20ce37723bebd866455c4","_id":"annotations/60c20ce37723bebd866455c4","_rev":"_cfFmVeO---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":39,"normalizedForm":"HADDOCK","offsetEnd":46,"rawForm":"HADDOCK","boundingBoxes":[{"x":307.802,"h":12,"y":194.684,"p":9,"w":53.724}]},"context":"The top-ranking pose was selected from HADDOCK showing Z-score of -1.9, the most  negative value amongst all poses (Z-score more negative is better)."},
  {"_key":"60c20ce37723bebd866455c5","_id":"annotations/60c20ce37723bebd866455c5","_rev":"_cfFmVea---","document":{"$oid":"60c20ce37723bebd866455b8"},"context":"T-cell  epitopes were predicted using Tepitool (Paul, Sidney, Sette, & Peters, 2016) of IEDB (Vita et  al., 2019) with IC-50 value more than 500 nM for MHC-I and MHC-II.","references":[{"offsetStart":29693,"normalizedForm":"Paul, Sidney, Sette, & Peters, 2016","refKey":19,"label":"(Paul, Sidney, Sette, & Peters, 2016)","reference_id":{"$oid":"60c20ce37723bebd866455ba"},"offsetEnd":29731,"boundingBoxes":[{"x":275.45,"h":12,"y":309.194,"p":14,"w":182.664}]}],"type":"software","software-name":{"offsetStart":39,"normalizedForm":"Tepitool","offsetEnd":47,"rawForm":"Tepitool","boundingBoxes":[{"x":229.644,"h":12,"y":309.194,"p":14,"w":43.092}]}},
  {"_key":"60c20ce37723bebd866455c6","_id":"annotations/60c20ce37723bebd866455c6","_rev":"_cfFmVem---","document":{"$oid":"60c20ce37723bebd866455b8"},"context":"The binding x, y, and z coordinates in  Autodock Vina were defined as 5.103, 13.862, and 146.304 respectively.","references":[{"offsetStart":30707,"normalizedForm":"Trott & Olson, 2009","refKey":34,"label":"(Trott & Olson, 2009)","reference_id":{"$oid":"60c20ce37723bebd866455b9"},"offsetEnd":30732,"boundingBoxes":[{"x":496.78,"h":12,"y":662.884,"p":14,"w":43.152000000000044},{"x":72.024,"h":12,"y":691.08,"p":14,"w":62.50266666666667}]}],"type":"software","software-name":{"offsetStart":41,"normalizedForm":"Autodock Vina","offsetEnd":54,"rawForm":"Autodock Vina","boundingBoxes":[{"x":72.024,"h":12,"y":102.164,"p":15,"w":74.832}]}},
  {"_key":"60c20ce37723bebd866455c7","_id":"annotations/60c20ce37723bebd866455c7","_rev":"_cfFmVey---","wikipediaExternalRef":39059578,"document":{"$oid":"60c20ce37723bebd866455b8"},"context":"Binding pocket and residues in HLA-B*15:03 were identified using the CASTp 3.0 server (Tian, Chen, Lei, Zhao, & Liang, 2018).","wikidataId":"Q17007097","type":"software","lang":"en","confidence":0.5179,"software-name":{"wikipediaExternalRef":39059578,"normalizedForm":"CASTp","offsetStart":69,"wikidataId":"Q17007097","offsetEnd":74,"lang":"en","confidence":0.5179,"rawForm":"CASTp","boundingBoxes":[{"x":506.02,"h":12,"y":691.08,"p":14,"w":33.936}]},"version":{"offsetStart":76,"normalizedForm":"3.0","offsetEnd":79,"rawForm":"3.0","boundingBoxes":[{"x":72.024,"h":12,"y":74.084,"p":15,"w":15.756}]}},
  {"_key":"60c20ce37723bebd866455c8","_id":"annotations/60c20ce37723bebd866455c8","_rev":"_cfFmVf----","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":70,"normalizedForm":"ToxinPred","offsetEnd":79,"rawForm":"ToxinPred","boundingBoxes":[{"x":237.816,"h":12,"y":421.774,"p":14,"w":53.568}]},"context":"The predicted potential immunogens  were analyzed for toxicity using ToxinPred (Gupta et al., 2013)."},
  {"_key":"60c20ce37723bebd866455c9","_id":"annotations/60c20ce37723bebd866455c9","_rev":"_cfFmVfK---","document":{"$oid":"60c20ce37723bebd866455b8"},"context":"Epitope prediction and selection  B-cell epitopes were predicted using SVMTrip (Yao, Zhang, Liang, & Zhang, 2012).","references":[{"offsetStart":29607,"normalizedForm":"Yao, Zhang, Liang, & Zhang, 2012","refKey":45,"label":"(Yao, Zhang, Liang, & Zhang, 2012)","reference_id":{"$oid":"60c20ce37723bebd866455bb"},"offsetEnd":29641,"boundingBoxes":[{"x":329.83,"h":12,"y":281.114,"p":14,"w":173.42499999999995}]}],"type":"software","software-name":{"offsetStart":72,"normalizedForm":"SVMTrip","offsetEnd":79,"rawForm":"SVMTrip","boundingBoxes":[{"x":282.08,"h":12,"y":281.114,"p":14,"w":45.024}]}},
  {"_key":"60c20ce37723bebd866455ca","_id":"annotations/60c20ce37723bebd866455ca","_rev":"_cfFmVfW---","document":{"$oid":"60c20ce37723bebd866455b8"},"context":"The antigenic sequences among the selected sequences were identified using the VaxiJen  server (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html).","type":"software","software-name":{"offsetStart":79,"normalizedForm":"VaxiJen","offsetEnd":88,"rawForm":"VaxiJen","boundingBoxes":[{"x":501.7,"h":12,"y":132.404,"p":14,"w":38.46}]},"url":{"offsetStart":97,"normalizedForm":"http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html","offsetEnd":153,"rawForm":"http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html","boundingBoxes":[{"x":114.89237288135594,"h":12,"y":160.484,"p":14,"w":310.9328813559322}]}},
  {"_key":"60c20ce37723bebd866455cb","_id":"annotations/60c20ce37723bebd866455cb","_rev":"_cfFmVfi---","wikipediaExternalRef":41452308,"document":{"$oid":"60c20ce37723bebd866455b8"},"context":"The ab-initio tertiary structure of designed multi-epitope was predicted  using I-Tasser (Yang & Zhang, 2015) server (https://zhanglab.ccmb.med.umich.edu/I- TASSER/).","wikidataId":"Q17029600","type":"software","confidence":0.7047,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-Tasser","offsetStart":81,"wikidataId":"Q17029600","offsetEnd":89,"lang":"en","confidence":0.7047,"rawForm":"I-Tasser","boundingBoxes":[{"x":106.212,"h":12,"y":596.644,"p":15,"w":41.92399999999999}]},"lang":"en"},
  {"_key":"60c20ce37723bebd866455cc","_id":"annotations/60c20ce37723bebd866455cc","_rev":"_cfFmVfu---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":84,"normalizedForm":"PROCHECK","offsetEnd":94,"rawForm":"PROCHECK","boundingBoxes":[{"x":481.61,"h":12,"y":102.164,"p":16,"w":58.284}]},"context":"The  predicted tertiary structure of the multi-epitope vaccine was validated using PROCHECK  (Laskowski et al., 1993)."},
  {"_key":"60c20ce37723bebd866455cd","_id":"annotations/60c20ce37723bebd866455cd","_rev":"_cfFmVf6---","document":{"$oid":"60c20ce37723bebd866455b8"},"publisher":{"offsetStart":98,"normalizedForm":"L. T","offsetEnd":102,"rawForm":"L. T","boundingBoxes":[{"x":305.38599999999997,"h":12,"y":198.044,"p":13,"w":17.32000000000005}]},"context":"A phylogenetic tree of spike glycoprotein sequences of  SARS-CoV-2 was constructed using IQTREE (L. T. Nguyen, Schmidt, Von Haeseler, & Minh,  2015).","type":"software","software-name":{"offsetStart":90,"normalizedForm":"IQTREE","offsetEnd":96,"rawForm":"IQTREE","boundingBoxes":[{"x":257.12,"h":12,"y":198.044,"p":13,"w":40.008}]}},
  {"_key":"60c20ce37723bebd866455ce","_id":"annotations/60c20ce37723bebd866455ce","_rev":"_cfFmVgC---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":99,"normalizedForm":"PRODIGY","offsetEnd":108,"rawForm":"PRODIGY","boundingBoxes":[{"x":492.1,"h":12,"y":250.994,"p":9,"w":48.012}]},"context":"Docked complex of multi- epitope vaccine candidate and HLA-B*15:03 subtype was analyzed using the PRODIGY  server and later by Pymol."},
  {"_key":"60c20ce37723bebd866455cf","_id":"annotations/60c20ce37723bebd866455cf","_rev":"_cfFmVgO---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":106,"normalizedForm":"PROCHECK","offsetEnd":114,"rawForm":"PROCHECK","boundingBoxes":[{"x":72.024,"h":12,"y":570.454,"p":14,"w":58.284}]},"context":"The predicted  structures of HLA-B*15:03 was further validated by creating the Ramachandran Plot using  PROCHECK (Laskowski, MacArthur, Moss, & Thornton, 1993)."},
  {"_key":"60c20ce37723bebd866455d0","_id":"annotations/60c20ce37723bebd866455d0","_rev":"_cfFmVga---","document":{"$oid":"60c20ce37723bebd866455b8"},"context":"The evolutionary analysis of SARS-CoV-2 spike glycoprotein sequences and GISAID  sequences was carried out at the Datamonkey server (https://www.datamonkey.org) of  HYPHY program (Pond & Muse, 2005).","type":"software","software-name":{"offsetStart":115,"normalizedForm":"Datamonkey","offsetEnd":125,"rawForm":"Datamonkey","boundingBoxes":[{"x":253.97,"h":12,"y":459.334,"p":13,"w":64.836}]},"url":{"offsetStart":134,"normalizedForm":"https://www.datamonkey.org","offsetEnd":160,"rawForm":"https://www.datamonkey.org","boundingBoxes":[{"x":366.7232857142857,"h":12,"y":459.334,"p":13,"w":152.60142857142853}]}},
  {"_key":"60c20ce37723bebd866455d1","_id":"annotations/60c20ce37723bebd866455d1","_rev":"_cfFmVgq---","wikipediaExternalRef":2324407,"document":{"$oid":"60c20ce37723bebd866455b8"},"context":"Docked complex of multi- epitope vaccine candidate and HLA-B*15:03 subtype was analyzed using the PRODIGY  server and later by Pymol.","wikidataId":"Q1373457","type":"software","confidence":0.7991,"software-name":{"wikipediaExternalRef":2324407,"normalizedForm":"Pymol","offsetStart":129,"wikidataId":"Q1373457","offsetEnd":134,"lang":"en","confidence":0.7991,"rawForm":"Pymol","boundingBoxes":[{"x":184.5,"h":12,"y":279.074,"p":9,"w":29.15}]},"lang":"en"},
  {"_key":"60c20ce37723bebd866455d2","_id":"annotations/60c20ce37723bebd866455d2","_rev":"_cfFmVg2---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":156,"normalizedForm":"TASSER","offsetEnd":165,"rawForm":"-\n\nTASSER","boundingBoxes":[{"x":534.5687692307692,"h":12,"y":596.644,"p":15,"w":5.555230769230769},{"x":72.024,"h":12,"y":624.724,"p":15,"w":35.89333333333333}]},"context":"The ab-initio tertiary structure of designed multi-epitope was predicted  using I-Tasser (Yang & Zhang, 2015) server (https://zhanglab.ccmb.med.umich.edu/I- TASSER/)."},
  {"_key":"60c20ce37723bebd866455d3","_id":"annotations/60c20ce37723bebd866455d3","_rev":"_cfFmVhC---","document":{"$oid":"60c20ce37723bebd866455b8"},"type":"software","software-name":{"offsetStart":164,"normalizedForm":"ModelFinder","offsetEnd":175,"rawForm":"ModelFinder","boundingBoxes":[{"x":234.792,"h":12,"y":310.634,"p":13,"w":65.868}]},"context":"The best model used was VT+G4, namely,  the 'Variable Time' matrix (Müller & Vingron, 2001) with Gamma distribution (under four  rate categories) as predicted by ModelFinder (Kalyaanamoorthy, Minh, Wong, Von Haeseler,  & Jermiin, 2017)."},
  {"_key":"60c20ce37723bebd866455d4","_id":"annotations/60c20ce37723bebd866455d4","_rev":"_cfFmVhO---","document":{"$oid":"60c20ce37723bebd866455b8"},"context":"Antigenic sequences from SARS-CoV-2 spike glycoproteins  15 antigenic high scoring (threshold >0.5) sequences were obtained out of 23 sequences  of SARS-CoV-2 spike glycoprotein submitted to the VaxiJen server.","type":"software","software-name":{"offsetStart":197,"normalizedForm":"VaxiJen","offsetEnd":204,"rawForm":"VaxiJen","boundingBoxes":[{"x":331.51,"h":12,"y":222.764,"p":7,"w":38.46}]},"url":{"offsetStart":97,"normalizedForm":"http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html","offsetEnd":153,"rawForm":"http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html","boundingBoxes":[{"x":114.89237288135594,"h":12,"y":160.484,"p":14,"w":310.9328813559322}]}},
  {"_key":"60c20ce77723bebd866455d6","_id":"annotations/60c20ce77723bebd866455d6","_rev":"_cfFmVha---","wikipediaExternalRef":179088,"document":{"$oid":"60c20ce77723bebd866455d5"},"context":"Statistical tests  were performed using SPSS ® software, version 23.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":41,"wikidataId":"Q181596","offsetEnd":45,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":131.642,"h":9.3201,"y":564.383,"p":2,"w":19.6602}]},"version":{"offsetStart":66,"normalizedForm":"23","offsetEnd":68,"rawForm":"23","boundingBoxes":[{"x":230.289,"h":9.3201,"y":564.374,"p":2,"w":7.840066666666666}]}},
  {"_key":"60c20cf57723bebd866455db","_id":"annotations/60c20cf57723bebd866455db","_rev":"_cfFmVhm---","document":{"$oid":"60c20cf57723bebd866455d7"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"PyRx","offsetEnd":4,"rawForm":"PyRx","boundingBoxes":[{"x":408.528,"h":8.3885,"y":126.091,"p":2,"w":19.038}]},"context":"PyRx Virtual Screening Tools incorpo- rated with Autodock Vina was used for virtual screening (Dallakyan & Olson, 2015)."},
  {"_key":"60c20cf57723bebd866455dc","_id":"annotations/60c20cf57723bebd866455dc","_rev":"_cfFmVhy---","wikipediaExternalRef":307123,"document":{"$oid":"60c20cf57723bebd866455d7"},"context":"AMBER14 force field (Dickson et al., 2014) was used on YASARA Dynamics (Krieger et al., 2013) for the simulation.","wikidataId":"Q2458963","type":"software","lang":"en","confidence":0.3031,"software-name":{"wikipediaExternalRef":307123,"normalizedForm":"AMBER","offsetStart":0,"wikidataId":"Q2458963","offsetEnd":5,"lang":"en","confidence":0.3031,"rawForm":"AMBER","boundingBoxes":[{"x":432.846,"h":8.3885,"y":491.815,"p":2,"w":38.133}]},"version":{"offsetStart":5,"normalizedForm":"14","offsetEnd":7,"rawForm":"14","boundingBoxes":[{"x":432.846,"h":8.3885,"y":491.815,"p":2,"w":38.133}]}},
  {"_key":"60c20cf57723bebd866455dd","_id":"annotations/60c20cf57723bebd866455dd","_rev":"_cfFmVi----","wikipediaExternalRef":307123,"document":{"$oid":"60c20cf57723bebd866455d7"},"context":"The AMBER14 force field was used during the binding free energy calculation.","wikidataId":"Q2458963","type":"software","lang":"en","confidence":0.3031,"software-name":{"wikipediaExternalRef":307123,"normalizedForm":"AMBER","offsetStart":4,"wikidataId":"Q2458963","offsetEnd":9,"lang":"en","confidence":0.3031,"rawForm":"AMBER","boundingBoxes":[{"x":462.273,"h":8.3885,"y":90.2593,"p":3,"w":38.133}]},"version":{"offsetStart":9,"normalizedForm":"14","offsetEnd":11,"rawForm":"14","boundingBoxes":[{"x":462.273,"h":8.3885,"y":90.2593,"p":3,"w":38.133}]}},
  {"_key":"60c20cf57723bebd866455de","_id":"annotations/60c20cf57723bebd866455de","_rev":"_cfFmViG---","document":{"$oid":"60c20cf57723bebd866455d7"},"type":"software","software-name":{"offsetStart":25,"normalizedForm":"XLSTAT","offsetEnd":31,"rawForm":"XLSTAT","boundingBoxes":[{"x":268.891,"h":8.3885,"y":457.628,"p":4,"w":29.849}]},"context":"MLR was carried out with XLSTAT (Adinsoft, 2010)."},
  {"_key":"60c20cf57723bebd866455df","_id":"annotations/60c20cf57723bebd866455df","_rev":"_cfFmViS---","wikipediaExternalRef":734158,"document":{"$oid":"60c20cf57723bebd866455d7"},"context":"The top-ranked drugs were then optimized by Gaussian 09 software using semi-empirical PM6 method (Frisch, 2009).","wikidataId":"Q901177","type":"software","confidence":0.9559,"software-name":{"wikipediaExternalRef":734158,"normalizedForm":"Gaussian 09","offsetStart":44,"wikidataId":"Q901177","offsetEnd":55,"lang":"en","confidence":0.9559,"rawForm":"Gaussian 09","boundingBoxes":[{"x":511.873,"h":8.388500000000022,"y":320.21,"p":2,"w":49.714999999999975}]},"lang":"en"},
  {"_key":"60c20cf57723bebd866455e0","_id":"annotations/60c20cf57723bebd866455e0","_rev":"_cfFmVie---","document":{"$oid":"60c20cf57723bebd866455d7"},"type":"software","software-name":{"offsetStart":49,"normalizedForm":"Autodock Vina","offsetEnd":62,"rawForm":"Autodock Vina","boundingBoxes":[{"x":361.018,"h":8.388499999999993,"y":138.223,"p":2,"w":61.934500000000014}]},"context":"PyRx Virtual Screening Tools incorpo- rated with Autodock Vina was used for virtual screening (Dallakyan & Olson, 2015)."},
  {"_key":"60c20cf57723bebd866455e1","_id":"annotations/60c20cf57723bebd866455e1","_rev":"_cfFmViq---","wikipediaExternalRef":19391960,"document":{"$oid":"60c20cf57723bebd866455d7"},"context":"AMBER14 force field (Dickson et al., 2014) was used on YASARA Dynamics (Krieger et al., 2013) for the simulation.","wikidataId":"Q8049645","type":"software","confidence":0.7475,"software-name":{"wikipediaExternalRef":19391960,"normalizedForm":"YASARA","offsetStart":56,"wikidataId":"Q8049645","offsetEnd":62,"lang":"en","confidence":0.7475,"rawForm":"YASARA","boundingBoxes":[{"x":422.984,"h":8.3885,"y":503.947,"p":2,"w":32.376}]},"lang":"en"},
  {"_key":"60c20cf57723bebd866455e2","_id":"annotations/60c20cf57723bebd866455e2","_rev":"_cfFmVi2---","wikipediaExternalRef":26322186,"document":{"$oid":"60c20cf57723bebd866455d7"},"context":"These optimized drug structures are then docked again using AutoDock Vina software and GOLD (Jones et al., 1997) docking programs.","wikidataId":"Q4826062","type":"software","confidence":0.9847,"software-name":{"wikipediaExternalRef":26322186,"normalizedForm":"AutoDock Vina","offsetStart":61,"wikidataId":"Q4826062","offsetEnd":74,"lang":"en","confidence":0.9847,"rawForm":"AutoDock Vina","boundingBoxes":[{"x":310.677,"h":8.388500000000022,"y":356.664,"p":2,"w":59.553499999999985}]},"lang":"en"},
  {"_key":"60c20cf57723bebd866455e3","_id":"annotations/60c20cf57723bebd866455e3","_rev":"_cfFmVjC---","wikipediaExternalRef":26322186,"document":{"$oid":"60c20cf57723bebd866455d7"},"context":"After optimizing by PM6 level of theory, the selected drugs are screened again in AutoDock Vina.","wikidataId":"Q4826062","type":"software","confidence":0.9722,"software-name":{"wikipediaExternalRef":26322186,"normalizedForm":"AutoDock Vina","offsetStart":83,"wikidataId":"Q4826062","offsetEnd":96,"lang":"en","confidence":0.9722,"rawForm":"AutoDock Vina","boundingBoxes":[{"x":207.545,"h":8.388500000000022,"y":673.343,"p":4,"w":59.46560000000002}]},"lang":"en"},
  {"_key":"60c20cf57723bebd866455e4","_id":"annotations/60c20cf57723bebd866455e4","_rev":"_cfFmVjO---","document":{"$oid":"60c20cf57723bebd866455d7"},"type":"software","software-name":{"offsetStart":84,"normalizedForm":"Autodock Vina","offsetEnd":97,"rawForm":"Autodock Vina","boundingBoxes":[{"x":143.373,"h":8.388500000000022,"y":551.115,"p":4,"w":57.42460000000003}]},"context":"The structure of 1615 FDA approved drugs is considered for virtual screening using Autodock Vina."},
  {"_key":"60c20cf57723bebd866455e5","_id":"annotations/60c20cf57723bebd866455e5","_rev":"_cfFmVja---","document":{"$oid":"60c20cf57723bebd866455d7"},"context":"These optimized drug structures are then docked again using AutoDock Vina software and GOLD (Jones et al., 1997) docking programs.","references":[{"offsetStart":9035,"normalizedForm":"Jones et al., 1997","refKey":25,"label":"(Jones et al., 1997)","reference_id":{"$oid":"60c20cf57723bebd866455d8"},"offsetEnd":9056,"boundingBoxes":[{"x":453.368,"h":8.388500000000022,"y":356.664,"p":2,"w":73.62560000000002}]}],"type":"software","software-name":{"offsetStart":88,"normalizedForm":"GOLD","offsetEnd":92,"rawForm":"GOLD","boundingBoxes":[{"x":427.346,"h":8.3885,"y":356.664,"p":2,"w":23.4935}]}},
  {"_key":"60c20cf57723bebd866455e6","_id":"annotations/60c20cf57723bebd866455e6","_rev":"_cfFmVjm---","wikipediaExternalRef":19391960,"document":{"$oid":"60c20cf57723bebd866455d7"},"context":"After completion of 100 ns MD simulation for all sys- tems, the results were analyzed in YASARA.","wikidataId":"Q8049645","type":"software","confidence":0.7475,"software-name":{"wikipediaExternalRef":19391960,"normalizedForm":"YASARA","offsetStart":89,"wikidataId":"Q8049645","offsetEnd":95,"lang":"en","confidence":0.7475,"rawForm":"YASARA","boundingBoxes":[{"x":473.437,"h":8.3885,"y":698.123,"p":2,"w":29.43642857142857}]},"lang":"en"},
  {"_key":"60c20cf57723bebd866455e7","_id":"annotations/60c20cf57723bebd866455e7","_rev":"_cfFmVju---","document":{"$oid":"60c20cf57723bebd866455d7"},"context":"The molecular interactions of the drugs as predicted by docking simulation were analyzed in BIOVIA Discovery Studio Visualizer (Studio, 2015).","references":[{"offsetStart":9204,"normalizedForm":"Studio, 2015","refKey":40,"label":"(Studio, 2015)","reference_id":{"$oid":"60c20cf57723bebd866455d9"},"offsetEnd":9218,"boundingBoxes":[{"x":378.82,"h":8.388500000000022,"y":393.062,"p":2,"w":53.02316666666667}]}],"type":"software","software-name":{"offsetStart":93,"normalizedForm":"BIOVIA Discovery Studio Visualizer","offsetEnd":128,"rawForm":"BIOVIA Discovery \nStudio Visualizer","boundingBoxes":[{"x":490.048,"h":8.388500000000022,"y":380.929,"p":2,"w":71.57449999999994},{"x":310.678,"h":8.388500000000022,"y":393.062,"p":2,"w":65.72850000000005}]}},
  {"_key":"60c20cf57723bebd866455e8","_id":"annotations/60c20cf57723bebd866455e8","_rev":"_cfFmVj6---","document":{"$oid":"60c20cf57723bebd866455d7"},"type":"software","software-name":{"offsetStart":121,"normalizedForm":"YASARA Dynamics","offsetEnd":136,"rawForm":"YASARA Dynamics","boundingBoxes":[{"x":321.051,"h":8.388500000000008,"y":77.9568,"p":3,"w":74.02199999999999}]},"context":"For binding free energy calculations, molecular mechanics/ Poisson-Boltzmann surface area (MM/PBSA) method was used in YASARA Dynamics software (Baker et al., 2001; Chirag et al., 2020; Massova & Kollman, 2000)."},
  {"_key":"60c20cf57723bebd866455e9","_id":"annotations/60c20cf57723bebd866455e9","_rev":"_cfFmVkG---","document":{"$oid":"60c20cf57723bebd866455d7"},"context":"All calculations were carried out on R platform employing in- house developed codes and plots were produced using the package ggplot2 (Kassambara, 2016).","references":[{"offsetStart":13139,"normalizedForm":"Kassambara, 2016","refKey":26,"label":"(Kassambara, 2016)","reference_id":{"$oid":"60c20cf57723bebd866455da"},"offsetEnd":13157,"boundingBoxes":[{"x":389.421,"h":8.388500000000022,"y":498.956,"p":3,"w":79.16874999999999}]}],"type":"software","software-name":{"offsetStart":127,"normalizedForm":"ggplot","offsetEnd":133,"rawForm":"ggplot","boundingBoxes":[{"x":350.985,"h":8.3885,"y":498.956,"p":3,"w":31.502}]},"version":{"offsetStart":133,"normalizedForm":"2","offsetEnd":134,"rawForm":"2","boundingBoxes":[{"x":350.985,"h":8.3885,"y":498.956,"p":3,"w":31.502}]}},
  {"_key":"60c20cfb7723bebd866455ed","_id":"annotations/60c20cfb7723bebd866455ed","_rev":"_cfFmVkS---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Spark application was developed to run data processing commands automatically and to generate the appropriate output data.","wikidataId":"Q7573619","type":"software","confidence":0.2975,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Spark","offsetStart":0,"wikidataId":"Q7573619","offsetEnd":5,"lang":"en","confidence":0.2975,"rawForm":"Spark","boundingBoxes":[{"x":190.715,"h":8.7472,"y":344.331,"p":1,"w":22.7267}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455ee","_id":"annotations/60c20cfb7723bebd866455ee","_rev":"_cfFmVke---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Spark can be run in a standalone cluster mode or take advantage of clusters based on a management framework like Yarn.","wikidataId":"Q7573619","type":"software","confidence":0.299,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Spark","offsetStart":0,"wikidataId":"Q7573619","offsetEnd":5,"lang":"en","confidence":0.299,"rawForm":"Spark","boundingBoxes":[{"x":317.479,"h":8.7472,"y":308.768,"p":6,"w":23.2936}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455ef","_id":"annotations/60c20cfb7723bebd866455ef","_rev":"_cfFmVkq---","wikipediaExternalRef":3254510,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Scala, as a native Spark language, was selected for developing of the application source code.","wikidataId":"Q460584","type":"software","confidence":0.3308,"software-name":{"wikipediaExternalRef":3254510,"normalizedForm":"Scala","offsetStart":0,"wikidataId":"Q460584","offsetEnd":5,"lang":"en","confidence":0.3308,"rawForm":"Scala","boundingBoxes":[{"x":350.531,"h":8.7472,"y":532.927,"p":6,"w":19.68775}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455f0","_id":"annotations/60c20cfb7723bebd866455f0","_rev":"_cfFmVk2---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"publisher":{"offsetStart":167,"normalizedForm":"Apache","offsetEnd":173,"rawForm":"Apache","boundingBoxes":[{"x":259.371,"h":8.7472,"y":134.455,"p":6,"w":29.8579}]},"context":"Hadoop .","wikidataId":"Q29120","type":"software","confidence":0.7327,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Hadoop","offsetStart":0,"wikidataId":"Q29120","offsetEnd":6,"lang":"en","confidence":0.7327,"rawForm":"Hadoop","boundingBoxes":[{"x":94.1099,"h":8.7472,"y":431.466,"p":1,"w":31.1092}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455f1","_id":"annotations/60c20cfb7723bebd866455f1","_rev":"_cfFmVl----","wikipediaExternalRef":30248516,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Apache Hive was found as optimal to play a database role in the architecture.","wikidataId":"Q4778914","type":"software","confidence":0.9824,"software-name":{"wikipediaExternalRef":30248516,"normalizedForm":"Apache Hive","offsetStart":0,"wikidataId":"Q4778914","offsetEnd":11,"lang":"en","confidence":0.9824,"rawForm":"Apache Hive","boundingBoxes":[{"x":124.78,"h":8.74720000000002,"y":395.973,"p":6,"w":51.00459999999998}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455f2","_id":"annotations/60c20cfb7723bebd866455f2","_rev":"_cfFmVlK---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Apache Spark was used for integrating frequent data into water-related models and analysis.","wikidataId":"Q7573619","references":[{"offsetStart":12147,"normalizedForm":"Shafiee et al. 2018","refKey":32,"label":"(Shafiee et al. 2018)","reference_id":{"$oid":"60c20cfb7723bebd866455eb"},"offsetEnd":12168,"boundingBoxes":[{"x":306.141,"h":8.74720000000002,"y":258.952,"p":3,"w":85.2495833333333}]}],"type":"software","confidence":0.9843,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Apache Spark","offsetStart":0,"wikidataId":"Q7573619","offsetEnd":12,"lang":"en","confidence":0.9843,"rawForm":"Apache Spark","boundingBoxes":[{"x":306.141,"h":8.74720000000002,"y":346.143,"p":3,"w":60.919299999999964}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455f3","_id":"annotations/60c20cfb7723bebd866455f3","_rev":"_cfFmVlW---","wikipediaExternalRef":40023747,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Apache Flume is a complex, distributed, and available service for collecting, aggregating, and moving large amounts of various data to a centralized data store.","wikidataId":"Q19599376","type":"software","confidence":0.969,"software-name":{"wikipediaExternalRef":40023747,"normalizedForm":"Apache Flume","offsetStart":0,"wikidataId":"Q19599376","offsetEnd":12,"lang":"en","confidence":0.969,"rawForm":"Apache Flume","boundingBoxes":[{"x":62.362,"h":8.74720000000002,"y":333.67,"p":4,"w":60.0208}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455f4","_id":"annotations/60c20cfb7723bebd866455f4","_rev":"_cfFmVli---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Scikit learn","offsetEnd":12,"rawForm":"Scikit learn","boundingBoxes":[{"x":62.362,"h":8.74720000000002,"y":420.861,"p":9,"w":52.211999999999996}]},"context":"Scikit learn (python library) helped us to build a Multinomial Naïve Bayes model in Python."},
  {"_key":"60c20cfb7723bebd866455f5","_id":"annotations/60c20cfb7723bebd866455f5","_rev":"_cfFmVlu---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"As Apache Spark engine has more advantages over the Map-Reduce like in-memory computation (Spark may be up to 100 times faster in memory, 10 times faster on disk), the Spark was decided to be a primary processing engine.","wikidataId":"Q7573619","references":[{"offsetStart":12147,"normalizedForm":"Shafiee et al. 2018","refKey":32,"label":"(Shafiee et al. 2018)","reference_id":{"$oid":"60c20cfb7723bebd866455eb"},"offsetEnd":12168,"boundingBoxes":[{"x":306.141,"h":8.74720000000002,"y":258.952,"p":3,"w":85.2495833333333}]}],"type":"software","confidence":0.9852,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Apache Spark","offsetStart":3,"wikidataId":"Q7573619","offsetEnd":15,"lang":"en","confidence":0.9852,"rawForm":"Apache Spark","boundingBoxes":[{"x":332.219,"h":8.747199999999992,"y":146.857,"p":6,"w":56.868600000000015}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455f6","_id":"annotations/60c20cfb7723bebd866455f6","_rev":"_cfFmVl6---","wikipediaExternalRef":30248516,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The Apache Hive is ideal for analysing, reading, writing, and managing large datasets that are stored in distributed stor- age and queried by HiveQL (SQL abstraction for integrating SQL-like queries).","wikidataId":"Q4778914","type":"software","confidence":0.9826,"software-name":{"wikipediaExternalRef":30248516,"normalizedForm":"Apache Hive","offsetStart":4,"wikidataId":"Q4778914","offsetEnd":15,"lang":"en","confidence":0.9826,"rawForm":"Apache Hive","boundingBoxes":[{"x":80.7302,"h":8.74720000000002,"y":420.86,"p":6,"w":51.9025}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455f7","_id":"annotations/60c20cfb7723bebd866455f7","_rev":"_cfFmVmC---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"publisher":{"offsetStart":167,"normalizedForm":"Apache","offsetEnd":173,"rawForm":"Apache","boundingBoxes":[{"x":259.371,"h":8.7472,"y":134.455,"p":6,"w":29.8579}]},"context":"Apache Hadoop Yarn was applied as a technology for re- source management in the proposed architecture.","wikidataId":"Q29120","type":"software","confidence":0.7278,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Hadoop","offsetStart":7,"wikidataId":"Q29120","offsetEnd":13,"lang":"en","confidence":0.7278,"rawForm":"Hadoop","boundingBoxes":[{"x":94.9608,"h":8.7472,"y":109.51,"p":6,"w":31.0524}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455f8","_id":"annotations/60c20cfb7723bebd866455f8","_rev":"_cfFmVmO---","wikipediaExternalRef":30248516,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"However, the Apache Hive is designed to meet mainly traditional warehousing tasks, and there- fore it is not fully prepared for OLTP (Online Transaction Processing) workloads.","wikidataId":"Q4778914","type":"software","confidence":0.9826,"software-name":{"wikipediaExternalRef":30248516,"normalizedForm":"Apache Hive","offsetStart":13,"wikidataId":"Q4778914","offsetEnd":24,"lang":"en","confidence":0.9826,"rawForm":"Apache Hive","boundingBoxes":[{"x":183.997,"h":8.74720000000002,"y":570.299,"p":6,"w":54.38749999999999}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455f9","_id":"annotations/60c20cfb7723bebd866455f9","_rev":"_cfFmVma---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The structure of Spark application is depicted in (Fig. 6).","wikidataId":"Q7573619","type":"software","confidence":0.2998,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Spark","offsetStart":17,"wikidataId":"Q7573619","offsetEnd":22,"lang":"en","confidence":0.2998,"rawForm":"Spark","boundingBoxes":[{"x":380.52,"h":8.7472,"y":645.006,"p":6,"w":22.7596}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455fa","_id":"annotations/60c20cfb7723bebd866455fa","_rev":"_cfFmVmm---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":18,"normalizedForm":"Spark SQL","offsetEnd":27,"rawForm":"Spark SQL","boundingBoxes":[{"x":483.307,"h":8.74720000000002,"y":694.781,"p":6,"w":43.43560000000002}]},"context":"In the next step, Spark SQL was used to read data from an existing Hive deployment."},
  {"_key":"60c20cfb7723bebd866455fb","_id":"annotations/60c20cfb7723bebd866455fb","_rev":"_cfFmVmy---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Scala, as a native Spark language, was selected for developing of the application source code.","wikidataId":"Q7573619","type":"software","confidence":0.3082,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Spark","offsetStart":19,"wikidataId":"Q7573619","offsetEnd":24,"lang":"en","confidence":0.3082,"rawForm":"Spark","boundingBoxes":[{"x":425.479,"h":8.7472,"y":532.927,"p":6,"w":22.896}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455fc","_id":"annotations/60c20cfb7723bebd866455fc","_rev":"_cfFmVm6---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":24,"normalizedForm":"SparkSession","offsetEnd":36,"rawForm":"SparkSession","boundingBoxes":[{"x":372.809,"h":8.7472,"y":657.421,"p":6,"w":52.3126}]},"context":"In the first part, the SparkSession object was created as an entry point to the Spark SQL."},
  {"_key":"60c20cfb7723bebd866455fd","_id":"annotations/60c20cfb7723bebd866455fd","_rev":"_cfFmVnG---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":29,"normalizedForm":"AVRO","offsetEnd":33,"rawForm":"AVRO","boundingBoxes":[{"x":169.765,"h":8.7472,"y":545.357,"p":4,"w":28.8298}]},"context":"All data were serialized by AVRO serialization system."},
  {"_key":"60c20cfb7723bebd866455fe","_id":"annotations/60c20cfb7723bebd866455fe","_rev":"_cfFmVnS---","wikipediaExternalRef":30248516,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"(3) Easy access to data via HiveQL, (4) Built on top of Apache Hadoop, (5) Query execution via Apache Spark engine.","wikidataId":"Q4778914","type":"software","confidence":0.2877,"software-name":{"wikipediaExternalRef":30248516,"normalizedForm":"HiveQL","offsetStart":29,"wikidataId":"Q4778914","offsetEnd":35,"lang":"en","confidence":0.2877,"rawForm":"HiveQL","boundingBoxes":[{"x":145.53,"h":8.7472,"y":532.94,"p":6,"w":29.500114285714286}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd866455ff","_id":"annotations/60c20cfb7723bebd866455ff","_rev":"_cfFmVne---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"publisher":{"offsetStart":167,"normalizedForm":"Apache","offsetEnd":173,"rawForm":"Apache","boundingBoxes":[{"x":259.371,"h":8.7472,"y":134.455,"p":6,"w":29.8579}]},"context":"Spark offers more features than Hadoop, but there is still a limitation -Spark does not provide its file management sys- tem, and therefore it is beneficial to integrate it with Hadoop.","wikidataId":"Q29120","type":"software","confidence":0.7238,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Hadoop","offsetStart":32,"wikidataId":"Q29120","offsetEnd":38,"lang":"en","confidence":0.7238,"rawForm":"Hadoop","boundingBoxes":[{"x":436.195,"h":8.7472,"y":221.576,"p":6,"w":28.709400000000002}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645600","_id":"annotations/60c20cfb7723bebd86645600","_rev":"_cfFmVnq---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":39,"normalizedForm":"HIVE","offsetEnd":43,"rawForm":"HIVE","boundingBoxes":[{"x":247.009,"h":8.7472,"y":455.734,"p":10,"w":23.3752}]},"context":"Built-in function ngrams() provided by HIVE was utilized to find the most frequent n-grams (word patterns) from the input dataset."},
  {"_key":"60c20cfb7723bebd86645601","_id":"annotations/60c20cfb7723bebd86645601","_rev":"_cfFmVny---","wikipediaExternalRef":3254510,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The Spark application was developed in Scala and sub- mitted to a preprepared Hadoop cluster using the master URL.","wikidataId":"Q460584","type":"software","confidence":0.3321,"software-name":{"wikipediaExternalRef":3254510,"normalizedForm":"Scala","offsetStart":39,"wikidataId":"Q460584","offsetEnd":44,"lang":"en","confidence":0.3321,"rawForm":"Scala","boundingBoxes":[{"x":487.785,"h":8.7472,"y":333.656,"p":6,"w":20.9902}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645602","_id":"annotations/60c20cfb7723bebd86645602","_rev":"_cfFmVo----","wikipediaExternalRef":30248516,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"There are a few main reasons for choosing Hive as a central warehouse: (1) It supports built-in connectors for various types of formats (CSV/TSV, JSON).","wikidataId":"Q4778914","type":"software","confidence":0.3191,"software-name":{"wikipediaExternalRef":30248516,"normalizedForm":"Hive","offsetStart":43,"wikidataId":"Q4778914","offsetEnd":47,"lang":"en","confidence":0.3191,"rawForm":"Hive","boundingBoxes":[{"x":51.0238,"h":8.7472,"y":470.692,"p":6,"w":19.0296}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645603","_id":"annotations/60c20cfb7723bebd86645603","_rev":"_cfFmVoK---","wikipediaExternalRef":3254510,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The connectivity between Spark application (Scala code) and Yarn cluster is provided by SparkContext telling to Spark how to access the cluster.","wikidataId":"Q460584","type":"software","confidence":0.3321,"software-name":{"wikipediaExternalRef":3254510,"normalizedForm":"Scala","offsetStart":44,"wikidataId":"Q460584","offsetEnd":49,"lang":"en","confidence":0.3321,"rawForm":"Scala","boundingBoxes":[{"x":497.19534999999996,"h":8.7472,"y":420.847,"p":6,"w":20.85175}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645604","_id":"annotations/60c20cfb7723bebd86645604","_rev":"_cfFmVoW---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Both platforms are based on the same core of Apache Hadoop, and therefore, they are expected to have more simi- larities than differences.","wikidataId":"Q29120","references":[{"offsetStart":12112,"normalizedForm":"(Lu et al. 2020","refKey":21,"label":"(Lu et al. 2020","reference_id":{"$oid":"60c20cfb7723bebd866455ec"},"offsetEnd":12127,"boundingBoxes":[{"x":382.172,"h":8.747199999999992,"y":246.536,"p":3,"w":69.11735999999996}]}],"type":"software","confidence":0.8861,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Apache Hadoop","offsetStart":45,"wikidataId":"Q29120","offsetEnd":59,"lang":"en","confidence":0.8861,"rawForm":"Apache \nHadoop","boundingBoxes":[{"x":514.485,"h":8.7472,"y":395.91,"p":4,"w":29.8579},{"x":306.14,"h":8.7472,"y":408.382,"p":4,"w":28.618885714285714}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645605","_id":"annotations/60c20cfb7723bebd86645605","_rev":"_cfFmVoi---","document":{"$oid":"60c20cfb7723bebd866455ea"},"publisher":{"offsetStart":38,"normalizedForm":"Apache","offsetEnd":44,"rawForm":"Apache","boundingBoxes":[{"x":258.494,"h":8.7472,"y":171.814,"p":6,"w":30.6539}]},"context":"In the proposed cluster architecture, Apache Hadoop Yarn resides between HDFS and the processing en- gine that is used for running applications.","type":"software","software-name":{"offsetStart":46,"normalizedForm":"Hadoop Yarn","offsetEnd":57,"rawForm":"Hadoop Yarn","boundingBoxes":[{"x":51.0238,"h":8.747199999999992,"y":184.23,"p":6,"w":53.487199999999994}]}},
  {"_key":"60c20cfb7723bebd86645606","_id":"annotations/60c20cfb7723bebd86645606","_rev":"_cfFmVou---","wikipediaExternalRef":40023747,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"As a suitable data ingestion tool for this study, Apache Flume was selected and used for the first step of the data handling process.","wikidataId":"Q19599376","type":"software","confidence":0.8763,"software-name":{"wikipediaExternalRef":40023747,"normalizedForm":"Apache Flume","offsetStart":50,"wikidataId":"Q19599376","offsetEnd":63,"lang":"en","confidence":0.8763,"rawForm":"Apache \nFlume","boundingBoxes":[{"x":258.97,"h":8.7472,"y":221.591,"p":4,"w":30.1767},{"x":51.0236,"h":8.7472,"y":234.063,"p":4,"w":25.1954}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645607","_id":"annotations/60c20cfb7723bebd86645607","_rev":"_cfFmVo2---","wikipediaExternalRef":27059655,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"(1) Hortonworks doesn't have any proprietary SW, whilst Cloudera has Cloudera Manager, Cloudera Search and Impala (SQL interface) (2) HDP is a native component on the windows server (3) slightly different security strategies.","wikidataId":"Q2979728","type":"software","confidence":0.7925,"software-name":{"wikipediaExternalRef":27059655,"normalizedForm":"Cloudera","offsetStart":57,"wikidataId":"Q2979728","offsetEnd":65,"lang":"en","confidence":0.7925,"rawForm":"Cloudera","boundingBoxes":[{"x":306.14,"h":8.7472,"y":458.214,"p":4,"w":38.3052}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645608","_id":"annotations/60c20cfb7723bebd86645608","_rev":"_cfFmVpC---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"There are two major representatives of such frameworks - Apache Hadoop (Lu et al. 2020) and Apache Spark (Shafiee et al. 2018).","wikidataId":"Q29120","references":[{"offsetStart":12112,"normalizedForm":"(Lu et al. 2020","refKey":21,"label":"(Lu et al. 2020","reference_id":{"$oid":"60c20cfb7723bebd866455ec"},"offsetEnd":12127,"boundingBoxes":[{"x":382.172,"h":8.747199999999992,"y":246.536,"p":3,"w":69.11735999999996}]}],"type":"software","confidence":0.9855,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Apache Hadoop","offsetStart":58,"wikidataId":"Q29120","offsetEnd":71,"lang":"en","confidence":0.9855,"rawForm":"Apache Hadoop","boundingBoxes":[{"x":306.141,"h":8.747199999999992,"y":246.536,"p":3,"w":70.12709999999998}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645609","_id":"annotations/60c20cfb7723bebd86645609","_rev":"_cfFmVpO---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Results confirmed the advantages of many well-known features of Spark and Hadoop in social media data processing.","wikidataId":"Q7573619","type":"software","confidence":0.2975,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Spark","offsetStart":64,"wikidataId":"Q7573619","offsetEnd":69,"lang":"en","confidence":0.2975,"rawForm":"Spark","boundingBoxes":[{"x":460.349,"h":8.7472,"y":356.747,"p":1,"w":22.6699}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664560a","_id":"annotations/60c20cfb7723bebd8664560a","_rev":"_cfFmVpa---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":64,"normalizedForm":"Kafka","offsetEnd":69,"rawForm":"Kafka","boundingBoxes":[{"x":230.682,"h":8.7472,"y":308.782,"p":4,"w":24.1882}]},"context":"There is no need (in our case) to use complex software such as Kafka or Nifi, which require a more robust implementation strategy."},
  {"_key":"60c20cfb7723bebd8664560b","_id":"annotations/60c20cfb7723bebd8664560b","_rev":"_cfFmVpm---","wikipediaExternalRef":40023747,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"There are plenty of options on the current data market such as Apache Flume, Apache Sqoop, Apache Kafka, Apache NIFI or Apache Storm.","wikidataId":"Q19599376","type":"software","confidence":0.9797,"software-name":{"wikipediaExternalRef":40023747,"normalizedForm":"Apache Flume","offsetStart":64,"wikidataId":"Q19599376","offsetEnd":76,"lang":"en","confidence":0.9797,"rawForm":"Apache Flume","boundingBoxes":[{"x":228.015,"h":8.747199999999992,"y":171.816,"p":4,"w":56.58116666666672}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664560c","_id":"annotations/60c20cfb7723bebd8664560c","_rev":"_cfFmVpu---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"publisher":{"offsetStart":57,"normalizedForm":"Apache","offsetEnd":63,"rawForm":"Apache","boundingBoxes":[{"x":259.368,"h":8.7472,"y":532.94,"p":6,"w":29.8579}]},"context":"(3) Easy access to data via HiveQL, (4) Built on top of Apache Hadoop, (5) Query execution via Apache Spark engine.","wikidataId":"Q29120","type":"software","confidence":0.7327,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Hadoop","offsetStart":65,"wikidataId":"Q29120","offsetEnd":71,"lang":"en","confidence":0.7327,"rawForm":"Hadoop","boundingBoxes":[{"x":51.0238,"h":8.7472,"y":545.412,"p":6,"w":28.618885714285714}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664560d","_id":"annotations/60c20cfb7723bebd8664560d","_rev":"_cfFmVp6---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":68,"normalizedForm":"Spark SQL","offsetEnd":77,"rawForm":"Spark SQL","boundingBoxes":[{"x":422.7,"h":8.74720000000002,"y":682.366,"p":6,"w":44.22840000000002}]},"context":"SparkSession allows basic configura- tions related to accessing the Spark SQL services or loading tables from Hive warehouse."},
  {"_key":"60c20cfb7723bebd8664560e","_id":"annotations/60c20cfb7723bebd8664560e","_rev":"_cfFmVqG---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":70,"normalizedForm":"Cloudera Manager","offsetEnd":86,"rawForm":"Cloudera Manager","boundingBoxes":[{"x":366.967,"h":8.74720000000002,"y":458.214,"p":4,"w":77.49419999999998}]},"context":"(1) Hortonworks doesn't have any proprietary SW, whilst Cloudera has Cloudera Manager, Cloudera Search and Impala (SQL interface) (2) HDP is a native component on the windows server (3) slightly different security strategies."},
  {"_key":"60c20cfb7723bebd8664560f","_id":"annotations/60c20cfb7723bebd8664560f","_rev":"_cfFmVqS---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":73,"normalizedForm":"Nifi","offsetEnd":77,"rawForm":"Nifi","boundingBoxes":[{"x":270.763,"h":8.7472,"y":308.782,"p":4,"w":14.647440000000001}]},"context":"There is no need (in our case) to use complex software such as Kafka or Nifi, which require a more robust implementation strategy."},
  {"_key":"60c20cfb7723bebd86645610","_id":"annotations/60c20cfb7723bebd86645610","_rev":"_cfFmVqe---","wikipediaExternalRef":30248516,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"All techniques were performed directly in the database with the help of Hive and Regex functions.","wikidataId":"Q4778914","type":"software","confidence":0.3191,"software-name":{"wikipediaExternalRef":30248516,"normalizedForm":"Hive","offsetStart":73,"wikidataId":"Q4778914","offsetEnd":77,"lang":"en","confidence":0.3191,"rawForm":"Hive","boundingBoxes":[{"x":525.313,"h":8.7472,"y":408.394,"p":9,"w":19.0296}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645611","_id":"annotations/60c20cfb7723bebd86645611","_rev":"_cfFmVqq---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"publisher":{"offsetStart":167,"normalizedForm":"Apache","offsetEnd":173,"rawForm":"Apache","boundingBoxes":[{"x":259.371,"h":8.7472,"y":134.455,"p":6,"w":29.8579}]},"context":"Results confirmed the advantages of many well-known features of Spark and Hadoop in social media data processing.","wikidataId":"Q29120","type":"software","confidence":0.7318,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Hadoop","offsetStart":74,"wikidataId":"Q29120","offsetEnd":80,"lang":"en","confidence":0.7318,"rawForm":"Hadoop","boundingBoxes":[{"x":502.812,"h":8.7472,"y":356.747,"p":1,"w":31.1092}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645612","_id":"annotations/60c20cfb7723bebd86645612","_rev":"_cfFmVqy---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"(Martin et al. 2019) proposed big data architecture and workflow based on Apache Spark.","wikidataId":"Q7573619","references":[{"offsetStart":12147,"normalizedForm":"Shafiee et al. 2018","refKey":32,"label":"(Shafiee et al. 2018)","reference_id":{"$oid":"60c20cfb7723bebd866455eb"},"offsetEnd":12168,"boundingBoxes":[{"x":306.141,"h":8.74720000000002,"y":258.952,"p":3,"w":85.2495833333333}]}],"type":"software","confidence":0.9843,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Apache Spark","offsetStart":76,"wikidataId":"Q7573619","offsetEnd":88,"lang":"en","confidence":0.9843,"rawForm":"Apache Spark","boundingBoxes":[{"x":352.967,"h":8.74720000000002,"y":383.503,"p":3,"w":61.29316666666671}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645613","_id":"annotations/60c20cfb7723bebd86645613","_rev":"_cfFmVr----","document":{"$oid":"60c20cfb7723bebd866455ea"},"publisher":{"offsetStart":70,"normalizedForm":"Apache","offsetEnd":76,"rawForm":"Apache","boundingBoxes":[{"x":51.0238,"h":8.7472,"y":221.589,"p":6,"w":29.8579}]},"context":"In our case, the slower processing engine MapReduce was replaced by Apache Spark engine.","type":"software","software-name":{"offsetStart":77,"normalizedForm":"Spark engine","offsetEnd":89,"rawForm":"Spark engine","boundingBoxes":[{"x":83.9621,"h":8.747199999999992,"y":221.589,"p":6,"w":50.15287142857143}]}},
  {"_key":"60c20cfb7723bebd86645614","_id":"annotations/60c20cfb7723bebd86645614","_rev":"_cfFmVrK---","wikipediaExternalRef":36956866,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"There are plenty of options on the current data market such as Apache Flume, Apache Sqoop, Apache Kafka, Apache NIFI or Apache Storm.","wikidataId":"Q773220","type":"software","confidence":0.9713,"software-name":{"wikipediaExternalRef":36956866,"normalizedForm":"Apache Sqoop","offsetStart":79,"wikidataId":"Q773220","offsetEnd":91,"lang":"en","confidence":0.9713,"rawForm":"Apache Sqoop","boundingBoxes":[{"x":51.0236,"h":8.747199999999992,"y":184.231,"p":4,"w":59.34599999999999}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645615","_id":"annotations/60c20cfb7723bebd86645615","_rev":"_cfFmVrW---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":82,"normalizedForm":"Spark SQL","offsetEnd":91,"rawForm":"Spark SQL","boundingBoxes":[{"x":352.12,"h":8.74720000000002,"y":669.893,"p":6,"w":40.575625}]},"context":"In the first part, the SparkSession object was created as an entry point to the Spark SQL."},
  {"_key":"60c20cfb7723bebd86645616","_id":"annotations/60c20cfb7723bebd86645616","_rev":"_cfFmVri---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":85,"normalizedForm":"Hadoop (","offsetEnd":93,"rawForm":"Hadoop (","boundingBoxes":[{"x":129.188,"h":8.74720000000002,"y":383.502,"p":4,"w":40.25380000000001}]},"context":"The main structure of the Flume is designed for the continuous data ingestion into Hadoop (HDFS) (Osman 2019)."},
  {"_key":"60c20cfb7723bebd86645617","_id":"annotations/60c20cfb7723bebd86645617","_rev":"_cfFmVru---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":88,"normalizedForm":"Cloudera Search","offsetEnd":103,"rawForm":"Cloudera Search","boundingBoxes":[{"x":453.798,"h":8.74720000000002,"y":458.214,"p":4,"w":71.08179999999993}]},"context":"(1) Hortonworks doesn't have any proprietary SW, whilst Cloudera has Cloudera Manager, Cloudera Search and Impala (SQL interface) (2) HDP is a native component on the windows server (3) slightly different security strategies."},
  {"_key":"60c20cfb7723bebd86645618","_id":"annotations/60c20cfb7723bebd86645618","_rev":"_cfFmVr6---","wikipediaExternalRef":2581,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The HDP is a secure, enterprise-ready Hadoop distribution and consists of all important Apache Hadoop projects including Hadoop Distributed File System (HDFS), Hive, Yarn, Ambari or HBase.","wikidataId":"Q11354","type":"software","confidence":0.4595,"software-name":{"wikipediaExternalRef":2581,"normalizedForm":"Apache","offsetStart":90,"wikidataId":"Q11354","offsetEnd":96,"lang":"en","confidence":0.4595,"rawForm":"Apache","boundingBoxes":[{"x":352.238,"h":8.7472,"y":308.775,"p":4,"w":32.1194}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645619","_id":"annotations/60c20cfb7723bebd86645619","_rev":"_cfFmVsG---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"There are two major representatives of such frameworks - Apache Hadoop (Lu et al. 2020) and Apache Spark (Shafiee et al. 2018).","wikidataId":"Q7573619","references":[{"offsetStart":12147,"normalizedForm":"Shafiee et al. 2018","refKey":32,"label":"(Shafiee et al. 2018)","reference_id":{"$oid":"60c20cfb7723bebd866455eb"},"offsetEnd":12168,"boundingBoxes":[{"x":306.141,"h":8.74720000000002,"y":258.952,"p":3,"w":85.2495833333333}]}],"type":"software","confidence":0.9843,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Apache Spark","offsetStart":93,"wikidataId":"Q7573619","offsetEnd":105,"lang":"en","confidence":0.9843,"rawForm":"Apache Spark","boundingBoxes":[{"x":482.738,"h":8.747199999999992,"y":246.536,"p":3,"w":61.49559999999991}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664561a","_id":"annotations/60c20cfb7723bebd8664561a","_rev":"_cfFmVsO---","wikipediaExternalRef":41321945,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"There are plenty of options on the current data market such as Apache Flume, Apache Sqoop, Apache Kafka, Apache NIFI or Apache Storm.","wikidataId":"Q16235208","type":"software","confidence":0.9808,"software-name":{"wikipediaExternalRef":41321945,"normalizedForm":"Apache Kafka","offsetStart":93,"wikidataId":"Q16235208","offsetEnd":105,"lang":"en","confidence":0.9808,"rawForm":"Apache Kafka","boundingBoxes":[{"x":119.323,"h":8.747199999999992,"y":184.231,"p":4,"w":58.20399999999999}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664561b","_id":"annotations/60c20cfb7723bebd8664561b","_rev":"_cfFmVsa---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The main objective of the article is to propose an advanced architecture and workflow based on Apache Hadoop and Apache Spark big data platforms.","wikidataId":"Q29120","references":[{"offsetStart":12112,"normalizedForm":"(Lu et al. 2020","refKey":21,"label":"(Lu et al. 2020","reference_id":{"$oid":"60c20cfb7723bebd866455ec"},"offsetEnd":12127,"boundingBoxes":[{"x":382.172,"h":8.747199999999992,"y":246.536,"p":3,"w":69.11735999999996}]}],"type":"software","confidence":0.9855,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Apache Hadoop","offsetStart":95,"wikidataId":"Q29120","offsetEnd":108,"lang":"en","confidence":0.9855,"rawForm":"Apache Hadoop","boundingBoxes":[{"x":430.925,"h":8.74720000000002,"y":257.139,"p":1,"w":63.76419999999996}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664561c","_id":"annotations/60c20cfb7723bebd8664561c","_rev":"_cfFmVsm---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The main objective of the article is to propose an advanced architecture and workflow based on Apache Hadoop and Apache Spark big data platforms.","wikidataId":"Q29120","references":[{"offsetStart":12112,"normalizedForm":"(Lu et al. 2020","refKey":21,"label":"(Lu et al. 2020","reference_id":{"$oid":"60c20cfb7723bebd866455ec"},"offsetEnd":12127,"boundingBoxes":[{"x":382.172,"h":8.747199999999992,"y":246.536,"p":3,"w":69.11735999999996}]}],"type":"software","confidence":0.9855,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Apache Hadoop","offsetStart":96,"wikidataId":"Q29120","offsetEnd":109,"lang":"en","confidence":0.9855,"rawForm":"Apache Hadoop","boundingBoxes":[{"x":204.275,"h":8.74720000000002,"y":331.577,"p":2,"w":66.30280000000002}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664561d","_id":"annotations/60c20cfb7723bebd8664561d","_rev":"_cfFmVsy---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"(3) Easy access to data via HiveQL, (4) Built on top of Apache Hadoop, (5) Query execution via Apache Spark engine.","wikidataId":"Q7573619","references":[{"offsetStart":12147,"normalizedForm":"Shafiee et al. 2018","refKey":32,"label":"(Shafiee et al. 2018)","reference_id":{"$oid":"60c20cfb7723bebd866455eb"},"offsetEnd":12168,"boundingBoxes":[{"x":306.141,"h":8.74720000000002,"y":258.952,"p":3,"w":85.2495833333333}]}],"type":"software","confidence":0.9852,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Apache Spark","offsetStart":97,"wikidataId":"Q7573619","offsetEnd":109,"lang":"en","confidence":0.9852,"rawForm":"Apache Spark","boundingBoxes":[{"x":186.803,"h":8.74720000000002,"y":545.412,"p":6,"w":55.981600000000014}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664561e","_id":"annotations/60c20cfb7723bebd8664561e","_rev":"_cfFmVt----","wikipediaExternalRef":50818838,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"There are plenty of options on the current data market such as Apache Flume, Apache Sqoop, Apache Kafka, Apache NIFI or Apache Storm.","wikidataId":"Q23691642","type":"software","confidence":0.8971,"software-name":{"wikipediaExternalRef":50818838,"normalizedForm":"Apache NIFI","offsetStart":107,"wikidataId":"Q23691642","offsetEnd":118,"lang":"en","confidence":0.8971,"rawForm":"Apache NIFI","boundingBoxes":[{"x":186.252,"h":8.747199999999992,"y":184.231,"p":4,"w":54.9752}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664561f","_id":"annotations/60c20cfb7723bebd8664561f","_rev":"_cfFmVtK---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":109,"normalizedForm":"Impala","offsetEnd":115,"rawForm":"Impala","boundingBoxes":[{"x":306.14,"h":8.7472,"y":470.63,"p":4,"w":27.0305}]},"context":"(1) Hortonworks doesn't have any proprietary SW, whilst Cloudera has Cloudera Manager, Cloudera Search and Impala (SQL interface) (2) HDP is a native component on the windows server (3) slightly different security strategies."},
  {"_key":"60c20cfb7723bebd86645620","_id":"annotations/60c20cfb7723bebd86645620","_rev":"_cfFmVtW---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The main objective of the article is to propose an advanced architecture and workflow based on Apache Hadoop and Apache Spark big data platforms.","wikidataId":"Q7573619","references":[{"offsetStart":12147,"normalizedForm":"Shafiee et al. 2018","refKey":32,"label":"(Shafiee et al. 2018)","reference_id":{"$oid":"60c20cfb7723bebd866455eb"},"offsetEnd":12168,"boundingBoxes":[{"x":306.141,"h":8.74720000000002,"y":258.952,"p":3,"w":85.2495833333333}]}],"type":"software","confidence":0.8944,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Apache Spark","offsetStart":113,"wikidataId":"Q7573619","offsetEnd":126,"lang":"en","confidence":0.8944,"rawForm":"Apache \nSpark","boundingBoxes":[{"x":514.491,"h":8.7472,"y":257.139,"p":1,"w":29.8579},{"x":51.0236,"h":8.7472,"y":269.612,"p":1,"w":22.7596}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645621","_id":"annotations/60c20cfb7723bebd86645621","_rev":"_cfFmVti---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The main objective of the article is to propose an advanced architecture and workflow based on Apache Hadoop and Apache Spark big data platforms.","wikidataId":"Q7573619","references":[{"offsetStart":12147,"normalizedForm":"Shafiee et al. 2018","refKey":32,"label":"(Shafiee et al. 2018)","reference_id":{"$oid":"60c20cfb7723bebd866455eb"},"offsetEnd":12168,"boundingBoxes":[{"x":306.141,"h":8.74720000000002,"y":258.952,"p":3,"w":85.2495833333333}]}],"type":"software","confidence":0.9852,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Apache Spark","offsetStart":115,"wikidataId":"Q7573619","offsetEnd":127,"lang":"en","confidence":0.9852,"rawForm":"Apache Spark","boundingBoxes":[{"x":51.0236,"h":8.74720000000002,"y":344.049,"p":2,"w":53.8528}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645622","_id":"annotations/60c20cfb7723bebd86645622","_rev":"_cfFmVtu---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Specifically, the first and major contribution is in the proposed big data archi- tecture based on the combination of Apache Spark and Apache Hadoop platforms.","wikidataId":"Q7573619","references":[{"offsetStart":12147,"normalizedForm":"Shafiee et al. 2018","refKey":32,"label":"(Shafiee et al. 2018)","reference_id":{"$oid":"60c20cfb7723bebd866455eb"},"offsetEnd":12168,"boundingBoxes":[{"x":306.141,"h":8.74720000000002,"y":258.952,"p":3,"w":85.2495833333333}]}],"type":"software","confidence":0.9852,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Apache Spark","offsetStart":119,"wikidataId":"Q7573619","offsetEnd":131,"lang":"en","confidence":0.9852,"rawForm":"Apache Spark","boundingBoxes":[{"x":465.809,"h":8.747199999999992,"y":159.339,"p":2,"w":59.4910999999999}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645623","_id":"annotations/60c20cfb7723bebd86645623","_rev":"_cfFmVt6---","wikipediaExternalRef":38576265,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"There are plenty of options on the current data market such as Apache Flume, Apache Sqoop, Apache Kafka, Apache NIFI or Apache Storm.","wikidataId":"Q7620099","type":"software","confidence":0.8719,"software-name":{"wikipediaExternalRef":38576265,"normalizedForm":"Apache Storm","offsetStart":122,"wikidataId":"Q7620099","offsetEnd":135,"lang":"en","confidence":0.8719,"rawForm":"Apache \nStorm","boundingBoxes":[{"x":257.918,"h":8.7472,"y":184.231,"p":4,"w":31.174},{"x":51.0236,"h":8.7472,"y":196.703,"p":4,"w":21.775750000000002}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645624","_id":"annotations/60c20cfb7723bebd86645624","_rev":"_cfFmVuG---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"Specifically, the first and major contribution is in the proposed big data archi- tecture based on the combination of Apache Spark and Apache Hadoop platforms.","wikidataId":"Q29120","references":[{"offsetStart":12112,"normalizedForm":"(Lu et al. 2020","refKey":21,"label":"(Lu et al. 2020","reference_id":{"$oid":"60c20cfb7723bebd866455ec"},"offsetEnd":12127,"boundingBoxes":[{"x":382.172,"h":8.747199999999992,"y":246.536,"p":3,"w":69.11735999999996}]}],"type":"software","confidence":0.9855,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Apache Hadoop","offsetStart":137,"wikidataId":"Q29120","offsetEnd":150,"lang":"en","confidence":0.9855,"rawForm":"Apache Hadoop","boundingBoxes":[{"x":306.139,"h":8.747199999999992,"y":171.811,"p":2,"w":63.02819999999997}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645625","_id":"annotations/60c20cfb7723bebd86645625","_rev":"_cfFmVuS---","wikipediaExternalRef":30248516,"document":{"$oid":"60c20cfb7723bebd866455ea"},"context":"The Apache Hive is ideal for analysing, reading, writing, and managing large datasets that are stored in distributed stor- age and queried by HiveQL (SQL abstraction for integrating SQL-like queries).","wikidataId":"Q4778914","type":"software","confidence":0.2877,"software-name":{"wikipediaExternalRef":30248516,"normalizedForm":"HiveQL","offsetStart":143,"wikidataId":"Q4778914","offsetEnd":149,"lang":"en","confidence":0.2877,"rawForm":"HiveQL","boundingBoxes":[{"x":128.978,"h":8.7472,"y":445.748,"p":6,"w":31.9929}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645626","_id":"annotations/60c20cfb7723bebd86645626","_rev":"_cfFmVue---","document":{"$oid":"60c20cfb7723bebd866455ea"},"type":"software","software-name":{"offsetStart":152,"normalizedForm":"CosmoHub","offsetEnd":160,"rawForm":"CosmoHub","boundingBoxes":[{"x":428.284,"h":8.7472,"y":433.278,"p":3,"w":46.0083}]},"context":"On the other hand, (Zvara et al. 2019) showed the optimization tech- niques of various data streams by means of the devel- oped tracing engine and the CosmoHub web application based on Hadoop is presented in (Tallada et al. 2020)."},
  {"_key":"60c20cfb7723bebd86645627","_id":"annotations/60c20cfb7723bebd86645627","_rev":"_cfFmVuq---","document":{"$oid":"60c20cfb7723bebd866455ea"},"publisher":{"offsetStart":169,"normalizedForm":"Apache","offsetEnd":175,"rawForm":"Apache","boundingBoxes":[{"x":514.371,"h":8.7472,"y":321.25,"p":2,"w":29.9147}]},"context":"The second contribution of the paper is in the Spark appli- cation that enables to process data in memory with Spark engine and at the same time, it takes advantage of Apache Hadoop Yarn cluster.","type":"software","software-name":{"offsetStart":177,"normalizedForm":"Hadoop Yarn","offsetEnd":188,"rawForm":"Hadoop Yarn","boundingBoxes":[{"x":306.139,"h":8.74720000000002,"y":333.665,"p":2,"w":55.24260000000004}]}},
  {"_key":"60c20cfb7723bebd86645628","_id":"annotations/60c20cfb7723bebd86645628","_rev":"_cfFmVu2---","wikipediaExternalRef":5919308,"document":{"$oid":"60c20cfb7723bebd866455ea"},"publisher":{"offsetStart":167,"normalizedForm":"Apache","offsetEnd":173,"rawForm":"Apache","boundingBoxes":[{"x":259.371,"h":8.7472,"y":134.455,"p":6,"w":29.8579}]},"context":"On the other hand, (Zvara et al. 2019) showed the optimization tech- niques of various data streams by means of the devel- oped tracing engine and the CosmoHub web application based on Hadoop is presented in (Tallada et al. 2020).","wikidataId":"Q29120","type":"software","confidence":0.7318,"software-name":{"wikipediaExternalRef":5919308,"normalizedForm":"Hadoop","offsetStart":187,"wikidataId":"Q29120","offsetEnd":193,"lang":"en","confidence":0.7318,"rawForm":"Hadoop","boundingBoxes":[{"x":348.33,"h":8.7472,"y":445.75,"p":3,"w":32.0009}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664562b","_id":"annotations/60c20cfb7723bebd8664562b","_rev":"_cfFmVvC---","wikipediaExternalRef":16161443,"document":{"$oid":"60c20cfb7723bebd86645629"},"context":"Devices consist of iOS and Android operating systems combining various location data sources such as GPS, Wi-Fi, beacons, and network.","wikidataId":"Q48493","type":"software","confidence":0.7161,"software-name":{"wikipediaExternalRef":16161443,"normalizedForm":"iOS","offsetStart":19,"wikidataId":"Q48493","offsetEnd":22,"lang":"en","confidence":0.7161,"rawForm":"iOS","boundingBoxes":[{"x":476.896,"h":8.8468,"y":137.232,"p":4,"w":12.3935}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd8664562c","_id":"annotations/60c20cfb7723bebd8664562c","_rev":"_cfFmVvO---","document":{"$oid":"60c20cfb7723bebd86645629"},"type":"software","software-name":{"offsetStart":28,"normalizedForm":"Android operating","offsetEnd":45,"rawForm":"Android operating","boundingBoxes":[{"x":39.0047,"h":8.846800000000002,"y":147.665,"p":4,"w":64.7643}]},"context":"Devices consist of iOS and Android operating systems combining various location data sources such as GPS, Wi-Fi, beacons, and network."},
  {"_key":"60c20cfb7723bebd8664562d","_id":"annotations/60c20cfb7723bebd8664562d","_rev":"_cfFmVva---","document":{"$oid":"60c20cfb7723bebd86645629"},"type":"software","software-name":{"offsetStart":39,"normalizedForm":"R 'MuMIn'","offsetEnd":48,"rawForm":"R 'MuMIn'","boundingBoxes":[{"x":436.817,"h":8.84680000000003,"y":557.159,"p":13,"w":37.11410000000001}]},"context":"Conditional R 2 is estimated using the R 'MuMIn' package (Nakagawa et al., 2017)."},
  {"_key":"60c20cfb7723bebd8664562e","_id":"annotations/60c20cfb7723bebd8664562e","_rev":"_cfFmVvm---","document":{"$oid":"60c20cfb7723bebd86645629"},"type":"software","software-name":{"offsetStart":54,"normalizedForm":"GAMM","offsetEnd":58,"rawForm":"GAMM","boundingBoxes":[{"x":250.694,"h":8.8468,"y":515.316,"p":13,"w":21.68504}]},"context":"Several benchmark models are tested and compared with GAMM, including the linear fixed model (expressed by Eq. (4)), the linear mixed model with random intercepts (Eq."},
  {"_key":"60c20cfb7723bebd8664562f","_id":"annotations/60c20cfb7723bebd8664562f","_rev":"_cfFmVvy---","wikipediaExternalRef":42164234,"document":{"$oid":"60c20cfb7723bebd86645629"},"context":"Hence, a cloud-based distributed cluster-computing framework (Spark) built on EMR (Amazon Elastic MapReduce) is employed to address the computation problem.","wikidataId":"Q7573619","type":"software","confidence":0.3029,"software-name":{"wikipediaExternalRef":42164234,"normalizedForm":"Spark","offsetStart":63,"wikidataId":"Q7573619","offsetEnd":68,"lang":"en","confidence":0.3029,"rawForm":"Spark","boundingBoxes":[{"x":189.10261428571428,"h":8.8468,"y":335.94,"p":4,"w":18.59307142857143}]},"lang":"en"},
  {"_key":"60c20cfb7723bebd86645630","_id":"annotations/60c20cfb7723bebd86645630","_rev":"_cfFmVw----","document":{"$oid":"60c20cfb7723bebd86645629"},"type":"software","software-name":{"offsetStart":82,"normalizedForm":"SafeGraph","offsetEnd":91,"rawForm":"SafeGraph","boundingBoxes":[{"x":65.5364,"h":8.8468,"y":179.015,"p":5,"w":36.4552}]},"context":"GeoDS Lab provides two mobility-related metrics at the county-level based on the SafeGraph data, namely Mobility (Median of Max Travel Distance) Over Time and Home Dwell Time (Gao et al., 2020)."},
  {"_key":"60c20cfb7723bebd86645631","_id":"annotations/60c20cfb7723bebd86645631","_rev":"_cfFmVwK---","document":{"$oid":"60c20cfb7723bebd86645629"},"type":"software","software-name":{"offsetStart":82,"normalizedForm":"R 'spdep' package","offsetEnd":99,"rawForm":"R 'spdep' package","boundingBoxes":[{"x":223.201,"h":8.846799999999973,"y":399.21,"p":12,"w":60.05367500000003}]},"context":"Moran's I was calculated based on queen neighbors with equal weighting using the R 'spdep' package."},
  {"_key":"60c20cfc7723bebd86645633","_id":"annotations/60c20cfc7723bebd86645633","_rev":"_cfFmVwe---","wikipediaExternalRef":20412,"document":{"$oid":"60c20cfc7723bebd86645632"},"context":"We solve the model using numerical integration in the software Matlab.","wikidataId":"Q169478","type":"software","confidence":0.7276,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"Matlab","offsetStart":63,"wikidataId":"Q169478","offsetEnd":69,"lang":"en","confidence":0.7276,"rawForm":"Matlab","boundingBoxes":[{"x":379.966,"h":10.8,"y":286.454,"p":8,"w":31.726285714285716}]},"lang":"en"},
  {"_key":"60c20d017723bebd86645635","_id":"annotations/60c20d017723bebd86645635","_rev":"_cfFmVwq---","document":{"$oid":"60c20d017723bebd86645634"},"publisher":{"offsetStart":37,"normalizedForm":"Cartesian Technologies, Inc","offsetEnd":64,"rawForm":"Cartesian Technologies, Inc","boundingBoxes":[{"x":100.12261000000001,"h":9.625,"y":290.742,"p":18,"w":119.51395}]},"context":"The complementary AxSysTM software (Cartesian Technologies, Inc., Irvine, CA) is used to instruct movement of pins about the dispense platform and the printing process.","type":"software","software-name":{"offsetStart":18,"normalizedForm":"AxSysTM","offsetEnd":25,"rawForm":"AxSysTM","boundingBoxes":[{"x":368.746,"h":9.625,"y":278.246,"p":18,"w":45.8304}]}},
  {"_key":"60c20d017723bebd86645636","_id":"annotations/60c20d017723bebd86645636","_rev":"_cfFmVw2---","document":{"$oid":"60c20d017723bebd86645634"},"publisher":{"offsetStart":4,"normalizedForm":"SAS Institute","offsetEnd":17,"rawForm":"SAS Institute","boundingBoxes":[{"x":305.357,"h":9.625,"y":423.783,"p":19,"w":66.43699999999995}]},"context":"and SAS Institute's JMP- Genomics, Proteomics, and Microarrays (http://www.jmp.com/).","type":"software","software-name":{"offsetStart":20,"normalizedForm":"JMP- Genomics, Proteomics, and Microarrays","offsetEnd":62,"rawForm":"JMP-\nGenomics, Proteomics, and Microarrays","boundingBoxes":[{"x":389.206,"h":9.625,"y":423.783,"p":19,"w":24.49369999999999},{"x":73.69,"h":9.625,"y":436.29,"p":19,"w":179.041}]},"url":{"offsetStart":64,"normalizedForm":"http://www.jmp.com","offsetEnd":82,"rawForm":"http://www.jmp.com","boundingBoxes":[{"x":260.7439090909091,"h":9.625,"y":436.29,"p":19,"w":84.92236363636363}]}},
  {"_key":"60c20d017723bebd86645637","_id":"annotations/60c20d017723bebd86645637","_rev":"_cfFmVxC---","document":{"$oid":"60c20d017723bebd86645634"},"publisher":{"offsetStart":20,"normalizedForm":"Stanford University","offsetEnd":39,"rawForm":"Stanford University","boundingBoxes":[{"x":73.69,"h":9.625,"y":411.276,"p":19,"w":93.79058333333333}]},"context":"We have been using Stanford University's Significance Analysis of Microarrays (SAM, http://www-stat.stanford.edu/ϳtibs/SAM/)","type":"software","software-name":{"offsetStart":42,"normalizedForm":"Significance Analysis of Microarrays (SAM","offsetEnd":83,"rawForm":"Significance Analysis of Microarrays (SAM","boundingBoxes":[{"x":185.313,"h":9.625,"y":411.276,"p":19,"w":222.17348000000004}]},"url":{"offsetStart":86,"normalizedForm":"http://www-stat.stanford.edu/ϳtibs/SAM","offsetEnd":124,"rawForm":"http://www-stat.stanford.edu/ϳtibs/SAM","boundingBoxes":[{"x":73.69,"h":9.625,"y":423.783,"p":19,"w":186.9201}]}},
  {"_key":"60c20d017723bebd86645638","_id":"annotations/60c20d017723bebd86645638","_rev":"_cfFmVxO---","document":{"$oid":"60c20d017723bebd86645634"},"publisher":{"offsetStart":95,"normalizedForm":"Packard Bioscience","offsetEnd":113,"rawForm":"Packard Bioscience","boundingBoxes":[{"x":134.236,"h":9.625,"y":298.768,"p":19,"w":83.28325000000001}]},"context":"• Fluorescence intensity values for each array spot and its background were cal- culated using Packard Bioscience's QuantArray software analysis packages or the updated ScanArray Express software.","type":"software","software-name":{"offsetStart":116,"normalizedForm":"QuantArray","offsetEnd":126,"rawForm":"QuantArray","boundingBoxes":[{"x":229.105,"h":9.625,"y":298.768,"p":19,"w":52.4711}]}},
  {"_key":"60c20d017723bebd86645639","_id":"annotations/60c20d017723bebd86645639","_rev":"_cfFmVxa---","document":{"$oid":"60c20d017723bebd86645634"},"type":"software","software-name":{"offsetStart":170,"normalizedForm":"ScanArray Express","offsetEnd":187,"rawForm":"ScanArray Express","boundingBoxes":[{"x":127.768,"h":9.625,"y":311.264,"p":19,"w":84.7004}]},"context":"• Fluorescence intensity values for each array spot and its background were cal- culated using Packard Bioscience's QuantArray software analysis packages or the updated ScanArray Express software."},
  {"_key":"60c20d037723bebd8664563b","_id":"annotations/60c20d037723bebd8664563b","_rev":"_cfFmVxm---","wikipediaExternalRef":990677,"document":{"$oid":"60c20d037723bebd8664563a"},"publisher":{"offsetStart":18,"normalizedForm":"SAS","offsetEnd":21,"rawForm":"SAS","boundingBoxes":[{"x":400.4291,"h":8.7372,"y":694.297,"p":3,"w":14.3103}]},"context":"SAS version 6.12 (SAS, Cary, NC, USA) was used to perform the statistical analysis for this study.","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":0,"wikidataId":"Q2003932","offsetEnd":3,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":318.671,"h":8.7372,"y":694.297,"p":3,"w":18.1519}]},"version":{"offsetStart":12,"normalizedForm":"6.12","offsetEnd":16,"rawForm":"6.12","boundingBoxes":[{"x":374.116,"h":8.73720000000003,"y":694.297,"p":3,"w":17.434499999999957}]}},
  {"_key":"60c20d057723bebd8664563d","_id":"annotations/60c20d057723bebd8664563d","_rev":"_cfFmVxy---","wikipediaExternalRef":21411241,"document":{"$oid":"60c20d057723bebd8664563c"},"context":"Analyses were performed using the StatView software.","wikidataId":"Q7602967","type":"software","confidence":0.7763,"software-name":{"wikipediaExternalRef":21411241,"normalizedForm":"StatView","offsetStart":35,"wikidataId":"Q7602967","offsetEnd":43,"lang":"en","confidence":0.7763,"rawForm":"StatView","boundingBoxes":[{"x":54.8399,"h":11.4926,"y":434.655,"p":5,"w":43.3673}]},"lang":"en"},
  {"_key":"60c20d057723bebd8664563e","_id":"annotations/60c20d057723bebd8664563e","_rev":"_cfFmVy----","wikipediaExternalRef":3793613,"document":{"$oid":"60c20d057723bebd8664563c"},"publisher":{"offsetStart":62,"normalizedForm":"FIJI","offsetEnd":66,"rawForm":"FIJI","boundingBoxes":[{"x":205.68066666666664,"h":11.4926,"y":370.416,"p":5,"w":17.090666666666664}]},"context":"Immunofluorescence signals were quantified using the ImageJ (FIJI) software with routine particle analysis procedures, to obtain nuclear masks, divided by the area to obtain cell density per mm 2 .","wikidataId":"Q1659584","type":"software","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":54,"wikidataId":"Q1659584","offsetEnd":60,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":162.056,"h":11.4926,"y":370.416,"p":5,"w":36.1118}]},"lang":"en"},
  {"_key":"60c20d077723bebd86645640","_id":"annotations/60c20d077723bebd86645640","_rev":"_cfFmVyK---","document":{"$oid":"60c20d077723bebd8664563f"},"type":"software","software-name":{"offsetStart":79,"normalizedForm":"MicroCal ORIGIN","offsetEnd":94,"rawForm":"MicroCal ORIGIN","boundingBoxes":[{"x":126.48,"h":9.014600000000002,"y":250.604,"p":4,"w":85.41590000000001}]},"context":"The resulting data were fitted to a single set of identical sites model using MicroCal ORIGIN software supplied with the instrument, and the standard molar enthalpy change for the binding, D b H 0 m ; the binding constant, K b , and the binding stoichiometry, n, which presents the number of bases covered by each complex, were thus obtained."},
  {"_key":"60c20d0f7723bebd86645643","_id":"annotations/60c20d0f7723bebd86645643","_rev":"_cfFmVyW---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"rSWeeP: A R/Bioconductor package deal with SWeeP  sequences representation","type":"software","software-name":{"offsetStart":0,"normalizedForm":"rSWeeP","offsetEnd":6,"rawForm":"rSWeeP","boundingBoxes":[{"x":83.808,"h":12.528,"y":81.2326,"p":1,"w":45.68537142857142}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645644","_id":"annotations/60c20d0f7723bebd86645644","_rev":"_cfFmVye---","document":{"$oid":"60c20d0f7723bebd86645642"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"rSweeP","offsetEnd":6,"rawForm":"rSweeP","boundingBoxes":[{"x":73.6742,"h":9.072,"y":426.455,"p":1,"w":30.7742}]},"context":"rSweeP meets to the growing demand for efficient methods of heuristic representation  in the field of Bioinformatics, on platforms accessible to the entire scientific community."},
  {"_key":"60c20d0f7723bebd86645645","_id":"annotations/60c20d0f7723bebd86645645","_rev":"_cfFmVyq---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"rSWeeP package is  freely available at https:","type":"software","software-name":{"offsetStart":0,"normalizedForm":"rSWeeP","offsetEnd":6,"rawForm":"rSWeeP","boundingBoxes":[{"x":346.03,"h":9.072,"y":541.465,"p":1,"w":32.0242}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645646","_id":"annotations/60c20d0f7723bebd86645646","_rev":"_cfFmVy2---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"rSWeeP input is a multiFASTA file or an \"AAStringSet\" class object,  containing amino acid sequences.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"rSWeeP","offsetEnd":6,"rawForm":"rSWeeP","boundingBoxes":[{"x":137.35,"h":9.1627,"y":580.724,"p":2,"w":32.9415}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645647","_id":"annotations/60c20d0f7723bebd86645647","_rev":"_cfFmVzC---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"rSWeeP consists in two main functions:","type":"software","software-name":{"offsetStart":0,"normalizedForm":"rSWeeP","offsetEnd":6,"rawForm":"rSWeeP","boundingBoxes":[{"x":186.6,"h":9.072,"y":603.895,"p":2,"w":32.9415}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645648","_id":"annotations/60c20d0f7723bebd86645648","_rev":"_cfFmVzO---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"rSWeeP had a processing time linear growth curve, as was already expected,  of near 500 sequences compared per minute.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"rSWeeP","offsetEnd":6,"rawForm":"rSWeeP","boundingBoxes":[{"x":119.35,"h":9.072,"y":528.025,"p":3,"w":32.0242}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645649","_id":"annotations/60c20d0f7723bebd86645649","_rev":"_cfFmVza---","document":{"$oid":"60c20d0f7723bebd86645642"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"rSWeeP package","offsetEnd":14,"rawForm":"rSWeeP package","boundingBoxes":[{"x":222.36,"h":9.072000000000003,"y":152.765,"p":5,"w":66.84989999999993}]},"context":"rSWeeP package presents a solution for the  taxonomic classification of organisms, freely available for the entire scientific community."},
  {"_key":"60c20d0f7723bebd8664564a","_id":"annotations/60c20d0f7723bebd8664564a","_rev":"_cfFmVzm---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"The rSWeeP package is an R implementation of the SWeeP model, designed to handle Big  Data.","type":"software","software-name":{"offsetStart":4,"normalizedForm":"rSWeeP","offsetEnd":10,"rawForm":"rSWeeP","boundingBoxes":[{"x":82.128,"h":9.072,"y":403.415,"p":1,"w":32.0242}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd8664564b","_id":"annotations/60c20d0f7723bebd8664564b","_rev":"_cfFmVzy---","document":{"$oid":"60c20d0f7723bebd86645642"},"type":"software","software-name":{"offsetStart":10,"normalizedForm":"R/Bioconductor","offsetEnd":24,"rawForm":"R/Bioconductor","boundingBoxes":[{"x":154.298,"h":12.528000000000006,"y":81.2326,"p":1,"w":94.6839}]},"context":"rSWeeP: A R/Bioconductor package deal with SWeeP  sequences representation"},
  {"_key":"60c20d0f7723bebd8664564c","_id":"annotations/60c20d0f7723bebd8664564c","_rev":"_cfFmV0----","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"All steps of rSWeeP implementation were performed on an Intel core I5 320Gz with 12  GB of RAM.","type":"software","software-name":{"offsetStart":13,"normalizedForm":"rSWeeP","offsetEnd":19,"rawForm":"rSWeeP","boundingBoxes":[{"x":112.52,"h":9.072,"y":534.985,"p":2,"w":32.9415}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd8664564d","_id":"annotations/60c20d0f7723bebd8664564d","_rev":"_cfFmV0K---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"Here, we present rSWeeP, an implementation of SWeeP model using  R/Bioconductor programming language.","type":"software","software-name":{"offsetStart":17,"normalizedForm":"rSWeeP","offsetEnd":23,"rawForm":"rSWeeP","boundingBoxes":[{"x":192.58,"h":9.072,"y":271.375,"p":2,"w":28.503428571428568}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd8664564e","_id":"annotations/60c20d0f7723bebd8664564e","_rev":"_cfFmV0a---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"A tutorial for running rSWeeP and the trees are available at  https://github.com/DanrleyRF/Suplementar.","type":"software","software-name":{"offsetStart":23,"normalizedForm":"rSWeeP","offsetEnd":29,"rawForm":"rSWeeP","boundingBoxes":[{"x":221.294,"h":9.072,"y":166.445,"p":3,"w":33.0505}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd8664564f","_id":"annotations/60c20d0f7723bebd8664564f","_rev":"_cfFmV0m---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"Our results showed that rSWeeP maintains the  effectiveness of SWeeP model in comparison of large numbers of sequences.","type":"software","software-name":{"offsetStart":24,"normalizedForm":"rSWeeP","offsetEnd":30,"rawForm":"rSWeeP","boundingBoxes":[{"x":286.94,"h":9.072,"y":340.275,"p":2,"w":32.0242}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645650","_id":"annotations/60c20d0f7723bebd86645650","_rev":"_cfFmV0y---","document":{"$oid":"60c20d0f7723bebd86645642"},"type":"software","software-name":{"offsetStart":30,"normalizedForm":"SWeeP","offsetEnd":35,"rawForm":"SWeeP","boundingBoxes":[{"x":191.86,"h":9.072,"y":106.685,"p":5,"w":28.8993}]},"context":"We show the implementation of SWeeP model in R language, rSWeeP package, is equally  accurate."},
  {"_key":"60c20d0f7723bebd86645651","_id":"annotations/60c20d0f7723bebd86645651","_rev":"_cfFmV1----","wikipediaExternalRef":20412,"document":{"$oid":"60c20d0f7723bebd86645642"},"context":"SWeeP is a model implemented in MatLab, which allows the representation of  biological information through the projection of DNA sequences in vectors with reduced  dimensionality [5] .","wikidataId":"Q169478","type":"software","confidence":0.7769,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MatLab","offsetStart":32,"wikidataId":"Q169478","offsetEnd":38,"lang":"en","confidence":0.7769,"rawForm":"MatLab","boundingBoxes":[{"x":235.17,"h":9.072,"y":224.545,"p":2,"w":29.459828571428567}]},"lang":"en"},
  {"_key":"60c20d0f7723bebd86645652","_id":"annotations/60c20d0f7723bebd86645652","_rev":"_cfFmV1K---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"To explore the potential of the rSWeeP package,  we created SWeeP vectors from the protein annotations of all the complete viral genomes  available at NCBI, in total, 31,386 proteomes sequences (31k).","type":"software","software-name":{"offsetStart":32,"normalizedForm":"rSWeeP","offsetEnd":38,"rawForm":"rSWeeP","boundingBoxes":[{"x":343.325,"h":9.072,"y":296.575,"p":3,"w":32.6996}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645653","_id":"annotations/60c20d0f7723bebd86645653","_rev":"_cfFmV1W---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"We  explored the implementation of rSWeeP using a dataset containing 31,386 viral proteomes,  performing phylogenetic and principal component analysis.","type":"software","software-name":{"offsetStart":36,"normalizedForm":"rSWeeP","offsetEnd":42,"rawForm":"rSWeeP","boundingBoxes":[{"x":178.18,"h":9.072,"y":472.325,"p":1,"w":32.0242}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645654","_id":"annotations/60c20d0f7723bebd86645654","_rev":"_cfFmV1i---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"Thereby, the functions presented by rSWeeP  package can give computational power to its users to manage biological big data variables in  a practical time.","type":"software","software-name":{"offsetStart":36,"normalizedForm":"rSWeeP","offsetEnd":44,"rawForm":"rSWeeP","boundingBoxes":[{"x":376.27,"h":9.072,"y":551.065,"p":3,"w":32.0242}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645655","_id":"annotations/60c20d0f7723bebd86645655","_rev":"_cfFmV1u---","document":{"$oid":"60c20d0f7723bebd86645642"},"type":"software","software-name":{"offsetStart":48,"normalizedForm":"SWeeP","offsetEnd":53,"rawForm":"SWeeP","boundingBoxes":[{"x":261.175,"h":9.936,"y":358.819,"p":7,"w":32.292}]},"context":"Phylogenetic tree generated using 4k data, with SWeeP default parameters: The enlarged branch containing the coronavirus specimens(red)."},
  {"_key":"60c20d0f7723bebd86645656","_id":"annotations/60c20d0f7723bebd86645656","_rev":"_cfFmV16---","document":{"$oid":"60c20d0f7723bebd86645642"},"type":"software","software-name":{"offsetStart":57,"normalizedForm":"rSWeeP package","offsetEnd":71,"rawForm":"rSWeeP package","boundingBoxes":[{"x":308.57,"h":9.072000000000003,"y":106.685,"p":5,"w":64.81819999999999}]},"context":"We show the implementation of SWeeP model in R language, rSWeeP package, is equally  accurate."},
  {"_key":"60c20d0f7723bebd86645657","_id":"annotations/60c20d0f7723bebd86645657","_rev":"_cfFmV2G---","wikipediaExternalRef":2383871,"document":{"$oid":"60c20d0f7723bebd86645642"},"context":"Here, we present rSWeeP, an implementation of SWeeP model using  R/Bioconductor programming language.","wikidataId":"Q2888953","type":"software","confidence":0.8008,"software-name":{"wikipediaExternalRef":2383871,"normalizedForm":"Bioconductor","offsetStart":68,"wikidataId":"Q2888953","offsetEnd":80,"lang":"en","confidence":0.8008,"rawForm":"Bioconductor","boundingBoxes":[{"x":58.85087142857143,"h":9.072,"y":294.175,"p":2,"w":54.881228571428565}]},"lang":"en"},
  {"_key":"60c20d0f7723bebd86645658","_id":"annotations/60c20d0f7723bebd86645658","_rev":"_cfFmV2S---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"The performance test, phylogenetics and PCA analyzes demonstrate the efficiency  of rSWeeP for analysis of viral proteomes.","type":"software","software-name":{"offsetStart":85,"normalizedForm":"rSWeeP","offsetEnd":91,"rawForm":"rSWeeP","boundingBoxes":[{"x":60.744,"h":9.072,"y":152.765,"p":5,"w":32.0242}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d0f7723bebd86645659","_id":"annotations/60c20d0f7723bebd86645659","_rev":"_cfFmV2e---","document":{"$oid":"60c20d0f7723bebd86645642"},"context":"As a case study we analyze the  viral strains closest to the SARS-CoV, responsible for the current pandemic of COVID-19,  confirming that rSWeeP can accurately classify organisms taxonomically.","type":"software","software-name":{"offsetStart":140,"normalizedForm":"rSWeeP","offsetEnd":146,"rawForm":"rSWeeP","boundingBoxes":[{"x":114.31,"h":9.072,"y":541.465,"p":1,"w":32.0242}]},"url":{"offsetStart":40,"normalizedForm":"https","offsetEnd":45,"rawForm":"https","boundingBoxes":[{"x":124.013,"h":9.072,"y":564.505,"p":1,"w":20.33044117647059}]}},
  {"_key":"60c20d157723bebd8664565b","_id":"annotations/60c20d157723bebd8664565b","_rev":"_cfFmV2q---","wikipediaExternalRef":20057286,"document":{"$oid":"60c20d157723bebd8664565a"},"publisher":{"offsetStart":87,"normalizedForm":"Molecular Biology Insights, Inc","offsetEnd":118,"rawForm":"Molecular Biology Insights, Inc","boundingBoxes":[{"x":409.15695,"h":9.205499999999972,"y":271.218,"p":2,"w":119.82254999999992}]},"context":"under the accession number HQ916317.1.The GSPs were designed using OLIGO 7 software (Molecular Biology Insights, Inc., Colorado Springs, CO, U.S.A.).","wikidataId":"Q7072663","type":"software","lang":"en","confidence":0.5102,"software-name":{"wikipediaExternalRef":20057286,"normalizedForm":"OLIGO","offsetStart":69,"wikidataId":"Q7072663","offsetEnd":74,"lang":"en","confidence":0.5102,"rawForm":"OLIGO","boundingBoxes":[{"x":329.527,"h":9.2055,"y":271.218,"p":2,"w":29.621}]},"version":{"offsetStart":75,"normalizedForm":"7","offsetEnd":76,"rawForm":"7","boundingBoxes":[{"x":361.874,"h":9.2055,"y":271.218,"p":2,"w":4.75}]}},
  {"_key":"60c20d157723bebd8664565c","_id":"annotations/60c20d157723bebd8664565c","_rev":"_cfFmV22---","document":{"$oid":"60c20d157723bebd8664565a"},"type":"software","software-name":{"offsetStart":72,"normalizedForm":"SeqMan","offsetEnd":78,"rawForm":"SeqMan","boundingBoxes":[{"x":468.55,"h":9.2055,"y":678.255,"p":2,"w":31.7585}]},"context":"Editing and assembly of nucleo- tide sequences were performed using the SeqMan program included in the Lasergene 7 Genomics Suite (DNAstar, Inc., Madison, WI, U.S.A.)."},
  {"_key":"60c20d157723bebd8664565d","_id":"annotations/60c20d157723bebd8664565d","_rev":"_cfFmV3C---","document":{"$oid":"60c20d157723bebd8664565a"},"publisher":{"offsetStart":132,"normalizedForm":"DNAstar, Inc","offsetEnd":144,"rawForm":"DNAstar, Inc","boundingBoxes":[{"x":481.2156111111111,"h":9.205500000000029,"y":689.256,"p":2,"w":47.772888888888815}]},"context":"Editing and assembly of nucleo- tide sequences were performed using the SeqMan program included in the Lasergene 7 Genomics Suite (DNAstar, Inc., Madison, WI, U.S.A.).","type":"software","software-name":{"offsetStart":104,"normalizedForm":"Lasergene 7 Genomics Suite","offsetEnd":130,"rawForm":"Lasergene 7 Genomics Suite","boundingBoxes":[{"x":365.209,"h":9.205500000000029,"y":689.256,"p":2,"w":109.21199999999999}]}},
  {"_key":"60c20d157723bebd8664565e","_id":"annotations/60c20d157723bebd8664565e","_rev":"_cfFmV3O---","wikipediaExternalRef":363695,"document":{"$oid":"60c20d157723bebd8664565a"},"context":"Some of the RT-PCR-positive samples were sequenced and primarily analyzed by comparison of nucleotide sequences using the online Basic Local Alignment Search Tool (http://blast.ncbi. nlm.nih.gov/Blast.cgi) to confirm the detection of astrovi- ruses.","wikidataId":"Q286820","type":"software","confidence":0.4452,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"Basic Local Alignment Search Tool","offsetStart":132,"wikidataId":"Q286820","offsetEnd":165,"lang":"en","confidence":0.4452,"rawForm":"Basic Local Alignment Search Tool","boundingBoxes":[{"x":85.7491,"h":9.205500000000029,"y":711.225,"p":2,"w":135.7734}]},"url":{"offsetStart":167,"normalizedForm":"http://blast.ncbi. nlm.nih.gov/Blast.cgi","offsetEnd":208,"rawForm":"http://blast.ncbi. \nnlm.nih.gov/Blast.cgi","boundingBoxes":[{"x":227.333,"h":9.205500000000029,"y":711.225,"p":2,"w":61.83000000000001},{"x":59.5291,"h":9.205500000000029,"y":722.226,"p":2,"w":81.74965909090909}]},"lang":"en"},
  {"_key":"60c20d157723bebd8664565f","_id":"annotations/60c20d157723bebd8664565f","_rev":"_cfFmV3a---","document":{"$oid":"60c20d157723bebd8664565a"},"context":"Pair distances of nucleotide sequences between bovine and water buffalo astroviruses, as well as the ORF1b/ORF2 junction, were analyzed using DNAstar software (Lasergene 7; MegAlign Program with the ClustalW sequence alignment algorithm).","type":"software","software-name":{"offsetStart":176,"normalizedForm":"MegAlign","offsetEnd":184,"rawForm":"MegAlign","boundingBoxes":[{"x":192.233,"h":9.2055,"y":557.222,"p":3,"w":39.1875}]},"version":{"offsetStart":173,"normalizedForm":"7","offsetEnd":174,"rawForm":"7","boundingBoxes":[{"x":180.861,"h":9.2055,"y":557.222,"p":3,"w":3.705}]}},
  {"_key":"60c20d157723bebd86645660","_id":"annotations/60c20d157723bebd86645660","_rev":"_cfFmV3i---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20d157723bebd8664565a"},"context":"Pair distances of nucleotide sequences between bovine and water buffalo astroviruses, as well as the ORF1b/ORF2 junction, were analyzed using DNAstar software (Lasergene 7; MegAlign Program with the ClustalW sequence alignment algorithm).","wikidataId":"Q866737","type":"software","confidence":0.7823,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"ClustalW","offsetStart":203,"wikidataId":"Q866737","offsetEnd":211,"lang":"en","confidence":0.7823,"rawForm":"ClustalW","boundingBoxes":[{"x":73.5876,"h":9.2055,"y":568.223,"p":3,"w":36.024}]},"lang":"en"},
  {"_key":"60c20d157723bebd86645661","_id":"annotations/60c20d157723bebd86645661","_rev":"_cfFmV3u---","document":{"$oid":"60c20d157723bebd8664565a"},"context":"Phylogenetic and genome analysis: Phylogenetic trees were constructed based on the nucleotide sequences of both partial and full-length ORF2 sequences using the Bootstrap Test Phylogeny algorithm with the neighbor-joining method included in the MEGA 4.1 software package (http://www. megasoftware.net/).","type":"software","software-name":{"offsetStart":249,"normalizedForm":"MEGA","offsetEnd":253,"rawForm":"MEGA","boundingBoxes":[{"x":122.493,"h":9.2055,"y":502.217,"p":3,"w":28.025}]},"url":{"offsetStart":276,"normalizedForm":"http://www. megasoftware.net","offsetEnd":305,"rawForm":"http://www. \nmegasoftware.net","boundingBoxes":[{"x":244.76433333333333,"h":9.205500000000029,"y":502.217,"p":3,"w":44.37766666666667},{"x":59.5276,"h":9.205500000000029,"y":513.218,"p":3,"w":63.82399999999999}]},"version":{"offsetStart":254,"normalizedForm":"4.1","offsetEnd":257,"rawForm":"4.1","boundingBoxes":[{"x":153.682,"h":9.205500000000029,"y":502.217,"p":3,"w":11.913000000000011}]}},
  {"_key":"60c20d177723bebd86645663","_id":"annotations/60c20d177723bebd86645663","_rev":"_cfFmV36---","wikipediaExternalRef":179088,"document":{"$oid":"60c20d177723bebd86645662"},"context":"Statistical analyses were performed using SPSS 20 software.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":42,"wikidataId":"Q181596","offsetEnd":46,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":215.149,"h":7.1839,"y":712.457,"p":2,"w":17.9702}]},"version":{"offsetStart":47,"normalizedForm":"20","offsetEnd":49,"rawForm":"20","boundingBoxes":[{"x":239.414,"h":7.1839,"y":712.457,"p":2,"w":9.3455}]}},
  {"_key":"60c20d197723bebd86645665","_id":"annotations/60c20d197723bebd86645665","_rev":"_cfFmV4G---","document":{"$oid":"60c20d197723bebd86645664"},"type":"software","software-name":{"offsetStart":7,"normalizedForm":"Scholar","offsetEnd":14,"rawForm":"Scholar","boundingBoxes":[{"x":183.34,"h":7.1652,"y":213.097,"p":3,"w":26.2777}]},"context":"Google Scholar was searched for the following keywords and their combinations: 1) SME(s), small firm(s), 2) crisis, hard economic times, disaster(s)."},
  {"_key":"60c20d1b7723bebd86645667","_id":"annotations/60c20d1b7723bebd86645667","_rev":"_cfFmV4S---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20d1b7723bebd86645666"},"context":"Data were analyzed using Stata version 14.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":25,"wikidataId":"Q1204300","offsetEnd":30,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":413.627,"h":8.9767,"y":376.698,"p":5,"w":20.523}]},"version":{"offsetStart":39,"normalizedForm":"14","offsetEnd":41,"rawForm":"14","boundingBoxes":[{"x":470.1,"h":8.9767,"y":376.698,"p":5,"w":8.092133333333333}]}},
  {"_key":"60c20d217723bebd86645669","_id":"annotations/60c20d217723bebd86645669","_rev":"_cfFmV4e---","wikipediaExternalRef":179088,"document":{"$oid":"60c20d217723bebd86645668"},"publisher":{"offsetStart":131,"normalizedForm":"IBM","offsetEnd":134,"rawForm":"IBM","boundingBoxes":[{"x":445.86,"h":9,"y":607.57,"p":3,"w":16.0425}]},"context":"Statistical significance was accepted when p < 0.05; all analyses were performed using a statistical software package (SPSS v.19, IBM, Somers, NY).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":120,"wikidataId":"Q181596","offsetEnd":124,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":401.054,"h":9,"y":607.57,"p":3,"w":20.456000000000003}]},"version":{"offsetStart":127,"normalizedForm":"19","offsetEnd":129,"rawForm":"19","boundingBoxes":[{"x":431.75,"h":9,"y":607.57,"p":3,"w":7.740000000000001}]}},
  {"_key":"60c20d277723bebd8664566f","_id":"annotations/60c20d277723bebd8664566f","_rev":"_cfFmV4m---","wikipediaExternalRef":34913748,"document":{"$oid":"60c20d277723bebd8664566a"},"context":"The SWISS-MODEL Repository (http://swissmodel.expasy. org/repository) [12] is also a database of annotated compara- tive protein 3D structure models, which have been generated using the fully automated homology-modeling pipeline SWISS-MODEL.","wikidataId":"Q7658835","references":[{"offsetStart":11119,"normalizedForm":"[12]","refKey":11,"label":"[12]","reference_id":{"$oid":"60c20d277723bebd8664566b"},"offsetEnd":11124,"boundingBoxes":[{"x":122.964,"h":8.549999999999955,"y":601.696,"p":4,"w":16.0128}]}],"type":"software","confidence":0.7562,"software-name":{"wikipediaExternalRef":34913748,"normalizedForm":"SWISS-MODEL","offsetStart":4,"wikidataId":"Q7658835","offsetEnd":15,"lang":"en","confidence":0.7562,"rawForm":"SWISS-MODEL","boundingBoxes":[{"x":87.4776,"h":8.549999999999955,"y":588.697,"p":4,"w":61.515000000000015}]},"url":{"offsetStart":28,"normalizedForm":"http://swissmodel.expasy. org/repository","offsetEnd":69,"rawForm":"http://swissmodel.expasy. \norg/repository","boundingBoxes":[{"x":201.20196153846155,"h":8.549999999999955,"y":588.697,"p":4,"w":104.29903846153843},{"x":59.5281,"h":8.549999999999955,"y":601.696,"p":4,"w":57.151079999999986}]},"lang":"en"},
  {"_key":"60c20d277723bebd86645670","_id":"annotations/60c20d277723bebd86645670","_rev":"_cfFmV4y---","wikipediaExternalRef":31070840,"document":{"$oid":"60c20d277723bebd8664566a"},"context":"[8] and PDBsum (http://www.biochem.ucl.ac.uk/bsm/pdbsum) [9].","wikidataId":"Q7118755","type":"software","confidence":0.5177,"software-name":{"wikipediaExternalRef":31070840,"normalizedForm":"PDBsum","offsetStart":9,"wikidataId":"Q7118755","offsetEnd":15,"lang":"en","confidence":0.5177,"rawForm":"PDBsum","boundingBoxes":[{"x":59.5276,"h":8.55,"y":198.696,"p":4,"w":35.473}]},"url":{"offsetStart":17,"normalizedForm":"http://www.biochem.ucl.ac.uk/bsm/pdbsum","offsetEnd":56,"rawForm":"http://www.biochem.ucl.ac.uk/bsm/pdbsum","boundingBoxes":[{"x":102.02581951219511,"h":8.550000000000011,"y":198.696,"p":4,"w":182.72356097560967}]},"lang":"en"},
  {"_key":"60c20d277723bebd86645671","_id":"annotations/60c20d277723bebd86645671","_rev":"_cfFmV5----","wikipediaExternalRef":363695,"document":{"$oid":"60c20d277723bebd8664566a"},"context":"The program PSI-BLAST was used to as- sign protein folds to all 1,182,126 unique sequence entries in Swiss-Prot-TrEMBL.","wikidataId":"Q286820","type":"software","confidence":0.9698,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"PSI-BLAST","offsetStart":12,"wikidataId":"Q286820","offsetEnd":21,"lang":"en","confidence":0.9698,"rawForm":"PSI-BLAST","boundingBoxes":[{"x":194.431,"h":8.550000000000011,"y":406.689,"p":4,"w":43.7526}]},"lang":"en"},
  {"_key":"60c20d277723bebd86645672","_id":"annotations/60c20d277723bebd86645672","_rev":"_cfFmV5K---","wikipediaExternalRef":31481256,"document":{"$oid":"60c20d277723bebd8664566a"},"context":"For exam- ple, the queryable database ModBase (http://alto.compbio. ucsf.edu/modbase-cgi/index.cgi) provides access to an enormous number of annotated comparative protein struc- ture models [10].","wikidataId":"Q6887948","type":"software","confidence":0.8125,"software-name":{"wikipediaExternalRef":31481256,"normalizedForm":"ModBase","offsetStart":38,"wikidataId":"Q6887948","offsetEnd":45,"lang":"en","confidence":0.8125,"rawForm":"ModBase","boundingBoxes":[{"x":176.147,"h":8.55,"y":367.69,"p":4,"w":37.6771}]},"url":{"offsetStart":47,"normalizedForm":"http://alto.compbio. ucsf.edu/modbase-cgi/index.cgi","offsetEnd":99,"rawForm":"http://alto.compbio. \nucsf.edu/modbase-cgi/index.cgi","boundingBoxes":[{"x":220.71821904761904,"h":8.550000000000011,"y":367.69,"p":4,"w":84.80438095238097},{"x":59.5303,"h":8.550000000000011,"y":380.69,"p":4,"w":136.9587096774194}]},"lang":"en"},
  {"_key":"60c20d277723bebd86645673","_id":"annotations/60c20d277723bebd86645673","_rev":"_cfFmV5W---","document":{"$oid":"60c20d277723bebd8664566a"},"context":"have created a database system called Target Informatics Platform™ [13] that currently includes homology models  for 55,000 proteins.","references":[{"offsetStart":11627,"normalizedForm":"[13]","refKey":12,"label":"[13]","reference_id":{"$oid":"60c20d277723bebd8664566c"},"offsetEnd":11632,"boundingBoxes":[{"x":108.239,"h":8.549999999999955,"y":718.693,"p":4,"w":16.571799999999996}]}],"type":"software","software-name":{"offsetStart":38,"normalizedForm":"Target Informatics Platform™","offsetEnd":67,"rawForm":"Target Informatics \nPlatform™","boundingBoxes":[{"x":226.003,"h":8.549999999999955,"y":705.693,"p":4,"w":79.50110000000001},{"x":59.529,"h":8.55,"y":718.693,"p":4,"w":45.7895}]}},
  {"_key":"60c20d277723bebd86645674","_id":"annotations/60c20d277723bebd86645674","_rev":"_cfFmV5i---","document":{"$oid":"60c20d277723bebd8664566a"},"context":"Information on binding sites and ligands can be retrieved from this database using LigBase [8].","references":[{"offsetStart":10832,"normalizedForm":"[8]","refKey":7,"label":"[8]","reference_id":{"$oid":"60c20d277723bebd8664566d"},"offsetEnd":10835,"boundingBoxes":[{"x":161.517,"h":8.549999999999955,"y":536.698,"p":4,"w":10.736924999999985}]}],"type":"software","software-name":{"offsetStart":85,"normalizedForm":"LigBase","offsetEnd":92,"rawForm":"LigBase","boundingBoxes":[{"x":126.302,"h":8.55,"y":536.698,"p":4,"w":32.1853}]},"url":{"offsetStart":275,"normalizedForm":"http://alto.compbio.ucsf.edu/ligbase","offsetEnd":311,"rawForm":"http://alto.compbio.ucsf.edu/ligbase","boundingBoxes":[{"x":115.04947368421053,"h":8.550000000000011,"y":185.696,"p":4,"w":152.98105263157896}]}},
  {"_key":"60c20d277723bebd86645675","_id":"annotations/60c20d277723bebd86645675","_rev":"_cfFmV5u---","document":{"$oid":"60c20d277723bebd8664566a"},"context":"The program PSI-BLAST was used to as- sign protein folds to all 1,182,126 unique sequence entries in Swiss-Prot-TrEMBL.","type":"software","software-name":{"offsetStart":102,"normalizedForm":"Swiss-Prot-TrEMBL","offsetEnd":119,"rawForm":"Swiss-Prot-TrEMBL","boundingBoxes":[{"x":71.3992,"h":8.550000000000011,"y":432.688,"p":4,"w":80.09833333333334}]},"url":{"offsetStart":200,"normalizedForm":"http://www.expasy.org/ sprot","offsetEnd":229,"rawForm":"http://www.expasy.org/ \nsprot","boundingBoxes":[{"x":205.9745652173913,"h":8.549999999999983,"y":250.694,"p":4,"w":99.54043478260863},{"x":59.5303,"h":8.55,"y":263.694,"p":4,"w":20.5275}]}},
  {"_key":"60c20d277723bebd86645676","_id":"annotations/60c20d277723bebd86645676","_rev":"_cfFmV56---","document":{"$oid":"60c20d277723bebd8664566a"},"type":"software","software-name":{"offsetStart":114,"normalizedForm":"Swiss","offsetEnd":119,"rawForm":"Swiss","boundingBoxes":[{"x":96.8248,"h":8.55,"y":666.694,"p":4,"w":22.414764705882355}]},"context":"As of August 2003, this database contained models for 282,096 different protein sequence entries (26%) from the Swiss-Prot-TrEMBL databases (1,073,566 sequences), with an average model size of ~200 amino acids."},
  {"_key":"60c20d277723bebd86645677","_id":"annotations/60c20d277723bebd86645677","_rev":"_cfFmV6G---","document":{"$oid":"60c20d277723bebd8664566a"},"type":"software","software-name":{"offsetStart":120,"normalizedForm":"Prot-TrEMBL","offsetEnd":131,"rawForm":"Prot-TrEMBL","boundingBoxes":[{"x":123.72251764705882,"h":8.549999999999955,"y":666.694,"p":4,"w":49.3124823529412}]},"context":"As of August 2003, this database contained models for 282,096 different protein sequence entries (26%) from the Swiss-Prot-TrEMBL databases (1,073,566 sequences), with an average model size of ~200 amino acids."},
  {"_key":"60c20d277723bebd86645678","_id":"annotations/60c20d277723bebd86645678","_rev":"_cfFmV6S---","wikipediaExternalRef":8011876,"document":{"$oid":"60c20d277723bebd8664566a"},"context":"For 56% of these sequences, com- parative models with an average model size of 235 amino acids could be built using the program MODELLER [11].","wikidataId":"Q3859815","references":[{"offsetStart":10513,"normalizedForm":"[11]","refKey":10,"label":"[11]","reference_id":{"$oid":"60c20d277723bebd8664566e"},"offsetEnd":10517,"boundingBoxes":[{"x":285.767,"h":8.550000000000011,"y":458.688,"p":4,"w":15.782560000000046}]}],"type":"software","confidence":0.3285,"software-name":{"wikipediaExternalRef":8011876,"normalizedForm":"MODELLER","offsetStart":129,"wikidataId":"Q3859815","offsetEnd":137,"lang":"en","confidence":0.3285,"rawForm":"MODELLER","boundingBoxes":[{"x":231.833,"h":8.55,"y":458.688,"p":4,"w":50.8734}]},"lang":"en"},
  {"_key":"60c20d277723bebd86645679","_id":"annotations/60c20d277723bebd86645679","_rev":"_cfFmV6e---","document":{"$oid":"60c20d277723bebd8664566a"},"context":"Although the experimental structure database is grow- ing rapidly, there is still a substantial gap between the number of known annotated sequences [1,182,126 unique sequences in Swiss-Prot-TrEMBL (http://www.expasy.org/ sprot) as of 29 August 2003] and known protein 3D struc- tures (23,000).","type":"software","software-name":{"offsetStart":181,"normalizedForm":"Swiss-Prot-TrEMBL","offsetEnd":198,"rawForm":"Swiss-Prot-TrEMBL","boundingBoxes":[{"x":117.13,"h":8.549999999999983,"y":250.694,"p":4,"w":81.36430000000001}]},"url":{"offsetStart":200,"normalizedForm":"http://www.expasy.org/ sprot","offsetEnd":229,"rawForm":"http://www.expasy.org/ \nsprot","boundingBoxes":[{"x":205.9745652173913,"h":8.549999999999983,"y":250.694,"p":4,"w":99.54043478260863},{"x":59.5303,"h":8.55,"y":263.694,"p":4,"w":20.5275}]}},
  {"_key":"60c20d277723bebd8664567a","_id":"annotations/60c20d277723bebd8664567a","_rev":"_cfFmV6q---","document":{"$oid":"60c20d277723bebd8664566a"},"context":"The PDB database encom- passes experimental information on an extensive array of ligands (small organic molecules and ions) bound to more than 50,000 different binding sites that can be analyzed using programs including ReliBase (http://relibase.ebi.ac.uk) [7], LigBase (http://alto.compbio.ucsf.edu/ligbase)","type":"software","software-name":{"offsetStart":223,"normalizedForm":"ReliBase","offsetEnd":231,"rawForm":"ReliBase","boundingBoxes":[{"x":167.371,"h":8.55,"y":172.696,"p":4,"w":33.2352}]},"url":{"offsetStart":233,"normalizedForm":"http://relibase.ebi.ac.uk","offsetEnd":258,"rawForm":"http://relibase.ebi.ac.uk","boundingBoxes":[{"x":206.8871851851852,"h":8.550000000000011,"y":172.696,"p":4,"w":94.82962962962964}]}},
  {"_key":"60c20d277723bebd8664567b","_id":"annotations/60c20d277723bebd8664567b","_rev":"_cfFmV62---","wikipediaExternalRef":34913748,"document":{"$oid":"60c20d277723bebd8664566a"},"context":"The SWISS-MODEL Repository (http://swissmodel.expasy. org/repository) [12] is also a database of annotated compara- tive protein 3D structure models, which have been generated using the fully automated homology-modeling pipeline SWISS-MODEL.","wikidataId":"Q7658835","references":[{"offsetStart":11119,"normalizedForm":"[12]","refKey":11,"label":"[12]","reference_id":{"$oid":"60c20d277723bebd8664566b"},"offsetEnd":11124,"boundingBoxes":[{"x":122.964,"h":8.549999999999955,"y":601.696,"p":4,"w":16.0128}]}],"type":"software","confidence":0.7562,"software-name":{"wikipediaExternalRef":34913748,"normalizedForm":"SWISS-MODEL","offsetStart":232,"wikidataId":"Q7658835","offsetEnd":243,"lang":"en","confidence":0.7562,"rawForm":"SWISS-MODEL","boundingBoxes":[{"x":59.5281,"h":8.549999999999955,"y":640.695,"p":4,"w":59.703508333333325}]},"url":{"offsetStart":28,"normalizedForm":"http://swissmodel.expasy. org/repository","offsetEnd":69,"rawForm":"http://swissmodel.expasy. \norg/repository","boundingBoxes":[{"x":201.20196153846155,"h":8.549999999999955,"y":588.697,"p":4,"w":104.29903846153843},{"x":59.5281,"h":8.549999999999955,"y":601.696,"p":4,"w":57.151079999999986}]},"lang":"en"},
  {"_key":"60c20d277723bebd8664567c","_id":"annotations/60c20d277723bebd8664567c","_rev":"_cfFmV7C---","document":{"$oid":"60c20d277723bebd8664566a"},"context":"The PDB database encom- passes experimental information on an extensive array of ligands (small organic molecules and ions) bound to more than 50,000 different binding sites that can be analyzed using programs including ReliBase (http://relibase.ebi.ac.uk) [7], LigBase (http://alto.compbio.ucsf.edu/ligbase)","references":[{"offsetStart":10832,"normalizedForm":"[8]","refKey":7,"label":"[8]","reference_id":{"$oid":"60c20d277723bebd8664566d"},"offsetEnd":10835,"boundingBoxes":[{"x":161.517,"h":8.549999999999955,"y":536.698,"p":4,"w":10.736924999999985}]}],"type":"software","software-name":{"offsetStart":266,"normalizedForm":"LigBase","offsetEnd":273,"rawForm":"LigBase","boundingBoxes":[{"x":76.404,"h":8.55,"y":185.696,"p":4,"w":31.4833}]},"url":{"offsetStart":275,"normalizedForm":"http://alto.compbio.ucsf.edu/ligbase","offsetEnd":311,"rawForm":"http://alto.compbio.ucsf.edu/ligbase","boundingBoxes":[{"x":115.04947368421053,"h":8.550000000000011,"y":185.696,"p":4,"w":152.98105263157896}]}},
  {"_key":"60c20d307723bebd8664567e","_id":"annotations/60c20d307723bebd8664567e","_rev":"_cfFmV7O---","document":{"$oid":"60c20d307723bebd8664567d"},"publisher":{"offsetStart":68,"normalizedForm":"StataCorp","offsetEnd":77,"rawForm":"StataCorp","boundingBoxes":[{"x":139.56398181818182,"h":10.536,"y":406.776,"p":4,"w":44.99083636363636}]},"context":"All analyses were conducted using Stata/SE for Mac,  version 16.1 (StataCorp, College Station, TX).","type":"software","software-name":{"offsetStart":34,"normalizedForm":"Stata/SE","offsetEnd":42,"rawForm":"Stata/SE","boundingBoxes":[{"x":436.471,"h":10.536000000000001,"y":386.136,"p":4,"w":41.33279999999996}]},"version":{"offsetStart":62,"normalizedForm":"16.1","offsetEnd":66,"rawForm":"16.1","boundingBoxes":[{"x":110.565,"h":10.536000000000001,"y":406.776,"p":4,"w":21}]}},
  {"_key":"60c20d3a7723bebd86645682","_id":"annotations/60c20d3a7723bebd86645682","_rev":"_cfFmV7a---","document":{"$oid":"60c20d3a7723bebd8664567f"},"context":"All analysis was conducted with R package dplyr (23) and graphically plotted with ggplot2  (24).","references":[{"offsetStart":40491,"normalizedForm":"23","refKey":23,"label":"(23)","reference_id":{"$oid":"60c20d3a7723bebd86645680"},"offsetEnd":40496,"boundingBoxes":[{"x":347.393,"h":10.21459999999999,"y":242.31,"p":17,"w":19.672300000000007}]}],"type":"software","software-name":{"offsetStart":32,"normalizedForm":"R package dplyr","offsetEnd":47,"rawForm":"R package dplyr","boundingBoxes":[{"x":265.073,"h":10.21459999999999,"y":242.31,"p":17,"w":79.26800000000003}]}},
  {"_key":"60c20d3a7723bebd86645683","_id":"annotations/60c20d3a7723bebd86645683","_rev":"_cfFmV7i---","document":{"$oid":"60c20d3a7723bebd8664567f"},"context":"We trimmed the full-length  alignment with trimAL3 v1.4.rev15 (21), which has the automated option -automated1 to remove any  spurious parts of the alignment, thus reducing noise introduced into the single nucleotide variant  analysis.","type":"software","software-name":{"offsetStart":44,"normalizedForm":"trimAL","offsetEnd":50,"rawForm":"trimAL","boundingBoxes":[{"x":130.903,"h":10.2146,"y":292.95,"p":16,"w":37.9144}]},"version":{"offsetStart":53,"normalizedForm":"1.4.rev15","offsetEnd":62,"rawForm":"1.4.rev15","boundingBoxes":[{"x":171.48,"h":10.214600000000019,"y":292.95,"p":16,"w":51.2636}]}},
  {"_key":"60c20d3a7723bebd86645684","_id":"annotations/60c20d3a7723bebd86645684","_rev":"_cfFmV7u---","document":{"$oid":"60c20d3a7723bebd8664567f"},"type":"software","software-name":{"offsetStart":79,"normalizedForm":"snp-sites","offsetEnd":90,"rawForm":"snp-sites","boundingBoxes":[{"x":507.555,"h":10.214600000000019,"y":402.15,"p":16,"w":44.0668}]},"context":"We extracted single nucleotide polymorphism (SNP) information with the program snp-sites  with default option (22)."},
  {"_key":"60c20d3a7723bebd86645685","_id":"annotations/60c20d3a7723bebd86645685","_rev":"_cfFmV76---","document":{"$oid":"60c20d3a7723bebd8664567f"},"context":"All analysis was conducted with R package dplyr (23) and graphically plotted with ggplot2  (24).","references":[{"offsetStart":40535,"normalizedForm":"24","refKey":24,"label":"(24)","reference_id":{"$oid":"60c20d3a7723bebd86645681"},"offsetEnd":40539,"boundingBoxes":[{"x":57.6,"h":10.214600000000019,"y":267.63,"p":17,"w":18.125440000000005}]}],"type":"software","software-name":{"offsetStart":82,"normalizedForm":"ggplot","offsetEnd":88,"rawForm":"ggplot","boundingBoxes":[{"x":505.713,"h":10.2146,"y":242.31,"p":17,"w":36.0813}]},"version":{"offsetStart":88,"normalizedForm":"2","offsetEnd":91,"rawForm":"2","boundingBoxes":[{"x":505.713,"h":10.2146,"y":242.31,"p":17,"w":36.0813}]}},
  {"_key":"60c20d3a7723bebd86645686","_id":"annotations/60c20d3a7723bebd86645686","_rev":"_cfFmV8G---","wikipediaExternalRef":6793476,"document":{"$oid":"60c20d3a7723bebd8664567f"},"publisher":{"offsetStart":174,"normalizedForm":"GISAID","offsetEnd":180,"rawForm":"GISAID","boundingBoxes":[{"x":57.6,"h":10.2146,"y":267.63,"p":16,"w":34.564971428571425}]},"context":"Duplicate and low-quality sequences (>5% NNNNs) were removed and alignment of  34,417 sequences was created based on the sequence multiple alignment program MAFFT (20) by  GISAID.","wikidataId":"Q6714151","type":"software","confidence":0.8157,"software-name":{"wikipediaExternalRef":6793476,"normalizedForm":"MAFFT","offsetStart":158,"wikidataId":"Q6714151","offsetEnd":163,"lang":"en","confidence":0.8157,"rawForm":"MAFFT","boundingBoxes":[{"x":465.843,"h":10.2146,"y":242.31,"p":16,"w":36.7118}]},"lang":"en"},
  {"_key":"60c20d3b7723bebd86645689","_id":"annotations/60c20d3b7723bebd86645689","_rev":"_cfFmV8S---","wikipediaExternalRef":34408890,"document":{"$oid":"60c20d3b7723bebd86645687"},"context":"1. Mobile communication applications, such as WeChat, 4 is an ef- fective and individualised method of information exchange.","wikidataId":"Q283233","references":[{"offsetStart":4068,"normalizedForm":"4","refKey":6,"label":"4","reference_id":{"$oid":"60c20d3b7723bebd86645688"},"offsetEnd":4070,"boundingBoxes":[{"x":515.67,"h":4.3189,"y":428.216,"p":1,"w":2.5932}]}],"type":"software","confidence":0.7626,"software-name":{"wikipediaExternalRef":34408890,"normalizedForm":"WeChat","offsetStart":46,"wikidataId":"Q283233","offsetEnd":52,"lang":"en","confidence":0.7626,"rawForm":"WeChat","boundingBoxes":[{"x":485.587,"h":7.408,"y":428.552,"p":1,"w":25.775999999999996}]},"lang":"en"},
  {"_key":"60c20d3e7723bebd8664568c","_id":"annotations/60c20d3e7723bebd8664568c","_rev":"_cfFmV8e---","document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"GeneAnalytics was used to identify diseases associated with the lncRNAs identified previously.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"GeneAnalytics","offsetEnd":13,"rawForm":"GeneAnalytics","boundingBoxes":[{"x":305.109,"h":9.1806,"y":97.3478,"p":3,"w":55.5208}]},"url":{"offsetStart":109,"normalizedForm":"geneanalytics.genecards.org","offsetEnd":136,"rawForm":"geneanalytics.genecards.org","boundingBoxes":[{"x":48.69948620689655,"h":9.180600000000027,"y":658.74,"p":3,"w":104.50582758620689}]}},
  {"_key":"60c20d3e7723bebd8664568d","_id":"annotations/60c20d3e7723bebd8664568d","_rev":"_cfFmV8q---","wikipediaExternalRef":363695,"document":{"$oid":"60c20d3e7723bebd8664568a"},"publisher":{"offsetStart":0,"normalizedForm":"NCBI","offsetEnd":4,"rawForm":"NCBI","boundingBoxes":[{"x":528.39,"h":9.1806,"y":287.382,"p":3,"w":22.0463}]},"context":"NCBI BLASTn was used to search for related lncRNAs in other species against the NORAD nucleotide sequence.","wikidataId":"Q286820","type":"software","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTn","offsetStart":6,"wikidataId":"Q286820","offsetEnd":12,"lang":"en","confidence":0.708,"rawForm":"BLASTn","boundingBoxes":[{"x":305.109,"h":9.1806,"y":298.839,"p":3,"w":32.645}]},"lang":"en"},
  {"_key":"60c20d3e7723bebd8664568e","_id":"annotations/60c20d3e7723bebd8664568e","_rev":"_cfFmV8y---","document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"The phylogenetic tree was imported to ITOL (itol.embl.de)","type":"software","software-name":{"offsetStart":38,"normalizedForm":"ITOL","offsetEnd":42,"rawForm":"ITOL","boundingBoxes":[{"x":529.219,"h":9.1806,"y":367.581,"p":3,"w":21.2379}]},"url":{"offsetStart":45,"normalizedForm":"itol.embl.de","offsetEnd":57,"rawForm":"itol.embl.de","boundingBoxes":[{"x":308.7869857142857,"h":9.180600000000027,"y":379.038,"p":3,"w":44.14782857142859}]}},
  {"_key":"60c20d3e7723bebd8664568f","_id":"annotations/60c20d3e7723bebd8664568f","_rev":"_cfFmV9----","document":{"$oid":"60c20d3e7723bebd8664568a"},"type":"software","software-name":{"offsetStart":47,"normalizedForm":"Molecular Complex Detection (MCODE)","offsetEnd":82,"rawForm":"Molecular Complex Detection (MCODE)","boundingBoxes":[{"x":112.905,"h":9.180600000000027,"y":462.774,"p":3,"w":162.89928749999999}]},"context":"To identify significant nodes in the network, Molecular Complex Detection (MCODE); a Cytoscape plug-in was used to generate network clustering based on regions with dense connections (Jiang et al., 2019)."},
  {"_key":"60c20d3e7723bebd86645690","_id":"annotations/60c20d3e7723bebd86645690","_rev":"_cfFmV9K---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"The lncRNA-target-pathways network was constructed with Cytoscape (v3.7.2) program (Smoot et al., 2011).","wikidataId":"Q3699942","type":"software","lang":"en","confidence":0.7953,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":57,"wikidataId":"Q3699942","offsetEnd":66,"lang":"en","confidence":0.7953,"rawForm":"Cytoscape","boundingBoxes":[{"x":117.107,"h":9.1806,"y":531.516,"p":3,"w":39.0597}]},"url":{"offsetStart":171,"normalizedForm":"cytoscape.org","offsetEnd":184,"rawForm":"cytoscape.org","boundingBoxes":[{"x":121.5899,"h":9.180600000000027,"y":451.317,"p":3,"w":49.02170000000001}]},"version":{"offsetStart":69,"normalizedForm":"3.7.2","offsetEnd":74,"rawForm":"3.7.2","boundingBoxes":[{"x":165.0080875,"h":9.180600000000027,"y":531.516,"p":3,"w":21.666525000000007}]}},
  {"_key":"60c20d3e7723bebd86645691","_id":"annotations/60c20d3e7723bebd86645691","_rev":"_cfFmV9W---","document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"A multiple sequence alignment and phylogenetic tree was created using MEGA (v7), with the neighbor-joining clustering method and bootstrapping with 500 iterations (Kumar et al., 2016).","type":"software","software-name":{"offsetStart":71,"normalizedForm":"MEGA","offsetEnd":75,"rawForm":"MEGA","boundingBoxes":[{"x":397.025,"h":9.1806,"y":344.667,"p":3,"w":27.1139}]},"version":{"offsetStart":78,"normalizedForm":"7","offsetEnd":79,"rawForm":"7","boundingBoxes":[{"x":431.44058,"h":9.1806,"y":344.667,"p":3,"w":7.05516}]}},
  {"_key":"60c20d3e7723bebd86645692","_id":"annotations/60c20d3e7723bebd86645692","_rev":"_cfFmV9i---","wikipediaExternalRef":363695,"document":{"$oid":"60c20d3e7723bebd8664568a"},"publisher":{"offsetStart":75,"normalizedForm":"NCBI","offsetEnd":79,"rawForm":"NCBI","boundingBoxes":[{"x":99.2246,"h":9.1806,"y":532.713,"p":7,"w":22.0464}]},"context":"Twenty three unique genera were represented in the top 100 results from a NCBI BLASTn search using the lncRNA NORAD.","wikidataId":"Q286820","type":"software","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTn","offsetStart":80,"wikidataId":"Q286820","offsetEnd":86,"lang":"en","confidence":0.708,"rawForm":"BLASTn","boundingBoxes":[{"x":123.47,"h":9.1806,"y":532.713,"p":7,"w":32.645}]},"lang":"en"},
  {"_key":"60c20d3e7723bebd86645693","_id":"annotations/60c20d3e7723bebd86645693","_rev":"_cfFmV9u---","wikipediaExternalRef":2039930,"document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"The gene sequences associated with the official gene names were retrieved from ensembl database (ensembl.org)","wikidataId":"Q1344256","type":"software","confidence":0.7343,"software-name":{"wikipediaExternalRef":2039930,"normalizedForm":"ensembl","offsetStart":80,"wikidataId":"Q1344256","offsetEnd":87,"lang":"en","confidence":0.7343,"rawForm":"ensembl","boundingBoxes":[{"x":126.539,"h":9.1806,"y":394.032,"p":3,"w":31.6445}]},"url":{"offsetStart":98,"normalizedForm":"ensembl.org","offsetEnd":109,"rawForm":"ensembl.org","boundingBoxes":[{"x":202.15236923076924,"h":9.180600000000027,"y":394.032,"p":3,"w":44.88406153846154}]},"lang":"en"},
  {"_key":"60c20d3e7723bebd86645694","_id":"annotations/60c20d3e7723bebd86645694","_rev":"_cfFmV92---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"A network analysis of lncRNA and cytokine pathway associations was created using Cytoscape (Figure 3).","wikidataId":"Q3699942","type":"software","lang":"en","confidence":0.8039,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":82,"wikidataId":"Q3699942","offsetEnd":91,"lang":"en","confidence":0.8039,"rawForm":"Cytoscape","boundingBoxes":[{"x":205.632,"h":9.1806,"y":693.111,"p":5,"w":39.0597}]},"url":{"offsetStart":171,"normalizedForm":"cytoscape.org","offsetEnd":184,"rawForm":"cytoscape.org","boundingBoxes":[{"x":121.5899,"h":9.180600000000027,"y":451.317,"p":3,"w":49.02170000000001}]},"version":{"offsetStart":163,"normalizedForm":"3.7.2","offsetEnd":168,"rawForm":"3.7.2","boundingBoxes":[{"x":90.02958749999999,"h":9.180600000000027,"y":451.317,"p":3,"w":21.666525000000007}]}},
  {"_key":"60c20d3e7723bebd86645695","_id":"annotations/60c20d3e7723bebd86645695","_rev":"_cfFmW-C---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"To identify significant nodes in the network, Molecular Complex Detection (MCODE); a Cytoscape plug-in was used to generate network clustering based on regions with dense connections (Jiang et al., 2019).","wikidataId":"Q3699942","type":"software","lang":"en","confidence":0.7953,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":87,"wikidataId":"Q3699942","offsetEnd":96,"lang":"en","confidence":0.7953,"rawForm":"Cytoscape","boundingBoxes":[{"x":44.829,"h":9.1806,"y":474.231,"p":3,"w":39.0597}]},"url":{"offsetStart":171,"normalizedForm":"cytoscape.org","offsetEnd":184,"rawForm":"cytoscape.org","boundingBoxes":[{"x":121.5899,"h":9.180600000000027,"y":451.317,"p":3,"w":49.02170000000001}]},"version":{"offsetStart":163,"normalizedForm":"3.7.2","offsetEnd":168,"rawForm":"3.7.2","boundingBoxes":[{"x":90.02958749999999,"h":9.180600000000027,"y":451.317,"p":3,"w":21.666525000000007}]}},
  {"_key":"60c20d3e7723bebd86645696","_id":"annotations/60c20d3e7723bebd86645696","_rev":"_cfFmW-O---","document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"In order to elucidate pathways that are significantly perturbed in COVID-19 cytokine storm, GeneAnalytics (geneanalytics.genecards.org) was used to identify metabolic pathways and gene ontology terms associated with such cytokines.","type":"software","software-name":{"offsetStart":93,"normalizedForm":"GeneAnalytics","offsetEnd":106,"rawForm":"GeneAnalytics","boundingBoxes":[{"x":234.657,"h":9.1806,"y":647.283,"p":3,"w":55.5208}]},"url":{"offsetStart":109,"normalizedForm":"geneanalytics.genecards.org","offsetEnd":136,"rawForm":"geneanalytics.genecards.org","boundingBoxes":[{"x":48.69948620689655,"h":9.180600000000027,"y":658.74,"p":3,"w":104.50582758620689}]}},
  {"_key":"60c20d3e7723bebd86645697","_id":"annotations/60c20d3e7723bebd86645697","_rev":"_cfFmW-e---","document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"Likewise, to understand the role that the identified lncRNAs play in disease pathology, we used GeneAnalytics to identify associated diseases, as described (Fuchs et al.,  2016).","type":"software","software-name":{"offsetStart":97,"normalizedForm":"GeneAnalytics","offsetEnd":110,"rawForm":"GeneAnalytics","boundingBoxes":[{"x":234.657,"h":9.1806,"y":693.111,"p":3,"w":55.5208}]},"url":{"offsetStart":109,"normalizedForm":"geneanalytics.genecards.org","offsetEnd":136,"rawForm":"geneanalytics.genecards.org","boundingBoxes":[{"x":48.69948620689655,"h":9.180600000000027,"y":658.74,"p":3,"w":104.50582758620689}]}},
  {"_key":"60c20d3e7723bebd86645698","_id":"annotations/60c20d3e7723bebd86645698","_rev":"_cfFmW-q---","wikipediaExternalRef":1092923,"document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"As of June 3, 2020, 210 papers appear in Web of Science, 518 papers in PubMed, and 6,420 results in Google Scholar for COVID-19 cytokine storm.","wikidataId":"Q95","type":"software","confidence":0.3333,"software-name":{"wikipediaExternalRef":1092923,"normalizedForm":"Google","offsetStart":101,"wikidataId":"Q95","offsetEnd":107,"lang":"en","confidence":0.3333,"rawForm":"Google","boundingBoxes":[{"x":473.776,"h":9.1806,"y":647.283,"p":3,"w":27.2604}]},"lang":"en"},
  {"_key":"60c20d3e7723bebd86645699","_id":"annotations/60c20d3e7723bebd86645699","_rev":"_cfFmW-2---","wikipediaExternalRef":1520204,"document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"Cytokines associated with increased COVID-19 cytokine storm were identified using the search engines Google Scholar, PubMed, and Web of Science, and a literature review by Costela-Ruiz et al. (2020) amongst others.","wikidataId":"Q494817","type":"software","confidence":0.9596,"software-name":{"wikipediaExternalRef":1520204,"normalizedForm":"Google Scholar","offsetStart":102,"wikidataId":"Q494817","offsetEnd":116,"lang":"en","confidence":0.9596,"rawForm":"Google Scholar","boundingBoxes":[{"x":455.032,"h":9.180600000000027,"y":601.455,"p":2,"w":55.26067499999999}]},"lang":"en"},
  {"_key":"60c20d3e7723bebd8664569a","_id":"annotations/60c20d3e7723bebd8664569a","_rev":"_cfFmW_C---","document":{"$oid":"60c20d3e7723bebd8664568a"},"type":"software","software-name":{"offsetStart":115,"normalizedForm":"UCSC genome browser","offsetEnd":134,"rawForm":"UCSC genome browser","boundingBoxes":[{"x":197.54,"h":9.180600000000027,"y":693.11,"p":7,"w":88.59398750000005}]},"context":"Figure 6A depicts annotated NORAD conserved regions across several mammalian genomic sequences and ESTs from the UCSC genome browser, while Figures 6B-E show two representation of significantly  conserved RNA folding and multiple sequence alignment among six mammals (human, chimpanzee, monkey, rat, mouse and dog) with p-values of 0.92 and 1.0, respectively."},
  {"_key":"60c20d3e7723bebd8664569b","_id":"annotations/60c20d3e7723bebd8664569b","_rev":"_cfFmW_O---","wikipediaExternalRef":503009,"document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"Cytokines associated with increased COVID-19 cytokine storm were identified using the search engines Google Scholar, PubMed, and Web of Science, and a literature review by Costela-Ruiz et al. (2020) amongst others.","wikidataId":"Q180686","type":"software","confidence":0.7721,"software-name":{"wikipediaExternalRef":503009,"normalizedForm":"PubMed","offsetStart":118,"wikidataId":"Q180686","offsetEnd":124,"lang":"en","confidence":0.7721,"rawForm":"PubMed","boundingBoxes":[{"x":515.728,"h":9.1806,"y":601.455,"p":2,"w":29.752714285714283}]},"lang":"en"},
  {"_key":"60c20d3e7723bebd8664569c","_id":"annotations/60c20d3e7723bebd8664569c","_rev":"_cfFmW_a---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"In order to visualize the functional relationships between lncRNAs, cytokines targets, and metabolic pathways, a network analysis was created using Cytoscape (v3.7.2) (cytoscape.org).","wikidataId":"Q3699942","type":"software","lang":"en","confidence":0.7953,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":151,"wikidataId":"Q3699942","offsetEnd":160,"lang":"en","confidence":0.7953,"rawForm":"Cytoscape","boundingBoxes":[{"x":44.829,"h":9.1806,"y":451.317,"p":3,"w":39.0597}]},"url":{"offsetStart":171,"normalizedForm":"cytoscape.org","offsetEnd":184,"rawForm":"cytoscape.org","boundingBoxes":[{"x":121.5899,"h":9.180600000000027,"y":451.317,"p":3,"w":49.02170000000001}]},"version":{"offsetStart":163,"normalizedForm":"3.7.2","offsetEnd":168,"rawForm":"3.7.2","boundingBoxes":[{"x":90.02958749999999,"h":9.180600000000027,"y":451.317,"p":3,"w":21.666525000000007}]}},
  {"_key":"60c20d3e7723bebd8664569d","_id":"annotations/60c20d3e7723bebd8664569d","_rev":"_cfFmW_i---","document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"To gain insight into molecular interactions between cytokines and pathogenic mechanisms, we performed a protein-protein interaction network analysis of the 10 most significant cytokines using Search Tool for the Retrieval of Interacting Genes database (STRING-DB;string-db.org, Szklarczyk et al., 2017).","references":[{"offsetStart":12344,"normalizedForm":"Szklarczyk et al., 2017)","refKey":66,"label":"Szklarczyk et al., 2017)","reference_id":{"$oid":"60c20d3e7723bebd8664568b"},"offsetEnd":12368,"boundingBoxes":[{"x":193.896,"h":9.180600000000027,"y":371.118,"p":3,"w":92.34425000000002}]}],"type":"software","software-name":{"offsetStart":195,"normalizedForm":"Search Tool for the Retrieval of Interacting Genes database (STRING-DB","offsetEnd":266,"rawForm":"Search Tool for the Retrieval of Interacting Genes \ndatabase (STRING-DB","boundingBoxes":[{"x":71.9278,"h":9.180600000000027,"y":359.661,"p":3,"w":218.24079999999998},{"x":44.829,"h":9.180600000000027,"y":371.118,"p":3,"w":80.21609999999998}]},"url":{"offsetStart":267,"normalizedForm":"string-db.org","offsetEnd":280,"rawForm":"string-db.org","boundingBoxes":[{"x":129.30562,"h":9.180600000000027,"y":371.118,"p":3,"w":55.38676000000001}]}},
  {"_key":"60c20d3e7723bebd8664569e","_id":"annotations/60c20d3e7723bebd8664569e","_rev":"_cfFmW_u---","document":{"$oid":"60c20d3e7723bebd8664568a"},"context":"In order to gain insight into the thermodynamic stability and evolutionary conservation of lncRNA NORAD secondary structure, we carried out a multiple sequence alignment of six mammals (human, chimpanzee, monkey, rat, mouse and dog) and transferred to RNAzWebServer (http://rna.tbi.univie.ac.at/cgi-bin/RNAz/ RNAz.cgi), using default parameter as described (Mathews et al., 2004; Lorenz et al., 2011).","type":"software","software-name":{"offsetStart":257,"normalizedForm":"RNAzWebServer","offsetEnd":270,"rawForm":"RNAzWebServer","boundingBoxes":[{"x":320.076,"h":9.1806,"y":493.608,"p":3,"w":65.2518}]},"url":{"offsetStart":272,"normalizedForm":"http://rna.tbi.univie.ac.at/cgi-bin/RNAz/ RNAz.cgi","offsetEnd":323,"rawForm":"http://rna.tbi.univie.ac.at/cgi-bin/RNAz/ \nRNAz.cgi","boundingBoxes":[{"x":396.348,"h":9.180600000000027,"y":493.608,"p":3,"w":154.11899999999997},{"x":305.108,"h":9.18059999999997,"y":505.065,"p":3,"w":33.298719999999946}]}},
  {"_key":"60c20d427723bebd866456a0","_id":"annotations/60c20d427723bebd866456a0","_rev":"_cfFmW_6---","document":{"$oid":"60c20d427723bebd8664569f"},"context":"In Arm 4, title-abstract screening by one reviewer excluded any studies clearly not meeting the inclusion  criteria, followed by independent title-abstract screening of the remaining studies by two reviewers in  EPPI Reviewer-4 systematic review management software (7).","type":"software","software-name":{"offsetStart":214,"normalizedForm":"EPPI Reviewer","offsetEnd":228,"rawForm":"EPPI Reviewer-","boundingBoxes":[{"x":72.024,"h":9.936000000000035,"y":523.889,"p":4,"w":71.43187000000003}]},"version":{"offsetStart":228,"normalizedForm":"4","offsetEnd":229,"rawForm":"4","boundingBoxes":[{"x":143.45587,"h":9.936,"y":523.889,"p":4,"w":5.124130000000001}]}},
  {"_key":"60c20d447723bebd866456a2","_id":"annotations/60c20d447723bebd866456a2","_rev":"_cfFmWAG---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20d447723bebd866456a1"},"publisher":{"offsetStart":63,"normalizedForm":"GraphPad Software","offsetEnd":80,"rawForm":"GraphPad Software","boundingBoxes":[{"x":350.8392333333333,"h":8.747199999999992,"y":171.811,"p":3,"w":73.14654444444443}]},"context":"Statistical analyses were performed using GraphPad Prism 7.0 (GraphPad Software, San Diego, CA, USA).","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.8862,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":42,"wikidataId":"Q5597066","offsetEnd":57,"lang":"en","confidence":0.8862,"rawForm":"GraphPad \nPrism","boundingBoxes":[{"x":504.567,"h":8.7472,"y":159.339,"p":3,"w":39.6651},{"x":306.142,"h":8.7472,"y":171.811,"p":3,"w":22.6181}]},"version":{"offsetStart":58,"normalizedForm":"7.0","offsetEnd":61,"rawForm":"7.0","boundingBoxes":[{"x":331.313,"h":8.747199999999992,"y":171.811,"p":3,"w":12.29480000000001}]}},
  {"_key":"60c20d487723bebd866456a4","_id":"annotations/60c20d487723bebd866456a4","_rev":"_cfFmWAS---","document":{"$oid":"60c20d487723bebd866456a3"},"type":"software","software-name":{"offsetStart":20,"normalizedForm":"Safe- Graph","offsetEnd":31,"rawForm":"Safe-\nGraph","boundingBoxes":[{"x":540.28,"h":8.5,"y":545.658,"p":7,"w":19.719999999999914},{"x":200.012,"h":8.5,"y":558.697,"p":7,"w":25.65}]},"context":"To enhance privacy, Safe- Graph excludes census block group information if fewer than five devices visited an establish- ment in a month from a given census block group."},
  {"_key":"60c20d487723bebd866456a5","_id":"annotations/60c20d487723bebd866456a5","_rev":"_cfFmWAe---","document":{"$oid":"60c20d487723bebd866456a3"},"type":"software","software-name":{"offsetStart":98,"normalizedForm":"SafeGraph","offsetEnd":107,"rawForm":"SafeGraph","boundingBoxes":[{"x":241.17,"h":8.5,"y":532.675,"p":7,"w":41.83}]},"context":"To measure how the number of interactions has changed due to social distancing, we use data from SafeGraph [21], a data company that aggregates anonymized location data from numerous applications to provide insights about physical places."},
  {"_key":"60c20d487723bebd866456a6","_id":"annotations/60c20d487723bebd866456a6","_rev":"_cfFmWAq---","document":{"$oid":"60c20d487723bebd866456a3"},"type":"software","software-name":{"offsetStart":110,"normalizedForm":"SafeGraph","offsetEnd":119,"rawForm":"SafeGraph","boundingBoxes":[{"x":277.057,"h":8.5,"y":701.676,"p":7,"w":39.672}]},"context":"When the industry-ZIP cell received fewer than ten visits in either month or when visits data are missing in SafeGraph, we replace the change in visits with the average of the ZIP code."},
  {"_key":"60c20d487723bebd866456a7","_id":"annotations/60c20d487723bebd866456a7","_rev":"_cfFmWAy---","document":{"$oid":"60c20d487723bebd866456a3"},"type":"software","software-name":{"offsetStart":133,"normalizedForm":"SafeGraph","offsetEnd":142,"rawForm":"SafeGraph","boundingBoxes":[{"x":374.229,"h":8.5,"y":389.921,"p":2,"w":41.83}]},"context":"To study how the patterns of interaction have changed in the U.S. during the Covid-19 pan- demic, we use customer mobility data from SafeGraph [21]."},
  {"_key":"60c20d4b7723bebd866456a9","_id":"annotations/60c20d4b7723bebd866456a9","_rev":"_cfFmWB----","document":{"$oid":"60c20d4b7723bebd866456a8"},"context":"Protein Pilot V.3.0 database software (with the MASCOT V.2.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"Protein Pilot","offsetEnd":13,"rawForm":"Protein Pilot","boundingBoxes":[{"x":499.115,"h":9.180600000000027,"y":429.596,"p":3,"w":51.32460000000003}]},"version":{"offsetStart":17,"normalizedForm":"3.0","offsetEnd":20,"rawForm":"3.0","boundingBoxes":[{"x":313.13356,"h":9.180600000000027,"y":441.053,"p":3,"w":12.03534000000002}]}},
  {"_key":"60c20d4b7723bebd866456aa","_id":"annotations/60c20d4b7723bebd866456aa","_rev":"_cfFmWBK---","document":{"$oid":"60c20d4b7723bebd866456a8"},"publisher":{"offsetStart":44,"normalizedForm":"Bio- Rad","offsetEnd":52,"rawForm":"Bio-\nRad","boundingBoxes":[{"x":274.50788,"h":9.180600000000027,"y":589.998,"p":3,"w":15.655520000000024},{"x":44.8291,"h":9.1806,"y":601.455,"p":3,"w":13.857149999999999}]},"context":"PDQUEST 2D Gel Analysis Software version 6 (Bio- Rad) was used to analyze spot intensities of each sample.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"PDQUEST 2D Gel Analysis","offsetEnd":23,"rawForm":"PDQUEST 2D Gel Analysis","boundingBoxes":[{"x":87.7057,"h":9.180600000000027,"y":589.998,"p":3,"w":106.6758}]},"version":{"offsetStart":41,"normalizedForm":"6","offsetEnd":42,"rawForm":"6","boundingBoxes":[{"x":263.385,"h":9.1806,"y":589.998,"p":3,"w":4.543}]}},
  {"_key":"60c20d4b7723bebd866456ab","_id":"annotations/60c20d4b7723bebd866456ab","_rev":"_cfFmWBW---","wikipediaExternalRef":4294204,"document":{"$oid":"60c20d4b7723bebd866456a8"},"publisher":{"offsetStart":71,"normalizedForm":"MedCalc Software","offsetEnd":88,"rawForm":"MedCalc \nSoftware","boundingBoxes":[{"x":257.2040625,"h":9.1806,"y":97.3478,"p":4,"w":32.9634375},{"x":44.8289,"h":9.1806,"y":108.804,"p":4,"w":31.350044444444443}]},"context":"ROC curve analysis was performed using MedCalc software version 19.4 (MedCalc Software, Ostend, Belgium).","wikidataId":"Q4272521","type":"software","lang":"en","confidence":0.7594,"software-name":{"wikipediaExternalRef":4294204,"normalizedForm":"MedCalc","offsetStart":40,"wikidataId":"Q4272521","offsetEnd":47,"lang":"en","confidence":0.7594,"rawForm":"MedCalc","boundingBoxes":[{"x":129.564,"h":9.1806,"y":97.3478,"p":4,"w":34.3964}]},"version":{"offsetStart":65,"normalizedForm":"19.4","offsetEnd":69,"rawForm":"19.4","boundingBoxes":[{"x":233.532,"h":9.180599999999998,"y":97.3478,"p":4,"w":15.793000000000006}]}},
  {"_key":"60c20d4b7723bebd866456ac","_id":"annotations/60c20d4b7723bebd866456ac","_rev":"_cfFmWBi---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20d4b7723bebd866456a8"},"publisher":{"offsetStart":128,"normalizedForm":"GraphPad Software, Inc","offsetEnd":150,"rawForm":"GraphPad Software, Inc","boundingBoxes":[{"x":328.1733,"h":9.180600000000027,"y":693.105,"p":3,"w":87.84604000000002}]},"context":"ANOVA with Tukey's post-hoc test between different infection groups was conducted using GraphPad Prism software version 7.00 (GraphPad Software, Inc., La Jolla, CA, USA).","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":89,"wikidataId":"Q5597066","offsetEnd":103,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":419.212,"h":9.180600000000027,"y":681.648,"p":3,"w":64.61340000000001}]},"version":{"offsetStart":122,"normalizedForm":"7.00","offsetEnd":126,"rawForm":"7.00","boundingBoxes":[{"x":305.11,"h":9.180600000000027,"y":693.105,"p":3,"w":15.793000000000006}]}},
  {"_key":"60c20d4b7723bebd866456ae","_id":"annotations/60c20d4b7723bebd866456ae","_rev":"_cfFmWBq---","wikipediaExternalRef":179088,"document":{"$oid":"60c20d4b7723bebd866456ad"},"context":"Statistical analyses were per- formed using SPSS software, version 26.0.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":44,"wikidataId":"Q181596","offsetEnd":48,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":123.023,"h":5.9138,"y":305.444,"p":3,"w":14.7356}]},"version":{"offsetStart":67,"normalizedForm":"26.0","offsetEnd":71,"rawForm":"26.0","boundingBoxes":[{"x":216.906,"h":8.448300000000017,"y":303.468,"p":3,"w":18.08408}]}},
  {"_key":"60c20d527723bebd866456b0","_id":"annotations/60c20d527723bebd866456b0","_rev":"_cfFmWB2---","document":{"$oid":"60c20d527723bebd866456af"},"publisher":{"offsetStart":49,"normalizedForm":"Department of Transportation, Division of New Technology and Research","offsetEnd":119,"rawForm":"Department \nof Transportation, Division of New Technology and Research","boundingBoxes":[{"x":508.56551818181816,"h":9.584,"y":600.509,"p":2,"w":50.70518181818181},{"x":167.265,"h":9.583999999999946,"y":613.062,"p":2,"w":268.66628888888886}]},"context":"The CALINE4 model allowed us to estimate the dispersion and deposition of pollutants such as particulate matter and other contaminants at predefined spatial receptors [32].","type":"software","software-name":{"offsetStart":4,"normalizedForm":"CALINE","offsetEnd":10,"rawForm":"CALINE","boundingBoxes":[{"x":448.801,"h":9.584,"y":625.615,"p":2,"w":42.9958}]},"version":{"offsetStart":10,"normalizedForm":"4","offsetEnd":11,"rawForm":"4","boundingBoxes":[{"x":448.801,"h":9.584,"y":625.615,"p":2,"w":42.9958}]}},
  {"_key":"60c20d527723bebd866456b1","_id":"annotations/60c20d527723bebd866456b1","_rev":"_cfFmWCC---","document":{"$oid":"60c20d527723bebd866456af"},"type":"software","software-name":{"offsetStart":12,"normalizedForm":"CAlifornia LINE","offsetEnd":27,"rawForm":"CAlifornia LINE","boundingBoxes":[{"x":334.528,"h":9.583999999999946,"y":600.509,"p":2,"w":72.29829999999998}]},"context":"We used the CAlifornia LINE version 4 (CALINE4) (Department of Transportation, Division of New Technology and Research."},
  {"_key":"60c20d527723bebd866456b2","_id":"annotations/60c20d527723bebd866456b2","_rev":"_cfFmWCO---","document":{"$oid":"60c20d527723bebd866456af"},"publisher":{"offsetStart":49,"normalizedForm":"Department of Transportation, Division of New Technology and Research","offsetEnd":119,"rawForm":"Department \nof Transportation, Division of New Technology and Research","boundingBoxes":[{"x":508.56551818181816,"h":9.584,"y":600.509,"p":2,"w":50.70518181818181},{"x":167.265,"h":9.583999999999946,"y":613.062,"p":2,"w":268.66628888888886}]},"context":"We used the CAlifornia LINE version 4 (CALINE4) (Department of Transportation, Division of New Technology and Research.","type":"software","software-name":{"offsetStart":39,"normalizedForm":"CALINE","offsetEnd":45,"rawForm":"CALINE","boundingBoxes":[{"x":456.9662222222222,"h":9.584,"y":600.509,"p":2,"w":38.529555555555554}]},"version":{"offsetStart":45,"normalizedForm":"4","offsetEnd":46,"rawForm":"4","boundingBoxes":[{"x":456.9662222222222,"h":9.584,"y":600.509,"p":2,"w":38.529555555555554}]}},
  {"_key":"60c20d527723bebd866456b3","_id":"annotations/60c20d527723bebd866456b3","_rev":"_cfFmWCa---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20d527723bebd866456af"},"publisher":{"offsetStart":69,"normalizedForm":"Stata Corp","offsetEnd":79,"rawForm":"Stata Corp","boundingBoxes":[{"x":215.53668333333334,"h":9.584000000000003,"y":390.385,"p":3,"w":41.60071666666667}]},"context":"We used 'logit', 'mkspline', and 'xblc' routines of the Stata 16.1 (Stata Corp., College Station, TX, USA) for all statistical analyses.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7154,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":57,"wikidataId":"Q1204300","offsetEnd":62,"lang":"en","confidence":0.7154,"rawForm":"Stata","boundingBoxes":[{"x":167.265,"h":9.584,"y":390.385,"p":3,"w":21.6886}]},"version":{"offsetStart":63,"normalizedForm":"16.1","offsetEnd":67,"rawForm":"16.1","boundingBoxes":[{"x":191.444,"h":9.584000000000003,"y":390.385,"p":3,"w":17.434600000000017}]}},
  {"_key":"60c20d5c7723bebd866456b5","_id":"annotations/60c20d5c7723bebd866456b5","_rev":"_cfFmWCm---","document":{"$oid":"60c20d5c7723bebd866456b4"},"type":"software","software-name":{"offsetStart":22,"normalizedForm":"Covasim","offsetEnd":29,"rawForm":"Covasim","boundingBoxes":[{"x":294.023,"h":8.2992,"y":287.083,"p":5,"w":36.614}]},"context":"In this paper, we use Covasim for two reasons."},
  {"_key":"60c20d5c7723bebd866456b6","_id":"annotations/60c20d5c7723bebd866456b6","_rev":"_cfFmWCy---","document":{"$oid":"60c20d5c7723bebd866456b4"},"type":"software","software-name":{"offsetStart":40,"normalizedForm":"Covasim","offsetEnd":47,"rawForm":"Covasim","boundingBoxes":[{"x":316.248,"h":8.2992,"y":254.596,"p":6,"w":36.614}]},"context":"Our simulations are performed using the Covasim platform as explained in our background section."},
  {"_key":"60c20d5c7723bebd866456b7","_id":"annotations/60c20d5c7723bebd866456b7","_rev":"_cfFmWC6---","wikipediaExternalRef":19961416,"document":{"$oid":"60c20d5c7723bebd866456b4"},"publisher":{"offsetStart":122,"normalizedForm":"Microsoft","offsetEnd":131,"rawForm":"Microsoft","boundingBoxes":[{"x":266.576,"h":8.7376,"y":641.036,"p":2,"w":41.0426}]},"context":"This requires a mas- sive number of computationally intensive experiments, which are performed through the cloud via the Microsoft Azure platform.","wikidataId":"Q725967","type":"software","confidence":0.3467,"software-name":{"wikipediaExternalRef":19961416,"normalizedForm":"Azure","offsetStart":132,"wikidataId":"Q725967","offsetEnd":137,"lang":"en","confidence":0.3467,"rawForm":"Azure","boundingBoxes":[{"x":310.946,"h":8.7376,"y":641.036,"p":2,"w":25.7653}]},"lang":"en"},
  {"_key":"60c20d5c7723bebd866456b8","_id":"annotations/60c20d5c7723bebd866456b8","_rev":"_cfFmWDG---","document":{"$oid":"60c20d5c7723bebd866456b4"},"type":"software","software-name":{"offsetStart":150,"normalizedForm":"COMOKIT","offsetEnd":157,"rawForm":"COMOKIT","boundingBoxes":[{"x":207.592,"h":8.2992,"y":275.128,"p":5,"w":36.614}]},"context":"After a proliferation of independently developed models, we started witnessing the emergence of COVID-19 ABM modeling packages or toolkits, such as COMOKIT [16] or Covasim, developed by the Institute of Disease Modeling [36]."},
  {"_key":"60c20d5c7723bebd866456b9","_id":"annotations/60c20d5c7723bebd866456b9","_rev":"_cfFmWDS---","document":{"$oid":"60c20d5c7723bebd866456b4"},"type":"software","software-name":{"offsetStart":166,"normalizedForm":"Covasim","offsetEnd":173,"rawForm":"Covasim","boundingBoxes":[{"x":277.873,"h":8.2992,"y":275.128,"p":5,"w":34.4584625}]},"context":"After a proliferation of independently developed models, we started witnessing the emergence of COVID-19 ABM modeling packages or toolkits, such as COMOKIT [16] or Covasim, developed by the Institute of Disease Modeling [36]."},
  {"_key":"60c20d5e7723bebd866456bb","_id":"annotations/60c20d5e7723bebd866456bb","_rev":"_cfFmWDe---","wikipediaExternalRef":179088,"document":{"$oid":"60c20d5e7723bebd866456ba"},"publisher":{"offsetStart":41,"normalizedForm":"IBM SPSS Inc","offsetEnd":53,"rawForm":"IBM SPSS Inc","boundingBoxes":[{"x":337.06805,"h":9.320100000000025,"y":398.593,"p":2,"w":53.63806999999997}]},"context":"This study used the SPSS22.0","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7435,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":20,"wikidataId":"Q181596","offsetEnd":24,"lang":"en","confidence":0.7435,"rawForm":"SPSS","boundingBoxes":[{"x":491.983,"h":9.3201,"y":387.203,"p":2,"w":27.1578}]},"version":{"offsetStart":24,"normalizedForm":"22.0","offsetEnd":28,"rawForm":"22.0","boundingBoxes":[{"x":491.983,"h":9.320100000000025,"y":387.203,"p":2,"w":36.21039999999999}]}},
  {"_key":"60c20d5e7723bebd866456bc","_id":"annotations/60c20d5e7723bebd866456bc","_rev":"_cfFmWDq---","wikipediaExternalRef":179088,"document":{"$oid":"60c20d5e7723bebd866456ba"},"publisher":{"offsetStart":41,"normalizedForm":"IBM SPSS Inc","offsetEnd":53,"rawForm":"IBM SPSS Inc","boundingBoxes":[{"x":337.06805,"h":9.320100000000025,"y":398.593,"p":2,"w":53.63806999999997}]},"context":"The quantile-quantile graph in SPSS22.0 was used to test the normality of the data, and single-factor ANOVA was used to detect the differences among multiple groups in this study.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7435,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":31,"wikidataId":"Q181596","offsetEnd":35,"lang":"en","confidence":0.7435,"rawForm":"SPSS","boundingBoxes":[{"x":513.692,"h":9.3201,"y":421.373,"p":2,"w":27.234299999999998}]},"version":{"offsetStart":35,"normalizedForm":"22.0","offsetEnd":39,"rawForm":"22.0","boundingBoxes":[{"x":513.692,"h":9.320100000000025,"y":421.373,"p":2,"w":36.312400000000025}]}},
  {"_key":"60c20d617723bebd866456be","_id":"annotations/60c20d617723bebd866456be","_rev":"_cfFmWD2---","wikipediaExternalRef":179088,"document":{"$oid":"60c20d617723bebd866456bd"},"publisher":{"offsetStart":40,"normalizedForm":"IBM","offsetEnd":43,"rawForm":"IBM","boundingBoxes":[{"x":498.42834,"h":9.584,"y":148.89,"p":5,"w":14.83602}]},"context":"All analyses were conducted in SPSS 26 (IBM, Armonk, NY, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":31,"wikidataId":"Q181596","offsetEnd":35,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":456.798,"h":9.584,"y":148.89,"p":5,"w":21.7519}]},"version":{"offsetStart":36,"normalizedForm":"26","offsetEnd":38,"rawForm":"26","boundingBoxes":[{"x":481.025,"h":9.584,"y":148.89,"p":5,"w":9.9825}]}},
  {"_key":"60c20d6a7723bebd866456c0","_id":"annotations/60c20d6a7723bebd866456c0","_rev":"_cfFmWEC---","document":{"$oid":"60c20d6a7723bebd866456bf"},"context":"CoMFA was performed using the QSAR module in Sybyl 6.91.","type":"software","software-name":{"offsetStart":46,"normalizedForm":"Sybyl","offsetEnd":51,"rawForm":"Sybyl","boundingBoxes":[{"x":50.6258,"h":8.9464,"y":201.856,"p":6,"w":23.715}]},"version":{"offsetStart":52,"normalizedForm":"6.91","offsetEnd":56,"rawForm":"6.91","boundingBoxes":[{"x":79.1418,"h":8.946400000000011,"y":201.856,"p":6,"w":16.258960000000002}]}},
  {"_key":"60c20d6a7723bebd866456c1","_id":"annotations/60c20d6a7723bebd866456c1","_rev":"_cfFmWEO---","document":{"$oid":"60c20d6a7723bebd866456bf"},"type":"software","software-name":{"offsetStart":77,"normalizedForm":"AOS/APS","offsetEnd":84,"rawForm":"AOS/APS","boundingBoxes":[{"x":119.053,"h":8.946400000000011,"y":165.97,"p":6,"w":43.766700000000014}]},"context":"The best orientation was searched by all-orientation search strategy using AOS/APS program [16], to minimize the effect of the initial orientation of the substrates."},
  {"_key":"60c20d6a7723bebd866456c2","_id":"annotations/60c20d6a7723bebd866456c2","_rev":"_cfFmWEW---","document":{"$oid":"60c20d6a7723bebd866456bf"},"context":"The complex structures of SARS 3C- like proteinase and substrates were generated based on the crystal structure of the enzyme (PDB code: 1UK4) using Sybyl 6.91, followed by energy minimiza- tion using 500 steps of steepest descents method.","type":"software","software-name":{"offsetStart":151,"normalizedForm":"Sybyl","offsetEnd":156,"rawForm":"Sybyl","boundingBoxes":[{"x":109.984,"h":8.9464,"y":106.217,"p":6,"w":23.6512}]},"version":{"offsetStart":157,"normalizedForm":"6.91","offsetEnd":161,"rawForm":"6.91","boundingBoxes":[{"x":137.195,"h":8.946399999999997,"y":106.217,"p":6,"w":16.258960000000002}]}},
  {"_key":"60c20d717723bebd866456c4","_id":"annotations/60c20d717723bebd866456c4","_rev":"_cfFmWEm---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20d717723bebd866456c3"},"context":"The 50% effective concentration (EC 50 ) and the compound-specific toxicity (50% cytotoxic concentration [CC 50 ]) were calculated with GraphPad Prism 5 software using the nonlinear regression model.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":138,"wikidataId":"Q5597066","offsetEnd":152,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":350.484,"h":7.556500000000028,"y":587.974,"p":2,"w":56.264999999999986}]},"version":{"offsetStart":153,"normalizedForm":"5","offsetEnd":154,"rawForm":"5","boundingBoxes":[{"x":408.121,"h":7.5565,"y":587.974,"p":2,"w":4.08}]}},
  {"_key":"60c20d727723bebd866456c6","_id":"annotations/60c20d727723bebd866456c6","_rev":"_cfFmWEy---","wikipediaExternalRef":179088,"document":{"$oid":"60c20d727723bebd866456c5"},"context":"The SPSS (version 21) was used to statistically analyze the data.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":4,"wikidataId":"Q181596","offsetEnd":8,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":323.092,"h":8.78,"y":530.602,"p":2,"w":21.88}]},"version":{"offsetStart":18,"normalizedForm":"21","offsetEnd":20,"rawForm":"21","boundingBoxes":[{"x":383.073,"h":8.78,"y":530.602,"p":2,"w":8.726666666666667}]}},
  {"_key":"60c20d787723bebd866456c8","_id":"annotations/60c20d787723bebd866456c8","_rev":"_cfFmWF----","wikipediaExternalRef":2317445,"document":{"$oid":"60c20d787723bebd866456c7"},"context":"The Adobe Connect online platform was used to conduct all focus groups, with technical assistance from Focus Vision.","wikidataId":"Q2551337","type":"software","confidence":0.9792,"software-name":{"wikipediaExternalRef":2317445,"normalizedForm":"Adobe Connect","offsetStart":4,"wikidataId":"Q2551337","offsetEnd":17,"lang":"en","confidence":0.9792,"rawForm":"Adobe Connect","boundingBoxes":[{"x":116.013,"h":9.584000000000003,"y":444.489,"p":3,"w":66.65399999999997}]},"lang":"en"},
  {"_key":"60c20d787723bebd866456c9","_id":"annotations/60c20d787723bebd866456c9","_rev":"_cfFmWFK---","wikipediaExternalRef":15441720,"document":{"$oid":"60c20d787723bebd866456c7"},"publisher":{"offsetStart":42,"normalizedForm":"QSR International","offsetEnd":59,"rawForm":"QSR International","boundingBoxes":[{"x":101.783975,"h":9.583999999999946,"y":568.246,"p":3,"w":76.03226785714287}]},"context":"Transcripts were coded using NVivo v.11 (QSR International, Melbourne, Australia) [25].","wikidataId":"Q6955723","type":"software","lang":"en","confidence":0.498,"software-name":{"wikipediaExternalRef":15441720,"normalizedForm":"NVivo","offsetStart":29,"wikidataId":"Q6955723","offsetEnd":34,"lang":"en","confidence":0.498,"rawForm":"NVivo","boundingBoxes":[{"x":489.7,"h":9.584,"y":554.736,"p":3,"w":29.036}]},"version":{"offsetStart":38,"normalizedForm":"11","offsetEnd":40,"rawForm":"11","boundingBoxes":[{"x":84.85105,"h":9.584,"y":568.246,"p":3,"w":8.59505}]}},
  {"_key":"60c20d7a7723bebd866456cb","_id":"annotations/60c20d7a7723bebd866456cb","_rev":"_cfFmWFW---","document":{"$oid":"60c20d7a7723bebd866456ca"},"publisher":{"offsetStart":53,"normalizedForm":"GraphPad Software","offsetEnd":71,"rawForm":"GraphPad \nSoftware","boundingBoxes":[{"x":498.9959111111111,"h":11.6816,"y":510.735,"p":3,"w":39.58328888888889},{"x":304.724,"h":11.6816,"y":522.73,"p":3,"w":34.20764444444445}]},"context":"The statistical analysis was performed using Prism (GraphPad Software, La Jolla, CA, USA).","type":"software","software-name":{"offsetStart":46,"normalizedForm":"Prism","offsetEnd":51,"rawForm":"Prism","boundingBoxes":[{"x":467.637,"h":11.6816,"y":510.735,"p":3,"w":24.108}]}},
  {"_key":"60c20d7a7723bebd866456cc","_id":"annotations/60c20d7a7723bebd866456cc","_rev":"_cfFmWFm---","document":{"$oid":"60c20d7a7723bebd866456ca"},"publisher":{"offsetStart":141,"normalizedForm":"Biopac Systems","offsetEnd":155,"rawForm":"Biopac Systems","boundingBoxes":[{"x":224.4706,"h":11.681600000000003,"y":294.73,"p":3,"w":61.67285000000004}]},"context":"Data acquisition from ASL 5000 was performed at 128 Hz and stored in a laptop computer for subsequent analysis with AcqKnowledge software (Biopac Systems, Goleta, CA, USA).","type":"software","software-name":{"offsetStart":118,"normalizedForm":"AcqKnowledge","offsetEnd":130,"rawForm":"AcqKnowledge","boundingBoxes":[{"x":114.796,"h":11.6816,"y":294.73,"p":3,"w":62.1712}]}},
  {"_key":"60c20d827723bebd866456ce","_id":"annotations/60c20d827723bebd866456ce","_rev":"_cfFmWFy---","document":{"$oid":"60c20d827723bebd866456cd"},"type":"software","software-name":{"offsetStart":38,"normalizedForm":"coarseDataTools","offsetEnd":53,"rawForm":"coarseDataTools","boundingBoxes":[{"x":210.596,"h":10.2023,"y":352.437,"p":7,"w":73.04109375}]},"context":"R Foundation;  Vienna, Austria) with coarseDataTools, tidyverse, and lubridate packages."},
  {"_key":"60c20d827723bebd866456cf","_id":"annotations/60c20d827723bebd866456cf","_rev":"_cfFmWG----","document":{"$oid":"60c20d827723bebd866456cd"},"type":"software","software-name":{"offsetStart":70,"normalizedForm":"lubridate","offsetEnd":79,"rawForm":"lubridate","boundingBoxes":[{"x":357.512,"h":10.2023,"y":352.437,"p":7,"w":39.9511}]},"context":"R Foundation;  Vienna, Austria) with coarseDataTools, tidyverse, and lubridate packages."},
  {"_key":"60c20d847723bebd866456d1","_id":"annotations/60c20d847723bebd866456d1","_rev":"_cfFmWGK---","wikipediaExternalRef":179088,"document":{"$oid":"60c20d847723bebd866456d0"},"publisher":{"offsetStart":106,"normalizedForm":"IBM","offsetEnd":109,"rawForm":"IBM","boundingBoxes":[{"x":191.143,"h":11.48,"y":270.16,"p":4,"w":14.025}]},"context":"Statistical analyses were performed using Statistical Package for the Social Sciences for Windows 22.0 (IBM).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.3713,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"Statistical Package for the Social Sciences","offsetStart":43,"wikidataId":"Q181596","offsetEnd":87,"lang":"en","confidence":0.3713,"rawForm":"Statistical Package for the \nSocial Sciences","boundingBoxes":[{"x":180.078,"h":11.480000000000018,"y":257.16,"p":4,"w":109.38000000000002},{"x":46.4882,"h":11.480000000000018,"y":270.16,"p":4,"w":62.490000000000016}]},"version":{"offsetStart":100,"normalizedForm":"22.0","offsetEnd":104,"rawForm":"22.0","boundingBoxes":[{"x":166.468,"h":11.480000000000018,"y":270.16,"p":4,"w":17.5}]}},
  {"_key":"60c20d847723bebd866456d2","_id":"annotations/60c20d847723bebd866456d2","_rev":"_cfFmWGW---","document":{"$oid":"60c20d847723bebd866456d0"},"type":"software","software-name":{"offsetStart":68,"normalizedForm":"Sojump","offsetEnd":74,"rawForm":"Sojump","boundingBoxes":[{"x":380.0325,"h":11.48,"y":686.16,"p":2,"w":28.335}]},"context":"The questionnaire was generated through an online survey platform (Sojump) and consists of five parts: online informed consent, sociodemographic information, epilepsy- related characteristics before and during the epidemic, di- rect and perceived threat related to the COVID-19 outbreak,  and the rating scales Patient Health Questionnaire-9 (PHQ- 9), Generalized Anxiety Disorder-7 items (GAD-7), and Insomnia Severity Index (ISI)."},
  {"_key":"60c20d847723bebd866456d3","_id":"annotations/60c20d847723bebd866456d3","_rev":"_cfFmWGi---","document":{"$oid":"60c20d847723bebd866456d0"},"context":"Two researchers entered data into the database double-blinded using EpiData 3.0 to guarantee accuracy.","type":"software","software-name":{"offsetStart":69,"normalizedForm":"EpiData","offsetEnd":76,"rawForm":"EpiData","boundingBoxes":[{"x":254.937,"h":11.48,"y":127.16,"p":3,"w":32.87}]},"version":{"offsetStart":78,"normalizedForm":"3.0","offsetEnd":81,"rawForm":"3.0","boundingBoxes":[{"x":44.7874,"h":11.47999999999999,"y":140.16,"p":3,"w":12.5}]}},
  {"_key":"60c20d847723bebd866456d4","_id":"annotations/60c20d847723bebd866456d4","_rev":"_cfFmWGu---","wikipediaExternalRef":34408890,"document":{"$oid":"60c20d847723bebd866456d0"},"context":"After excluding 225 patients who (1) were unable to read, (2) had a history of psychiatric illness, or (3) were younger than 10 years in terms of understanding the illness, 13 570 patients received self-reported questionnaires individually by researchers via WeChat.","wikidataId":"Q283233","type":"software","confidence":0.7543,"software-name":{"wikipediaExternalRef":34408890,"normalizedForm":"WeChat","offsetStart":264,"wikidataId":"Q283233","offsetEnd":270,"lang":"en","confidence":0.7543,"rawForm":"WeChat","boundingBoxes":[{"x":307.49,"h":11.48,"y":673.16,"p":2,"w":30.231428571428573}]},"lang":"en"},
  {"_key":"60c20d857723bebd866456d8","_id":"annotations/60c20d857723bebd866456d8","_rev":"_cfFmWG6---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes","type":"software","software-name":{"offsetStart":0,"normalizedForm":"CVTree","offsetEnd":6,"rawForm":"CVTree","boundingBoxes":[{"x":42.463,"h":18.1121,"y":74.4978,"p":1,"w":69.878}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456d9","_id":"annotations/60c20d857723bebd866456d9","_rev":"_cfFmWHG---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"CVTree provides such an alignment-free and parameter- free phylogenetic tool using composition vectors (CVs) inferred from whole genome data (1).","type":"software","software-name":{"offsetStart":0,"normalizedForm":"CVTree","offsetEnd":6,"rawForm":"CVTree","boundingBoxes":[{"x":319.405,"h":8.8667,"y":332.782,"p":1,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456da","_id":"annotations/60c20d857723bebd866456da","_rev":"_cfFmWHS---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"CVTree reads amino acid or nucleotide sequences in FASTA format.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"CVTree","offsetEnd":6,"rawForm":"CVTree","boundingBoxes":[{"x":55.7849,"h":8.8667,"y":631.339,"p":2,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456db","_id":"annotations/60c20d857723bebd866456db","_rev":"_cfFmWHe---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"CVTree also provides a useful tool to find the phylogenetic position of the user's-specific genome data.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"CVTree","offsetEnd":6,"rawForm":"CVTree","boundingBoxes":[{"x":368.843,"h":8.8667,"y":459.83,"p":4,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456dc","_id":"annotations/60c20d857723bebd866456dc","_rev":"_cfFmWHm---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"The CVTree web server (http://tlife.fudan.edu.cn/ cvtree) presented here is a new implementation of the whole genome-based, alignment-free compo- sition vector (CV) method for phylogenetic analysis.","type":"software","software-name":{"offsetStart":4,"normalizedForm":"CVTree","offsetEnd":10,"rawForm":"CVTree","boundingBoxes":[{"x":66.7269,"h":9.056,"y":261.214,"p":1,"w":34.9388}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456dd","_id":"annotations/60c20d857723bebd866456dd","_rev":"_cfFmWHy---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"The CVTree home page contains a link to an online user's manual and provides several ways to get to the project page.","type":"software","software-name":{"offsetStart":4,"normalizedForm":"CVTree","offsetEnd":10,"rawForm":"CVTree","boundingBoxes":[{"x":61.6251,"h":8.8667,"y":375.253,"p":3,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456de","_id":"annotations/60c20d857723bebd866456de","_rev":"_cfFmWI----","document":{"$oid":"60c20d857723bebd866456d5"},"context":"The CVTree result page shows the run-time information and displays the final results when calculation ends.","type":"software","software-name":{"offsetStart":4,"normalizedForm":"CVTree","offsetEnd":10,"rawForm":"CVTree","boundingBoxes":[{"x":76.1384,"h":8.8667,"y":89.0631,"p":4,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456df","_id":"annotations/60c20d857723bebd866456df","_rev":"_cfFmWIK---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"The CVTree web server returns three kinds of result files:","type":"software","software-name":{"offsetStart":4,"normalizedForm":"CVTree","offsetEnd":10,"rawForm":"CVTree","boundingBoxes":[{"x":86.9667,"h":8.8667,"y":111.06,"p":4,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456e0","_id":"annotations/60c20d857723bebd866456e0","_rev":"_cfFmWIW---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"In the CVTree web server, the processing is carried out in two steps (Figure 1).","type":"software","software-name":{"offsetStart":7,"normalizedForm":"CVTree","offsetEnd":13,"rawForm":"CVTree","boundingBoxes":[{"x":94.5045,"h":8.8667,"y":429.226,"p":2,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456e1","_id":"annotations/60c20d857723bebd866456e1","_rev":"_cfFmWIe---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"The new CVTree web server comes with a greater, monthly auto-updated inbuilt database, with a more user-friendly and intuitive interface and a faster data pro- cessing pipeline.","type":"software","software-name":{"offsetStart":8,"normalizedForm":"CVTree","offsetEnd":14,"rawForm":"CVTree","boundingBoxes":[{"x":370.204,"h":8.8667,"y":381.881,"p":4,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456e2","_id":"annotations/60c20d857723bebd866456e2","_rev":"_cfFmWIq---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"This new CVTree web server provides a faster and stable research platform.","type":"software","software-name":{"offsetStart":9,"normalizedForm":"CVTree","offsetEnd":15,"rawForm":"CVTree","boundingBoxes":[{"x":195.246,"h":9.056,"y":452.494,"p":1,"w":34.9388}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456e3","_id":"annotations/60c20d857723bebd866456e3","_rev":"_cfFmWI2---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"(4) The efficiency of CVTree has been significantly enhanced to meet the requirement of treating thou- sands of genomes in a single run.","type":"software","software-name":{"offsetStart":22,"normalizedForm":"CVTree","offsetEnd":28,"rawForm":"CVTree","boundingBoxes":[{"x":414.367,"h":8.8667,"y":627.867,"p":1,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456e4","_id":"annotations/60c20d857723bebd866456e4","_rev":"_cfFmWJC---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"An overview of the new CVTree web server is given in Figure 2. Once connected to CVTree's interface, a user may alternate between six pages shown in the figure, depending on how the job is being submitted and pro- cessed.","type":"software","software-name":{"offsetStart":23,"normalizedForm":"CVTree","offsetEnd":29,"rawForm":"CVTree","boundingBoxes":[{"x":154.487,"h":8.8667,"y":294.466,"p":3,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456e5","_id":"annotations/60c20d857723bebd866456e5","_rev":"_cfFmWJO---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"Since the algorithm used in CVTree has been described previously (1,2,6), we only give a brief account here.","type":"software","software-name":{"offsetStart":28,"normalizedForm":"CVTree","offsetEnd":34,"rawForm":"CVTree","boundingBoxes":[{"x":182.266,"h":8.8667,"y":164.919,"p":2,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456e6","_id":"annotations/60c20d857723bebd866456e6","_rev":"_cfFmWJa---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"These files can be viewed in MEGA and in some other phylogenetic programs.","references":[{"offsetStart":3848,"normalizedForm":"11","refKey":10,"label":"(11)","reference_id":{"$oid":"60c20d857723bebd866456d6"},"offsetEnd":3853,"boundingBoxes":[{"x":461.14,"h":8.866700000000037,"y":594.701,"p":1,"w":16.59770000000003}]}],"type":"software","software-name":{"offsetStart":29,"normalizedForm":"MEGA","offsetEnd":33,"rawForm":"MEGA","boundingBoxes":[{"x":250.919,"h":8.8667,"y":195.308,"p":4,"w":32.3486}]}},
  {"_key":"60c20d857723bebd866456e7","_id":"annotations/60c20d857723bebd866456e7","_rev":"_cfFmWJm---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"All these improvements make the CVTree server a useful complement to various phylogenetic projects  *To whom correspondence should be addressed.","type":"software","software-name":{"offsetStart":32,"normalizedForm":"CVTree","offsetEnd":38,"rawForm":"CVTree","boundingBoxes":[{"x":489.883,"h":8.8667,"y":668.004,"p":1,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456e8","_id":"annotations/60c20d857723bebd866456e8","_rev":"_cfFmWJy---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"The key improvement to accelerate CVTree's speed consists in avoiding repeated calculations among all jobs submitted after a major update of the database.","type":"software","software-name":{"offsetStart":34,"normalizedForm":"CVTree","offsetEnd":40,"rawForm":"CVTree","boundingBoxes":[{"x":233.342,"h":8.8667,"y":341.18,"p":2,"w":30.00735}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456e9","_id":"annotations/60c20d857723bebd866456e9","_rev":"_cfFmWK----","document":{"$oid":"60c20d857723bebd866456d5"},"context":"The program neighbor is borrowed from the PHYLIP package (19).","references":[{"offsetStart":6872,"normalizedForm":"19","refKey":18,"label":"(19)","reference_id":{"$oid":"60c20d857723bebd866456d7"},"offsetEnd":6876,"boundingBoxes":[{"x":135.493,"h":8.866700000000037,"y":583.377,"p":2,"w":15.430080000000004}]}],"type":"software","software-name":{"offsetStart":43,"normalizedForm":"PHYLIP package","offsetEnd":57,"rawForm":"PHYLIP package","boundingBoxes":[{"x":55.7849,"h":8.866700000000037,"y":583.377,"p":2,"w":76.3752}]}},
  {"_key":"60c20d857723bebd866456ea","_id":"annotations/60c20d857723bebd866456ea","_rev":"_cfFmWKO---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"Some tree files are directly uploadable to MEGA (11) or the Interactive Tree Of Life (iTOL) project (12) in order to display the results in different ways.","references":[{"offsetStart":3848,"normalizedForm":"11","refKey":10,"label":"(11)","reference_id":{"$oid":"60c20d857723bebd866456d6"},"offsetEnd":3853,"boundingBoxes":[{"x":461.14,"h":8.866700000000037,"y":594.701,"p":1,"w":16.59770000000003}]}],"type":"software","software-name":{"offsetStart":44,"normalizedForm":"MEGA","offsetEnd":48,"rawForm":"MEGA","boundingBoxes":[{"x":425.197,"h":8.8667,"y":594.701,"p":1,"w":32.3486}]}},
  {"_key":"60c20d857723bebd866456eb","_id":"annotations/60c20d857723bebd866456eb","_rev":"_cfFmWKe---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"We will further improve the implementation of CVTree to meet the need of efficiently processing thousands of genomes.","type":"software","software-name":{"offsetStart":47,"normalizedForm":"CVTree","offsetEnd":53,"rawForm":"CVTree","boundingBoxes":[{"x":405.126,"h":8.8667,"y":526.611,"p":4,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456ec","_id":"annotations/60c20d857723bebd866456ec","_rev":"_cfFmWKq---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"Users may upload their own genomic sequences to the CVTree web server.","type":"software","software-name":{"offsetStart":53,"normalizedForm":"CVTree","offsetEnd":59,"rawForm":"CVTree","boundingBoxes":[{"x":341.232,"h":8.8667,"y":686.169,"p":2,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456ed","_id":"annotations/60c20d857723bebd866456ed","_rev":"_cfFmWK6---","document":{"$oid":"60c20d857723bebd866456d5"},"type":"software","software-name":{"offsetStart":61,"normalizedForm":"Interactive Tree Of Life (iTOL)","offsetEnd":93,"rawForm":"Interactive \nTree Of Life (iTOL)","boundingBoxes":[{"x":510.973,"h":8.8667,"y":594.701,"p":1,"w":45.5191},{"x":326.665,"h":8.866700000000037,"y":605.757,"p":1,"w":89.45339999999993}]},"context":"Some tree files are directly uploadable to MEGA (11) or the Interactive Tree Of Life (iTOL) project (12) in order to display the results in different ways."},
  {"_key":"60c20d857723bebd866456ee","_id":"annotations/60c20d857723bebd866456ee","_rev":"_cfFmWLG---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"One may consult (1,2,6) or the online user's manual (available from the CVTree home page or http://tlife.","type":"software","software-name":{"offsetStart":73,"normalizedForm":"CVTree","offsetEnd":79,"rawForm":"CVTree","boundingBoxes":[{"x":147.965,"h":8.8667,"y":308.184,"p":2,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456ef","_id":"annotations/60c20d857723bebd866456ef","_rev":"_cfFmWLW---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"However, there are still many eukaryote genomes not included in the new CVTree web server.","type":"software","software-name":{"offsetStart":73,"normalizedForm":"CVTree","offsetEnd":79,"rawForm":"CVTree","boundingBoxes":[{"x":413.631,"h":8.8667,"y":493.221,"p":4,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456f0","_id":"annotations/60c20d857723bebd866456f0","_rev":"_cfFmWLi---","wikipediaExternalRef":19133401,"document":{"$oid":"60c20d857723bebd866456d5"},"context":"To upload, first click the 'Browse'  button (or 'Choose File' button in Google Chrome web browser) to find a sequence file locally, and then press 'Upload this file' to transfer.","wikidataId":"Q777","type":"software","confidence":0.9785,"software-name":{"wikipediaExternalRef":19133401,"normalizedForm":"Google Chrome","offsetStart":73,"wikidataId":"Q777","offsetEnd":86,"lang":"en","confidence":0.9785,"rawForm":"Google Chrome","boundingBoxes":[{"x":465.559,"h":8.866700000000009,"y":233.303,"p":3,"w":69.85039999999998}]},"lang":"en"},
  {"_key":"60c20d857723bebd866456f1","_id":"annotations/60c20d857723bebd866456f1","_rev":"_cfFmWLy---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"An overview of the new CVTree web server is given in Figure 2. Once connected to CVTree's interface, a user may alternate between six pages shown in the figure, depending on how the job is being submitted and pro- cessed.","type":"software","software-name":{"offsetStart":82,"normalizedForm":"CVTree","offsetEnd":88,"rawForm":"CVTree","boundingBoxes":[{"x":174.047,"h":8.8667,"y":305.464,"p":3,"w":30.00735}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456f2","_id":"annotations/60c20d857723bebd866456f2","_rev":"_cfFmWMC---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"We suggest users always to create a new project to do their analysis, in this way the CVTree server does the garbage collection more efficiently.","type":"software","software-name":{"offsetStart":87,"normalizedForm":"CVTree","offsetEnd":93,"rawForm":"CVTree","boundingBoxes":[{"x":255.965,"h":8.8667,"y":496.012,"p":3,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456f3","_id":"annotations/60c20d857723bebd866456f3","_rev":"_cfFmWMO---","wikipediaExternalRef":3678414,"document":{"$oid":"60c20d857723bebd866456d5"},"context":"The ffn files are locally extracted from the gbk files by the program extractfeat in the EMBOSS  package (20).","wikidataId":"Q690201","type":"software","confidence":0.8057,"software-name":{"wikipediaExternalRef":3678414,"normalizedForm":"EMBOSS","offsetStart":90,"wikidataId":"Q690201","offsetEnd":98,"lang":"en","confidence":0.8057,"rawForm":"EMBOSS","boundingBoxes":[{"x":261.012,"h":8.8667,"y":730.441,"p":2,"w":41.7931}]},"lang":"en"},
  {"_key":"60c20d857723bebd866456f4","_id":"annotations/60c20d857723bebd866456f4","_rev":"_cfFmWMe---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"In order to catch up with the increasing amount of geno- mic data, we have redesigned the data processing strategy and implemented a new user-friendly web interface to improve the new CVTree server in several aspects:","type":"software","software-name":{"offsetStart":186,"normalizedForm":"CVTree","offsetEnd":192,"rawForm":"CVTree","boundingBoxes":[{"x":384.661,"h":8.8667,"y":499.29,"p":1,"w":33.4843}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d857723bebd866456f5","_id":"annotations/60c20d857723bebd866456f5","_rev":"_cfFmWMu---","document":{"$oid":"60c20d857723bebd866456d5"},"context":"One collects all protein products in a genome and counts the number of (overlapping) K-tuples to form a raw CV with 20 K or 4 K components, depending on whether protein or coding DNA sequences are used (both options are allowed in CVTree, but protein sequences are recommended).","type":"software","software-name":{"offsetStart":235,"normalizedForm":"CVTree","offsetEnd":241,"rawForm":"CVTree","boundingBoxes":[{"x":205.453,"h":8.8667,"y":231.022,"p":2,"w":31.00645714285714}]},"url":{"offsetStart":23,"normalizedForm":"http://tlife.fudan.edu.cn/ cvtree","offsetEnd":57,"rawForm":"http://tlife.fudan.edu.cn/ \ncvtree","boundingBoxes":[{"x":175.36762962962965,"h":9.055999999999983,"y":261.214,"p":1,"w":114.00037037037035},{"x":42.463,"h":9.056,"y":273.176,"p":1,"w":27.88962857142857}]}},
  {"_key":"60c20d867723bebd866456f7","_id":"annotations/60c20d867723bebd866456f7","_rev":"_cfFmWNC---","wikipediaExternalRef":28309569,"document":{"$oid":"60c20d867723bebd866456f6"},"context":"Eligible patients who were informed of the study and agreed to be contacted were invited to complete an online de-identified survey via email using REDCap.","wikidataId":"Q7305527","type":"software","confidence":0.5069,"software-name":{"wikipediaExternalRef":28309569,"normalizedForm":"REDCap","offsetStart":150,"wikidataId":"Q7305527","offsetEnd":156,"lang":"en","confidence":0.5069,"rawForm":"REDCap","boundingBoxes":[{"x":46.7716,"h":8.3099,"y":525.798,"p":2,"w":30.721285714285717}]},"lang":"en"},
  {"_key":"60c20d897723bebd866456fa","_id":"annotations/60c20d897723bebd866456fa","_rev":"_cfFmWNS---","document":{"$oid":"60c20d897723bebd866456f9"},"context":"Using NanoAnalyze Software (version 3.11.0),","type":"software","software-name":{"offsetStart":6,"normalizedForm":"NanoAnalyze","offsetEnd":17,"rawForm":"NanoAnalyze","boundingBoxes":[{"x":472.818,"h":8.9901,"y":583.239,"p":2,"w":51.2005}]},"version":{"offsetStart":37,"normalizedForm":"3.11.0","offsetEnd":43,"rawForm":"3.11.0","boundingBoxes":[{"x":360.168,"h":8.990099999999984,"y":594.634,"p":2,"w":21.907725000000028}]}},
  {"_key":"60c20d897723bebd866456fb","_id":"annotations/60c20d897723bebd866456fb","_rev":"_cfFmWNq---","document":{"$oid":"60c20d897723bebd866456f9"},"type":"software","software-name":{"offsetStart":43,"normalizedForm":"DIALS","offsetEnd":48,"rawForm":"DIALS","boundingBoxes":[{"x":138.613,"h":8.9901,"y":344.384,"p":3,"w":26.7703}]},"context":"The data were indexed and integrated with DIALS 15,16 as implemented in version 7.2 of the CCP4 software suite. 17,18"},
  {"_key":"60c20d897723bebd866456fc","_id":"annotations/60c20d897723bebd866456fc","_rev":"_cfFmWN6---","document":{"$oid":"60c20d897723bebd866456f9"},"type":"software","software-name":{"offsetStart":49,"normalizedForm":"AIMLESS","offsetEnd":56,"rawForm":"AIMLESS","boundingBoxes":[{"x":164.802,"h":8.9901,"y":366.388,"p":3,"w":36.80635}]},"context":"Data scaling and reduction were performed using AIMLESS. 19"},
  {"_key":"60c20d897723bebd866456fd","_id":"annotations/60c20d897723bebd866456fd","_rev":"_cfFmWOK---","document":{"$oid":"60c20d897723bebd866456f9"},"type":"software","software-name":{"offsetStart":84,"normalizedForm":"PHENIX","offsetEnd":90,"rawForm":"PHENIX","boundingBoxes":[{"x":223.881,"h":8.9901,"y":432.379,"p":3,"w":26.052685714285712}]},"context":"The model underwent iterative rounds of (re)- building in COOT 23 and refinement in PHENIX.refine. 24,25"},
  {"_key":"60c20d897723bebd866456fe","_id":"annotations/60c20d897723bebd866456fe","_rev":"_cfFmWOa---","wikipediaExternalRef":5268864,"document":{"$oid":"60c20d897723bebd866456f9"},"context":"The data were indexed and integrated with DIALS 15,16 as implemented in version 7.2 of the CCP4 software suite. 17,18","wikidataId":"Q5145814","type":"software","lang":"en","confidence":0.3545,"software-name":{"wikipediaExternalRef":5268864,"normalizedForm":"CCP4","offsetStart":93,"wikidataId":"Q5145814","offsetEnd":97,"lang":"en","confidence":0.3545,"rawForm":"CCP4","boundingBoxes":[{"x":88.7809,"h":8.990099999999984,"y":355.39,"p":3,"w":23.6802}]},"version":{"offsetStart":81,"normalizedForm":"7.2","offsetEnd":84,"rawForm":"7.2","boundingBoxes":[{"x":288.907,"h":8.990099999999984,"y":344.392,"p":3,"w":11.560099999999977}]}},
  {"_key":"60c20d8d7723bebd86645700","_id":"annotations/60c20d8d7723bebd86645700","_rev":"_cfFmWOq---","document":{"$oid":"60c20d8d7723bebd866456ff"},"type":"software","software-name":{"offsetStart":57,"normalizedForm":"Imaging and","offsetEnd":68,"rawForm":"Imaging and","boundingBoxes":[{"x":143.329,"h":11.480000000000018,"y":282.755,"p":5,"w":55.41999999999999}]},"context":"Further development of image stand- ards such as Digital Imaging and Communications in Medicine (DICOM) for dermatology imaging could also improve interoperability and security of image ingestion [16]."},
  {"_key":"60c20d8d7723bebd86645701","_id":"annotations/60c20d8d7723bebd86645701","_rev":"_cfFmWO2---","document":{"$oid":"60c20d8d7723bebd866456ff"},"type":"software","software-name":{"offsetStart":84,"normalizedForm":"in Medicine (","offsetEnd":98,"rawForm":"in \nMedicine (","boundingBoxes":[{"x":280.919,"h":11.48,"y":282.755,"p":5,"w":8.27},{"x":51.0236,"h":11.480000000000018,"y":295.255,"p":5,"w":52.66428571428571}]},"context":"Further development of image stand- ards such as Digital Imaging and Communications in Medicine (DICOM) for dermatology imaging could also improve interoperability and security of image ingestion [16]."},
  {"_key":"60c20d8d7723bebd86645702","_id":"annotations/60c20d8d7723bebd86645702","_rev":"_cfFmWPG---","document":{"$oid":"60c20d8d7723bebd866456ff"},"publisher":{"offsetStart":104,"normalizedForm":"Can- field Scientific","offsetEnd":125,"rawForm":"Can-\nfield Scientific","boundingBoxes":[{"x":525.409,"h":11.480000000000018,"y":358.635,"p":2,"w":18.823999999999955},{"x":306.143,"h":11.480000000000018,"y":371.135,"p":2,"w":62.22000000000003}]},"context":"Image Ingestion: All images reviewed were ultimately uploaded into our secure image database, Vectra™ (Can- field Scientific, Parsippany, NY) imaging software, by a member of the office or clinical staff.","type":"software","software-name":{"offsetStart":95,"normalizedForm":"Vectra™","offsetEnd":102,"rawForm":"Vectra™","boundingBoxes":[{"x":481.003,"h":11.48,"y":358.635,"p":2,"w":36.87}]}},
  {"_key":"60c20d8d7723bebd86645703","_id":"annotations/60c20d8d7723bebd86645703","_rev":"_cfFmWPW---","document":{"$oid":"60c20d8d7723bebd866456ff"},"type":"software","software-name":{"offsetStart":232,"normalizedForm":"Voalte™","offsetEnd":239,"rawForm":"Voalte™","boundingBoxes":[{"x":335.381,"h":11.48,"y":402.323,"p":4,"w":36.668}]},"context":"Figure 3 shows the proportion of inpatient consulta- tions, where PPE was at a particular premium, that were able to be converted to interprofessional e-consults on the basis of smartphone photography and secure messaging on the Voalte™ platform."},
  {"_key":"60c20d937723bebd8664570a","_id":"annotations/60c20d937723bebd8664570a","_rev":"_cfFmWPm---","document":{"$oid":"60c20d937723bebd86645704"},"context":"and MATLAB_R2018a packages.","type":"software","software-name":{"offsetStart":4,"normalizedForm":"MATLAB_R","offsetEnd":12,"rawForm":"MATLAB_R","boundingBoxes":[{"x":441.695,"h":6.4159,"y":322.876,"p":11,"w":55.1294}]},"version":{"offsetStart":16,"normalizedForm":"a","offsetEnd":17,"rawForm":"a","boundingBoxes":[{"x":441.695,"h":6.4159,"y":322.876,"p":11,"w":55.1294}]}},
  {"_key":"60c20d937723bebd8664570b","_id":"annotations/60c20d937723bebd8664570b","_rev":"_cfFmWPy---","document":{"$oid":"60c20d937723bebd86645704"},"type":"software","software-name":{"offsetStart":13,"normalizedForm":"HT-AM pipeline","offsetEnd":27,"rawForm":"HT-AM pipeline","boundingBoxes":[{"x":161.4,"h":8.311800000000005,"y":350.393,"p":10,"w":65.393}]},"context":"Although the HT-AM pipeline does not cap- ture temporal dynamics, we found that the probabilistic networks reported here closely resembled the ones derived from the MD simulations, and the two lead to similar predictions, for instance, the clustering of glycans into larger microdomains (SI Appendix, Fig. S10)."},
  {"_key":"60c20d937723bebd8664570c","_id":"annotations/60c20d937723bebd8664570c","_rev":"_cfFmWQC---","wikipediaExternalRef":5269034,"document":{"$oid":"60c20d937723bebd86645704"},"context":"Model building and refinement were carried out with UCSF Chimera (67), Coot (68, 69), and Rosetta (70).","wikidataId":"Q7864121","type":"software","confidence":0.9776,"software-name":{"wikipediaExternalRef":5269034,"normalizedForm":"UCSF Chimera","offsetStart":53,"wikidataId":"Q7864121","offsetEnd":65,"lang":"en","confidence":0.9776,"rawForm":"UCSF Chimera","boundingBoxes":[{"x":359.664,"h":6.415900000000022,"y":259.889,"p":11,"w":46.54170000000005}]},"lang":"en"},
  {"_key":"60c20d937723bebd8664570d","_id":"annotations/60c20d937723bebd8664570d","_rev":"_cfFmWQS---","wikipediaExternalRef":20412,"document":{"$oid":"60c20d937723bebd86645704"},"context":"All custom analysis of cryo-EM maps was performed in MATLAB (2018b) (MATLAB and Image Processing Toolbox Release 2018b, The MathWorks).","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7687,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":54,"wikidataId":"Q169478","offsetEnd":60,"lang":"en","confidence":0.7687,"rawForm":"MATLAB","boundingBoxes":[{"x":489.499,"h":6.4159,"y":268.903,"p":11,"w":28.1013}]},"version":{"offsetStart":62,"normalizedForm":"2018b","offsetEnd":67,"rawForm":"2018b","boundingBoxes":[{"x":525.7697285714286,"h":6.415900000000022,"y":268.903,"p":11,"w":17.218642857142868}]}},
  {"_key":"60c20d937723bebd8664570e","_id":"annotations/60c20d937723bebd8664570e","_rev":"_cfFmWQe---","document":{"$oid":"60c20d937723bebd86645704"},"context":"The HT- AM pipeline was carried out by implementing the ALLOSMOD (29, 71) package of MODELLER (72, 73) in a streamlined pipeline.","references":[{"offsetStart":63082,"normalizedForm":"(29","refKey":28,"label":"(29,","reference_id":{"$oid":"60c20d937723bebd86645705"},"offsetEnd":63092,"boundingBoxes":[{"x":520.796,"h":6.415900000000022,"y":295.89,"p":11,"w":25.651199999999903}]},{"offsetStart":63082,"normalizedForm":"71)","refKey":70,"label":"71)","reference_id":{"$oid":"60c20d937723bebd86645706"},"offsetEnd":63092,"boundingBoxes":[{"x":520.796,"h":6.415900000000022,"y":295.89,"p":11,"w":25.651199999999903}]}],"type":"software","software-name":{"offsetStart":56,"normalizedForm":"ALLOSMOD","offsetEnd":64,"rawForm":"ALLOSMOD","boundingBoxes":[{"x":479.124,"h":6.4159,"y":295.89,"p":11,"w":37.8341}]}},
  {"_key":"60c20d937723bebd8664570f","_id":"annotations/60c20d937723bebd8664570f","_rev":"_cfFmWQq---","wikipediaExternalRef":5269034,"document":{"$oid":"60c20d937723bebd86645704"},"context":"All cryo-EM map and model visualization was performed with UCSF Chimera.","wikidataId":"Q7864121","type":"software","confidence":0.9776,"software-name":{"wikipediaExternalRef":5269034,"normalizedForm":"UCSF Chimera","offsetStart":60,"wikidataId":"Q7864121","offsetEnd":72,"lang":"en","confidence":0.9776,"rawForm":"UCSF Chimera","boundingBoxes":[{"x":492.387,"h":6.415900000000022,"y":340.904,"p":11,"w":42.587199999999996}]},"lang":"en"},
  {"_key":"60c20d937723bebd86645710","_id":"annotations/60c20d937723bebd86645710","_rev":"_cfFmWQ6---","wikipediaExternalRef":23862,"document":{"$oid":"60c20d937723bebd86645704"},"context":"All graph theory and network-based analysis was performed using Python (Python Software Foundation; https://www.python.org/)","wikidataId":"Q28865","type":"software","confidence":0.6136,"software-name":{"wikipediaExternalRef":23862,"normalizedForm":"Python","offsetStart":65,"wikidataId":"Q28865","offsetEnd":71,"lang":"en","confidence":0.6136,"rawForm":"Python","boundingBoxes":[{"x":464.896,"h":6.4159,"y":313.861,"p":11,"w":22.6617}]},"lang":"en"},
  {"_key":"60c20d937723bebd86645711","_id":"annotations/60c20d937723bebd86645711","_rev":"_cfFmWRO---","document":{"$oid":"60c20d937723bebd86645704"},"type":"software","software-name":{"offsetStart":67,"normalizedForm":"RELION","offsetEnd":73,"rawForm":"RELION","boundingBoxes":[{"x":510.544,"h":6.4159,"y":331.89,"p":11,"w":21.0204}]},"context":"Sim- ulated cryo-EM data generation and analysis were performed in RELION."},
  {"_key":"60c20d937723bebd86645712","_id":"annotations/60c20d937723bebd86645712","_rev":"_cfFmWRa---","wikipediaExternalRef":20412,"document":{"$oid":"60c20d937723bebd86645704"},"context":"All custom analysis of cryo-EM maps was performed in MATLAB (2018b) (MATLAB and Image Processing Toolbox Release 2018b, The MathWorks).","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7687,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":71,"wikidataId":"Q169478","offsetEnd":77,"lang":"en","confidence":0.7687,"rawForm":"MATLAB","boundingBoxes":[{"x":305.71437142857144,"h":6.4159,"y":277.918,"p":11,"w":26.01222857142857}]},"version":{"offsetStart":62,"normalizedForm":"2018b","offsetEnd":67,"rawForm":"2018b","boundingBoxes":[{"x":525.7697285714286,"h":6.415900000000022,"y":268.903,"p":11,"w":17.218642857142868}]}},
  {"_key":"60c20d937723bebd86645713","_id":"annotations/60c20d937723bebd86645713","_rev":"_cfFmWRq---","wikipediaExternalRef":696712,"document":{"$oid":"60c20d937723bebd86645704"},"context":"All graph theory and network-based analysis was performed using Python (Python Software Foundation; https://www.python.org/)","wikidataId":"Q83818","type":"software","confidence":0.8988,"software-name":{"wikipediaExternalRef":696712,"normalizedForm":"Python Software Foundation","offsetStart":73,"wikidataId":"Q83818","offsetEnd":100,"lang":"en","confidence":0.8988,"rawForm":"Python Software \nFoundation","boundingBoxes":[{"x":493.4677571428571,"h":6.415900000000022,"y":313.861,"p":11,"w":52.95024285714288},{"x":301.379,"h":6.4159,"y":322.876,"p":11,"w":35.51627272727273}]},"url":{"offsetStart":102,"normalizedForm":"https://www.python.org","offsetEnd":124,"rawForm":"https://www.python.org","boundingBoxes":[{"x":342.935,"h":6.415900000000022,"y":322.876,"p":11,"w":74.76269166666663}]},"lang":"en"},
  {"_key":"60c20d937723bebd86645714","_id":"annotations/60c20d937723bebd86645714","_rev":"_cfFmWR6---","document":{"$oid":"60c20d937723bebd86645704"},"publisher":{"offsetStart":122,"normalizedForm":"The MathWorks","offsetEnd":135,"rawForm":"The MathWorks","boundingBoxes":[{"x":489.728,"h":6.415900000000022,"y":277.918,"p":11,"w":49.073490909090935}]},"context":"All custom analysis of cryo-EM maps was performed in MATLAB (2018b) (MATLAB and Image Processing Toolbox Release 2018b, The MathWorks).","type":"software","software-name":{"offsetStart":82,"normalizedForm":"Image Processing Toolbox","offsetEnd":106,"rawForm":"Image Processing Toolbox","boundingBoxes":[{"x":349.911,"h":6.415900000000022,"y":277.918,"p":11,"w":85.26569999999998}]},"version":{"offsetStart":115,"normalizedForm":"2018b","offsetEnd":120,"rawForm":"2018b","boundingBoxes":[{"x":465.292,"h":6.415900000000022,"y":277.918,"p":11,"w":17.91424999999998}]}},
  {"_key":"60c20d937723bebd86645715","_id":"annotations/60c20d937723bebd86645715","_rev":"_cfFmWSG---","wikipediaExternalRef":8011876,"document":{"$oid":"60c20d937723bebd86645704"},"context":"The HT- AM pipeline was carried out by implementing the ALLOSMOD (29, 71) package of MODELLER (72, 73) in a streamlined pipeline.","wikidataId":"Q3859815","references":[{"offsetStart":63112,"normalizedForm":"(72","refKey":71,"label":"(72,","reference_id":{"$oid":"60c20d937723bebd86645707"},"offsetEnd":63121,"boundingBoxes":[{"x":378.827,"h":6.415900000000022,"y":304.904,"p":11,"w":24.40420000000006}]},{"offsetStart":63112,"normalizedForm":"73)","refKey":72,"label":"73)","reference_id":{"$oid":"60c20d937723bebd86645708"},"offsetEnd":63121,"boundingBoxes":[{"x":378.827,"h":6.415900000000022,"y":304.904,"p":11,"w":24.40420000000006}]}],"type":"software","confidence":0.3285,"software-name":{"wikipediaExternalRef":8011876,"normalizedForm":"MODELLER","offsetStart":86,"wikidataId":"Q3859815","offsetEnd":94,"lang":"en","confidence":0.3285,"rawForm":"MODELLER","boundingBoxes":[{"x":340.387,"h":6.4159,"y":304.904,"p":11,"w":35.8019}]},"lang":"en"},
  {"_key":"60c20d937723bebd86645716","_id":"annotations/60c20d937723bebd86645716","_rev":"_cfFmWSW---","wikipediaExternalRef":2001990,"document":{"$oid":"60c20d937723bebd86645704"},"context":"Model building and refinement were carried out with UCSF Chimera (67), Coot (68, 69), and Rosetta (70).","wikidataId":"Q1196945","references":[{"offsetStart":62804,"normalizedForm":"70","refKey":69,"label":"(70)","reference_id":{"$oid":"60c20d937723bebd86645709"},"offsetEnd":62808,"boundingBoxes":[{"x":520.117,"h":6.415900000000022,"y":259.889,"p":11,"w":11.260960000000068}]}],"type":"software","confidence":0.3932,"software-name":{"wikipediaExternalRef":2001990,"normalizedForm":"Rosetta","offsetStart":91,"wikidataId":"Q1196945","offsetEnd":98,"lang":"en","confidence":0.3932,"rawForm":"Rosetta","boundingBoxes":[{"x":492.448,"h":6.4159,"y":259.889,"p":11,"w":24.1828}]},"lang":"en"},
  {"_key":"60c20d937723bebd86645717","_id":"annotations/60c20d937723bebd86645717","_rev":"_cfFmWSi---","document":{"$oid":"60c20d937723bebd86645704"},"context":"To overcome the sampling limitations of MD simulations, we employed a high-throughput at- omistic modeling (HT-AM) pipeline based around the ALLOSMOD package of the MODELLER software suite (29), which has been used previously to generate small ensembles of glycosylated Env (30).","references":[{"offsetStart":63082,"normalizedForm":"(29","refKey":28,"label":"(29,","reference_id":{"$oid":"60c20d937723bebd86645705"},"offsetEnd":63092,"boundingBoxes":[{"x":520.796,"h":6.415900000000022,"y":295.89,"p":11,"w":25.651199999999903}]},{"offsetStart":63082,"normalizedForm":"71)","refKey":70,"label":"71)","reference_id":{"$oid":"60c20d937723bebd86645706"},"offsetEnd":63092,"boundingBoxes":[{"x":520.796,"h":6.415900000000022,"y":295.89,"p":11,"w":25.651199999999903}]}],"type":"software","software-name":{"offsetStart":142,"normalizedForm":"ALLOSMOD","offsetEnd":150,"rawForm":"ALLOSMOD","boundingBoxes":[{"x":495.483,"h":8.3118,"y":487.192,"p":3,"w":51.0209}]}},
  {"_key":"60c20d937723bebd86645718","_id":"annotations/60c20d937723bebd86645718","_rev":"_cfFmWSu---","wikipediaExternalRef":8011876,"document":{"$oid":"60c20d937723bebd86645704"},"context":"To overcome the sampling limitations of MD simulations, we employed a high-throughput at- omistic modeling (HT-AM) pipeline based around the ALLOSMOD package of the MODELLER software suite (29), which has been used previously to generate small ensembles of glycosylated Env (30).","wikidataId":"Q3859815","references":[{"offsetStart":63112,"normalizedForm":"(72","refKey":71,"label":"(72,","reference_id":{"$oid":"60c20d937723bebd86645707"},"offsetEnd":63121,"boundingBoxes":[{"x":378.827,"h":6.415900000000022,"y":304.904,"p":11,"w":24.40420000000006}]},{"offsetStart":63112,"normalizedForm":"73)","refKey":72,"label":"73)","reference_id":{"$oid":"60c20d937723bebd86645708"},"offsetEnd":63121,"boundingBoxes":[{"x":378.827,"h":6.415900000000022,"y":304.904,"p":11,"w":24.40420000000006}]}],"type":"software","confidence":0.3285,"software-name":{"wikipediaExternalRef":8011876,"normalizedForm":"MODELLER","offsetStart":167,"wikidataId":"Q3859815","offsetEnd":175,"lang":"en","confidence":0.3285,"rawForm":"MODELLER","boundingBoxes":[{"x":359.204,"h":8.3118,"y":497.397,"p":3,"w":52.6214}]},"lang":"en"},
  {"_key":"60c20d937723bebd8664571a","_id":"annotations/60c20d937723bebd8664571a","_rev":"_cfFmWT----","document":{"$oid":"60c20d937723bebd86645719"},"context":"and Phenograph (59) (https://github.com/JinmiaoChenLab/Rphenograph).","type":"software","software-name":{"offsetStart":4,"normalizedForm":"Phenograph","offsetEnd":14,"rawForm":"Phenograph","boundingBoxes":[{"x":491.585,"h":6.4159,"y":538.25,"p":10,"w":39.5916}]},"url":{"offsetStart":22,"normalizedForm":"https://github.com/JinmiaoChenLab/Rphenograph","offsetEnd":67,"rawForm":"https://github.com/JinmiaoChenLab/Rphenograph","boundingBoxes":[{"x":304.8453333333334,"h":6.415899999999965,"y":547.321,"p":10,"w":155.98499999999996}]}},
  {"_key":"60c20d937723bebd8664571b","_id":"annotations/60c20d937723bebd8664571b","_rev":"_cfFmWTK---","document":{"$oid":"60c20d937723bebd86645719"},"context":"UMAP coordinates and Phenograph cluster annotation were assigned to each cell in each sample in the concatenated sample file, and from there, subset-specific phenotypic changes of mean fluorescence intensity (MFI) were analyzed by gating di- rectly in the UMAP space on the concatenated samples using FlowJo v.10.5.3 (BD Biosciences).","type":"software","software-name":{"offsetStart":22,"normalizedForm":"Phenograph","offsetEnd":32,"rawForm":"Phenograph","boundingBoxes":[{"x":301.379,"h":6.4159,"y":556.392,"p":10,"w":39.5916}]},"url":{"offsetStart":22,"normalizedForm":"https://github.com/JinmiaoChenLab/Rphenograph","offsetEnd":67,"rawForm":"https://github.com/JinmiaoChenLab/Rphenograph","boundingBoxes":[{"x":304.8453333333334,"h":6.415899999999965,"y":547.321,"p":10,"w":155.98499999999996}]}},
  {"_key":"60c20d937723bebd8664571c","_id":"annotations/60c20d937723bebd8664571c","_rev":"_cfFmWTW---","document":{"$oid":"60c20d937723bebd86645719"},"publisher":{"offsetStart":40,"normalizedForm":"BD Bio- sciences","offsetEnd":56,"rawForm":"BD Bio-\nsciences","boundingBoxes":[{"x":523.8189333333332,"h":6.415900000000022,"y":501.849,"p":10,"w":22.623166666666748},{"x":301.379,"h":6.4159,"y":510.976,"p":10,"w":23.510080000000002}]},"context":"Acquired data were analyzed using DIVA (BD Bio- sciences), FlowJo v.10.5.3 (BD Biosciences), and Prism v8.0.2 (GraphPad Software).","type":"software","software-name":{"offsetStart":34,"normalizedForm":"DIVA","offsetEnd":38,"rawForm":"DIVA","boundingBoxes":[{"x":501.003,"h":6.4159,"y":501.849,"p":10,"w":16.5442}]}},
  {"_key":"60c20d937723bebd8664571d","_id":"annotations/60c20d937723bebd8664571d","_rev":"_cfFmWTi---","document":{"$oid":"60c20d937723bebd86645719"},"context":"Algorithms used for dimensionality reduction were UMAP (58) (https://github.com/lmcinnes/umap)","type":"software","software-name":{"offsetStart":51,"normalizedForm":"UMAP","offsetEnd":55,"rawForm":"UMAP","boundingBoxes":[{"x":320.599,"h":6.4159,"y":538.25,"p":10,"w":20.4007}]},"url":{"offsetStart":62,"normalizedForm":"https://github.com/lmcinnes/umap","offsetEnd":94,"rawForm":"https://github.com/lmcinnes/umap","boundingBoxes":[{"x":362.7247941176471,"h":6.415899999999965,"y":538.25,"p":10,"w":107.06541176470586}]}},
  {"_key":"60c20d937723bebd8664571e","_id":"annotations/60c20d937723bebd8664571e","_rev":"_cfFmWTu---","wikipediaExternalRef":24666773,"document":{"$oid":"60c20d937723bebd86645719"},"publisher":{"offsetStart":76,"normalizedForm":"BD Biosciences","offsetEnd":90,"rawForm":"BD Biosciences","boundingBoxes":[{"x":394.5416333333334,"h":6.415899999999965,"y":510.976,"p":10,"w":45.715428205128205}]},"context":"Acquired data were analyzed using DIVA (BD Bio- sciences), FlowJo v.10.5.3 (BD Biosciences), and Prism v8.0.2 (GraphPad Software).","wikidataId":"Q5462055","type":"software","lang":"en","confidence":0.4725,"software-name":{"wikipediaExternalRef":24666773,"normalizedForm":"FlowJo","offsetStart":59,"wikidataId":"Q5462055","offsetEnd":65,"lang":"en","confidence":0.4725,"rawForm":"FlowJo","boundingBoxes":[{"x":335.165,"h":6.4159,"y":510.976,"p":10,"w":22.2959}]},"version":{"offsetStart":68,"normalizedForm":"10.5.3","offsetEnd":74,"rawForm":"10.5.3","boundingBoxes":[{"x":367.94245,"h":6.415899999999965,"y":510.976,"p":10,"w":18.40035000000006}]}},
  {"_key":"60c20d937723bebd8664571f","_id":"annotations/60c20d937723bebd8664571f","_rev":"_cfFmWU----","document":{"$oid":"60c20d937723bebd86645719"},"publisher":{"offsetStart":111,"normalizedForm":"GraphPad Software","offsetEnd":129,"rawForm":"GraphPad \nSoftware","boundingBoxes":[{"x":516.0544222222222,"h":6.4159,"y":510.976,"p":10,"w":30.331377777777774},{"x":301.379,"h":6.4159,"y":520.047,"p":10,"w":26.725760000000005}]},"context":"Acquired data were analyzed using DIVA (BD Bio- sciences), FlowJo v.10.5.3 (BD Biosciences), and Prism v8.0.2 (GraphPad Software).","type":"software","software-name":{"offsetStart":97,"normalizedForm":"Prism","offsetEnd":102,"rawForm":"Prism","boundingBoxes":[{"x":467.364,"h":6.4159,"y":510.976,"p":10,"w":17.2741}]},"version":{"offsetStart":104,"normalizedForm":"8.0.2","offsetEnd":109,"rawForm":"8.0.2","boundingBoxes":[{"x":489.02,"h":6.415899999999965,"y":510.976,"p":10,"w":18.871800000000007}]}},
  {"_key":"60c20d937723bebd86645720","_id":"annotations/60c20d937723bebd86645720","_rev":"_cfFmWUK---","wikipediaExternalRef":24666773,"document":{"$oid":"60c20d937723bebd86645719"},"publisher":{"offsetStart":322,"normalizedForm":"BD Biosciences","offsetEnd":336,"rawForm":"BD Biosciences","boundingBoxes":[{"x":305.20063333333337,"h":6.415899999999965,"y":592.788,"p":10,"w":43.59995128205122}]},"context":"UMAP coordinates and Phenograph cluster annotation were assigned to each cell in each sample in the concatenated sample file, and from there, subset-specific phenotypic changes of mean fluorescence intensity (MFI) were analyzed by gating di- rectly in the UMAP space on the concatenated samples using FlowJo v.10.5.3 (BD Biosciences).","wikidataId":"Q5462055","type":"software","lang":"en","confidence":0.4725,"software-name":{"wikipediaExternalRef":24666773,"normalizedForm":"FlowJo","offsetStart":304,"wikidataId":"Q5462055","offsetEnd":310,"lang":"en","confidence":0.4725,"rawForm":"FlowJo","boundingBoxes":[{"x":497.779,"h":6.4159,"y":583.661,"p":10,"w":22.2991}]},"version":{"offsetStart":313,"normalizedForm":"10.5.3","offsetEnd":319,"rawForm":"10.5.3","boundingBoxes":[{"x":528.0098,"h":6.415899999999965,"y":583.661,"p":10,"w":18.40440000000001}]}},
  {"_key":"60c20da27723bebd86645722","_id":"annotations/60c20da27723bebd86645722","_rev":"_cfFmWUW---","document":{"$oid":"60c20da27723bebd86645721"},"context":"Re- cent eff orts have produced a software program (Ladybug: http://www.stat.uni-muenchen. de/~hoehle/software/ladybug/) for the sim- ulation and parameter estimation of suscep- tible-exposed-infectious-recovered (SEIR) compartmental epidemic models, but the application of complex transmission models will probably require custom-written code for some time to come.","type":"software","software-name":{"offsetStart":53,"normalizedForm":"Ladybug","offsetEnd":60,"rawForm":"Ladybug","boundingBoxes":[{"x":401.78911111111114,"h":9.93,"y":404.404,"p":3,"w":30.499777777777776}]},"url":{"offsetStart":62,"normalizedForm":"http://www.stat.uni-muenchen. de/~hoehle/software/ladybug","offsetEnd":120,"rawForm":"http://www.stat.uni-muenchen. \nde/~hoehle/software/ladybug","boundingBoxes":[{"x":448.089,"h":9.930000000000007,"y":404.404,"p":3,"w":121.76400000000007},{"x":397.432,"h":9.930000000000007,"y":416.404,"p":3,"w":115.03489655172416}]}},
  {"_key":"60c20da37723bebd86645724","_id":"annotations/60c20da37723bebd86645724","_rev":"_cfFmWUi---","wikipediaExternalRef":363695,"document":{"$oid":"60c20da37723bebd86645723"},"context":"Sequences were identified by BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi).","wikidataId":"Q286820","type":"software","confidence":0.2845,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":29,"wikidataId":"Q286820","offsetEnd":34,"lang":"en","confidence":0.2845,"rawForm":"BLAST","boundingBoxes":[{"x":486.729,"h":9.69,"y":542.95,"p":1,"w":31.67}]},"url":{"offsetStart":37,"normalizedForm":"http://blast.ncbi.nlm.nih.gov/Blast.cgi","offsetEnd":76,"rawForm":"http://blast.ncbi.nlm.nih.gov/Blast.cgi","boundingBoxes":[{"x":287.0420952380952,"h":9.690000000000055,"y":554.95,"p":1,"w":149.10071428571428}]},"lang":"en"},
  {"_key":"60c20dac7723bebd86645726","_id":"annotations/60c20dac7723bebd86645726","_rev":"_cfFmWUy---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20dac7723bebd86645725"},"context":"The sequences of nucleotides and deduced amino acids were analyzed by ClustalW, version 1.82 using  data available from GenBank and the European Molecular Biology Laboratory (EMBL).","wikidataId":"Q866737","type":"software","lang":"en","confidence":0.7823,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"ClustalW","offsetStart":71,"wikidataId":"Q866737","offsetEnd":79,"lang":"en","confidence":0.7823,"rawForm":"ClustalW","boundingBoxes":[{"x":167.469,"h":9.9626,"y":720.8,"p":3,"w":35.843199999999996}]},"version":{"offsetStart":89,"normalizedForm":"1.82","offsetEnd":93,"rawForm":"1.82","boundingBoxes":[{"x":243.153,"h":9.962599999999952,"y":720.8,"p":3,"w":17.434499999999986}]}},
  {"_key":"60c20dac7723bebd86645727","_id":"annotations/60c20dac7723bebd86645727","_rev":"_cfFmWV----","document":{"$oid":"60c20dac7723bebd86645725"},"publisher":{"offsetStart":104,"normalizedForm":"Pasteur Institute","offsetEnd":121,"rawForm":"Pasteur Institute","boundingBoxes":[{"x":452.521175,"h":9.962600000000009,"y":206.711,"p":3,"w":68.26449499999995}]},"context":"The protein chemistry of Chinju99 amino acids was analyzed using protein statistic programs PEPSTATS (Pasteur Institute, France) and PredictProtein (EMBL).","type":"software","software-name":{"offsetStart":94,"normalizedForm":"PEPSTATS","offsetEnd":102,"rawForm":"PEPSTATS","boundingBoxes":[{"x":393.05,"h":9.9626,"y":206.711,"p":3,"w":47.6162}]}},
  {"_key":"60c20dac7723bebd86645728","_id":"annotations/60c20dac7723bebd86645728","_rev":"_cfFmWVK---","wikipediaExternalRef":37922760,"document":{"$oid":"60c20dac7723bebd86645725"},"publisher":{"offsetStart":152,"normalizedForm":"EMBL","offsetEnd":156,"rawForm":"EMBL","boundingBoxes":[{"x":426.6667857142857,"h":9.9626,"y":218.673,"p":3,"w":21.087142857142858}]},"context":"The protein chemistry of Chinju99 amino acids was analyzed using protein statistic programs PEPSTATS (Pasteur Institute, France) and PredictProtein (EMBL).","wikidataId":"Q7239681","type":"software","confidence":0.4751,"software-name":{"wikipediaExternalRef":37922760,"normalizedForm":"PredictProtein","offsetStart":136,"wikidataId":"Q7239681","offsetEnd":150,"lang":"en","confidence":0.4751,"rawForm":"PredictProtein","boundingBoxes":[{"x":360.791,"h":9.9626,"y":218.673,"p":3,"w":57.2341}]},"lang":"en"},
  {"_key":"60c20dae7723bebd8664572a","_id":"annotations/60c20dae7723bebd8664572a","_rev":"_cfFmWVW---","wikipediaExternalRef":179088,"document":{"$oid":"60c20dae7723bebd86645729"},"context":"Statistical analysis was performed using SPSS12 (Illinois, Chicago).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":41,"wikidataId":"Q181596","offsetEnd":45,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":510.984,"h":8.7472,"y":371.007,"p":2,"w":33.295}]},"version":{"offsetStart":45,"normalizedForm":"12","offsetEnd":47,"rawForm":"12","boundingBoxes":[{"x":510.984,"h":8.7472,"y":371.007,"p":2,"w":33.295}]}},
  {"_key":"60c20db07723bebd8664572c","_id":"annotations/60c20db07723bebd8664572c","_rev":"_cfFmWVi---","wikipediaExternalRef":3524766,"document":{"$oid":"60c20db07723bebd8664572b"},"context":"There are concerns over the quality of videos such as those available for free, in YouTube, which may demonstrate improper or poor surgical techni- ques.","wikidataId":"Q866","type":"software","confidence":0.4534,"software-name":{"wikipediaExternalRef":3524766,"normalizedForm":"YouTube","offsetStart":84,"wikidataId":"Q866","offsetEnd":91,"lang":"en","confidence":0.4534,"rawForm":"YouTube","boundingBoxes":[{"x":222.972,"h":9.7861,"y":106.977,"p":6,"w":36.60335}]},"lang":"en"},
  {"_key":"60c20db27723bebd8664572e","_id":"annotations/60c20db27723bebd8664572e","_rev":"_cfFmWVu---","wikipediaExternalRef":376707,"document":{"$oid":"60c20db27723bebd8664572d"},"publisher":{"offsetStart":0,"normalizedForm":"R Core Team","offsetEnd":11,"rawForm":"R Core Team","boundingBoxes":[{"x":427.502,"h":11.100000000000023,"y":350.484,"p":10,"w":74.17779999999999}]},"context":"R Core Team, R  Foundation for Statistical Computing, Vienna, Austria).","wikidataId":"Q206904","type":"software","confidence":0.3562,"software-name":{"wikipediaExternalRef":376707,"normalizedForm":"R Foundation for Statistical Computing","offsetStart":13,"wikidataId":"Q206904","offsetEnd":53,"lang":"en","confidence":0.3562,"rawForm":"R \n\nFoundation for Statistical Computing","boundingBoxes":[{"x":514.683,"h":11.1,"y":350.484,"p":10,"w":8.664},{"x":72,"h":11.100000000000023,"y":378.084,"p":10,"w":197.66348}]},"lang":"en"},
  {"_key":"60c20db37723bebd86645730","_id":"annotations/60c20db37723bebd86645730","_rev":"_cfFmWW----","wikipediaExternalRef":179088,"document":{"$oid":"60c20db37723bebd8664572f"},"context":"All analyses were conducted using SPSS for Windows (version 16.0).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":34,"wikidataId":"Q181596","offsetEnd":38,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":500.654,"h":8.9767,"y":652.739,"p":2,"w":20.3711}]},"version":{"offsetStart":61,"normalizedForm":"16.0","offsetEnd":65,"rawForm":"16.0","boundingBoxes":[{"x":380.126,"h":8.97670000000005,"y":664.757,"p":2,"w":14.564599999999984}]}},
  {"_key":"60c20db57723bebd86645732","_id":"annotations/60c20db57723bebd86645732","_rev":"_cfFmWWO---","document":{"$oid":"60c20db57723bebd86645731"},"type":"software","software-name":{"offsetStart":74,"normalizedForm":"ML platform","offsetEnd":85,"rawForm":"ML platform","boundingBoxes":[{"x":91.8811,"h":8.625300000000038,"y":607.812,"p":2,"w":54.374071428571426}]},"context":"The data-set used in the implementation can be found on Kag- gle(Google's ML platform)(Link for Data Used[17]).It is an accession-based data originally downloaded by performing a BLAST exhaustive search from NCBI(National Center for Biotech- nology Information) database.The data has been described as per the following taxonomy."},
  {"_key":"60c20db87723bebd86645735","_id":"annotations/60c20db87723bebd86645735","_rev":"_cfFmWWy---","document":{"$oid":"60c20db87723bebd86645733"},"context":"We conducted an a priori power analysis using G*Power Version 3.1 [34] (F-tests, multiple re- gression with six predictors, and R 2 deviation from 0).","references":[{"offsetStart":14935,"normalizedForm":"[34]","refKey":31,"label":"[34]","reference_id":{"$oid":"60c20db87723bebd86645734"},"offsetEnd":14940,"boundingBoxes":[{"x":460.417,"h":8.948999999999955,"y":512.26,"p":3,"w":15.807999999999993}]}],"type":"software","software-name":{"offsetStart":47,"normalizedForm":"G*Power","offsetEnd":54,"rawForm":"G*Power","boundingBoxes":[{"x":362.13,"h":8.948999999999955,"y":512.26,"p":3,"w":36.94549999999998}]},"version":{"offsetStart":63,"normalizedForm":"3.1","offsetEnd":66,"rawForm":"3.1","boundingBoxes":[{"x":441.882,"h":8.948999999999955,"y":512.26,"p":3,"w":12.387999999999977}]}},
  {"_key":"60c20db87723bebd86645737","_id":"annotations/60c20db87723bebd86645737","_rev":"_cfFmWXG---","wikipediaExternalRef":179088,"document":{"$oid":"60c20db87723bebd86645736"},"publisher":{"offsetStart":43,"normalizedForm":"IBM","offsetEnd":46,"rawForm":"IBM","boundingBoxes":[{"x":202.452,"h":8.379,"y":493.713,"p":3,"w":14.458}]},"context":"Statistical analysis was carried out using IBM SPSS 25.0 soft- ware.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":47,"wikidataId":"Q181596","offsetEnd":51,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":219.244,"h":8.379,"y":493.713,"p":3,"w":18.2372}]},"version":{"offsetStart":52,"normalizedForm":"25.0","offsetEnd":56,"rawForm":"25.0","boundingBoxes":[{"x":239.816,"h":8.379000000000019,"y":493.713,"p":3,"w":15.902999999999992}]}},
  {"_key":"60c20dc07723bebd86645739","_id":"annotations/60c20dc07723bebd86645739","_rev":"_cfFmWXe---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20dc07723bebd86645738"},"context":" All analyses were performed with Stata 16.0. 28","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":35,"wikidataId":"Q1204300","offsetEnd":40,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":261.898,"h":10.4857,"y":667.94,"p":6,"w":26.4659}]},"version":{"offsetStart":41,"normalizedForm":"16.0","offsetEnd":45,"rawForm":"16.0","boundingBoxes":[{"x":291.421,"h":10.485699999999952,"y":667.94,"p":6,"w":19.949360000000013}]}},
  {"_key":"60c20dc17723bebd8664573b","_id":"annotations/60c20dc17723bebd8664573b","_rev":"_cfFmWXu---","wikipediaExternalRef":34408890,"document":{"$oid":"60c20dc17723bebd8664573a"},"context":"We screened the men- tal health status of suspected cases, medical staffs and general population via WeChat platform and/or telephone by using questionnaires (e.g.","wikidataId":"Q283233","type":"software","confidence":0.7626,"software-name":{"wikipediaExternalRef":34408890,"normalizedForm":"WeChat","offsetStart":102,"wikidataId":"Q283233","offsetEnd":108,"lang":"en","confidence":0.7626,"rawForm":"WeChat","boundingBoxes":[{"x":180.989,"h":8.993,"y":668.239,"p":4,"w":32.8986}]},"lang":"en"},
  {"_key":"60c20dc37723bebd8664573d","_id":"annotations/60c20dc37723bebd8664573d","_rev":"_cfFmWY----","wikipediaExternalRef":20268,"document":{"$oid":"60c20dc37723bebd8664573c"},"publisher":{"offsetStart":43,"normalizedForm":"Microsoft","offsetEnd":52,"rawForm":"Microsoft","boundingBoxes":[{"x":461.651,"h":6.9637,"y":704.236,"p":8,"w":29.0795}]},"context":"Statistic significances were calculated by Microsoft Excel version 16.30 and all the data were shown as mean ± s.d.","wikidataId":"Q11272","type":"software","lang":"en","confidence":0.378,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Excel","offsetStart":53,"wikidataId":"Q11272","offsetEnd":58,"lang":"en","confidence":0.378,"rawForm":"Excel","boundingBoxes":[{"x":493.23,"h":6.9637,"y":704.236,"p":8,"w":15.7804}]},"version":{"offsetStart":67,"normalizedForm":"16.30","offsetEnd":72,"rawForm":"16.30","boundingBoxes":[{"x":535.693,"h":6.963700000000017,"y":704.236,"p":8,"w":15.944799999999987}]}},
  {"_key":"60c20dc37723bebd8664573e","_id":"annotations/60c20dc37723bebd8664573e","_rev":"_cfFmWYS---","document":{"$oid":"60c20dc37723bebd8664573c"},"type":"software","software-name":{"offsetStart":164,"normalizedForm":"PSTrace","offsetEnd":171,"rawForm":"PSTrace","boundingBoxes":[{"x":265.44,"h":6.9637,"y":715.237,"p":7,"w":24.562}]},"context":"For electrochemical measurements, two-electrode screen-printed carbon electrodes (SPCE) were obtained from Quasense, Thailand and the PalmSens4 potentiostat with PSTrace software was obtained from Palmsens, The Netherlands."},
  {"_key":"60c20dc57723bebd86645740","_id":"annotations/60c20dc57723bebd86645740","_rev":"_cfFmWYi---","document":{"$oid":"60c20dc57723bebd8664573f"},"type":"software","software-name":{"offsetStart":42,"normalizedForm":"e-Outbreak Platform","offsetEnd":61,"rawForm":"e-Outbreak Platform","boundingBoxes":[{"x":475.143,"h":7.571700000000021,"y":458.055,"p":6,"w":72.94420000000008}]},"context":"We create an online input platform called e-Outbreak Platform that allows the health authorities to implement a disease- specific questionnaire."},
  {"_key":"60c20dc57723bebd86645741","_id":"annotations/60c20dc57723bebd86645741","_rev":"_cfFmWYy---","document":{"$oid":"60c20dc57723bebd8664573f"},"type":"software","software-name":{"offsetStart":91,"normalizedForm":"e-Outbreak Platform","offsetEnd":112,"rawForm":"e-Outbreak \n\nPlatform","boundingBoxes":[{"x":505.869,"h":7.09820000000002,"y":560.509,"p":1,"w":37.41129999999998},{"x":211.691,"h":7.0982,"y":571.961,"p":1,"w":28.7888}]},"context":"To meet the  various needs of the epidemiological investigation, we decided to develop an e-Outbreak  Platform that provides a semi-structured, multifaceted, computer-aided questionnaire for  outbreak investigation."},
  {"_key":"60c20dc87723bebd86645743","_id":"annotations/60c20dc87723bebd86645743","_rev":"_cfFmWZG---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20dc87723bebd86645742"},"publisher":{"offsetStart":115,"normalizedForm":"National Institutes of Health","offsetEnd":144,"rawForm":"National Institutes of Health","boundingBoxes":[{"x":205.976,"h":9.584000000000003,"y":239.677,"p":11,"w":125.9190857142857}]},"context":"ImageJ was used to enumerate GFP signal in random sections of infected cells for confocal microscopy and was also used to estimate relative density and size of samples in the dot blot.","wikidataId":"Q1659584","type":"software","lang":"en","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":0,"wikidataId":"Q1659584","offsetEnd":6,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":433.555,"h":9.584,"y":678.493,"p":11,"w":30.6415}]},"version":{"offsetStart":108,"normalizedForm":"1.52p","offsetEnd":113,"rawForm":"1.52p","boundingBoxes":[{"x":177.056,"h":9.584000000000003,"y":239.677,"p":11,"w":22.02583333333331}]}},
  {"_key":"60c20dc87723bebd86645744","_id":"annotations/60c20dc87723bebd86645744","_rev":"_cfFmWZa---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20dc87723bebd86645742"},"publisher":{"offsetStart":115,"normalizedForm":"National Institutes of Health","offsetEnd":144,"rawForm":"National Institutes of Health","boundingBoxes":[{"x":205.976,"h":9.584000000000003,"y":239.677,"p":11,"w":125.9190857142857}]},"context":"Using ImageJ, the immunolabeled punctae with SPGG treatment were quantified as compared to the mock-treated cell lines.","wikidataId":"Q1659584","type":"software","lang":"en","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":6,"wikidataId":"Q1659584","offsetEnd":12,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":303.858,"h":9.96,"y":759.477,"p":4,"w":28.4628}]},"version":{"offsetStart":108,"normalizedForm":"1.52p","offsetEnd":113,"rawForm":"1.52p","boundingBoxes":[{"x":177.056,"h":9.584000000000003,"y":239.677,"p":11,"w":22.02583333333331}]}},
  {"_key":"60c20dc87723bebd86645745","_id":"annotations/60c20dc87723bebd86645745","_rev":"_cfFmWZq---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20dc87723bebd86645742"},"publisher":{"offsetStart":115,"normalizedForm":"National Institutes of Health","offsetEnd":144,"rawForm":"National Institutes of Health","boundingBoxes":[{"x":205.976,"h":9.584000000000003,"y":239.677,"p":11,"w":125.9190857142857}]},"context":"Using ImageJ, the immunolabeled punctae with SPGG treatment were quantified as compared to the mock-treated cell lines.","wikidataId":"Q1659584","type":"software","lang":"en","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":6,"wikidataId":"Q1659584","offsetEnd":12,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":258.515,"h":9.584,"y":735.689,"p":4,"w":28.989}]},"version":{"offsetStart":108,"normalizedForm":"1.52p","offsetEnd":113,"rawForm":"1.52p","boundingBoxes":[{"x":177.056,"h":9.584000000000003,"y":239.677,"p":11,"w":22.02583333333331}]}},
  {"_key":"60c20dc87723bebd86645746","_id":"annotations/60c20dc87723bebd86645746","_rev":"_cfFmWa----","wikipediaExternalRef":3793613,"document":{"$oid":"60c20dc87723bebd86645742"},"publisher":{"offsetStart":115,"normalizedForm":"National Institutes of Health","offsetEnd":144,"rawForm":"National Institutes of Health","boundingBoxes":[{"x":205.976,"h":9.584000000000003,"y":239.677,"p":11,"w":125.9190857142857}]},"context":"The intensity of the signal was quantified using ImageJ gel analysis function to calculate and plot the area under each peak.","wikidataId":"Q1659584","type":"software","lang":"en","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":49,"wikidataId":"Q1659584","offsetEnd":55,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":287.189,"h":9.584,"y":595.265,"p":11,"w":30.703}]},"version":{"offsetStart":108,"normalizedForm":"1.52p","offsetEnd":113,"rawForm":"1.52p","boundingBoxes":[{"x":177.056,"h":9.584000000000003,"y":239.677,"p":11,"w":22.02583333333331}]}},
  {"_key":"60c20dc87723bebd86645747","_id":"annotations/60c20dc87723bebd86645747","_rev":"_cfFmWae---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20dc87723bebd86645742"},"publisher":{"offsetStart":115,"normalizedForm":"National Institutes of Health","offsetEnd":144,"rawForm":"National Institutes of Health","boundingBoxes":[{"x":205.976,"h":9.584000000000003,"y":239.677,"p":11,"w":125.9190857142857}]},"context":"The signal was then quantified for size and pixel density using ImageJ gel analysis function and the profile plot was generated with each curve representing a respective spot on the original blot (panel A).","wikidataId":"Q1659584","type":"software","lang":"en","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":65,"wikidataId":"Q1659584","offsetEnd":71,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":209.381,"h":8.6257,"y":505.313,"p":8,"w":27.4302}]},"version":{"offsetStart":108,"normalizedForm":"1.52p","offsetEnd":113,"rawForm":"1.52p","boundingBoxes":[{"x":177.056,"h":9.584000000000003,"y":239.677,"p":11,"w":22.02583333333331}]}},
  {"_key":"60c20dc87723bebd86645748","_id":"annotations/60c20dc87723bebd86645748","_rev":"_cfFmWb----","wikipediaExternalRef":3793613,"document":{"$oid":"60c20dc87723bebd86645742"},"publisher":{"offsetStart":115,"normalizedForm":"National Institutes of Health","offsetEnd":144,"rawForm":"National Institutes of Health","boundingBoxes":[{"x":205.976,"h":9.584000000000003,"y":239.677,"p":11,"w":125.9190857142857}]},"context":"Slides were imaged using the Nikon A1R confocal microscope and images were processed using ImageJ (version 1.52p, National Institutes of Health, USA) [78] and the GFP-positive punctae were enumerated in 3 random views per slide.","wikidataId":"Q1659584","type":"software","lang":"en","confidence":0.7992,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"ImageJ","offsetStart":92,"wikidataId":"Q1659584","offsetEnd":98,"lang":"en","confidence":0.7992,"rawForm":"ImageJ","boundingBoxes":[{"x":103.972,"h":9.584,"y":239.677,"p":11,"w":31.3798}]},"version":{"offsetStart":108,"normalizedForm":"1.52p","offsetEnd":113,"rawForm":"1.52p","boundingBoxes":[{"x":177.056,"h":9.584000000000003,"y":239.677,"p":11,"w":22.02583333333331}]}},
  {"_key":"60c20dcb7723bebd8664574a","_id":"annotations/60c20dcb7723bebd8664574a","_rev":"_cfFmWbi---","wikipediaExternalRef":8109474,"document":{"$oid":"60c20dcb7723bebd86645749"},"publisher":{"offsetStart":61,"normalizedForm":"OriginLab Corporation","offsetEnd":82,"rawForm":"OriginLab Corporation","boundingBoxes":[{"x":104.43975,"h":8.025999999999954,"y":513.277,"p":3,"w":91.11336666666665}]},"context":"The IC 50 values were determined using ORIGIN 7.5 software (OriginLab Corporation, Northampton, MA, USA).","wikidataId":"Q31708","type":"software","lang":"en","confidence":0.297,"software-name":{"wikipediaExternalRef":8109474,"normalizedForm":"ORIGIN","offsetStart":39,"wikidataId":"Q31708","offsetEnd":45,"lang":"en","confidence":0.297,"rawForm":"ORIGIN","boundingBoxes":[{"x":244.798,"h":8.026,"y":500.805,"p":3,"w":25.9292}]},"version":{"offsetStart":46,"normalizedForm":"7.5","offsetEnd":49,"rawForm":"7.5","boundingBoxes":[{"x":273.429,"h":8.02600000000001,"y":500.805,"p":3,"w":13.496499999999969}]}},
  {"_key":"60c20dcb7723bebd8664574b","_id":"annotations/60c20dcb7723bebd8664574b","_rev":"_cfFmWcC---","document":{"$oid":"60c20dcb7723bebd86645749"},"type":"software","software-name":{"offsetStart":39,"normalizedForm":"Sybyl/Sketch","offsetEnd":51,"rawForm":"Sybyl/Sketch","boundingBoxes":[{"x":479.903,"h":8.025999999999954,"y":587.885,"p":3,"w":52.093200000000024}]},"context":"All 28 molecules were constructed with Sybyl/Sketch module and geometry optimized using Powell's method [29] with the Tripos force field with convergence criterion set at 0.05 kcal/(A ˚• mol) and assigned with Gasteiger-HU ¨ckel method [30]."},
  {"_key":"60c20dcb7723bebd8664574c","_id":"annotations/60c20dcb7723bebd8664574c","_rev":"_cfFmWcm---","document":{"$oid":"60c20dcb7723bebd86645749"},"type":"software","software-name":{"offsetStart":77,"normalizedForm":"Sybyl/QSAR","offsetEnd":87,"rawForm":"Sybyl/QSAR","boundingBoxes":[{"x":373.435,"h":8.025999999999954,"y":687.551,"p":3,"w":49.25380000000001}]},"context":"In brief, the molecular force field of the molecule 13f was computed using Sybyl/QSAR module first and then the steric and electrostatic fields were extracted individually."},
  {"_key":"60c20dd27723bebd8664574e","_id":"annotations/60c20dd27723bebd8664574e","_rev":"_cfFmWdK---","document":{"$oid":"60c20dd27723bebd8664574d"},"publisher":{"offsetStart":59,"normalizedForm":"Systat Software, Inc","offsetEnd":79,"rawForm":"Systat Software, Inc","boundingBoxes":[{"x":60.559200000000004,"h":8.943300000000022,"y":292.766,"p":3,"w":77.85455999999999}]},"context":"Statistical analysis was performed using Sigma Plot 11.0 (Systat Software, Inc., San Jose, CA, USA).","type":"software","software-name":{"offsetStart":41,"normalizedForm":"Sigma Plot","offsetEnd":51,"rawForm":"Sigma Plot","boundingBoxes":[{"x":225.228,"h":8.943300000000022,"y":280.805,"p":3,"w":44.863099999999974}]},"version":{"offsetStart":52,"normalizedForm":"11.0","offsetEnd":56,"rawForm":"11.0","boundingBoxes":[{"x":273.528,"h":8.943300000000022,"y":280.805,"p":3,"w":17.01759999999996}]}},
  {"_key":"60c20dd67723bebd86645750","_id":"annotations/60c20dd67723bebd86645750","_rev":"_cfFmWdu---","wikipediaExternalRef":20412,"document":{"$oid":"60c20dd67723bebd8664574f"},"publisher":{"offsetStart":212,"normalizedForm":"Hughey Lab","offsetEnd":225,"rawForm":"Hughey Lab","boundingBoxes":[{"x":435.178,"h":10.536699999999996,"y":654.815,"p":28,"w":69.97340000000003}]},"context":"Custom-written software in MATLAB was used to segment and identify the 3D  volume, mean intensity, and number of RNA dots in each field of view using the  nestedSortStruct algorithm for MATLAB written by the Hughey Lab  (https://www.github.com/hugheylab/nestedSortStruct,","wikidataId":"Q169478","type":"software","confidence":0.7679,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":27,"wikidataId":"Q169478","offsetEnd":33,"lang":"en","confidence":0.7679,"rawForm":"MATLAB","boundingBoxes":[{"x":233.495,"h":10.5367,"y":613.415,"p":28,"w":50.6573}]},"url":{"offsetStart":278,"normalizedForm":"GitHub","offsetEnd":284,"rawForm":"GitHub","boundingBoxes":[{"x":358.455,"h":10.5367,"y":675.455,"p":28,"w":32.2491}]},"lang":"en"},
  {"_key":"60c20dd67723bebd86645751","_id":"annotations/60c20dd67723bebd86645751","_rev":"_cfFmWeS---","document":{"$oid":"60c20dd67723bebd8664574f"},"publisher":{"offsetStart":56,"normalizedForm":"OriginLabs","offsetEnd":66,"rawForm":"OriginLabs","boundingBoxes":[{"x":258.76034166666665,"h":10.5367,"y":696.215,"p":28,"w":52.09341666666666}]},"context":"Statistical analysis  was performed using Origin 9.2 (OriginLabs) and P-values were calculated using a  Kruskal-Wallis one-way ANOVA test, with the null hypothesis that the medians of  each population were equal.","type":"software","software-name":{"offsetStart":44,"normalizedForm":"Origin","offsetEnd":50,"rawForm":"Origin","boundingBoxes":[{"x":198.097,"h":10.5367,"y":696.215,"p":28,"w":31.332}]},"version":{"offsetStart":51,"normalizedForm":"9.2","offsetEnd":54,"rawForm":"9.2","boundingBoxes":[{"x":233.989,"h":10.536699999999996,"y":696.215,"p":28,"w":15.000900000000001}]}},
  {"_key":"60c20dd67723bebd86645752","_id":"annotations/60c20dd67723bebd86645752","_rev":"_cfFmWeu---","document":{"$oid":"60c20dd67723bebd8664574f"},"publisher":{"offsetStart":84,"normalizedForm":"Scientific Volume Imaging","offsetEnd":112,"rawForm":"Scientific \n\n\nVolume Imaging","boundingBoxes":[{"x":459.67403636363633,"h":10.5367,"y":572.015,"p":28,"w":45.43036363636363},{"x":89.88,"h":10.536699999999996,"y":592.655,"p":28,"w":80.85578750000002}]},"context":"Z stacks were  subsequently deconvolved using the Huygens Deconvolution Software (Scientific  Volume Imaging) and 3D views were rendered using the FIJI ClearVolume plugin 64 .","type":"software","software-name":{"offsetStart":52,"normalizedForm":"Huygens Deconvolution","offsetEnd":73,"rawForm":"Huygens Deconvolution","boundingBoxes":[{"x":279.348,"h":10.536699999999996,"y":572.015,"p":28,"w":120.06359999999995}]}},
  {"_key":"60c20dd67723bebd86645753","_id":"annotations/60c20dd67723bebd86645753","_rev":"_cfFmWfS---","document":{"$oid":"60c20dd67723bebd8664574f"},"type":"software","software-name":{"offsetStart":151,"normalizedForm":"FIJI ClearVolume","offsetEnd":167,"rawForm":"FIJI ClearVolume","boundingBoxes":[{"x":372.083,"h":10.536699999999996,"y":592.655,"p":28,"w":87.83919999999995}]},"context":"Z stacks were  subsequently deconvolved using the Huygens Deconvolution Software (Scientific  Volume Imaging) and 3D views were rendered using the FIJI ClearVolume plugin 64 ."},
  {"_key":"60c20dd67723bebd86645754","_id":"annotations/60c20dd67723bebd86645754","_rev":"_cfFmWf2---","wikipediaExternalRef":20412,"document":{"$oid":"60c20dd67723bebd8664574f"},"publisher":{"offsetStart":212,"normalizedForm":"Hughey Lab","offsetEnd":225,"rawForm":"Hughey Lab","boundingBoxes":[{"x":435.178,"h":10.536699999999996,"y":654.815,"p":28,"w":69.97340000000003}]},"context":"Custom-written software in MATLAB was used to segment and identify the 3D  volume, mean intensity, and number of RNA dots in each field of view using the  nestedSortStruct algorithm for MATLAB written by the Hughey Lab  (https://www.github.com/hugheylab/nestedSortStruct,","wikidataId":"Q169478","type":"software","confidence":0.7679,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":190,"wikidataId":"Q169478","offsetEnd":196,"lang":"en","confidence":0.7679,"rawForm":"MATLAB","boundingBoxes":[{"x":270.091,"h":10.5367,"y":654.815,"p":28,"w":50.6573}]},"url":{"offsetStart":278,"normalizedForm":"GitHub","offsetEnd":284,"rawForm":"GitHub","boundingBoxes":[{"x":358.455,"h":10.5367,"y":675.455,"p":28,"w":32.2491}]},"lang":"en"},
  {"_key":"60c20dd77723bebd86645756","_id":"annotations/60c20dd77723bebd86645756","_rev":"_cfFmWge---","document":{"$oid":"60c20dd77723bebd86645755"},"context":"We predicted the domains and GO functions of these virus proteins based on their sequences using InterProScan (http:// www.ebi.ac.uk/interpro/search/sequence/), and the InterPro results are given in Supplementary file 2. The 20 GO terms with level ≥ 3 were selected for the following analysis, as listed in Supplementary file 3. Next, we extracted the human proteins shared with the same 20 GO functions and these candidate human proteins are listed in Supplementary file 4.","type":"software","software-name":{"offsetStart":98,"normalizedForm":"InterProScan","offsetEnd":110,"rawForm":"InterProScan","boundingBoxes":[{"x":207.753,"h":9.3201,"y":590.653,"p":3,"w":52.5445}]},"url":{"offsetStart":112,"normalizedForm":"http:// www.ebi.ac.uk/interpro/search/sequence","offsetEnd":159,"rawForm":"http:// \nwww.ebi.ac.uk/interpro/search/sequence","boundingBoxes":[{"x":265.93591250000003,"h":9.320100000000025,"y":590.653,"p":3,"w":25.031387499999994},{"x":50.0031,"h":9.320100000000025,"y":602.043,"p":3,"w":157.4998048780488}]}},
  {"_key":"60c20dda7723bebd86645758","_id":"annotations/60c20dda7723bebd86645758","_rev":"_cfFmWh----","wikipediaExternalRef":21572326,"document":{"$oid":"60c20dda7723bebd86645757"},"context":"Graphs were generated using GraphPad Prism v8.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":28,"wikidataId":"Q5597066","offsetEnd":42,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":447.764,"h":9.289100000000019,"y":320.188,"p":7,"w":70.5199}]},"version":{"offsetStart":45,"normalizedForm":"8","offsetEnd":46,"rawForm":"8","boundingBoxes":[{"x":314.819,"h":9.2891,"y":332.068,"p":7,"w":8.5604}]}},
  {"_key":"60c20dda7723bebd86645759","_id":"annotations/60c20dda7723bebd86645759","_rev":"_cfFmWhm---","document":{"$oid":"60c20dda7723bebd86645757"},"publisher":{"offsetStart":43,"normalizedForm":"Bio-Rad","offsetEnd":50,"rawForm":"Bio-Rad","boundingBoxes":[{"x":477.86746,"h":9.289100000000019,"y":367.708,"p":8,"w":31.167219999999986}]},"context":"Blot analysis was performed in Image-Lab (Bio-Rad).","type":"software","software-name":{"offsetStart":32,"normalizedForm":"Image-Lab","offsetEnd":41,"rawForm":"Image-Lab","boundingBoxes":[{"x":425.528,"h":9.289100000000019,"y":367.708,"p":8,"w":45.30799999999999}]}},
  {"_key":"60c20dda7723bebd8664575a","_id":"annotations/60c20dda7723bebd8664575a","_rev":"_cfFmWiC---","document":{"$oid":"60c20dda7723bebd86645757"},"publisher":{"offsetStart":69,"normalizedForm":"UIowa Bioinformatics Core","offsetEnd":95,"rawForm":"UIowa \nBioinformatics Core","boundingBoxes":[{"x":490.318,"h":9.2891,"y":248.728,"p":7,"w":27.8032},{"x":314.819,"h":9.289100000000019,"y":260.608,"p":7,"w":87.74609999999996}]},"context":"All other datasets where analyzed from GEO data using DESeq2 by the UIowa Bioinformatics Core (see Code Availability).","type":"software","software-name":{"offsetStart":55,"normalizedForm":"DESeq","offsetEnd":60,"rawForm":"DESeq","boundingBoxes":[{"x":404.117,"h":9.2891,"y":248.728,"p":7,"w":34.5316}]},"version":{"offsetStart":60,"normalizedForm":"2","offsetEnd":61,"rawForm":"2","boundingBoxes":[{"x":404.117,"h":9.2891,"y":248.728,"p":7,"w":34.5316}]}},
  {"_key":"60c20dda7723bebd8664575b","_id":"annotations/60c20dda7723bebd8664575b","_rev":"_cfFmWia---","document":{"$oid":"60c20dda7723bebd86645757"},"type":"software","software-name":{"offsetStart":87,"normalizedForm":"DESeq2","offsetEnd":93,"rawForm":"DESeq2","boundingBoxes":[{"x":263.355,"h":9.289099999999962,"y":699.444,"p":7,"w":34.30720000000002}]},"context":"RNA was collected, and differential gene expression analysis was performed using the DESeq2 package."},
  {"_key":"60c20ddc7723bebd8664575d","_id":"annotations/60c20ddc7723bebd8664575d","_rev":"_cfFmWiu---","wikipediaExternalRef":179088,"document":{"$oid":"60c20ddc7723bebd8664575c"},"publisher":{"offsetStart":63,"normalizedForm":"SPSS","offsetEnd":67,"rawForm":"SPSS","boundingBoxes":[{"x":116.34105,"h":10.2023,"y":603.357,"p":7,"w":21.1282}]},"context":"Statistical analyses were conducted using SPSS version 18•0  (SPSS, Chicago, IL, USA) and SAS version 9•4 (SAS Institute, Cary, North Carolina).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7466,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":42,"wikidataId":"Q181596","offsetEnd":46,"lang":"en","confidence":0.7466,"rawForm":"SPSS","boundingBoxes":[{"x":415.787,"h":10.2023,"y":581.217,"p":7,"w":25.024}]},"version":{"offsetStart":55,"normalizedForm":"18•0","offsetEnd":61,"rawForm":"18•0","boundingBoxes":[{"x":481.666,"h":10.202300000000037,"y":581.217,"p":7,"w":19.887699999999995}]}},
  {"_key":"60c20ddc7723bebd8664575e","_id":"annotations/60c20ddc7723bebd8664575e","_rev":"_cfFmWjS---","wikipediaExternalRef":990677,"document":{"$oid":"60c20ddc7723bebd8664575c"},"publisher":{"offsetStart":108,"normalizedForm":"SAS Institute","offsetEnd":121,"rawForm":"SAS Institute","boundingBoxes":[{"x":336.13485,"h":10.202300000000037,"y":603.357,"p":7,"w":57.01920000000001}]},"context":"Statistical analyses were conducted using SPSS version 18•0  (SPSS, Chicago, IL, USA) and SAS version 9•4 (SAS Institute, Cary, North Carolina).","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":91,"wikidataId":"Q2003932","offsetEnd":94,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":253.465,"h":10.2023,"y":603.357,"p":7,"w":20.7189}]},"version":{"offsetStart":103,"normalizedForm":"9•4","offsetEnd":106,"rawForm":"9•4","boundingBoxes":[{"x":312.907,"h":10.202300000000037,"y":603.357,"p":7,"w":14.128199999999993}]}},
  {"_key":"60c20de17723bebd86645760","_id":"annotations/60c20de17723bebd86645760","_rev":"_cfFmWjq---","wikipediaExternalRef":12610483,"document":{"$oid":"60c20de17723bebd8664575f"},"context":"In addition, Android smartphone users could download the CoVidAffect app, available on the website.","wikidataId":"Q94","type":"software","confidence":0.4457,"software-name":{"wikipediaExternalRef":12610483,"normalizedForm":"Android","offsetStart":14,"wikidataId":"Q94","offsetEnd":21,"lang":"en","confidence":0.4457,"rawForm":"Android","boundingBoxes":[{"x":155.635,"h":9.099,"y":730.8,"p":2,"w":31.347}]},"lang":"en"},
  {"_key":"60c20de17723bebd86645761","_id":"annotations/60c20de17723bebd86645761","_rev":"_cfFmWj6---","wikipediaExternalRef":12610483,"document":{"$oid":"60c20de17723bebd8664575f"},"context":"The app was developed only for Android OS, and was not available for smartphones with different operating systems.","wikidataId":"Q94","type":"software","confidence":0.6908,"software-name":{"wikipediaExternalRef":12610483,"normalizedForm":"Android OS","offsetStart":32,"wikidataId":"Q94","offsetEnd":42,"lang":"en","confidence":0.6908,"rawForm":"Android OS","boundingBoxes":[{"x":185.817,"h":9.099000000000046,"y":695.402,"p":4,"w":41.42999999999998}]},"lang":"en"},
  {"_key":"60c20de17723bebd86645762","_id":"annotations/60c20de17723bebd86645762","_rev":"_cfFmWkS---","document":{"$oid":"60c20de17723bebd8664575f"},"type":"software","software-name":{"offsetStart":56,"normalizedForm":"CoVidAffect","offsetEnd":67,"rawForm":"CoVidAffect","boundingBoxes":[{"x":168.628,"h":9.099,"y":580.016,"p":2,"w":45.1089}]},"context":"They were also offered the possibility to download the CoVidAffect Android app, which sent regular reminder notifications and allowed the participants to rate their mood directly from the app."},
  {"_key":"60c20de17723bebd86645763","_id":"annotations/60c20de17723bebd86645763","_rev":"_cfFmWky---","document":{"$oid":"60c20de17723bebd8664575f"},"type":"software","software-name":{"offsetStart":58,"normalizedForm":"CoVidAffect","offsetEnd":69,"rawForm":"CoVidAffect","boundingBoxes":[{"x":332.997,"h":9.099,"y":730.8,"p":2,"w":46.3941}]},"context":"In addition, Android smartphone users could download the CoVidAffect app, available on the website."},
  {"_key":"60c20de17723bebd86645764","_id":"annotations/60c20de17723bebd86645764","_rev":"_cfFmWlW---","wikipediaExternalRef":12610483,"document":{"$oid":"60c20de17723bebd8664575f"},"context":"At the time of the study, the mobile devices market share of Android OS in Spain was 78% 19 , meaning that a significant number of participants may not have been able to use their smartphones for data recording.","wikidataId":"Q94","type":"software","confidence":0.6908,"software-name":{"wikipediaExternalRef":12610483,"normalizedForm":"Android OS","offsetStart":62,"wikidataId":"Q94","offsetEnd":72,"lang":"en","confidence":0.6908,"rawForm":"Android OS","boundingBoxes":[{"x":304.542,"h":9.099000000000046,"y":705.401,"p":4,"w":43.70500000000004}]},"lang":"en"},
  {"_key":"60c20de17723bebd86645765","_id":"annotations/60c20de17723bebd86645765","_rev":"_cfFmWly---","wikipediaExternalRef":12610483,"document":{"$oid":"60c20de17723bebd8664575f"},"context":"They were also offered the possibility to download the CoVidAffect Android app, which sent regular reminder notifications and allowed the participants to rate their mood directly from the app.","wikidataId":"Q94","type":"software","confidence":0.4457,"software-name":{"wikipediaExternalRef":12610483,"normalizedForm":"Android","offsetStart":68,"wikidataId":"Q94","offsetEnd":75,"lang":"en","confidence":0.4457,"rawForm":"Android","boundingBoxes":[{"x":215.402,"h":9.099,"y":580.016,"p":2,"w":30.4902}]},"lang":"en"},
  {"_key":"60c20de17723bebd86645766","_id":"annotations/60c20de17723bebd86645766","_rev":"_cfFmWmC---","document":{"$oid":"60c20de17723bebd8664575f"},"type":"software","software-name":{"offsetStart":153,"normalizedForm":"CoVidAffect","offsetEnd":164,"rawForm":"CoVidAffect","boundingBoxes":[{"x":360.421,"h":9.099,"y":685.403,"p":4,"w":45.8685}]},"context":"The methodology of data collection designed for this study offered participants two channels to  report their mood: through the website and through the CoVidAffect smartphone app."},
  {"_key":"60c20dec7723bebd86645768","_id":"annotations/60c20dec7723bebd86645768","_rev":"_cfFmWmS---","wikipediaExternalRef":179088,"document":{"$oid":"60c20dec7723bebd86645767"},"context":"All analyses were carried out using SPSS-v25 software.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":37,"wikidataId":"Q181596","offsetEnd":41,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":407.69,"h":9.3201,"y":301.871,"p":3,"w":18.7307}]},"version":{"offsetStart":43,"normalizedForm":"25","offsetEnd":45,"rawForm":"25","boundingBoxes":[{"x":431.10337499999997,"h":9.3201,"y":301.871,"p":3,"w":14.048024999999999}]}},
  {"_key":"60c20df17723bebd8664576a","_id":"annotations/60c20df17723bebd8664576a","_rev":"_cfFmWmi---","wikipediaExternalRef":20412,"document":{"$oid":"60c20df17723bebd86645769"},"context":"We used a MATLAB implementation of weighted kappa 24 to perform this calculation.","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":10,"wikidataId":"Q169478","offsetEnd":16,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":195.544,"h":9.099,"y":523.18,"p":8,"w":35.8956}]},"url":{"offsetStart":135,"normalizedForm":"a.html","offsetEnd":141,"rawForm":"a.html","boundingBoxes":[{"x":503.107,"h":9.099000000000046,"y":550.591,"p":10,"w":25.483499999999992}]},"version":{"offsetStart":134,"normalizedForm":"8","offsetEnd":135,"rawForm":"8","boundingBoxes":[{"x":503.107,"h":9.099,"y":550.591,"p":10,"w":7.281}]}},
  {"_key":"60c20df17723bebd8664576b","_id":"annotations/60c20df17723bebd8664576b","_rev":"_cfFmWmy---","wikipediaExternalRef":179088,"document":{"$oid":"60c20df17723bebd86645769"},"context":"Finally, using SPSS v25.0 we calculated ICC(A, 1) both over only the ratings of the human special- ists and over all raters at once, to measure its change with the exclusion or inclusion of our method respectively.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":15,"wikidataId":"Q181596","offsetEnd":19,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":251.936,"h":9.099,"y":583.18,"p":8,"w":17.8794}]},"version":{"offsetStart":21,"normalizedForm":"25.0","offsetEnd":25,"rawForm":"25.0","boundingBoxes":[{"x":271.755,"h":9.099000000000046,"y":583.18,"p":8,"w":19.350000000000023}]}},
  {"_key":"60c20df17723bebd8664576c","_id":"annotations/60c20df17723bebd8664576c","_rev":"_cfFmWnC---","wikipediaExternalRef":20412,"document":{"$oid":"60c20df17723bebd86645769"},"context":"Figure created using MATLAB 2018a, http:// mathw orks.com/produ cts/new_produ cts/relea se201 8a.html.","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":21,"wikidataId":"Q169478","offsetEnd":27,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":467.561,"h":9.099,"y":257.957,"p":11,"w":35.406}]},"url":{"offsetStart":35,"normalizedForm":"http:// mathw orks.com/produ cts/new_produ","offsetEnd":78,"rawForm":"http:// \nmathw orks.com/produ cts/new_produ","boundingBoxes":[{"x":529.931,"h":9.09899999999999,"y":257.957,"p":11,"w":22.400999999999954},{"x":155.901,"h":9.09899999999999,"y":267.956,"p":11,"w":135.65609999999998}]},"version":{"offsetStart":28,"normalizedForm":"2018a","offsetEnd":33,"rawForm":"2018a","boundingBoxes":[{"x":504.92,"h":9.09899999999999,"y":257.957,"p":11,"w":19.214999999999975}]}},
  {"_key":"60c20df17723bebd8664576d","_id":"annotations/60c20df17723bebd8664576d","_rev":"_cfFmWnS---","wikipediaExternalRef":23862,"document":{"$oid":"60c20df17723bebd86645769"},"context":"We used the Keras framework 17 for Tensorflow 18 in Python to implement and train our architectures.","wikidataId":"Q28865","type":"software","confidence":0.6138,"software-name":{"wikipediaExternalRef":23862,"normalizedForm":"Python","offsetStart":52,"wikidataId":"Q28865","offsetEnd":58,"lang":"en","confidence":0.6138,"rawForm":"Python","boundingBoxes":[{"x":439.5,"h":9.099,"y":605.182,"p":5,"w":26.28}]},"lang":"en"},
  {"_key":"60c20df17723bebd8664576e","_id":"annotations/60c20df17723bebd8664576e","_rev":"_cfFmWni---","wikipediaExternalRef":20412,"document":{"$oid":"60c20df17723bebd86645769"},"context":"The overlays with the detection results were created through MATLAB 2018a, http://mathw orks.com/produ","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":62,"wikidataId":"Q169478","offsetEnd":68,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":233.25,"h":9.099,"y":550.591,"p":10,"w":35.4051}]},"url":{"offsetStart":135,"normalizedForm":"a.html","offsetEnd":141,"rawForm":"a.html","boundingBoxes":[{"x":503.107,"h":9.099000000000046,"y":550.591,"p":10,"w":25.483499999999992}]},"version":{"offsetStart":134,"normalizedForm":"8","offsetEnd":135,"rawForm":"8","boundingBoxes":[{"x":503.107,"h":9.099,"y":550.591,"p":10,"w":7.281}]}},
  {"_key":"60c20df17723bebd8664576f","_id":"annotations/60c20df17723bebd8664576f","_rev":"_cfFmWnu---","document":{"$oid":"60c20df17723bebd86645769"},"context":"A gastroen- terologist extracted the parts corresponding to the small intestine through their official RAPID Reader v8.3 software, capable of reading the proprietary file format of the video recordings, from which we subsequently systematically extracted all frames at regular intervals of one minute.","type":"software","software-name":{"offsetStart":103,"normalizedForm":"RAPID Reader","offsetEnd":115,"rawForm":"RAPID Reader","boundingBoxes":[{"x":481.215,"h":9.09899999999999,"y":283.445,"p":3,"w":54.99899999999997}]},"version":{"offsetStart":117,"normalizedForm":"8.3","offsetEnd":120,"rawForm":"8.3","boundingBoxes":[{"x":539.301,"h":9.09899999999999,"y":283.445,"p":3,"w":14.858999999999924}]}},
  {"_key":"60c20df17723bebd86645770","_id":"annotations/60c20df17723bebd86645770","_rev":"_cfFmWo----","document":{"$oid":"60c20df17723bebd86645769"},"context":"Original images were extracted from videos of CE procedures performed with the PillCam SB 3 model, obtained as explained in \"Data conditioning\" section through the Rapid Reader v8.3 software, http://medtr onic.com/covid","type":"software","software-name":{"offsetStart":166,"normalizedForm":"Rapid Reader","offsetEnd":178,"rawForm":"Rapid Reader","boundingBoxes":[{"x":278.601,"h":9.099000000000046,"y":530.593,"p":10,"w":48.21300000000002}]},"url":{"offsetStart":271,"normalizedForm":"-","offsetEnd":272,"rawForm":"-","boundingBoxes":[{"x":253.88542857142855,"h":9.099,"y":540.592,"p":10,"w":3.8764285714285713}]},"version":{"offsetStart":180,"normalizedForm":"8.3","offsetEnd":183,"rawForm":"8.3","boundingBoxes":[{"x":328.767,"h":9.099000000000046,"y":530.593,"p":10,"w":14.72399999999999}]}},
  {"_key":"60c20df17723bebd86645771","_id":"annotations/60c20df17723bebd86645771","_rev":"_cfFmWoO---","wikipediaExternalRef":20412,"document":{"$oid":"60c20df17723bebd86645769"},"context":"We also evaluated the size of each model, in terms of number of parameters and storage space, along with the average time required for a prediction of a batch of 2000 patch images, measured over the processing of 100 of such batches on an NVIDIA GeForce GTX 950 GPU using a MATLAB 2018a implementation.","wikidataId":"Q169478","type":"software","lang":"en","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":277,"wikidataId":"Q169478","offsetEnd":283,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":272.919,"h":9.099,"y":233.174,"p":8,"w":35.838}]},"url":{"offsetStart":135,"normalizedForm":"a.html","offsetEnd":141,"rawForm":"a.html","boundingBoxes":[{"x":503.107,"h":9.099000000000046,"y":550.591,"p":10,"w":25.483499999999992}]},"version":{"offsetStart":134,"normalizedForm":"8","offsetEnd":135,"rawForm":"8","boundingBoxes":[{"x":503.107,"h":9.099,"y":550.591,"p":10,"w":7.281}]}},
  {"_key":"60c20df47723bebd86645773","_id":"annotations/60c20df47723bebd86645773","_rev":"_cfFmWoe---","document":{"$oid":"60c20df47723bebd86645772"},"context":"The average cycle threshold value (C T ) for each individual assay was calculated from triplicate measurements by means of the instrument's software in the auto C T mode (7500 FAST System Software, version 1.3.0).","type":"software","software-name":{"offsetStart":173,"normalizedForm":"7500 FAST System","offsetEnd":189,"rawForm":"7500 FAST System","boundingBoxes":[{"x":431.57620000000003,"h":6.272000000000048,"y":547.013,"p":2,"w":55.88779999999997}]},"version":{"offsetStart":209,"normalizedForm":"1.3.0","offsetEnd":214,"rawForm":"1.3.0","boundingBoxes":[{"x":300.499,"h":6.272000000000048,"y":556.157,"p":2,"w":13.164999999999964}]}},
  {"_key":"60c20df87723bebd86645775","_id":"annotations/60c20df87723bebd86645775","_rev":"_cfFmWoq---","wikipediaExternalRef":179088,"document":{"$oid":"60c20df87723bebd86645774"},"publisher":{"offsetStart":69,"normalizedForm":"SPSS IBM","offsetEnd":77,"rawForm":"SPSS IBM","boundingBoxes":[{"x":48.78894,"h":7.183899999999994,"y":729.295,"p":3,"w":32.05564000000001}]},"context":"The data were analyzed using the IBM SPSS Statistics 22.0 program  (SPSS IBM).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.4875,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS Statistics","offsetStart":37,"wikidataId":"Q181596","offsetEnd":52,"lang":"en","confidence":0.4875,"rawForm":"SPSS Statistics","boundingBoxes":[{"x":184.876,"h":7.183899999999994,"y":716.256,"p":3,"w":52.14959999999999}]},"version":{"offsetStart":53,"normalizedForm":"22.0","offsetEnd":57,"rawForm":"22.0","boundingBoxes":[{"x":239.471,"h":7.183899999999994,"y":716.256,"p":3,"w":15.615800000000007}]}},
  {"_key":"60c20e097723bebd86645777","_id":"annotations/60c20e097723bebd86645777","_rev":"_cfFmWo6---","wikipediaExternalRef":990677,"document":{"$oid":"60c20e097723bebd86645776"},"publisher":{"offsetStart":69,"normalizedForm":"SAS Insti- tute","offsetEnd":84,"rawForm":"SAS Insti-\ntute","boundingBoxes":[{"x":516.71465,"h":7.539800000000014,"y":257.537,"p":3,"w":34.727750000000015},{"x":300.473,"h":7.5398,"y":267.968,"p":3,"w":13.198640000000001}]},"context":"All statis- tical calculations were performed using SAS version 9.4 (SAS Insti- tute, Cary, NC).","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":52,"wikidataId":"Q2003932","offsetEnd":55,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":451.611,"h":7.5398,"y":257.537,"p":3,"w":13.5175}]},"version":{"offsetStart":64,"normalizedForm":"9.4","offsetEnd":67,"rawForm":"9.4","boundingBoxes":[{"x":498.437,"h":7.539800000000014,"y":257.537,"p":3,"w":10.943099999999959}]}},
  {"_key":"60c20e0d7723bebd86645779","_id":"annotations/60c20e0d7723bebd86645779","_rev":"_cfFmWpK---","document":{"$oid":"60c20e0d7723bebd86645778"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"CAMY","offsetEnd":4,"rawForm":"CAMY","boundingBoxes":[{"x":176.994,"h":6.0317,"y":408.208,"p":5,"w":18.6591}]},"context":"CAMY is designed to predict disease outbreaks using social media and other existing channels of communication while connecting physicians and patients in under-resourced areas."},
  {"_key":"60c20e0d7723bebd8664577a","_id":"annotations/60c20e0d7723bebd8664577a","_rev":"_cfFmWpa---","document":{"$oid":"60c20e0d7723bebd86645778"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Multiplexed Early Warning System -MEWS MEWS","offsetEnd":43,"rawForm":"Multiplexed Early Warning System -MEWS MEWS","boundingBoxes":[{"x":39.6849,"h":6.375999999999976,"y":442.355,"p":5,"w":157.6401}]},"context":"Multiplexed Early Warning System -MEWS MEWS proposed a software toolkit that utilizes the many disease tracking models published in the literature combined with cost-benefit analysis of prevention and treatment options."},
  {"_key":"60c20e107723bebd8664577c","_id":"annotations/60c20e107723bebd8664577c","_rev":"_cfFmWpm---","document":{"$oid":"60c20e107723bebd8664577b"},"context":"This identification of efficient diets was solved in two stages (12,32) , using Xpress-IVE release 1•24.","type":"software","software-name":{"offsetStart":81,"normalizedForm":"Xpress-IVE","offsetEnd":91,"rawForm":"Xpress-IVE","boundingBoxes":[{"x":437.273,"h":8.435999999999979,"y":485.739,"p":2,"w":44.19399999999996}]},"version":{"offsetStart":100,"normalizedForm":"1•24","offsetEnd":104,"rawForm":"1•24","boundingBoxes":[{"x":516.534,"h":8.435999999999979,"y":485.739,"p":2,"w":15.200000000000045}]}},
  {"_key":"60c20e137723bebd8664577e","_id":"annotations/60c20e137723bebd8664577e","_rev":"_cfFmWp6---","document":{"$oid":"60c20e137723bebd8664577d"},"publisher":{"offsetStart":65,"normalizedForm":"Bio-Rad","offsetEnd":72,"rawForm":"Bio-Rad","boundingBoxes":[{"x":389.409,"h":9.09899999999999,"y":480.737,"p":6,"w":30.048299999999983}]},"context":"Cq was evaluated with a threshold of 30 flourescence units using Bio-Rad CFX Manager software.","type":"software","software-name":{"offsetStart":73,"normalizedForm":"CFX Manager","offsetEnd":84,"rawForm":"CFX Manager","boundingBoxes":[{"x":421.455,"h":9.09899999999999,"y":480.737,"p":6,"w":50.70780000000002}]}},
  {"_key":"60c20e137723bebd8664577f","_id":"annotations/60c20e137723bebd8664577f","_rev":"_cfFmWqG---","document":{"$oid":"60c20e137723bebd8664577d"},"context":"The sequences of GII.4 New Orleans and Sydney strains as well as a GII.3 strain were aligned using the Mega 6 software package.","type":"software","software-name":{"offsetStart":104,"normalizedForm":"Mega","offsetEnd":108,"rawForm":"Mega","boundingBoxes":[{"x":346.221,"h":9.099,"y":115.487,"p":5,"w":19.773}]},"version":{"offsetStart":109,"normalizedForm":"6","offsetEnd":110,"rawForm":"6","boundingBoxes":[{"x":367.83,"h":9.099,"y":115.487,"p":5,"w":4.32}]}},
  {"_key":"60c20e137723bebd86645780","_id":"annotations/60c20e137723bebd86645780","_rev":"_cfFmWqS---","wikipediaExternalRef":20268,"document":{"$oid":"60c20e137723bebd8664577d"},"publisher":{"offsetStart":161,"normalizedForm":"Microsoft","offsetEnd":170,"rawForm":"Microsoft","boundingBoxes":[{"x":519.483,"h":9.099,"y":70.6408,"p":7,"w":35.0892}]},"context":"The degree of correlation between RT-RPA time to detection (in min) and log 10 genomic copy input (by standard curve) was determined by linear regression using Microsoft Excel 2013 (Figure S2).","wikidataId":"Q11272","type":"software","lang":"en","confidence":0.378,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Excel","offsetStart":172,"wikidataId":"Q11272","offsetEnd":177,"lang":"en","confidence":0.378,"rawForm":"Excel","boundingBoxes":[{"x":155.638,"h":9.099,"y":80.6398,"p":7,"w":19.4418}]},"version":{"offsetStart":178,"normalizedForm":"2013","offsetEnd":182,"rawForm":"2013","boundingBoxes":[{"x":177.185,"h":9.099,"y":80.6398,"p":7,"w":17.4645}]}},
  {"_key":"60c20e137723bebd86645781","_id":"annotations/60c20e137723bebd86645781","_rev":"_cfFmWqi---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20e137723bebd8664577d"},"context":"To analyze the degree of sequence difference between GII.4 New Orleans, for which the primers were designed, and two other human norovirus strains (GII.3 and GII.4 Sydney), sequences were aligned by performing Clustal W analysis using the MEGA 6 Software suite 39 .","wikidataId":"Q866737","type":"software","confidence":0.8955,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"Clustal W","offsetStart":212,"wikidataId":"Q866737","offsetEnd":221,"lang":"en","confidence":0.8955,"rawForm":"Clustal W","boundingBoxes":[{"x":453.148,"h":9.09899999999999,"y":191.192,"p":7,"w":36.178999999999974}]},"lang":"en"},
  {"_key":"60c20e137723bebd86645782","_id":"annotations/60c20e137723bebd86645782","_rev":"_cfFmWqy---","document":{"$oid":"60c20e137723bebd8664577d"},"context":"To analyze the degree of sequence difference between GII.4 New Orleans, for which the primers were designed, and two other human norovirus strains (GII.3 and GII.4 Sydney), sequences were aligned by performing Clustal W analysis using the MEGA 6 Software suite 39 .","type":"software","software-name":{"offsetStart":242,"normalizedForm":"MEGA","offsetEnd":246,"rawForm":"MEGA","boundingBoxes":[{"x":155.636,"h":9.099,"y":201.191,"p":7,"w":25.785}]},"version":{"offsetStart":247,"normalizedForm":"6","offsetEnd":248,"rawForm":"6","boundingBoxes":[{"x":183.257,"h":9.099,"y":201.191,"p":7,"w":4.32}]}},
  {"_key":"60c20e137723bebd86645783","_id":"annotations/60c20e137723bebd86645783","_rev":"_cfFmWr----","wikipediaExternalRef":1979375,"document":{"$oid":"60c20e137723bebd8664577d"},"publisher":{"offsetStart":297,"normalizedForm":"SAS","offsetEnd":300,"rawForm":"SAS","boundingBoxes":[{"x":497.22702000000004,"h":9.099,"y":100.637,"p":7,"w":12.06306}]},"context":"For evaluating the RT-RPA assay analytical sensitivity, serial dilutions of purified RNA from three selected stool samples (samples 29, 47, and 58) were tested using as described above for a total of 8 replicates and a probit regression was performed for each using the JMP 12 software package (SAS, Cary, NC).","wikidataId":"Q1161680","type":"software","lang":"en","confidence":0.3648,"software-name":{"wikipediaExternalRef":1979375,"normalizedForm":"JMP","offsetStart":272,"wikidataId":"Q1161680","offsetEnd":275,"lang":"en","confidence":0.3648,"rawForm":"JMP","boundingBoxes":[{"x":400.397,"h":9.099,"y":100.637,"p":7,"w":16.155}]},"version":{"offsetStart":276,"normalizedForm":"12","offsetEnd":278,"rawForm":"12","boundingBoxes":[{"x":418.631,"h":9.099,"y":100.637,"p":7,"w":8.694}]}},
  {"_key":"60c20e147723bebd86645786","_id":"annotations/60c20e147723bebd86645786","_rev":"_cfFmWrK---","document":{"$oid":"60c20e147723bebd86645784"},"context":"This was achieved using  LLMapReduce [12], with a task created for each of the 770,661 non-empty bottom level directories.","references":[{"offsetStart":17091,"normalizedForm":"[12]","refKey":12,"label":"[12]","reference_id":{"$oid":"60c20e147723bebd86645785"},"offsetEnd":17095,"boundingBoxes":[{"x":107.78,"h":8.963999999999999,"y":55.8373,"p":4,"w":15.240000000000009}]}],"type":"software","software-name":{"offsetStart":26,"normalizedForm":"LLMapReduce","offsetEnd":37,"rawForm":"LLMapReduce","boundingBoxes":[{"x":45.36,"h":8.964,"y":55.8373,"p":4,"w":60.0488}]}},
  {"_key":"60c20e147723bebd86645787","_id":"annotations/60c20e147723bebd86645787","_rev":"_cfFmWrW---","document":{"$oid":"60c20e147723bebd86645784"},"context":"Once organized into individual csv files, LLMapReduce can be used again to update the existing archives.","references":[{"offsetStart":17091,"normalizedForm":"[12]","refKey":12,"label":"[12]","reference_id":{"$oid":"60c20e147723bebd86645785"},"offsetEnd":17095,"boundingBoxes":[{"x":107.78,"h":8.963999999999999,"y":55.8373,"p":4,"w":15.240000000000009}]}],"type":"software","software-name":{"offsetStart":42,"normalizedForm":"LLMapReduce","offsetEnd":53,"rawForm":"LLMapReduce","boundingBoxes":[{"x":208.803,"h":8.964,"y":181.977,"p":4,"w":59.9293}]}},
  {"_key":"60c20e157723bebd8664578a","_id":"annotations/60c20e157723bebd8664578a","_rev":"_cfFmWri---","document":{"$oid":"60c20e157723bebd86645788"},"type":"software","software-name":{"offsetStart":4,"normalizedForm":"Basic Local Alignment Search Tool (BLAST)","offsetEnd":45,"rawForm":"Basic Local Alignment Search Tool (BLAST)","boundingBoxes":[{"x":81.1836,"h":11.480000000000018,"y":671.135,"p":2,"w":189.27639999999997}]},"context":"The Basic Local Alignment Search Tool (BLAST) was used to identify regions of sequence similarity [27]."},
  {"_key":"60c20e157723bebd8664578b","_id":"annotations/60c20e157723bebd8664578b","_rev":"_cfFmWru---","document":{"$oid":"60c20e157723bebd86645788"},"context":"Sequence alignments were made with Multalin [28].","references":[{"offsetStart":6980,"normalizedForm":"[28]","refKey":27,"label":"[28]","reference_id":{"$oid":"60c20e157723bebd86645789"},"offsetEnd":6984,"boundingBoxes":[{"x":505.448,"h":11.480000000000004,"y":71.1358,"p":2,"w":15.67999999999995}]}],"type":"software","software-name":{"offsetStart":35,"normalizedForm":"Multalin","offsetEnd":43,"rawForm":"Multalin","boundingBoxes":[{"x":466.727,"h":11.48,"y":71.1358,"p":2,"w":35.321}]},"url":{"offsetStart":153,"normalizedForm":".","offsetEnd":154,"rawForm":".","boundingBoxes":[{"x":463.145,"h":11.48,"y":96.1358,"p":2,"w":4.683}]}},
  {"_key":"60c20e157723bebd8664578c","_id":"annotations/60c20e157723bebd8664578c","_rev":"_cfFmWs----","wikipediaExternalRef":17420591,"document":{"$oid":"60c20e157723bebd86645788"},"context":"Nucleo- tide sequence were translated into amino acid sequences using the Translate tool at the Expasy website of the Swiss  Institute of Bioinformatics (https ://web.expas","wikidataId":"Q4462013","type":"software","confidence":0.296,"software-name":{"wikipediaExternalRef":17420591,"normalizedForm":"Translate","offsetStart":75,"wikidataId":"Q4462013","offsetEnd":84,"lang":"en","confidence":0.296,"rawForm":"Translate","boundingBoxes":[{"x":90.6406,"h":11.48,"y":708.635,"p":2,"w":37.067}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd8664578f","_id":"annotations/60c20e1b7723bebd8664578f","_rev":"_cfFmWsO---","document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"AMBER14: EHT force field was used for energy minimisation of the generated compound library using steepest descent algorithm until RMS gra- dient of 0.1 Kcal/Mol/A is reached 16 .","type":"software","software-name":{"offsetStart":0,"normalizedForm":"AMBER","offsetEnd":5,"rawForm":"AMBER","boundingBoxes":[{"x":532.006,"h":7.947,"y":391.746,"p":3,"w":33.240375}]},"version":{"offsetStart":5,"normalizedForm":"14: EHT","offsetEnd":13,"rawForm":"14: \nEHT","boundingBoxes":[{"x":532.006,"h":7.947000000000003,"y":391.746,"p":3,"w":37.98899999999992},{"x":311.98,"h":7.947,"y":402.971,"p":3,"w":14.769}]}},
  {"_key":"60c20e1b7723bebd86645790","_id":"annotations/60c20e1b7723bebd86645790","_rev":"_cfFmWse---","wikipediaExternalRef":306766,"document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"GROMACS has built-in commands that were used to measure the distances of the formed hydrogen bonds between compound 11 and SARS-COV-2 2 0 -O-methyltransferase (nsp16).","wikidataId":"Q905302","type":"software","confidence":0.8007,"software-name":{"wikipediaExternalRef":306766,"normalizedForm":"GROMACS","offsetStart":0,"wikidataId":"Q905302","offsetEnd":7,"lang":"en","confidence":0.8007,"rawForm":"GROMACS","boundingBoxes":[{"x":311.981,"h":7.947,"y":578.891,"p":8,"w":39.258}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd86645791","_id":"annotations/60c20e1b7723bebd86645791","_rev":"_cfFmWsq---","document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"MGL tools 1.5.7 was implemented to pre- pare the equilibrated nsp16, Sinefungin and the successful candi- dates from the pharmacophore search were converted into pdbqt format; a prerequisite for Vina Autodock software 20,21 .","type":"software","software-name":{"offsetStart":0,"normalizedForm":"MGL tools","offsetEnd":9,"rawForm":"MGL tools","boundingBoxes":[{"x":136.18,"h":7.947000000000003,"y":674.418,"p":4,"w":39.468999999999994}]},"version":{"offsetStart":10,"normalizedForm":"1.5.7","offsetEnd":15,"rawForm":"1.5.7","boundingBoxes":[{"x":179.268,"h":7.947000000000003,"y":674.418,"p":4,"w":17.576999999999998}]}},
  {"_key":"60c20e1b7723bebd86645792","_id":"annotations/60c20e1b7723bebd86645792","_rev":"_cfFmWs6---","wikipediaExternalRef":26322186,"document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"AutoDock Vina software was used to conduct the previous step in addition to the successful candidates from the pharmacophore search.","wikidataId":"Q4826062","type":"software","confidence":0.9722,"software-name":{"wikipediaExternalRef":26322186,"normalizedForm":"AutoDock Vina","offsetStart":0,"wikidataId":"Q4826062","offsetEnd":13,"lang":"en","confidence":0.9722,"rawForm":"AutoDock Vina","boundingBoxes":[{"x":95.6983,"h":7.947000000000003,"y":651.401,"p":4,"w":58.868700000000004}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd86645793","_id":"annotations/60c20e1b7723bebd86645793","_rev":"_cfFmWtK---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":4,"normalizedForm":"g_mmpbsa","offsetEnd":12,"rawForm":"g_mmpbsa","boundingBoxes":[{"x":59.8114,"h":7.947,"y":665.628,"p":9,"w":42.687}]},"context":"The g_mmpbsa package was used to calculate all those types of energies along with the values standard deviation and then summed together to yield the average total free energy of each component."},
  {"_key":"60c20e1b7723bebd86645794","_id":"annotations/60c20e1b7723bebd86645794","_rev":"_cfFmWta---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":11,"normalizedForm":"g_mmpbsa","offsetEnd":19,"rawForm":"g_mmpbsa","boundingBoxes":[{"x":114.43609000000001,"h":9,"y":531.605,"p":5,"w":39.24072}]},"context":"Thus, the \"g_mmpbsa\" 27 package of GROMACS was used perform MM-PBSA calculations through all the MD trajectories."},
  {"_key":"60c20e1b7723bebd86645795","_id":"annotations/60c20e1b7723bebd86645795","_rev":"_cfFmWtm---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":17,"normalizedForm":"g_mmpbsa","offsetEnd":25,"rawForm":"g_mmpbsa","boundingBoxes":[{"x":110.836,"h":7.947,"y":521.347,"p":9,"w":42.687}]},"context":"Accordingly, the g_mmpbsa package was used to calculate the MM-PBSA binding free energy for the two complexes of SARS COV-2 2 0 -O-methyltransferase enzyme with compound 11 and with Sinefungine by the employment of MmPbSaStat.py python script."},
  {"_key":"60c20e1b7723bebd86645796","_id":"annotations/60c20e1b7723bebd86645796","_rev":"_cfFmWt2---","document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"The latest version of GROningen MAchine for Chemical Simulations (GROMACS 2020.3) was employed to conduct the entire MD simulation experiments 23 .","type":"software","software-name":{"offsetStart":23,"normalizedForm":"GROningen MAchine for Chemical Simulations (GROMACS","offsetEnd":74,"rawForm":"GROningen MAchine for Chemical Simulations (GROMACS","boundingBoxes":[{"x":311.98,"h":7.947000000000003,"y":177.447,"p":4,"w":226.75199999999995}]},"version":{"offsetStart":75,"normalizedForm":"2020.3","offsetEnd":81,"rawForm":"2020.3","boundingBoxes":[{"x":542.5,"h":7.947000000000003,"y":177.447,"p":4,"w":23.574857142857127}]}},
  {"_key":"60c20e1b7723bebd86645797","_id":"annotations/60c20e1b7723bebd86645797","_rev":"_cfFmWuG---","wikipediaExternalRef":306766,"document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"Thus, the \"g_mmpbsa\" 27 package of GROMACS was used perform MM-PBSA calculations through all the MD trajectories.","wikidataId":"Q905302","type":"software","confidence":0.8007,"software-name":{"wikipediaExternalRef":306766,"normalizedForm":"GROMACS","offsetStart":35,"wikidataId":"Q905302","offsetEnd":42,"lang":"en","confidence":0.8007,"rawForm":"GROMACS","boundingBoxes":[{"x":218.779,"h":7.947,"y":532.29,"p":5,"w":39.258}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd86645798","_id":"annotations/60c20e1b7723bebd86645798","_rev":"_cfFmWuW---","wikipediaExternalRef":26322186,"document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"Based on the results obtained from AutoDock Vina, only four compounds (5, 9, 11 and 24, Figure 4), among the 24 potential leads, were able to achieve better docking score (S ¼ À10.1, À10.3, À10.6 and À9.9 Kcal/mol, respectively) than Sinefungine (S ¼ À8.5 Kcal/mol), and thus were selected for further analysis.","wikidataId":"Q4826062","type":"software","confidence":0.9722,"software-name":{"wikipediaExternalRef":26322186,"normalizedForm":"AutoDock Vina","offsetStart":35,"wikidataId":"Q4826062","offsetEnd":48,"lang":"en","confidence":0.9722,"rawForm":"AutoDock Vina","boundingBoxes":[{"x":200.071,"h":7.947000000000003,"y":423.041,"p":7,"w":56.33020000000002}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd86645799","_id":"annotations/60c20e1b7723bebd86645799","_rev":"_cfFmWuq---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":43,"normalizedForm":"CHARMM General Force Field CGENFF","offsetEnd":77,"rawForm":"CHARMM General \nForce Field CGENFF","boundingBoxes":[{"x":499.809,"h":7.947000000000003,"y":199.559,"p":4,"w":70.2229999999999},{"x":311.981,"h":7.947000000000003,"y":210.615,"p":4,"w":78.56599999999997}]},"context":"The ligand topologies were obtained by the CHARMM General Force Field CGENFF server and converted into the desired gro- macs format using the \"cgenff_charmm2gmx_py3_nx2.py\""},
  {"_key":"60c20e1b7723bebd8664579a","_id":"annotations/60c20e1b7723bebd8664579a","_rev":"_cfFmWu6---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":61,"normalizedForm":"2","offsetEnd":62,"rawForm":"2","boundingBoxes":[{"x":531.7434000000001,"h":9,"y":232.098,"p":4,"w":33.476800000000004}]},"context":"script, while the receptor topology was obtained by the \"pdb2gmx\" script 24 ."},
  {"_key":"60c20e1b7723bebd8664579b","_id":"annotations/60c20e1b7723bebd8664579b","_rev":"_cfFmWvK---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":61,"normalizedForm":"MM-PBSA","offsetEnd":68,"rawForm":"MM-PBSA","boundingBoxes":[{"x":75.5724,"h":7.947000000000003,"y":543.628,"p":5,"w":36.846000000000004}]},"context":"Thus, the \"g_mmpbsa\" 27 package of GROMACS was used perform MM-PBSA calculations through all the MD trajectories."},
  {"_key":"60c20e1b7723bebd8664579c","_id":"annotations/60c20e1b7723bebd8664579c","_rev":"_cfFmWvW---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":61,"normalizedForm":"MM-PBSA","offsetEnd":68,"rawForm":"MM-PBSA","boundingBoxes":[{"x":42.0094,"h":7.947000000000003,"y":532.458,"p":9,"w":36.846000000000004}]},"context":"Accordingly, the g_mmpbsa package was used to calculate the MM-PBSA binding free energy for the two complexes of SARS COV-2 2 0 -O-methyltransferase enzyme with compound 11 and with Sinefungine by the employment of MmPbSaStat.py python script."},
  {"_key":"60c20e1b7723bebd8664579d","_id":"annotations/60c20e1b7723bebd8664579d","_rev":"_cfFmWvm---","document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"was downloaded as smiles files and then converted into single database file with extension mdb by MOE suite (MOE, 2019 (https://www.chemcomp.com)).","type":"software","software-name":{"offsetStart":100,"normalizedForm":"MOE","offsetEnd":103,"rawForm":"MOE","boundingBoxes":[{"x":311.98,"h":7.947,"y":391.746,"p":3,"w":17.865}]},"url":{"offsetStart":122,"normalizedForm":"https://www.chemcomp.com","offsetEnd":146,"rawForm":"https://www.chemcomp.com","boundingBoxes":[{"x":411.6783571428572,"h":7.947000000000003,"y":391.746,"p":3,"w":102.7765714285714}]},"version":{"offsetStart":116,"normalizedForm":"2019","offsetEnd":120,"rawForm":"2019","boundingBoxes":[{"x":384.265,"h":7.947,"y":391.746,"p":3,"w":18.468}]}},
  {"_key":"60c20e1b7723bebd8664579e","_id":"annotations/60c20e1b7723bebd8664579e","_rev":"_cfFmWv2---","document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"was downloaded as smiles files and then converted into single database file with extension mdb by MOE suite (MOE, 2019 (https://www.chemcomp.com)).","type":"software","software-name":{"offsetStart":111,"normalizedForm":"MOE","offsetEnd":114,"rawForm":"MOE","boundingBoxes":[{"x":361.79179999999997,"h":7.947,"y":391.746,"p":3,"w":13.370399999999998}]},"url":{"offsetStart":122,"normalizedForm":"https://www.chemcomp.com","offsetEnd":146,"rawForm":"https://www.chemcomp.com","boundingBoxes":[{"x":411.6783571428572,"h":7.947000000000003,"y":391.746,"p":3,"w":102.7765714285714}]},"version":{"offsetStart":116,"normalizedForm":"2019","offsetEnd":120,"rawForm":"2019","boundingBoxes":[{"x":384.265,"h":7.947,"y":391.746,"p":3,"w":18.468}]}},
  {"_key":"60c20e1b7723bebd8664579f","_id":"annotations/60c20e1b7723bebd8664579f","_rev":"_cfFmWwG---","document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"The best candi- dates were selected for further analysis based on the docking and  the interaction diagram generated by Discovery Studio Visualiser 22 .","type":"software","software-name":{"offsetStart":121,"normalizedForm":"Discovery Studio Visualiser","offsetEnd":149,"rawForm":"Discovery Studio \nVisualiser","boundingBoxes":[{"x":498.221,"h":7.947000000000003,"y":53.0078,"p":4,"w":71.78100000000006},{"x":311.981,"h":7.947,"y":64.0625,"p":4,"w":35.235}]},"version":{"offsetStart":171,"normalizedForm":"2020","offsetEnd":175,"rawForm":"2020","boundingBoxes":[{"x":417.887,"h":7.947,"y":210.103,"p":3,"w":18.468}]}},
  {"_key":"60c20e1b7723bebd866457a0","_id":"annotations/60c20e1b7723bebd866457a0","_rev":"_cfFmWwW---","document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"The interaction dia- gram between Sinefungin and the minimised and equilibrated SARS COV-2 2 0 -O-methyltransferase (nsp16) was generated by Discovery Studio Visualiser 2020 to determine the types and num- ber of the formed interactions, as well as the functional groups in Sinefungin responsible for those interactions (Figure 2).","type":"software","software-name":{"offsetStart":143,"normalizedForm":"Discovery Studio Visualiser","offsetEnd":170,"rawForm":"Discovery Studio Visualiser","boundingBoxes":[{"x":311.981,"h":7.947000000000003,"y":210.103,"p":3,"w":102.75800000000004}]},"version":{"offsetStart":171,"normalizedForm":"2020","offsetEnd":175,"rawForm":"2020","boundingBoxes":[{"x":417.887,"h":7.947,"y":210.103,"p":3,"w":18.468}]}},
  {"_key":"60c20e1b7723bebd866457a1","_id":"annotations/60c20e1b7723bebd866457a1","_rev":"_cfFmWwi---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":149,"normalizedForm":"MM-PBSA","offsetEnd":156,"rawForm":"MM-PBSA","boundingBoxes":[{"x":359.036,"h":7.947000000000003,"y":731.904,"p":8,"w":36.846000000000004}]},"context":"Another important indicator that gives account for the potential affinity of a ligand with its target is the binding free energy calcu- lated using MM-PBSA and MD calculations."},
  {"_key":"60c20e1b7723bebd866457a2","_id":"annotations/60c20e1b7723bebd866457a2","_rev":"_cfFmWwy---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":157,"normalizedForm":"2","offsetEnd":158,"rawForm":"2","boundingBoxes":[{"x":412.13323333333335,"h":9,"y":221.042,"p":4,"w":112.78083333333333}]},"context":"The ligand topologies were obtained by the CHARMM General Force Field CGENFF server and converted into the desired gro- macs format using the \"cgenff_charmm2gmx_py3_nx2.py\""},
  {"_key":"60c20e1b7723bebd866457a3","_id":"annotations/60c20e1b7723bebd866457a3","_rev":"_cfFmWx----","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":164,"normalizedForm":"3","offsetEnd":165,"rawForm":"3","boundingBoxes":[{"x":412.13323333333335,"h":9,"y":221.042,"p":4,"w":112.78083333333333}]},"context":"The ligand topologies were obtained by the CHARMM General Force Field CGENFF server and converted into the desired gro- macs format using the \"cgenff_charmm2gmx_py3_nx2.py\""},
  {"_key":"60c20e1b7723bebd866457a4","_id":"annotations/60c20e1b7723bebd866457a4","_rev":"_cfFmWxO---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":168,"normalizedForm":"2","offsetEnd":169,"rawForm":"2","boundingBoxes":[{"x":412.13323333333335,"h":9,"y":221.042,"p":4,"w":112.78083333333333}]},"context":"The ligand topologies were obtained by the CHARMM General Force Field CGENFF server and converted into the desired gro- macs format using the \"cgenff_charmm2gmx_py3_nx2.py\""},
  {"_key":"60c20e1b7723bebd866457a5","_id":"annotations/60c20e1b7723bebd866457a5","_rev":"_cfFmWxe---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":196,"normalizedForm":"Vina Autodock","offsetEnd":209,"rawForm":"Vina Autodock","boundingBoxes":[{"x":145.023,"h":7.947000000000003,"y":708.886,"p":4,"w":57.010999999999996}]},"context":"MGL tools 1.5.7 was implemented to pre- pare the equilibrated nsp16, Sinefungin and the successful candi- dates from the pharmacophore search were converted into pdbqt format; a prerequisite for Vina Autodock software 20,21 ."},
  {"_key":"60c20e1b7723bebd866457a6","_id":"annotations/60c20e1b7723bebd866457a6","_rev":"_cfFmWxu---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":218,"normalizedForm":"MmPbSaStat.py","offsetEnd":231,"rawForm":"MmPbSaStat.py","boundingBoxes":[{"x":208.862,"h":7.947000000000003,"y":554.683,"p":9,"w":59.38199999999998}]},"context":"Accordingly, the g_mmpbsa package was used to calculate the MM-PBSA binding free energy for the two complexes of SARS COV-2 2 0 -O-methyltransferase enzyme with compound 11 and with Sinefungine by the employment of MmPbSaStat.py python script."},
  {"_key":"60c20e1b7723bebd866457a7","_id":"annotations/60c20e1b7723bebd866457a7","_rev":"_cfFmWx6---","wikipediaExternalRef":306766,"document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"The root mean square deviation (RMSD) was calculated from the generated trajectories of the MD simulations as well as the distances of the formed hydrogen bonds between the receptor and the ligands by various scripts of GROMACS.","wikidataId":"Q905302","type":"software","confidence":0.8007,"software-name":{"wikipediaExternalRef":306766,"normalizedForm":"GROMACS","offsetStart":224,"wikidataId":"Q905302","offsetEnd":231,"lang":"en","confidence":0.8007,"rawForm":"GROMACS","boundingBoxes":[{"x":380.071,"h":7.947,"y":553.546,"p":4,"w":35.980875000000005}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd866457a8","_id":"annotations/60c20e1b7723bebd866457a8","_rev":"_cfFmWyK---","wikipediaExternalRef":21490336,"document":{"$oid":"60c20e1b7723bebd8664578d"},"context":"Accordingly, the g_mmpbsa package was used to calculate the MM-PBSA binding free energy for the two complexes of SARS COV-2 2 0 -O-methyltransferase enzyme with compound 11 and with Sinefungine by the employment of MmPbSaStat.py python script.","wikidataId":"Q187432","references":[{"offsetStart":14982,"normalizedForm":"24","refKey":22,"label":"24","reference_id":{"$oid":"60c20e1b7723bebd8664578e"},"offsetEnd":14985,"boundingBoxes":[{"x":332.73,"h":5.2973,"y":241.833,"p":4,"w":6.9254}]}],"type":"software","confidence":0.2792,"software-name":{"wikipediaExternalRef":21490336,"normalizedForm":"script","offsetStart":240,"wikidataId":"Q187432","offsetEnd":246,"lang":"en","confidence":0.2792,"rawForm":"script","boundingBoxes":[{"x":42.0094,"h":7.947,"y":565.794,"p":9,"w":19.378285714285713}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd866457a9","_id":"annotations/60c20e1b7723bebd866457a9","_rev":"_cfFmWya---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":314,"normalizedForm":"2","offsetEnd":315,"rawForm":"2","boundingBoxes":[{"x":452.0006,"h":17.91,"y":173.353,"p":1,"w":10.121400000000001}]},"context":"In silico identification of novel SARS-COV-2 2′-O- methyltransferase (nsp16) inhibitors: structure- based virtual screening, molecular dynamics simulation and MM-PBSA approaches In silico identification of novel SARS-COV-2 2 0 -O-methyltransferase (nsp16) inhibitors: structure-based virtual screening, molecular dynamics simulation and MM-PBSA approaches"},
  {"_key":"60c20e1b7723bebd866457aa","_id":"annotations/60c20e1b7723bebd866457aa","_rev":"_cfFmWyq---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":337,"normalizedForm":"PBSA","offsetEnd":341,"rawForm":"PBSA","boundingBoxes":[{"x":75.20544285714286,"h":7.947,"y":483.589,"p":3,"w":21.05485714285714}]},"context":"Herein in this study, we report the application of Structure- Based Virtual Screening (SBVS) strategies with the prime goal of identification of novel potential inhibitors for SARS COV-2 2 0 -O- methyltransferase (nsp16) utilising integrated Structure-based vir- tual screening, molecular docking, molecular dynamics simulation and MM-PBSA approaches, as illustrated in (Figure 1)."},
  {"_key":"60c20e1b7723bebd866457ab","_id":"annotations/60c20e1b7723bebd866457ab","_rev":"_cfFmWz----","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":1391,"normalizedForm":"2","offsetEnd":1392,"rawForm":"2","boundingBoxes":[{"x":302.13419999999996,"h":12.88,"y":103.885,"p":2,"w":7.4228}]}},
  {"_key":"60c20e1b7723bebd866457ac","_id":"annotations/60c20e1b7723bebd866457ac","_rev":"_cfFmWzO---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":1393,"normalizedForm":"2","offsetEnd":1394,"rawForm":"2","boundingBoxes":[{"x":314.189,"h":12.88,"y":103.885,"p":2,"w":7.504}]}},
  {"_key":"60c20e1b7723bebd866457ad","_id":"annotations/60c20e1b7723bebd866457ad","_rev":"_cfFmWze---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":2078,"normalizedForm":"2","offsetEnd":2079,"rawForm":"2","boundingBoxes":[{"x":329.4442,"h":7.947,"y":257.045,"p":2,"w":4.02405}]}},
  {"_key":"60c20e1b7723bebd866457ae","_id":"annotations/60c20e1b7723bebd866457ae","_rev":"_cfFmWzu---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":2467,"normalizedForm":"2","offsetEnd":2468,"rawForm":"2","boundingBoxes":[{"x":168.42188000000002,"h":7.947,"y":297.015,"p":2,"w":4.73022}]}},
  {"_key":"60c20e1b7723bebd866457af","_id":"annotations/60c20e1b7723bebd866457af","_rev":"_cfFmW0----","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":2469,"normalizedForm":"2","offsetEnd":2470,"rawForm":"2","boundingBoxes":[{"x":176.487,"h":7.947,"y":297.015,"p":2,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457b0","_id":"annotations/60c20e1b7723bebd866457b0","_rev":"_cfFmW0O---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":3544,"normalizedForm":"2","offsetEnd":3545,"rawForm":"2","boundingBoxes":[{"x":513.90044,"h":7.0399,"y":301.94,"p":2,"w":3.8783600000000003}]}},
  {"_key":"60c20e1b7723bebd866457b1","_id":"annotations/60c20e1b7723bebd866457b1","_rev":"_cfFmW0e---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":3546,"normalizedForm":"2","offsetEnd":3547,"rawForm":"2","boundingBoxes":[{"x":520.44,"h":7.0399,"y":301.94,"p":2,"w":3.8}]}},
  {"_key":"60c20e1b7723bebd866457b2","_id":"annotations/60c20e1b7723bebd866457b2","_rev":"_cfFmW0q---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":3779,"normalizedForm":"2","offsetEnd":3780,"rawForm":"2","boundingBoxes":[{"x":144.37,"h":7.947,"y":468.283,"p":2,"w":4.243499999999999}]}},
  {"_key":"60c20e1b7723bebd866457b3","_id":"annotations/60c20e1b7723bebd866457b3","_rev":"_cfFmW06---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":4677,"normalizedForm":"2","offsetEnd":4678,"rawForm":"2","boundingBoxes":[{"x":93.6566,"h":5.2973,"y":628.139,"p":2,"w":2.8360666666666665}]}},
  {"_key":"60c20e1b7723bebd866457b4","_id":"annotations/60c20e1b7723bebd866457b4","_rev":"_cfFmW1K---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":4679,"normalizedForm":"3","offsetEnd":4680,"rawForm":"3","boundingBoxes":[{"x":99.32873333333333,"h":5.2973,"y":628.139,"p":2,"w":2.8360666666666665}]}},
  {"_key":"60c20e1b7723bebd866457b5","_id":"annotations/60c20e1b7723bebd866457b5","_rev":"_cfFmW1W---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":5117,"normalizedForm":"2","offsetEnd":5118,"rawForm":"2","boundingBoxes":[{"x":565.405,"h":7.947,"y":451.444,"p":2,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457b6","_id":"annotations/60c20e1b7723bebd866457b6","_rev":"_cfFmW1m---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":5614,"normalizedForm":"2","offsetEnd":5615,"rawForm":"2","boundingBoxes":[{"x":497.257,"h":7.947,"y":541.02,"p":2,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457b7","_id":"annotations/60c20e1b7723bebd866457b7","_rev":"_cfFmW12---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":7580,"normalizedForm":"2","offsetEnd":7581,"rawForm":"2","boundingBoxes":[{"x":168.392,"h":7.947,"y":86.1164,"p":3,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457b8","_id":"annotations/60c20e1b7723bebd866457b8","_rev":"_cfFmW2G---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":7875,"normalizedForm":"2","offsetEnd":7876,"rawForm":"2","boundingBoxes":[{"x":74.6092,"h":7.947,"y":141.333,"p":3,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457b9","_id":"annotations/60c20e1b7723bebd866457b9","_rev":"_cfFmW2W---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":7974,"normalizedForm":"2","offsetEnd":7975,"rawForm":"2","boundingBoxes":[{"x":106.9905,"h":7.947,"y":163.388,"p":3,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457ba","_id":"annotations/60c20e1b7723bebd866457ba","_rev":"_cfFmW2m---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":7976,"normalizedForm":"2","offsetEnd":7977,"rawForm":"2","boundingBoxes":[{"x":118.887,"h":7.947,"y":163.388,"p":3,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457bb","_id":"annotations/60c20e1b7723bebd866457bb","_rev":"_cfFmW3C---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":8090,"normalizedForm":"2","offsetEnd":8091,"rawForm":"2","boundingBoxes":[{"x":61.0681,"h":7.947,"y":185.498,"p":3,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457bc","_id":"annotations/60c20e1b7723bebd866457bc","_rev":"_cfFmW3W---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":8092,"normalizedForm":"2","offsetEnd":8093,"rawForm":"2","boundingBoxes":[{"x":70.2436,"h":7.947,"y":185.498,"p":3,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457bd","_id":"annotations/60c20e1b7723bebd866457bd","_rev":"_cfFmW3m---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":9172,"normalizedForm":"2","offsetEnd":9173,"rawForm":"2","boundingBoxes":[{"x":172.3024,"h":7.947,"y":362.154,"p":3,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457be","_id":"annotations/60c20e1b7723bebd866457be","_rev":"_cfFmW32---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":9174,"normalizedForm":"2","offsetEnd":9175,"rawForm":"2","boundingBoxes":[{"x":181.421,"h":7.947,"y":362.154,"p":3,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457bf","_id":"annotations/60c20e1b7723bebd866457bf","_rev":"_cfFmW4G---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":9470,"normalizedForm":"2","offsetEnd":9471,"rawForm":"2","boundingBoxes":[{"x":295.445,"h":7.947,"y":406.317,"p":3,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457c0","_id":"annotations/60c20e1b7723bebd866457c0","_rev":"_cfFmW4W---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":9683,"normalizedForm":"2","offsetEnd":9684,"rawForm":"2","boundingBoxes":[{"x":271.9714,"h":7.947,"y":450.482,"p":3,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457c1","_id":"annotations/60c20e1b7723bebd866457c1","_rev":"_cfFmW4m---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":9685,"normalizedForm":"2","offsetEnd":9686,"rawForm":"2","boundingBoxes":[{"x":281.43,"h":7.947,"y":450.482,"p":3,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457c2","_id":"annotations/60c20e1b7723bebd866457c2","_rev":"_cfFmW4y---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":9975,"normalizedForm":"2","offsetEnd":9976,"rawForm":"2","boundingBoxes":[{"x":473.79540000000003,"h":7.947,"y":86.684,"p":3,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457c3","_id":"annotations/60c20e1b7723bebd866457c3","_rev":"_cfFmW5C---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":9977,"normalizedForm":"2","offsetEnd":9978,"rawForm":"2","boundingBoxes":[{"x":483.821,"h":7.947,"y":86.684,"p":3,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457c4","_id":"annotations/60c20e1b7723bebd866457c4","_rev":"_cfFmW5S---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":10581,"normalizedForm":"2","offsetEnd":10582,"rawForm":"2","boundingBoxes":[{"x":356.6084,"h":7.947,"y":198.876,"p":3,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457c5","_id":"annotations/60c20e1b7723bebd866457c5","_rev":"_cfFmW5q---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":10583,"normalizedForm":"2","offsetEnd":10584,"rawForm":"2","boundingBoxes":[{"x":367.711,"h":7.947,"y":198.876,"p":3,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457c6","_id":"annotations/60c20e1b7723bebd866457c6","_rev":"_cfFmW56---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":10822,"normalizedForm":"2","offsetEnd":10823,"rawForm":"2","boundingBoxes":[{"x":518.174,"h":7.947,"y":232.553,"p":3,"w":3.0035999999999996}]}},
  {"_key":"60c20e1b7723bebd866457c7","_id":"annotations/60c20e1b7723bebd866457c7","_rev":"_cfFmW6K---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":11134,"normalizedForm":"2","offsetEnd":11135,"rawForm":"2","boundingBoxes":[{"x":485.7584,"h":7.947,"y":288.623,"p":3,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457c8","_id":"annotations/60c20e1b7723bebd866457c8","_rev":"_cfFmW6a---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":11136,"normalizedForm":"2","offsetEnd":11137,"rawForm":"2","boundingBoxes":[{"x":493.459,"h":7.947,"y":288.623,"p":3,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457c9","_id":"annotations/60c20e1b7723bebd866457c9","_rev":"_cfFmW6u---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":11947,"normalizedForm":"2","offsetEnd":11948,"rawForm":"2","boundingBoxes":[{"x":442.00104,"h":7.0399,"y":744.088,"p":3,"w":3.83276}]}},
  {"_key":"60c20e1b7723bebd866457ca","_id":"annotations/60c20e1b7723bebd866457ca","_rev":"_cfFmW7C---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":11949,"normalizedForm":"2","offsetEnd":11950,"rawForm":"2","boundingBoxes":[{"x":448.44,"h":7.0399,"y":744.088,"p":3,"w":3.8}]}},
  {"_key":"60c20e1b7723bebd866457cb","_id":"annotations/60c20e1b7723bebd866457cb","_rev":"_cfFmW7W---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":12466,"normalizedForm":"2","offsetEnd":12467,"rawForm":"2","boundingBoxes":[{"x":161.067,"h":7.947,"y":417.996,"p":4,"w":3.699}]}},
  {"_key":"60c20e1b7723bebd866457cc","_id":"annotations/60c20e1b7723bebd866457cc","_rev":"_cfFmW7m---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":12952,"normalizedForm":"2","offsetEnd":12953,"rawForm":"2","boundingBoxes":[{"x":244.3034,"h":7.947,"y":536.425,"p":4,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457cd","_id":"annotations/60c20e1b7723bebd866457cd","_rev":"_cfFmW72---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":12954,"normalizedForm":"2","offsetEnd":12955,"rawForm":"2","boundingBoxes":[{"x":253.592,"h":7.947,"y":536.425,"p":4,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457ce","_id":"annotations/60c20e1b7723bebd866457ce","_rev":"_cfFmW8G---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":14429,"normalizedForm":"2","offsetEnd":14430,"rawForm":"2","boundingBoxes":[{"x":374.92040000000003,"h":7.947,"y":144.284,"p":4,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457cf","_id":"annotations/60c20e1b7723bebd866457cf","_rev":"_cfFmW8y---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":14431,"normalizedForm":"2","offsetEnd":14432,"rawForm":"2","boundingBoxes":[{"x":386.761,"h":7.947,"y":144.284,"p":4,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457d0","_id":"annotations/60c20e1b7723bebd866457d0","_rev":"_cfFmW9K---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":14573,"normalizedForm":"2","offsetEnd":14574,"rawForm":"2","boundingBoxes":[{"x":455.76640000000003,"h":7.947,"y":166.393,"p":4,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457d1","_id":"annotations/60c20e1b7723bebd866457d1","_rev":"_cfFmW9a---","wikipediaExternalRef":21490336,"document":{"$oid":"60c20e1b7723bebd8664578d"},"wikidataId":"Q187432","references":[{"offsetStart":14982,"normalizedForm":"24","refKey":22,"label":"24","reference_id":{"$oid":"60c20e1b7723bebd8664578e"},"offsetEnd":14985,"boundingBoxes":[{"x":332.73,"h":5.2973,"y":241.833,"p":4,"w":6.9254}]}],"type":"software","confidence":0.2792,"software-name":{"wikipediaExternalRef":21490336,"normalizedForm":"script","offsetStart":14907,"wikidataId":"Q187432","offsetEnd":14913,"lang":"en","confidence":0.2792,"rawForm":"script","boundingBoxes":[{"x":547.37,"h":7.947,"y":221.726,"p":4,"w":19.378285714285713}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd866457d2","_id":"annotations/60c20e1b7723bebd866457d2","_rev":"_cfFmW9q---","wikipediaExternalRef":21490336,"document":{"$oid":"60c20e1b7723bebd8664578d"},"wikidataId":"Q187432","references":[{"offsetStart":14982,"normalizedForm":"24","refKey":22,"label":"24","reference_id":{"$oid":"60c20e1b7723bebd8664578e"},"offsetEnd":14985,"boundingBoxes":[{"x":332.73,"h":5.2973,"y":241.833,"p":4,"w":6.9254}]}],"type":"software","confidence":0.2792,"software-name":{"wikipediaExternalRef":21490336,"normalizedForm":"script","offsetStart":14975,"wikidataId":"Q187432","offsetEnd":14981,"lang":"en","confidence":0.2792,"rawForm":"script","boundingBoxes":[{"x":311.982,"h":7.947,"y":243.837,"p":4,"w":20.745}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd866457d3","_id":"annotations/60c20e1b7723bebd866457d3","_rev":"_cfFmW96---","wikipediaExternalRef":21490336,"document":{"$oid":"60c20e1b7723bebd8664578d"},"wikidataId":"Q187432","references":[{"offsetStart":14982,"normalizedForm":"24","refKey":22,"label":"24","reference_id":{"$oid":"60c20e1b7723bebd8664578e"},"offsetEnd":14985,"boundingBoxes":[{"x":332.73,"h":5.2973,"y":241.833,"p":4,"w":6.9254}]}],"type":"software","confidence":0.2792,"software-name":{"wikipediaExternalRef":21490336,"normalizedForm":"script","offsetStart":15442,"wikidataId":"Q187432","offsetEnd":15448,"lang":"en","confidence":0.2792,"rawForm":"script","boundingBoxes":[{"x":463.577,"h":7.947,"y":321.22,"p":4,"w":19.378285714285713}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd866457d4","_id":"annotations/60c20e1b7723bebd866457d4","_rev":"_cfFmX-K---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":15840,"normalizedForm":"2","offsetEnd":15841,"rawForm":"2","boundingBoxes":[{"x":538.702,"h":7.947,"y":387.605,"p":4,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457d5","_id":"annotations/60c20e1b7723bebd866457d5","_rev":"_cfFmX-a---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":16441,"normalizedForm":"2","offsetEnd":16442,"rawForm":"2","boundingBoxes":[{"x":322.583,"h":7.947,"y":498.216,"p":4,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457d6","_id":"annotations/60c20e1b7723bebd866457d6","_rev":"_cfFmX-q---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":18047,"normalizedForm":"2","offsetEnd":18048,"rawForm":"2","boundingBoxes":[{"x":135.5104,"h":7.947,"y":607.124,"p":5,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457d7","_id":"annotations/60c20e1b7723bebd866457d7","_rev":"_cfFmX-6---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":18049,"normalizedForm":"2","offsetEnd":18050,"rawForm":"2","boundingBoxes":[{"x":147.233,"h":7.947,"y":607.124,"p":5,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457d8","_id":"annotations/60c20e1b7723bebd866457d8","_rev":"_cfFmX_K---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":18988,"normalizedForm":"2","offsetEnd":18989,"rawForm":"2","boundingBoxes":[{"x":466.301,"h":7.947,"y":532.058,"p":5,"w":3.0035999999999996}]}},
  {"_key":"60c20e1b7723bebd866457d9","_id":"annotations/60c20e1b7723bebd866457d9","_rev":"_cfFmX_a---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":19186,"normalizedForm":"3","offsetEnd":19187,"rawForm":"3","boundingBoxes":[{"x":342.428,"h":7.947,"y":576.447,"p":5,"w":3.0035999999999996}]}},
  {"_key":"60c20e1b7723bebd866457da","_id":"annotations/60c20e1b7723bebd866457da","_rev":"_cfFmX_q---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":19975,"normalizedForm":"2","offsetEnd":19976,"rawForm":"2","boundingBoxes":[{"x":541.8844,"h":7.947,"y":710.01,"p":5,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457db","_id":"annotations/60c20e1b7723bebd866457db","_rev":"_cfFmX_6---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":19977,"normalizedForm":"2","offsetEnd":19978,"rawForm":"2","boundingBoxes":[{"x":551.457,"h":7.947,"y":710.01,"p":5,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457dc","_id":"annotations/60c20e1b7723bebd866457dc","_rev":"_cfFmXAG---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":20107,"normalizedForm":"2","offsetEnd":20108,"rawForm":"2","boundingBoxes":[{"x":543.4184,"h":7.947,"y":732.302,"p":5,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457dd","_id":"annotations/60c20e1b7723bebd866457dd","_rev":"_cfFmXAW---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":20109,"normalizedForm":"2","offsetEnd":20110,"rawForm":"2","boundingBoxes":[{"x":551.459,"h":7.947,"y":732.302,"p":5,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457de","_id":"annotations/60c20e1b7723bebd866457de","_rev":"_cfFmXAi---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":21748,"normalizedForm":"3","offsetEnd":21749,"rawForm":"3","boundingBoxes":[{"x":58.3366,"h":9,"y":455.521,"p":7,"w":4.08225}]}},
  {"_key":"60c20e1b7723bebd866457df","_id":"annotations/60c20e1b7723bebd866457df","_rev":"_cfFmXAy---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":22330,"normalizedForm":"2","offsetEnd":22331,"rawForm":"2","boundingBoxes":[{"x":83.23750000000001,"h":7.947,"y":555.641,"p":7,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457e0","_id":"annotations/60c20e1b7723bebd866457e0","_rev":"_cfFmXB----","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":22332,"normalizedForm":"2","offsetEnd":22333,"rawForm":"2","boundingBoxes":[{"x":90.8227,"h":7.947,"y":555.641,"p":7,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457e1","_id":"annotations/60c20e1b7723bebd866457e1","_rev":"_cfFmXBO---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":22482,"normalizedForm":"3","offsetEnd":22483,"rawForm":"3","boundingBoxes":[{"x":178.6574,"h":9,"y":577.017,"p":7,"w":4.5261000000000005}]}},
  {"_key":"60c20e1b7723bebd866457e2","_id":"annotations/60c20e1b7723bebd866457e2","_rev":"_cfFmXBa---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":22621,"normalizedForm":"3","offsetEnd":22622,"rawForm":"3","boundingBoxes":[{"x":247.181,"h":5.2973,"y":603.307,"p":7,"w":3.4627}]}},
  {"_key":"60c20e1b7723bebd866457e3","_id":"annotations/60c20e1b7723bebd866457e3","_rev":"_cfFmXBm---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":22787,"normalizedForm":"2","offsetEnd":22788,"rawForm":"2","boundingBoxes":[{"x":131.697,"h":5.2973,"y":636.473,"p":7,"w":3.4627}]}},
  {"_key":"60c20e1b7723bebd866457e4","_id":"annotations/60c20e1b7723bebd866457e4","_rev":"_cfFmXBy---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":23240,"normalizedForm":"2","offsetEnd":23241,"rawForm":"2","boundingBoxes":[{"x":191.735,"h":5.2973,"y":724.857,"p":7,"w":3.4627}]}},
  {"_key":"60c20e1b7723bebd866457e5","_id":"annotations/60c20e1b7723bebd866457e5","_rev":"_cfFmXCC---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":23659,"normalizedForm":"2","offsetEnd":23660,"rawForm":"2","boundingBoxes":[{"x":311.979,"h":7.947,"y":435.966,"p":7,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457e6","_id":"annotations/60c20e1b7723bebd866457e6","_rev":"_cfFmXCS---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":23661,"normalizedForm":"2","offsetEnd":23662,"rawForm":"2","boundingBoxes":[{"x":319.633,"h":7.947,"y":435.966,"p":7,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457e7","_id":"annotations/60c20e1b7723bebd866457e7","_rev":"_cfFmXCe---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":24205,"normalizedForm":"2","offsetEnd":24206,"rawForm":"2","boundingBoxes":[{"x":444.2584,"h":7.947,"y":566.701,"p":7,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457e8","_id":"annotations/60c20e1b7723bebd866457e8","_rev":"_cfFmXCu---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":24207,"normalizedForm":"2","offsetEnd":24208,"rawForm":"2","boundingBoxes":[{"x":452.356,"h":7.947,"y":566.701,"p":7,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457e9","_id":"annotations/60c20e1b7723bebd866457e9","_rev":"_cfFmXC6---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":24480,"normalizedForm":"2","offsetEnd":24481,"rawForm":"2","boundingBoxes":[{"x":473.34499999999997,"h":7.947,"y":651.4,"p":7,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457ea","_id":"annotations/60c20e1b7723bebd866457ea","_rev":"_cfFmXDK---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":24482,"normalizedForm":"2","offsetEnd":24483,"rawForm":"2","boundingBoxes":[{"x":483.765,"h":7.947,"y":651.4,"p":7,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457eb","_id":"annotations/60c20e1b7723bebd866457eb","_rev":"_cfFmXDa---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":24815,"normalizedForm":"2","offsetEnd":24816,"rawForm":"2","boundingBoxes":[{"x":534.008,"h":7.947,"y":708.888,"p":7,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457ec","_id":"annotations/60c20e1b7723bebd866457ec","_rev":"_cfFmXDq---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":24817,"normalizedForm":"2","offsetEnd":24818,"rawForm":"2","boundingBoxes":[{"x":551.458,"h":7.947,"y":708.888,"p":7,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457ed","_id":"annotations/60c20e1b7723bebd866457ed","_rev":"_cfFmXD2---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":25005,"normalizedForm":"3","offsetEnd":25006,"rawForm":"3","boundingBoxes":[{"x":543.633,"h":7.947,"y":743.413,"p":7,"w":3.9285}]}},
  {"_key":"60c20e1b7723bebd866457ee","_id":"annotations/60c20e1b7723bebd866457ee","_rev":"_cfFmXEG---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":25263,"normalizedForm":"2","offsetEnd":25264,"rawForm":"2","boundingBoxes":[{"x":272.088,"h":7.947,"y":567.439,"p":8,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457ef","_id":"annotations/60c20e1b7723bebd866457ef","_rev":"_cfFmXEW---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":25265,"normalizedForm":"2","offsetEnd":25266,"rawForm":"2","boundingBoxes":[{"x":281.431,"h":7.947,"y":567.439,"p":8,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457f0","_id":"annotations/60c20e1b7723bebd866457f0","_rev":"_cfFmXEi---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":25684,"normalizedForm":"2","offsetEnd":25685,"rawForm":"2","boundingBoxes":[{"x":245.61100000000002,"h":7.947,"y":644.43,"p":8,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457f1","_id":"annotations/60c20e1b7723bebd866457f1","_rev":"_cfFmXEu---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":25686,"normalizedForm":"2","offsetEnd":25687,"rawForm":"2","boundingBoxes":[{"x":253.593,"h":7.947,"y":644.43,"p":8,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457f2","_id":"annotations/60c20e1b7723bebd866457f2","_rev":"_cfFmXF----","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":25760,"normalizedForm":"2","offsetEnd":25761,"rawForm":"2","boundingBoxes":[{"x":282.576,"h":7.947,"y":655.427,"p":8,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457f3","_id":"annotations/60c20e1b7723bebd866457f3","_rev":"_cfFmXFK---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":25762,"normalizedForm":"2","offsetEnd":25763,"rawForm":"2","boundingBoxes":[{"x":290.388,"h":7.947,"y":655.427,"p":8,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457f4","_id":"annotations/60c20e1b7723bebd866457f4","_rev":"_cfFmXFW---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":25973,"normalizedForm":"2","offsetEnd":25974,"rawForm":"2","boundingBoxes":[{"x":237.317,"h":7.947,"y":699.42,"p":8,"w":3.9285}]}},
  {"_key":"60c20e1b7723bebd866457f5","_id":"annotations/60c20e1b7723bebd866457f5","_rev":"_cfFmXFm---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":26075,"normalizedForm":"2","offsetEnd":26076,"rawForm":"2","boundingBoxes":[{"x":128.4204,"h":7.947,"y":721.416,"p":8,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457f6","_id":"annotations/60c20e1b7723bebd866457f6","_rev":"_cfFmXFy---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":26077,"normalizedForm":"2","offsetEnd":26078,"rawForm":"2","boundingBoxes":[{"x":136.746,"h":7.947,"y":721.416,"p":8,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457f7","_id":"annotations/60c20e1b7723bebd866457f7","_rev":"_cfFmXG----","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":26245,"normalizedForm":"2","offsetEnd":26246,"rawForm":"2","boundingBoxes":[{"x":295.2094,"h":7.947,"y":743.413,"p":8,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457f8","_id":"annotations/60c20e1b7723bebd866457f8","_rev":"_cfFmXGK---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":26249,"normalizedForm":"2","offsetEnd":26250,"rawForm":"2","boundingBoxes":[{"x":311.98,"h":7.947,"y":567.438,"p":8,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457f9","_id":"annotations/60c20e1b7723bebd866457f9","_rev":"_cfFmXGW---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":26451,"normalizedForm":"2","offsetEnd":26452,"rawForm":"2","boundingBoxes":[{"x":374.866,"h":7.947,"y":601.907,"p":8,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd866457fa","_id":"annotations/60c20e1b7723bebd866457fa","_rev":"_cfFmXGm---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":26453,"normalizedForm":"2","offsetEnd":26454,"rawForm":"2","boundingBoxes":[{"x":386.646,"h":7.947,"y":601.907,"p":8,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457fb","_id":"annotations/60c20e1b7723bebd866457fb","_rev":"_cfFmXGy---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":26621,"normalizedForm":"3","offsetEnd":26622,"rawForm":"3","boundingBoxes":[{"x":311.98,"h":7.947,"y":636.433,"p":8,"w":3.699}]}},
  {"_key":"60c20e1b7723bebd866457fc","_id":"annotations/60c20e1b7723bebd866457fc","_rev":"_cfFmXH----","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":26771,"normalizedForm":"2","offsetEnd":26772,"rawForm":"2","boundingBoxes":[{"x":403.37,"h":7.947,"y":659.394,"p":8,"w":3.0225}]}},
  {"_key":"60c20e1b7723bebd866457fd","_id":"annotations/60c20e1b7723bebd866457fd","_rev":"_cfFmXHK---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":29868,"normalizedForm":"2","offsetEnd":29869,"rawForm":"2","boundingBoxes":[{"x":61.0678,"h":7.947,"y":543.569,"p":9,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd866457fe","_id":"annotations/60c20e1b7723bebd866457fe","_rev":"_cfFmXHW---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":29870,"normalizedForm":"2","offsetEnd":29871,"rawForm":"2","boundingBoxes":[{"x":71.7742,"h":7.947,"y":543.569,"p":9,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd866457ff","_id":"annotations/60c20e1b7723bebd866457ff","_rev":"_cfFmXHi---","wikipediaExternalRef":21490336,"document":{"$oid":"60c20e1b7723bebd8664578d"},"wikidataId":"Q187432","references":[{"offsetStart":14982,"normalizedForm":"24","refKey":22,"label":"24","reference_id":{"$oid":"60c20e1b7723bebd8664578e"},"offsetEnd":14985,"boundingBoxes":[{"x":332.73,"h":5.2973,"y":241.833,"p":4,"w":6.9254}]}],"type":"software","confidence":0.2792,"software-name":{"wikipediaExternalRef":21490336,"normalizedForm":"script","offsetStart":29997,"wikidataId":"Q187432","offsetEnd":30003,"lang":"en","confidence":0.2792,"rawForm":"script","boundingBoxes":[{"x":89.236,"h":7.947,"y":565.794,"p":9,"w":20.745}]},"lang":"en"},
  {"_key":"60c20e1b7723bebd86645800","_id":"annotations/60c20e1b7723bebd86645800","_rev":"_cfFmXHu---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":30963,"normalizedForm":"3","offsetEnd":30964,"rawForm":"3","boundingBoxes":[{"x":86.6836,"h":7.947,"y":732.301,"p":9,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd86645801","_id":"annotations/60c20e1b7723bebd86645801","_rev":"_cfFmXH6---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":31087,"normalizedForm":"2","offsetEnd":31088,"rawForm":"2","boundingBoxes":[{"x":473.2254,"h":7.947,"y":488.011,"p":9,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd86645802","_id":"annotations/60c20e1b7723bebd86645802","_rev":"_cfFmXIG---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":31089,"normalizedForm":"2","offsetEnd":31090,"rawForm":"2","boundingBoxes":[{"x":483.761,"h":7.947,"y":488.011,"p":9,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd86645803","_id":"annotations/60c20e1b7723bebd86645803","_rev":"_cfFmXIS---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":31583,"normalizedForm":"2","offsetEnd":31584,"rawForm":"2","boundingBoxes":[{"x":366.2464,"h":7.947,"y":580.022,"p":9,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd86645804","_id":"annotations/60c20e1b7723bebd86645804","_rev":"_cfFmXIe---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":31585,"normalizedForm":"2","offsetEnd":31586,"rawForm":"2","boundingBoxes":[{"x":374.004,"h":7.947,"y":580.022,"p":9,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd86645805","_id":"annotations/60c20e1b7723bebd86645805","_rev":"_cfFmXIm---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":31775,"normalizedForm":"2","offsetEnd":31776,"rawForm":"2","boundingBoxes":[{"x":367.8334,"h":7.947,"y":651.401,"p":9,"w":4.764600000000001}]}},
  {"_key":"60c20e1b7723bebd86645806","_id":"annotations/60c20e1b7723bebd86645806","_rev":"_cfFmXIy---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":31777,"normalizedForm":"2","offsetEnd":31778,"rawForm":"2","boundingBoxes":[{"x":376.159,"h":7.947,"y":651.401,"p":9,"w":4.617}]}},
  {"_key":"60c20e1b7723bebd86645807","_id":"annotations/60c20e1b7723bebd86645807","_rev":"_cfFmXJ----","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":31847,"normalizedForm":"2","offsetEnd":31848,"rawForm":"2","boundingBoxes":[{"x":388.133,"h":7.947,"y":662.91,"p":9,"w":4.581}]}},
  {"_key":"60c20e1b7723bebd86645808","_id":"annotations/60c20e1b7723bebd86645808","_rev":"_cfFmXJK---","document":{"$oid":"60c20e1b7723bebd8664578d"},"type":"software","software-name":{"offsetStart":31849,"normalizedForm":"2","offsetEnd":31850,"rawForm":"2","boundingBoxes":[{"x":398.724,"h":7.947,"y":662.91,"p":9,"w":4.617}]}},
  {"_key":"60c20e247723bebd8664580a","_id":"annotations/60c20e247723bebd8664580a","_rev":"_cfFmXJW---","document":{"$oid":"60c20e247723bebd86645809"},"type":"software","software-name":{"offsetStart":40,"normalizedForm":"Covidence","offsetEnd":49,"rawForm":"Covidence","boundingBoxes":[{"x":453.036,"h":9.32,"y":540.74,"p":2,"w":45.8}]},"context":"Unique records were then imported into Covidence software for screening."},
  {"_key":"60c20e247723bebd8664580b","_id":"annotations/60c20e247723bebd8664580b","_rev":"_cfFmXJi---","wikipediaExternalRef":6664689,"document":{"$oid":"60c20e247723bebd86645809"},"context":"All identified indexed records were downloaded into EndNote software and duplicates were removed.","wikidataId":"Q1340244","type":"software","confidence":0.794,"software-name":{"wikipediaExternalRef":6664689,"normalizedForm":"EndNote","offsetStart":53,"wikidataId":"Q1340244","offsetEnd":60,"lang":"en","confidence":0.794,"rawForm":"EndNote","boundingBoxes":[{"x":306.885,"h":9.32,"y":528.74,"p":2,"w":39.4}]},"lang":"en"},
  {"_key":"60c20e247723bebd8664580c","_id":"annotations/60c20e247723bebd8664580c","_rev":"_cfFmXJu---","wikipediaExternalRef":424589,"document":{"$oid":"60c20e247723bebd86645809"},"context":"They were therefore forced to organize and supervise the program via the Internet, Skype, and by telephone\" 152  Infrastructure  ►  \"Poor network coverage and phone charging facilities in the settlement makes community mobilisation processes difficult for the implementation team\" 103  ►  \"The recent bombing and closure of the clinic resulted in a huge loss for the local communities' leaving a gap in critical services for the health system of this war ravaged region\" 73  ►  \"In these settings, the context is likely to change abruptly at any moment, and the research subjects who are participating out of goodwill alone may no longer be available.","wikidataId":"Q40984","type":"software","confidence":0.7288,"software-name":{"wikipediaExternalRef":424589,"normalizedForm":"Skype","offsetStart":84,"wikidataId":"Q40984","offsetEnd":89,"lang":"en","confidence":0.7288,"rawForm":"Skype","boundingBoxes":[{"x":176.122,"h":7.888,"y":199.813,"p":11,"w":21.78125}]},"lang":"en"},
  {"_key":"60c20e247723bebd8664580d","_id":"annotations/60c20e247723bebd8664580d","_rev":"_cfFmXJ6---","wikipediaExternalRef":28309569,"document":{"$oid":"60c20e247723bebd86645809"},"context":"We extracted data and information from all indexed and grey literature publications that met the eligibility criteria in duplicate, using a customised form in REDCap software.","wikidataId":"Q7305527","type":"software","confidence":0.5069,"software-name":{"wikipediaExternalRef":28309569,"normalizedForm":"REDCap","offsetStart":161,"wikidataId":"Q7305527","offsetEnd":167,"lang":"en","confidence":0.5069,"rawForm":"REDCap","boundingBoxes":[{"x":515.645,"h":9.32,"y":612.74,"p":2,"w":37.6}]},"lang":"en"},
  {"_key":"60c20e257723bebd86645810","_id":"annotations/60c20e257723bebd86645810","_rev":"_cfFmXKC---","document":{"$oid":"60c20e257723bebd8664580e"},"context":"We used Alexnet [21], a widely used deep network, for the CXR processing.","references":[{"offsetStart":14023,"normalizedForm":"[21]","refKey":20,"label":"[21]","reference_id":{"$oid":"60c20e257723bebd8664580f"},"offsetEnd":14027,"boundingBoxes":[{"x":378.537,"h":10.039999999999992,"y":220.956,"p":3,"w":15.350640000000055}]}],"type":"software","software-name":{"offsetStart":9,"normalizedForm":"Alexnet","offsetEnd":16,"rawForm":"Alexnet","boundingBoxes":[{"x":339.899,"h":10.04,"y":220.956,"p":3,"w":34.582}]}},
  {"_key":"60c20e257723bebd86645811","_id":"annotations/60c20e257723bebd86645811","_rev":"_cfFmXKO---","document":{"$oid":"60c20e257723bebd8664580e"},"type":"software","software-name":{"offsetStart":10,"normalizedForm":"torchvision","offsetEnd":21,"rawForm":"torchvision","boundingBoxes":[{"x":194.649,"h":10.04,"y":646.836,"p":3,"w":49.8735}]},"context":"Using the torchvision toolbox of Pytorch, the augmentation was done automatically in the training process and a sampler is introduced to make sure that influenza cases and COVID-19 cases are in the same amount in every batch."},
  {"_key":"60c20e257723bebd86645812","_id":"annotations/60c20e257723bebd86645812","_rev":"_cfFmXKa---","wikipediaExternalRef":54022970,"document":{"$oid":"60c20e257723bebd8664580e"},"context":"Using the torchvision toolbox of Pytorch, the augmentation was done automatically in the training process and a sampler is introduced to make sure that influenza cases and COVID-19 cases are in the same amount in every batch.","wikidataId":"Q47509047","type":"software","confidence":0.7809,"software-name":{"wikipediaExternalRef":54022970,"normalizedForm":"Pytorch","offsetStart":34,"wikidataId":"Q47509047","offsetEnd":41,"lang":"en","confidence":0.7809,"rawForm":"Pytorch","boundingBoxes":[{"x":58.68,"h":10.04,"y":659.256,"p":3,"w":32.433625}]},"lang":"en"},
  {"_key":"60c20e257723bebd86645813","_id":"annotations/60c20e257723bebd86645813","_rev":"_cfFmXKm---","wikipediaExternalRef":54022970,"document":{"$oid":"60c20e257723bebd8664580e"},"context":"The DNN parts were all implemented based on Pytorch tools [22].","wikidataId":"Q47509047","type":"software","confidence":0.7809,"software-name":{"wikipediaExternalRef":54022970,"normalizedForm":"Pytorch","offsetStart":45,"wikidataId":"Q47509047","offsetEnd":52,"lang":"en","confidence":0.7809,"rawForm":"Pytorch","boundingBoxes":[{"x":493.013,"h":10.04,"y":394.896,"p":3,"w":34.569}]},"lang":"en"},
  {"_key":"60c20e297723bebd86645815","_id":"annotations/60c20e297723bebd86645815","_rev":"_cfFmXKu---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20e297723bebd86645814"},"publisher":{"offsetStart":90,"normalizedForm":"NIH","offsetEnd":93,"rawForm":"NIH","boundingBoxes":[{"x":238.841,"h":8.1324,"y":481.057,"p":3,"w":12.88458}]},"context":"The wound and reference ring areas were measured with Image J software (public software, NIH).","wikidataId":"Q1659584","type":"software","confidence":0.9507,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":55,"wikidataId":"Q1659584","offsetEnd":62,"lang":"en","confidence":0.9507,"rawForm":"Image J","boundingBoxes":[{"x":113.667,"h":8.132400000000018,"y":481.057,"p":3,"w":28.40210000000002}]},"lang":"en"},
  {"_key":"60c20e297723bebd86645816","_id":"annotations/60c20e297723bebd86645816","_rev":"_cfFmXK6---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20e297723bebd86645814"},"publisher":{"offsetStart":90,"normalizedForm":"NIH","offsetEnd":93,"rawForm":"NIH","boundingBoxes":[{"x":238.841,"h":8.1324,"y":481.057,"p":3,"w":12.88458}]},"context":"The wound and reference ring areas were measured with Image J software.","wikidataId":"Q1659584","type":"software","confidence":0.9507,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":55,"wikidataId":"Q1659584","offsetEnd":62,"lang":"en","confidence":0.9507,"rawForm":"Image J","boundingBoxes":[{"x":116.728,"h":8.132399999999961,"y":704.258,"p":3,"w":29.932100000000005}]},"lang":"en"},
  {"_key":"60c20e297723bebd86645817","_id":"annotations/60c20e297723bebd86645817","_rev":"_cfFmXLG---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20e297723bebd86645814"},"publisher":{"offsetStart":90,"normalizedForm":"NIH","offsetEnd":93,"rawForm":"NIH","boundingBoxes":[{"x":238.841,"h":8.1324,"y":481.057,"p":3,"w":12.88458}]},"context":"The wound and reference ring areas were measured with Image J software.","wikidataId":"Q1659584","type":"software","confidence":0.9507,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":55,"wikidataId":"Q1659584","offsetEnd":62,"lang":"en","confidence":0.9507,"rawForm":"Image J","boundingBoxes":[{"x":132.091,"h":8.132400000000004,"y":72.0168,"p":4,"w":27.94810000000001}]},"lang":"en"},
  {"_key":"60c20e297723bebd86645818","_id":"annotations/60c20e297723bebd86645818","_rev":"_cfFmXLS---","document":{"$oid":"60c20e297723bebd86645814"},"type":"software","software-name":{"offsetStart":159,"normalizedForm":"EDAX","offsetEnd":163,"rawForm":"EDAX","boundingBoxes":[{"x":63.01604999999999,"h":8.1324,"y":182.115,"p":3,"w":19.851399999999998}]},"context":"The nanoparticles were imaged with a scanning electron microscope (XL30 Sirion, FEI, Hillsboro, Oregon) and EDX was performed with the associated software (EDAX, Ametek, NJ)."},
  {"_key":"60c20e297723bebd86645819","_id":"annotations/60c20e297723bebd86645819","_rev":"_cfFmXLe---","wikipediaExternalRef":3793613,"document":{"$oid":"60c20e297723bebd86645814"},"publisher":{"offsetStart":184,"normalizedForm":"NIH","offsetEnd":187,"rawForm":"NIH","boundingBoxes":[{"x":277.4742,"h":8.1324,"y":478.107,"p":4,"w":11.8086}]},"context":"The 24 well plate was scanned digitally (Scanjets 5370C and c7671b, Hewlett-Packard, Palo Alto, CA) and the size of the FPCL was measured daily and calculated with Image J software (NIH), normalizing to the day 0 value.","wikidataId":"Q1659584","type":"software","confidence":0.9507,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":166,"wikidataId":"Q1659584","offsetEnd":173,"lang":"en","confidence":0.9507,"rawForm":"Image J","boundingBoxes":[{"x":208.171,"h":8.132400000000018,"y":478.107,"p":4,"w":29.026100000000014}]},"lang":"en"},
  {"_key":"60c20e2a7723bebd8664581b","_id":"annotations/60c20e2a7723bebd8664581b","_rev":"_cfFmXLm---","document":{"$oid":"60c20e2a7723bebd8664581a"},"publisher":{"offsetStart":44,"normalizedForm":"Agilent","offsetEnd":51,"rawForm":"Agilent","boundingBoxes":[{"x":256.074,"h":8.2759,"y":176.905,"p":5,"w":28.3694}]},"context":"Hierarchical clustering was performed using Agilent GeneSpring GX software (version 12.0).","type":"software","software-name":{"offsetStart":53,"normalizedForm":"GeneSpring GX","offsetEnd":66,"rawForm":"GeneSpring GX","boundingBoxes":[{"x":45.3543,"h":8.275900000000007,"y":187.846,"p":5,"w":59.46619999999999}]},"version":{"offsetStart":85,"normalizedForm":"12.0","offsetEnd":89,"rawForm":"12.0","boundingBoxes":[{"x":180.221,"h":8.275900000000007,"y":187.846,"p":5,"w":15.852399999999989}]}},
  {"_key":"60c20e2a7723bebd8664581c","_id":"annotations/60c20e2a7723bebd8664581c","_rev":"_cfFmXLy---","document":{"$oid":"60c20e2a7723bebd8664581a"},"publisher":{"offsetStart":118,"normalizedForm":"Agilent","offsetEnd":125,"rawForm":"Agilent","boundingBoxes":[{"x":253.37642222222223,"h":8.2759,"y":122.084,"p":5,"w":27.141955555555555}]},"context":"Quantile normal- ization and subsequent data processing were performed using a GeneSpring GX v12.0 software package (Agilent, Santa Clara, CA, USA).","type":"software","software-name":{"offsetStart":80,"normalizedForm":"GeneSpring GX","offsetEnd":93,"rawForm":"GeneSpring GX","boundingBoxes":[{"x":79.8234,"h":8.275900000000007,"y":122.084,"p":5,"w":61.33679999999997}]},"version":{"offsetStart":95,"normalizedForm":"12.0","offsetEnd":99,"rawForm":"12.0","boundingBoxes":[{"x":145.755,"h":8.275900000000007,"y":122.084,"p":5,"w":21.635699999999986}]}},
  {"_key":"60c20e2a7723bebd8664581d","_id":"annotations/60c20e2a7723bebd8664581d","_rev":"_cfFmXM----","wikipediaExternalRef":2039930,"document":{"$oid":"60c20e2a7723bebd8664581a"},"context":"After data normalization, we determined hundreds of differentially expressed lncRNAs between groups in Ensembl, RNAdb, NRED, lincRNA, misc_RNA, UCSC_knowngene, H-invDB, HOX cluster, RefSeq_NR and UCR (FDR <0.05).","wikidataId":"Q1344256","type":"software","confidence":0.7716,"software-name":{"wikipediaExternalRef":2039930,"normalizedForm":"Ensembl","offsetStart":105,"wikidataId":"Q1344256","offsetEnd":112,"lang":"en","confidence":0.7716,"rawForm":"Ensembl","boundingBoxes":[{"x":469.809,"h":8.2759,"y":321.019,"p":5,"w":32.17445}]},"lang":"en"},
  {"_key":"60c20e2f7723bebd8664581f","_id":"annotations/60c20e2f7723bebd8664581f","_rev":"_cfFmXMK---","document":{"$oid":"60c20e2f7723bebd8664581e"},"publisher":{"offsetStart":85,"normalizedForm":"Media Cybernetics","offsetEnd":102,"rawForm":"Media Cybernetics","boundingBoxes":[{"x":454.4799666666667,"h":9.180599999999998,"y":120.262,"p":3,"w":68.42260833333324}]},"context":"RGCs were counted in each field by a blinded investigator using Image-Pro Plus 5.0 (Media Cybernetics, Silver Spring, MD) software.","type":"software","software-name":{"offsetStart":65,"normalizedForm":"Image-Pro Plus","offsetEnd":79,"rawForm":"Image-Pro Plus","boundingBoxes":[{"x":375.074,"h":9.180599999999998,"y":120.262,"p":3,"w":59.048899999999946}]},"version":{"offsetStart":80,"normalizedForm":"5.0","offsetEnd":83,"rawForm":"5.0","boundingBoxes":[{"x":436.401,"h":9.180599999999998,"y":120.262,"p":3,"w":11.247900000000016}]}},
  {"_key":"60c20e317723bebd86645821","_id":"annotations/60c20e317723bebd86645821","_rev":"_cfFmXMS---","document":{"$oid":"60c20e317723bebd86645820"},"publisher":{"offsetStart":179,"normalizedForm":"IBM Corp","offsetEnd":187,"rawForm":"IBM Corp","boundingBoxes":[{"x":420.72155,"h":9.319400000000002,"y":67.6734,"p":3,"w":26.47784999999999}]},"context":"The laboratory records and clinical data of the patients were accessed and analyzed on IBM Statistical Package for the Social Sciences (SPSS) Statistics for Windows, version 27 (IBM Corp., Armonk, NY).","type":"software","software-name":{"offsetStart":91,"normalizedForm":"Statistical Package for the Social Sciences (SPSS)","offsetEnd":142,"rawForm":"Statistical \nPackage for the Social Sciences (SPSS)","boundingBoxes":[{"x":475.512,"h":9.3194,"y":57.4705,"p":3,"w":32.042},{"x":183.343,"h":9.319400000000002,"y":67.6734,"p":3,"w":121.66619999999998}]},"version":{"offsetStart":175,"normalizedForm":"27","offsetEnd":177,"rawForm":"27","boundingBoxes":[{"x":407.402,"h":9.3194,"y":67.6734,"p":3,"w":7.6453}]}},
  {"_key":"60c20e3a7723bebd86645823","_id":"annotations/60c20e3a7723bebd86645823","_rev":"_cfFmXMe---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20e3a7723bebd86645822"},"publisher":{"offsetStart":106,"normalizedForm":"GraphPad Software Inc","offsetEnd":127,"rawForm":"GraphPad Software Inc","boundingBoxes":[{"x":197.8665,"h":7.183899999999994,"y":625.263,"p":4,"w":83.21239999999997}]},"context":"All statistical analyses and preparation of graphs were done using  GraphPad Prism software version 8.0 (GraphPad Software Inc.).","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":69,"wikidataId":"Q5597066","offsetEnd":83,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":46.4882,"h":7.183899999999994,"y":625.263,"p":4,"w":60.338400000000014}]},"version":{"offsetStart":101,"normalizedForm":"8.0","offsetEnd":104,"rawForm":"8.0","boundingBoxes":[{"x":178.016,"h":7.183899999999994,"y":625.263,"p":4,"w":10.975899999999996}]}},
  {"_key":"60c20e3a7723bebd86645824","_id":"annotations/60c20e3a7723bebd86645824","_rev":"_cfFmXMq---","document":{"$oid":"60c20e3a7723bebd86645822"},"publisher":{"offsetStart":303,"normalizedForm":"Treestar","offsetEnd":311,"rawForm":"Treestar","boundingBoxes":[{"x":71.36436363636365,"h":7.1839,"y":222.287,"p":4,"w":27.14610909090909}]},"context":"The frequency and number of CD4 + T cells, CD8 + T cells, CD19 +  B cells, CD16 + or CD56 + NK cells, and CD14 + monocytes were  measured by flow cytometry method using human monoclonal  A number of 20,000 events were counted  for each sample and the results were analyzed using Flowjo soft- ware (Treestar).","type":"software","software-name":{"offsetStart":283,"normalizedForm":"Flowjo","offsetEnd":289,"rawForm":"Flowjo","boundingBoxes":[{"x":245.376,"h":7.1839,"y":209.248,"p":4,"w":24.0117}]}},
  {"_key":"60c20e3f7723bebd86645826","_id":"annotations/60c20e3f7723bebd86645826","_rev":"_cfFmXM2---","document":{"$oid":"60c20e3f7723bebd86645825"},"type":"software","software-name":{"offsetStart":31,"normalizedForm":"DIVA","offsetEnd":35,"rawForm":"DIVA","boundingBoxes":[{"x":117.407,"h":7.1652,"y":729.283,"p":3,"w":18.8416}]},"context":"Analyses were performed using DIVA software focusing on T-and B-cell subsets."},
  {"_key":"60c20e3f7723bebd86645827","_id":"annotations/60c20e3f7723bebd86645827","_rev":"_cfFmXN----","wikipediaExternalRef":24666773,"document":{"$oid":"60c20e3f7723bebd86645825"},"context":"T-cell proliferation was quantified using FlowJo software.","wikidataId":"Q5462055","type":"software","confidence":0.4725,"software-name":{"wikipediaExternalRef":24666773,"normalizedForm":"FlowJo","offsetStart":42,"wikidataId":"Q5462055","offsetEnd":48,"lang":"en","confidence":0.4725,"rawForm":"FlowJo","boundingBoxes":[{"x":492.829,"h":7.1652,"y":630.924,"p":3,"w":25.4249}]},"lang":"en"},
  {"_key":"60c20e3f7723bebd86645828","_id":"annotations/60c20e3f7723bebd86645828","_rev":"_cfFmXNK---","document":{"$oid":"60c20e3f7723bebd86645825"},"context":"Data were acquired on FACSCanto II flow-cyt- ometer and data were analyzed by FCAP v3 array software.","type":"software","software-name":{"offsetStart":78,"normalizedForm":"FCAP","offsetEnd":82,"rawForm":"FCAP","boundingBoxes":[{"x":163.782,"h":7.1652,"y":122.558,"p":4,"w":19.2799}]},"version":{"offsetStart":84,"normalizedForm":"3","offsetEnd":85,"rawForm":"3","boundingBoxes":[{"x":185.721,"h":7.1652,"y":122.558,"p":4,"w":8.6875}]}},
  {"_key":"60c20e417723bebd8664582a","_id":"annotations/60c20e417723bebd8664582a","_rev":"_cfFmXNW---","wikipediaExternalRef":15441720,"document":{"$oid":"60c20e417723bebd86645829"},"context":"We used NVivo 12.0 software to complement our manual coding.","wikidataId":"Q6955723","type":"software","lang":"en","confidence":0.498,"software-name":{"wikipediaExternalRef":15441720,"normalizedForm":"NVivo","offsetStart":8,"wikidataId":"Q6955723","offsetEnd":13,"lang":"en","confidence":0.498,"rawForm":"NVivo","boundingBoxes":[{"x":143.831,"h":6.6112,"y":691.082,"p":2,"w":18.4318}]},"version":{"offsetStart":14,"normalizedForm":"12.0","offsetEnd":18,"rawForm":"12.0","boundingBoxes":[{"x":164.638,"h":6.6112000000000535,"y":691.082,"p":2,"w":12.413399999999996}]}},
  {"_key":"60c20e4a7723bebd8664582d","_id":"annotations/60c20e4a7723bebd8664582d","_rev":"_cfFmXNi---","document":{"$oid":"60c20e4a7723bebd8664582b"},"context":"Therefore, as a replication convention [9,10], we halved the effect size of the original experiment (Cohen's f = 0.151), and used G Ã Power [11] to conduct a power analysis (Cohen's f = 0.151, α = 0.05, 1−β = 0.99, number of groups = 3), as a result of which we set N = 942 as the required sample size.","references":[{"offsetStart":11551,"normalizedForm":"[11]","refKey":11,"label":"[11]","reference_id":{"$oid":"60c20e4a7723bebd8664582c"},"offsetEnd":11556,"boundingBoxes":[{"x":395.319,"h":8.793000000000006,"y":540.613,"p":3,"w":14.31450000000001}]}],"type":"software","software-name":{"offsetStart":131,"normalizedForm":"G Ã Power","offsetEnd":140,"rawForm":"G Ã Power","boundingBoxes":[{"x":352.121,"h":8.793,"y":540.61,"p":3,"w":6.84},{"x":360.736,"h":6.3,"y":538.846,"p":3,"w":3.15},{"x":366.179,"h":8.793,"y":540.613,"p":3,"w":24.7977}]}},
  {"_key":"60c20e4a7723bebd8664582f","_id":"annotations/60c20e4a7723bebd8664582f","_rev":"_cfFmXNq---","document":{"$oid":"60c20e4a7723bebd8664582e"},"context":"For measurement of leakage, data from the ventilator memory using specific software (PS Live software 3.0) was recorded on two consecutive nights (coinciding with NHPO), including: hours of treatment, mean leakage value (meanL), and a complete graphic record of leakage for the entire session.","type":"software","software-name":{"offsetStart":86,"normalizedForm":"PS Live","offsetEnd":93,"rawForm":"PS Live","boundingBoxes":[{"x":396.65363333333335,"h":8.844499999999996,"y":106.31,"p":2,"w":26.448666666666668}]},"version":{"offsetStart":103,"normalizedForm":"3.0","offsetEnd":106,"rawForm":"3.0","boundingBoxes":[{"x":459.394,"h":8.844499999999996,"y":106.31,"p":2,"w":10.707449999999994}]}},
  {"_key":"60c20e4e7723bebd86645831","_id":"annotations/60c20e4e7723bebd86645831","_rev":"_cfFmXN2---","document":{"$oid":"60c20e4e7723bebd86645830"},"publisher":{"offsetStart":92,"normalizedForm":"SynGene","offsetEnd":99,"rawForm":"SynGene","boundingBoxes":[{"x":73.1336,"h":8.7472,"y":296.31,"p":3,"w":36.3774}]},"context":"In some experiments, pro- tein band intensity was quantified using GeneTools software from SynGene (Cambridge, UK).","type":"software","software-name":{"offsetStart":67,"normalizedForm":"GeneTools","offsetEnd":76,"rawForm":"GeneTools","boundingBoxes":[{"x":210.043,"h":8.7472,"y":283.895,"p":3,"w":42.7934}]}},
  {"_key":"60c20e4e7723bebd86645832","_id":"annotations/60c20e4e7723bebd86645832","_rev":"_cfFmXOC---","document":{"$oid":"60c20e4e7723bebd86645830"},"type":"software","software-name":{"offsetStart":256,"normalizedForm":"CellQuest","offsetEnd":265,"rawForm":"CellQuest","boundingBoxes":[{"x":504.4,"h":8.7472,"y":333.659,"p":2,"w":39.8046}]},"context":"After two washes with PBS, cells were stained with Fluorescein isothiocyanate-conjugated rabbit anti-goat IgG for 30 min at 4 °C, washed with PBS, fixed in 1 % paraformaldehyde, and subjected to flow cytometry on a FACSCalibur (BD, San Jose, CA) using CellQuest software for data acquisition and analysis."},
  {"_key":"60c20e4e7723bebd86645835","_id":"annotations/60c20e4e7723bebd86645835","_rev":"_cfFmXOK---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20e4e7723bebd86645833"},"context":"Sequences were aligned with Clustal W 40 using default parameters (gap opening penalty: 15, extension penalty: 6, IUB matrix).","wikidataId":"Q866737","type":"software","confidence":0.8955,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"Clustal W","offsetStart":28,"wikidataId":"Q866737","offsetEnd":37,"lang":"en","confidence":0.8955,"rawForm":"Clustal W","boundingBoxes":[{"x":433.136,"h":7.428199999999947,"y":638.256,"p":7,"w":30.271199999999965}]},"lang":"en"},
  {"_key":"60c20e4e7723bebd86645836","_id":"annotations/60c20e4e7723bebd86645836","_rev":"_cfFmXOW---","document":{"$oid":"60c20e4e7723bebd86645833"},"context":"Molecular dynamics simulations were performed with Amber 12 with the ff10 Cornell force field for RNA.","type":"software","software-name":{"offsetStart":51,"normalizedForm":"Amber","offsetEnd":56,"rawForm":"Amber","boundingBoxes":[{"x":485.684,"h":7.4282,"y":381.785,"p":7,"w":22.1492}]},"version":{"offsetStart":57,"normalizedForm":"12","offsetEnd":59,"rawForm":"12","boundingBoxes":[{"x":509.491,"h":7.4282,"y":381.785,"p":7,"w":7.6355}]}},
  {"_key":"60c20e4e7723bebd86645837","_id":"annotations/60c20e4e7723bebd86645837","_rev":"_cfFmXOi---","document":{"$oid":"60c20e4e7723bebd86645833"},"context":"The resulting alignment was manually edited using seaview 41 to trim especially long 39 UTR and long 59 UTR sequences (notably Danio rerio, sheep, goat, rat, and mouse).","references":[{"offsetStart":58218,"normalizedForm":"41","refKey":40,"label":"41","reference_id":{"$oid":"60c20e4e7723bebd86645834"},"offsetEnd":58221,"boundingBoxes":[{"x":401.669,"h":4.2088,"y":656.573,"p":7,"w":4.8674}]}],"type":"software","software-name":{"offsetStart":51,"normalizedForm":"seaview","offsetEnd":58,"rawForm":"seaview","boundingBoxes":[{"x":377.678,"h":7.4282,"y":657.247,"p":7,"w":24.0142}]}},
  {"_key":"60c20e4e7723bebd86645838","_id":"annotations/60c20e4e7723bebd86645838","_rev":"_cfFmXOu---","document":{"$oid":"60c20e4e7723bebd86645833"},"context":"The solvent boxes had a clearance distance of 10 A ˚(also named 'buffer' in Amber, that is, the minimum distance between the solute and the solvent box wall).","type":"software","software-name":{"offsetStart":77,"normalizedForm":"Amber","offsetEnd":82,"rawForm":"Amber","boundingBoxes":[{"x":435.39,"h":7.4282,"y":571.475,"p":7,"w":19.905583333333336}]},"version":{"offsetStart":57,"normalizedForm":"12","offsetEnd":59,"rawForm":"12","boundingBoxes":[{"x":509.491,"h":7.4282,"y":381.785,"p":7,"w":7.6355}]}},
  {"_key":"60c20e4e7723bebd86645839","_id":"annotations/60c20e4e7723bebd86645839","_rev":"_cfFmXO2---","wikipediaExternalRef":363695,"document":{"$oid":"60c20e4e7723bebd86645833"},"context":"Sequences for CCR5 coding sequences were chosen for 39 primates and a naive BLAST search extended these candidates to 45 sequences with the CCR5 mRNA from Danio rerio chosen as an outgroup.","wikidataId":"Q286820","type":"software","confidence":0.2946,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":77,"wikidataId":"Q286820","offsetEnd":82,"lang":"en","confidence":0.2946,"rawForm":"BLAST","boundingBoxes":[{"x":484.648,"h":7.4282,"y":619.318,"p":7,"w":22.8506}]},"lang":"en"},
  {"_key":"60c20e4e7723bebd8664583a","_id":"annotations/60c20e4e7723bebd8664583a","_rev":"_cfFmXPC---","document":{"$oid":"60c20e4e7723bebd86645833"},"type":"software","software-name":{"offsetStart":102,"normalizedForm":"ptraj","offsetEnd":107,"rawForm":"ptraj","boundingBoxes":[{"x":543.466,"h":7.4282,"y":590.468,"p":7,"w":14.9282}]},"context":"Analyses of the molecular dyna- mics results excluded the equilibrations and were performed using the ptraj module of Amber."},
  {"_key":"60c20e4e7723bebd8664583b","_id":"annotations/60c20e4e7723bebd8664583b","_rev":"_cfFmXPO---","document":{"$oid":"60c20e4e7723bebd86645833"},"context":"Analyses of the molecular dyna- mics results excluded the equilibrations and were performed using the ptraj module of Amber.","type":"software","software-name":{"offsetStart":119,"normalizedForm":"Amber","offsetEnd":124,"rawForm":"Amber","boundingBoxes":[{"x":340.6,"h":7.4282,"y":599.936,"p":7,"w":19.825833333333335}]},"version":{"offsetStart":57,"normalizedForm":"12","offsetEnd":59,"rawForm":"12","boundingBoxes":[{"x":509.491,"h":7.4282,"y":381.785,"p":7,"w":7.6355}]}},
  {"_key":"60c20e507723bebd8664583d","_id":"annotations/60c20e507723bebd8664583d","_rev":"_cfFmXPa---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20e507723bebd8664583c"},"context":"Sequences retrieved from GenBank database (accession num- bers: AF434165, AF434164, AF434163, AF434162, and AF434161) were aligned using Clustal W 1.7.","wikidataId":"Q866737","type":"software","lang":"en","confidence":0.8955,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"Clustal W","offsetStart":138,"wikidataId":"Q866737","offsetEnd":147,"lang":"en","confidence":0.8955,"rawForm":"Clustal W","boundingBoxes":[{"x":115.157,"h":7.523799999999994,"y":434.686,"p":3,"w":36.4046}]},"version":{"offsetStart":148,"normalizedForm":"1.7","offsetEnd":152,"rawForm":"1.7.","boundingBoxes":[{"x":153.312,"h":7.523799999999994,"y":434.686,"p":3,"w":13.485399999999998}]}},
  {"_key":"60c20e507723bebd86645840","_id":"annotations/60c20e507723bebd86645840","_rev":"_cfFmXPm---","wikipediaExternalRef":652617,"document":{"$oid":"60c20e507723bebd8664583e"},"context":"The bootscanning analysis using RDP v. 4.58 was performed to identify the presumed recombinant breakpoints.","wikidataId":"Q49150","type":"software","lang":"en","confidence":0.4233,"software-name":{"wikipediaExternalRef":652617,"normalizedForm":"RDP","offsetStart":33,"wikidataId":"Q49150","offsetEnd":36,"lang":"en","confidence":0.4233,"rawForm":"RDP","boundingBoxes":[{"x":331.369,"h":7.5398,"y":528.527,"p":3,"w":14.8541}]},"version":{"offsetStart":40,"normalizedForm":"4.58","offsetEnd":44,"rawForm":"4.58","boundingBoxes":[{"x":355.464,"h":7.539800000000014,"y":528.527,"p":3,"w":15.216699999999946}]}},
  {"_key":"60c20e507723bebd86645841","_id":"annotations/60c20e507723bebd86645841","_rev":"_cfFmXPy---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20e507723bebd8664583e"},"context":"The sequences were aligned using ClustalW in MEGA5.22 (Tamura et al., 2011).","wikidataId":"Q866737","type":"software","confidence":0.7823,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"ClustalW","offsetStart":34,"wikidataId":"Q866737","offsetEnd":42,"lang":"en","confidence":0.7823,"rawForm":"ClustalW","boundingBoxes":[{"x":119.223,"h":7.5398,"y":570.423,"p":3,"w":33.1791}]},"lang":"en"},
  {"_key":"60c20e507723bebd86645842","_id":"annotations/60c20e507723bebd86645842","_rev":"_cfFmXQ----","document":{"$oid":"60c20e507723bebd8664583e"},"context":"The sequences were aligned using ClustalW in MEGA5.22 (Tamura et al., 2011).","references":[{"offsetStart":9138,"normalizedForm":"Tamura et al., 2011","refKey":36,"label":"(Tamura et al., 2011)","reference_id":{"$oid":"60c20e507723bebd8664583f"},"offsetEnd":9159,"boundingBoxes":[{"x":209.475,"h":7.539800000000014,"y":570.423,"p":3,"w":80.09350000000003}]}],"type":"software","software-name":{"offsetStart":46,"normalizedForm":"MEGA","offsetEnd":50,"rawForm":"MEGA","boundingBoxes":[{"x":167.183,"h":7.5398,"y":570.423,"p":3,"w":24.017187500000002}]},"version":{"offsetStart":50,"normalizedForm":"5.22","offsetEnd":54,"rawForm":"5.22","boundingBoxes":[{"x":167.183,"h":7.539800000000014,"y":570.423,"p":3,"w":38.42750000000001}]}},
  {"_key":"60c20e507723bebd86645843","_id":"annotations/60c20e507723bebd86645843","_rev":"_cfFmXQG---","document":{"$oid":"60c20e507723bebd8664583e"},"publisher":{"offsetStart":92,"normalizedForm":"CLC bio","offsetEnd":99,"rawForm":"CLC bio","boundingBoxes":[{"x":154.78722499999998,"h":7.539800000000014,"y":591.342,"p":3,"w":26.734655000000004}]},"context":"Pairwise sequence identity calculations were performed using CLC Genomics Workbench 6.5.1 (CLC bio).","type":"software","software-name":{"offsetStart":61,"normalizedForm":"CLC Genomics Workbench","offsetEnd":84,"rawForm":"CLC \nGenomics Workbench","boundingBoxes":[{"x":280.115,"h":7.5398,"y":580.854,"p":3,"w":13.4569},{"x":42.5186,"h":7.539800000000014,"y":591.342,"p":3,"w":82.87810000000002}]},"version":{"offsetStart":85,"normalizedForm":"6.5.1","offsetEnd":90,"rawForm":"6.5.1","boundingBoxes":[{"x":129.143,"h":7.539800000000014,"y":591.342,"p":3,"w":17.59820000000002}]}},
  {"_key":"60c20e507723bebd86645844","_id":"annotations/60c20e507723bebd86645844","_rev":"_cfFmXQS---","document":{"$oid":"60c20e507723bebd8664583e"},"publisher":{"offsetStart":114,"normalizedForm":"CLC bio","offsetEnd":121,"rawForm":"CLC bio","boundingBoxes":[{"x":145.387425,"h":7.539800000000014,"y":559.935,"p":3,"w":23.76004999999998}]},"context":"Collected reads were trimmed and assembled into contigs by de novo assembly using CLC Genomics Workbench 6.5.1 (CLC bio, Aarhus, Denmark).","type":"software","software-name":{"offsetStart":83,"normalizedForm":"CLC Genomics Workbench","offsetEnd":106,"rawForm":"CLC \nGenomics Workbench","boundingBoxes":[{"x":280.119,"h":7.5398,"y":549.503,"p":3,"w":13.4569},{"x":42.5186,"h":7.539800000000014,"y":559.935,"p":3,"w":78.5017}]},"version":{"offsetStart":107,"normalizedForm":"6.5.1","offsetEnd":112,"rawForm":"6.5.1","boundingBoxes":[{"x":122.567,"h":7.539800000000014,"y":559.935,"p":3,"w":16.917500000000004}]}},
  {"_key":"60c20e507723bebd86645845","_id":"annotations/60c20e507723bebd86645845","_rev":"_cfFmXQe---","document":{"$oid":"60c20e507723bebd8664583e"},"context":"The phylogenetic tree was constructed by the maximum likelihood method statistically supported by bootstrapping with 1000 replicates by using MEGA5.22.","references":[{"offsetStart":9138,"normalizedForm":"Tamura et al., 2011","refKey":36,"label":"(Tamura et al., 2011)","reference_id":{"$oid":"60c20e507723bebd8664583f"},"offsetEnd":9159,"boundingBoxes":[{"x":209.475,"h":7.539800000000014,"y":570.423,"p":3,"w":80.09350000000003}]}],"type":"software","software-name":{"offsetStart":144,"normalizedForm":"MEGA","offsetEnd":148,"rawForm":"MEGA","boundingBoxes":[{"x":210.1,"h":7.5398,"y":612.262,"p":3,"w":21.73827777777778}]},"version":{"offsetStart":148,"normalizedForm":"5.22","offsetEnd":152,"rawForm":"5.22","boundingBoxes":[{"x":210.1,"h":7.539800000000014,"y":612.262,"p":3,"w":34.78124444444447}]}},
  {"_key":"60c20e507723bebd86645846","_id":"annotations/60c20e507723bebd86645846","_rev":"_cfFmXQq---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20e507723bebd8664583e"},"context":"To investigate the recombination events, the complete genomes of BToV Ishi, BToV Kago, PToV NPL/2014, PToV SH1, and BToV Breda1 were aligned using ClustalW program in MEGA5.22 and standard similarity plot analysis was performed using SimPlot software v. 3.5.1 with BToV Ishi (Fig. 1) and BToV Kagoshima/2014 sequences as sepa- rate queries.","wikidataId":"Q866737","type":"software","confidence":0.7823,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"ClustalW","offsetStart":149,"wikidataId":"Q866737","offsetEnd":157,"lang":"en","confidence":0.7823,"rawForm":"ClustalW","boundingBoxes":[{"x":386.7,"h":7.5398,"y":455.337,"p":3,"w":33.2357}]},"lang":"en"},
  {"_key":"60c20e507723bebd86645847","_id":"annotations/60c20e507723bebd86645847","_rev":"_cfFmXQ2---","document":{"$oid":"60c20e507723bebd8664583e"},"context":"To investigate the recombination events, the complete genomes of BToV Ishi, BToV Kago, PToV NPL/2014, PToV SH1, and BToV Breda1 were aligned using ClustalW program in MEGA5.22 and standard similarity plot analysis was performed using SimPlot software v. 3.5.1 with BToV Ishi (Fig. 1) and BToV Kagoshima/2014 sequences as sepa- rate queries.","references":[{"offsetStart":9138,"normalizedForm":"Tamura et al., 2011","refKey":36,"label":"(Tamura et al., 2011)","reference_id":{"$oid":"60c20e507723bebd8664583f"},"offsetEnd":9159,"boundingBoxes":[{"x":209.475,"h":7.539800000000014,"y":570.423,"p":3,"w":80.09350000000003}]}],"type":"software","software-name":{"offsetStart":169,"normalizedForm":"MEGA","offsetEnd":173,"rawForm":"MEGA","boundingBoxes":[{"x":469.64,"h":7.5398,"y":455.337,"p":3,"w":24.108874999999998}]},"version":{"offsetStart":173,"normalizedForm":"5.22","offsetEnd":177,"rawForm":"5.22","boundingBoxes":[{"x":469.64,"h":7.539800000000014,"y":455.337,"p":3,"w":38.57420000000002}]}},
  {"_key":"60c20e5e7723bebd8664584b","_id":"annotations/60c20e5e7723bebd8664584b","_rev":"_cfFmXRC---","document":{"$oid":"60c20e5e7723bebd86645848"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Pyrx","offsetEnd":4,"rawForm":"Pyrx","boundingBoxes":[{"x":249.564,"h":8.7472,"y":335.489,"p":4,"w":19.0973}]},"context":"Pyrx tool was used for energy minimizing and preparing ligands in PDBQT format, and AutoDock Vina was applied for virtual screening."},
  {"_key":"60c20e5e7723bebd8664584c","_id":"annotations/60c20e5e7723bebd8664584c","_rev":"_cfFmXRO---","document":{"$oid":"60c20e5e7723bebd86645848"},"type":"software","software-name":{"offsetStart":1,"normalizedForm":"Drefine","offsetEnd":8,"rawForm":"Drefine","boundingBoxes":[{"x":440.884,"h":8.7472,"y":682.391,"p":2,"w":36.5438}]},"context":"3Drefine server and the package of GROMACS 5.1.4"},
  {"_key":"60c20e5e7723bebd8664584d","_id":"annotations/60c20e5e7723bebd8664584d","_rev":"_cfFmXRa---","wikipediaExternalRef":26322186,"document":{"$oid":"60c20e5e7723bebd86645848"},"context":"It was used AutoDock Vina for drug discovery to screen libraries of compounds against targets [16, 17].","wikidataId":"Q4826062","type":"software","confidence":0.9728,"software-name":{"wikipediaExternalRef":26322186,"normalizedForm":"AutoDock Vina","offsetStart":12,"wikidataId":"Q4826062","offsetEnd":25,"lang":"en","confidence":0.9728,"rawForm":"AutoDock Vina","boundingBoxes":[{"x":182.757,"h":8.74720000000002,"y":372.848,"p":4,"w":66.65630000000002}]},"lang":"en"},
  {"_key":"60c20e5e7723bebd8664584e","_id":"annotations/60c20e5e7723bebd8664584e","_rev":"_cfFmXRm---","document":{"$oid":"60c20e5e7723bebd86645848"},"type":"software","software-name":{"offsetStart":21,"normalizedForm":"PockDrug","offsetEnd":29,"rawForm":"PockDrug","boundingBoxes":[{"x":112.372,"h":8.7472,"y":410.208,"p":4,"w":40.9084}]},"context":"This position using PockDrug server and it was determined by  using data in uniprot about the main amino acids in the bond."},
  {"_key":"60c20e5e7723bebd8664584f","_id":"annotations/60c20e5e7723bebd8664584f","_rev":"_cfFmXRy---","wikipediaExternalRef":306766,"document":{"$oid":"60c20e5e7723bebd86645848"},"context":"3Drefine server and the package of GROMACS 5.1.4","wikidataId":"Q905302","type":"software","lang":"en","confidence":0.8007,"software-name":{"wikipediaExternalRef":306766,"normalizedForm":"GROMACS","offsetStart":36,"wikidataId":"Q905302","offsetEnd":43,"lang":"en","confidence":0.8007,"rawForm":"GROMACS","boundingBoxes":[{"x":356.511,"h":8.7472,"y":694.806,"p":2,"w":49.7841}]},"version":{"offsetStart":44,"normalizedForm":"5.1.4","offsetEnd":49,"rawForm":"5.1.4","boundingBoxes":[{"x":410.887,"h":8.74720000000002,"y":694.806,"p":2,"w":20.338599999999985}]}},
  {"_key":"60c20e5e7723bebd86645850","_id":"annotations/60c20e5e7723bebd86645850","_rev":"_cfFmXS----","wikipediaExternalRef":34913748,"document":{"$oid":"60c20e5e7723bebd86645848"},"context":"The homology models of these proteins were done in the SWISS-MODEL workspace [11, 12] (https://swissmodel.expasy.org/docs/","wikidataId":"Q7658835","references":[{"offsetStart":8366,"normalizedForm":"[11","refKey":10,"label":"[11,","reference_id":{"$oid":"60c20e5e7723bebd86645849"},"offsetEnd":8375,"boundingBoxes":[{"x":354.272,"h":8.74720000000002,"y":620.086,"p":2,"w":34.27720000000005}]},{"offsetStart":8366,"normalizedForm":"12]","refKey":11,"label":"12]","reference_id":{"$oid":"60c20e5e7723bebd8664584a"},"offsetEnd":8375,"boundingBoxes":[{"x":354.272,"h":8.74720000000002,"y":620.086,"p":2,"w":34.27720000000005}]}],"type":"software","confidence":0.7591,"software-name":{"wikipediaExternalRef":34913748,"normalizedForm":"SWISS-MODEL","offsetStart":56,"wikidataId":"Q7658835","offsetEnd":67,"lang":"en","confidence":0.7591,"rawForm":"SWISS-MODEL","boundingBoxes":[{"x":472.028,"h":8.74720000000002,"y":607.671,"p":2,"w":72.18899999999996}]},"url":{"offsetStart":221,"normalizedForm":"https://www. rcsb.org/structure","offsetEnd":253,"rawForm":"https://www. \nrcsb.org/structure","boundingBoxes":[{"x":492.5480615384615,"h":8.74720000000002,"y":645.031,"p":2,"w":51.696738461538416},{"x":306.142,"h":8.74720000000002,"y":657.446,"p":2,"w":71.09805600000004}]},"lang":"en"},
  {"_key":"60c20e5e7723bebd86645851","_id":"annotations/60c20e5e7723bebd86645851","_rev":"_cfFmXSK---","wikipediaExternalRef":26322186,"document":{"$oid":"60c20e5e7723bebd86645848"},"context":"Pyrx tool was used for energy minimizing and preparing ligands in PDBQT format, and AutoDock Vina was applied for virtual screening.","wikidataId":"Q4826062","type":"software","confidence":0.9728,"software-name":{"wikipediaExternalRef":26322186,"normalizedForm":"AutoDock Vina","offsetStart":86,"wikidataId":"Q4826062","offsetEnd":99,"lang":"en","confidence":0.9728,"rawForm":"AutoDock Vina","boundingBoxes":[{"x":153.123,"h":8.74720000000002,"y":360.376,"p":4,"w":65.96090000000001}]},"lang":"en"},
  {"_key":"60c20e5e7723bebd86645852","_id":"annotations/60c20e5e7723bebd86645852","_rev":"_cfFmXSW---","document":{"$oid":"60c20e5e7723bebd86645848"},"type":"software","software-name":{"offsetStart":181,"normalizedForm":"LigPlot","offsetEnd":188,"rawForm":"LigPlot","boundingBoxes":[{"x":354.603,"h":8.7472,"y":393.029,"p":5,"w":27.8574}]},"context":"The protein complexes with these seven drugs are shown in Figs. 2, 3, 4, 5, 6, 7, and 8. Hydrophobic and hydrogen bonding interactions of docked molecules were visu- alized using LigPlot program (Table 2)."},
  {"_key":"60c20e607723bebd86645854","_id":"annotations/60c20e607723bebd86645854","_rev":"_cfFmXSi---","wikipediaExternalRef":179088,"document":{"$oid":"60c20e607723bebd86645853"},"publisher":{"offsetStart":43,"normalizedForm":"IBM Corp","offsetEnd":51,"rawForm":"IBM Corp","boundingBoxes":[{"x":254.32452500000002,"h":10.20229999999998,"y":315.717,"p":7,"w":42.12603499999997}]},"context":"Data  was analysed using SPSS version 26 (IBM Corp, New York, USA) and Stata version 16.0 (Stata  Corp LLC, Texas, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":26,"wikidataId":"Q181596","offsetEnd":30,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":169.936,"h":10.2023,"y":315.717,"p":7,"w":25.2621}]},"version":{"offsetStart":39,"normalizedForm":"26","offsetEnd":41,"rawForm":"26","boundingBoxes":[{"x":233.896,"h":10.2023,"y":315.717,"p":7,"w":11.4277}]}},
  {"_key":"60c20e607723bebd86645855","_id":"annotations/60c20e607723bebd86645855","_rev":"_cfFmXSu---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20e607723bebd86645853"},"publisher":{"offsetStart":92,"normalizedForm":"Stata Corp","offsetEnd":104,"rawForm":"Stata \n\nCorp","boundingBoxes":[{"x":493.70776666666666,"h":10.2023,"y":315.717,"p":7,"w":21.903833333333335},{"x":79.9188,"h":10.2023,"y":341.636,"p":7,"w":22.5876}]},"context":"Data  was analysed using SPSS version 26 (IBM Corp, New York, USA) and Stata version 16.0 (Stata  Corp LLC, Texas, USA).","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7154,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":72,"wikidataId":"Q1204300","offsetEnd":77,"lang":"en","confidence":0.7154,"rawForm":"Stata","boundingBoxes":[{"x":405.447,"h":10.2023,"y":315.717,"p":7,"w":22.5131}]},"version":{"offsetStart":86,"normalizedForm":"16.0","offsetEnd":90,"rawForm":"16.0","boundingBoxes":[{"x":466.677,"h":10.20229999999998,"y":315.717,"p":7,"w":19.858199999999954}]}},
  {"_key":"60c20e627723bebd86645857","_id":"annotations/60c20e627723bebd86645857","_rev":"_cfFmXS6---","wikipediaExternalRef":38833779,"document":{"$oid":"60c20e627723bebd86645856"},"context":"and Pandas v1.0.3.","wikidataId":"Q15967387","type":"software","lang":"en","confidence":0.3629,"software-name":{"wikipediaExternalRef":38833779,"normalizedForm":"Pandas","offsetStart":4,"wikidataId":"Q15967387","offsetEnd":10,"lang":"en","confidence":0.3629,"rawForm":"Pandas","boundingBoxes":[{"x":356.714,"h":8.8468,"y":495.419,"p":3,"w":24.9145}]},"version":{"offsetStart":12,"normalizedForm":"1.0.3","offsetEnd":17,"rawForm":"1.0.3","boundingBoxes":[{"x":389.085,"h":8.846799999999973,"y":495.419,"p":3,"w":20.890800000000013}]}},
  {"_key":"60c20e627723bebd86645858","_id":"annotations/60c20e627723bebd86645858","_rev":"_cfFmXTG---","document":{"$oid":"60c20e627723bebd86645856"},"context":"A McNemar test for paired samples was performed using Researchpy v0.1.9","type":"software","software-name":{"offsetStart":54,"normalizedForm":"Researchpy","offsetEnd":64,"rawForm":"Researchpy","boundingBoxes":[{"x":517.38,"h":8.8468,"y":484.988,"p":3,"w":40.2968}]},"version":{"offsetStart":67,"normalizedForm":"0.1.9","offsetEnd":72,"rawForm":"0.1.9","boundingBoxes":[{"x":306.597,"h":8.846799999999973,"y":495.419,"p":3,"w":22.140899999999988}]}},
  {"_key":"60c20e627723bebd86645859","_id":"annotations/60c20e627723bebd86645859","_rev":"_cfFmXTS---","wikipediaExternalRef":381782,"document":{"$oid":"60c20e627723bebd86645856"},"context":"The adjusted Wald confidence interval of the proportion of invalid test results per specimen type was calculated using NumPy v1.18.4 and SciPy v1.4.1.","wikidataId":"Q197520","type":"software","lang":"en","confidence":0.8008,"software-name":{"wikipediaExternalRef":381782,"normalizedForm":"NumPy","offsetStart":121,"wikidataId":"Q197520","offsetEnd":126,"lang":"en","confidence":0.8008,"rawForm":"NumPy","boundingBoxes":[{"x":327.8,"h":8.8468,"y":662.775,"p":3,"w":25.8949}]},"version":{"offsetStart":128,"normalizedForm":"1.18.4","offsetEnd":134,"rawForm":"1.18.4","boundingBoxes":[{"x":356.089,"h":8.84680000000003,"y":662.775,"p":3,"w":26.628100000000018}]}},
  {"_key":"60c20e627723bebd8664585a","_id":"annotations/60c20e627723bebd8664585a","_rev":"_cfFmXTe---","wikipediaExternalRef":263472,"document":{"$oid":"60c20e627723bebd86645856"},"context":"The adjusted Wald confidence interval of the proportion of invalid test results per specimen type was calculated using NumPy v1.18.4 and SciPy v1.4.1.","wikidataId":"Q197492","type":"software","lang":"en","confidence":0.7981,"software-name":{"wikipediaExternalRef":263472,"normalizedForm":"SciPy","offsetStart":139,"wikidataId":"Q197492","offsetEnd":144,"lang":"en","confidence":0.7981,"rawForm":"SciPy","boundingBoxes":[{"x":400.593,"h":8.8468,"y":662.775,"p":3,"w":19.1203}]},"version":{"offsetStart":146,"normalizedForm":"1.4.1","offsetEnd":151,"rawForm":"1.4.1","boundingBoxes":[{"x":422.079,"h":8.84680000000003,"y":662.775,"p":3,"w":20.890800000000013}]}},
  {"_key":"60c20e627723bebd8664585b","_id":"annotations/60c20e627723bebd8664585b","_rev":"_cfFmXTm---","wikipediaExternalRef":381782,"document":{"$oid":"60c20e627723bebd86645856"},"context":"The mean of the differences (and 95 % confidence interval) be- tween the cobas®6800 assay and LDA Ct-values and between the cobas®6800 SARS-CoV-2 Ct-values before and after a freeze-thaw cycle was calculated using NumPy v1.18.4 and SciPy v1.4.1.","wikidataId":"Q197520","type":"software","lang":"en","confidence":0.8008,"software-name":{"wikipediaExternalRef":381782,"normalizedForm":"NumPy","offsetStart":216,"wikidataId":"Q197520","offsetEnd":221,"lang":"en","confidence":0.8008,"rawForm":"NumPy","boundingBoxes":[{"x":384.606,"h":8.8468,"y":568.666,"p":3,"w":25.8949}]},"version":{"offsetStart":223,"normalizedForm":"1.18.4","offsetEnd":229,"rawForm":"1.18.4","boundingBoxes":[{"x":413.746,"h":8.84680000000003,"y":568.666,"p":3,"w":26.628100000000018}]}},
  {"_key":"60c20e627723bebd8664585c","_id":"annotations/60c20e627723bebd8664585c","_rev":"_cfFmXTy---","wikipediaExternalRef":2901907,"document":{"$oid":"60c20e627723bebd86645856"},"context":"Bland-Altman plots comparing the cobas®6800 and LDA SARS-CoV-2 Ct-values of the prospectively collected samples and comparing the cobas®6800 SARS-CoV-2 Ct- values before and after a freeze-thaw cycle, were drawn using Matplotlib v3.2.1.","wikidataId":"Q2985668","type":"software","lang":"en","confidence":0.8108,"software-name":{"wikipediaExternalRef":2901907,"normalizedForm":"Matplotlib","offsetStart":220,"wikidataId":"Q2985668","offsetEnd":230,"lang":"en","confidence":0.8108,"rawForm":"Matplotlib","boundingBoxes":[{"x":520.838,"h":8.8468,"y":526.827,"p":3,"w":36.8219}]},"version":{"offsetStart":233,"normalizedForm":"3.2.1","offsetEnd":238,"rawForm":"3.2.1","boundingBoxes":[{"x":306.597,"h":8.84680000000003,"y":537.258,"p":3,"w":20.890800000000013}]}},
  {"_key":"60c20e627723bebd8664585d","_id":"annotations/60c20e627723bebd8664585d","_rev":"_cfFmXU----","wikipediaExternalRef":263472,"document":{"$oid":"60c20e627723bebd86645856"},"context":"A Mann- Whitney U test was performed between the median Ct-values of the LDA E-gene, cobas®6800 E-gene and cobas®6800 RdRp of the pro- spectively collected deep respiratory specimens and oro-/nasopharyn- geal swabs using SciPy v1.4.1.","wikidataId":"Q197492","type":"software","lang":"en","confidence":0.7981,"software-name":{"wikipediaExternalRef":263472,"normalizedForm":"SciPy","offsetStart":222,"wikidataId":"Q197492","offsetEnd":227,"lang":"en","confidence":0.7981,"rawForm":"SciPy","boundingBoxes":[{"x":366.861,"h":8.8468,"y":641.856,"p":3,"w":19.1203}]},"version":{"offsetStart":229,"normalizedForm":"1.4.1","offsetEnd":234,"rawForm":"1.4.1","boundingBoxes":[{"x":387.951,"h":8.84680000000003,"y":641.856,"p":3,"w":20.890800000000013}]}},
  {"_key":"60c20e627723bebd8664585e","_id":"annotations/60c20e627723bebd8664585e","_rev":"_cfFmXUK---","wikipediaExternalRef":263472,"document":{"$oid":"60c20e627723bebd86645856"},"context":"The mean of the differences (and 95 % confidence interval) be- tween the cobas®6800 assay and LDA Ct-values and between the cobas®6800 SARS-CoV-2 Ct-values before and after a freeze-thaw cycle was calculated using NumPy v1.18.4 and SciPy v1.4.1.","wikidataId":"Q197492","type":"software","lang":"en","confidence":0.7981,"software-name":{"wikipediaExternalRef":263472,"normalizedForm":"SciPy","offsetStart":234,"wikidataId":"Q197492","offsetEnd":239,"lang":"en","confidence":0.7981,"rawForm":"SciPy","boundingBoxes":[{"x":459.95,"h":8.8468,"y":568.666,"p":3,"w":19.1203}]},"version":{"offsetStart":241,"normalizedForm":"1.4.1","offsetEnd":246,"rawForm":"1.4.1","boundingBoxes":[{"x":482.344,"h":8.84680000000003,"y":568.666,"p":3,"w":20.890800000000013}]}},
  {"_key":"60c20e637723bebd86645860","_id":"annotations/60c20e637723bebd86645860","_rev":"_cfFmXUW---","document":{"$oid":"60c20e637723bebd8664585f"},"context":" Generalized linear models (R stats v3.6.2) were used to estimate the correlation of population density, percent minority, percent uninsured and median income on median travel time, by county.","type":"software","software-name":{"offsetStart":28,"normalizedForm":"R stats","offsetEnd":35,"rawForm":"R stats","boundingBoxes":[{"x":186.0924,"h":8.205699999999979,"y":532.619,"p":2,"w":25.747600000000006}]},"version":{"offsetStart":37,"normalizedForm":"3.6.2","offsetEnd":42,"rawForm":"3.6.2","boundingBoxes":[{"x":216.682,"h":8.205699999999979,"y":532.619,"p":2,"w":22.18911428571431}]}},
  {"_key":"60c20e657723bebd86645862","_id":"annotations/60c20e657723bebd86645862","_rev":"_cfFmXUi---","document":{"$oid":"60c20e657723bebd86645861"},"publisher":{"offsetStart":81,"normalizedForm":"GraphPad","offsetEnd":89,"rawForm":"GraphPad","boundingBoxes":[{"x":322.039,"h":8.424,"y":715.216,"p":3,"w":34.92}]},"context":"Data were an- alyzed by two-way repeated-measures ANOVA using Prism ver- sion 6 (GraphPad).","type":"software","software-name":{"offsetStart":62,"normalizedForm":"Prism","offsetEnd":67,"rawForm":"Prism","boundingBoxes":[{"x":497.908,"h":8.424,"y":703.216,"p":3,"w":21.996}]},"version":{"offsetStart":78,"normalizedForm":"6","offsetEnd":79,"rawForm":"6","boundingBoxes":[{"x":311.09,"h":8.424,"y":715.216,"p":3,"w":5.004}]}},
  {"_key":"60c20e6a7723bebd86645864","_id":"annotations/60c20e6a7723bebd86645864","_rev":"_cfFmXUu---","document":{"$oid":"60c20e6a7723bebd86645863"},"publisher":{"offsetStart":71,"normalizedForm":"SSRI","offsetEnd":75,"rawForm":"SSRI","boundingBoxes":[{"x":310.6009166666667,"h":8.7571,"y":346.075,"p":2,"w":17.839666666666666}]},"context":"All statistical analyses were performed using Excel Statistics 2008 (SSRI, Japan).","type":"software","software-name":{"offsetStart":47,"normalizedForm":"Excel Statistics","offsetEnd":63,"rawForm":"Excel Statistics","boundingBoxes":[{"x":451.103,"h":8.75709999999998,"y":333.603,"p":2,"w":66.00859999999994}]},"version":{"offsetStart":64,"normalizedForm":"2008","offsetEnd":68,"rawForm":"2008","boundingBoxes":[{"x":524.293,"h":8.7571,"y":333.603,"p":2,"w":19.9252}]}},
  {"_key":"60c20e717723bebd86645866","_id":"annotations/60c20e717723bebd86645866","_rev":"_cfFmXU6---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20e717723bebd86645865"},"context":"GraphPad Prism software was used for statistical analysis.","wikidataId":"Q5597066","type":"software","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":0,"wikidataId":"Q5597066","offsetEnd":14,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":183.287,"h":7.539800000000014,"y":539.017,"p":5,"w":59.197299999999984}]},"lang":"en"},
  {"_key":"60c20e727723bebd86645867","_id":"annotations/60c20e727723bebd86645867","_rev":"_cfFmXVG---","document":{"$oid":"60c20e717723bebd86645865"},"context":"Emerging in silico methods-in particular, a novel bioinfor- matics tool called prediction of protease specificity (PoPS; http://pops. csse.monash.edu.au/home.html)-have","type":"software","software-name":{"offsetStart":115,"normalizedForm":"PoPS","offsetEnd":119,"rawForm":"PoPS","boundingBoxes":[{"x":220.83026666666666,"h":7.5398,"y":685.455,"p":8,"w":15.697066666666666}]},"url":{"offsetStart":121,"normalizedForm":"http://pops. csse.monash.edu.au/home.html","offsetEnd":163,"rawForm":"http://pops. \ncsse.monash.edu.au/home.html","boundingBoxes":[{"x":242.532,"h":7.539800000000014,"y":685.455,"p":8,"w":42.32729999999995},{"x":33.7315,"h":7.539800000000014,"y":695.943,"p":8,"w":118.12541176470585}]}},
  {"_key":"60c20e757723bebd8664586d","_id":"annotations/60c20e757723bebd8664586d","_rev":"_cfFmXVS---","wikipediaExternalRef":363695,"document":{"$oid":"60c20e757723bebd86645868"},"context":"BLASTP (vers.","wikidataId":"Q286820","type":"software","lang":"en","confidence":0.7063,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTP","offsetStart":0,"wikidataId":"Q286820","offsetEnd":6,"lang":"en","confidence":0.7063,"rawForm":"BLASTP","boundingBoxes":[{"x":471.647,"h":9.099,"y":440.76,"p":13,"w":31.0347}]},"version":{"offsetStart":14,"normalizedForm":"2.3.0","offsetEnd":19,"rawForm":"2.3.0","boundingBoxes":[{"x":525.588,"h":9.09899999999999,"y":440.76,"p":13,"w":21.786299999999983}]}},
  {"_key":"60c20e757723bebd8664586e","_id":"annotations/60c20e757723bebd8664586e","_rev":"_cfFmXVe---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"HMMSCAN","offsetEnd":7,"rawForm":"HMMSCAN","boundingBoxes":[{"x":155.639,"h":9.099,"y":450.759,"p":13,"w":45.981}]},"context":"HMMSCAN against Pfam, SignalP, TMHMM, and RNAMMER."},
  {"_key":"60c20e757723bebd8664586f","_id":"annotations/60c20e757723bebd8664586f","_rev":"_cfFmXVq---","wikipediaExternalRef":10921962,"document":{"$oid":"60c20e757723bebd86645868"},"context":"Cytoscape software with Biological Network Gene Ontology (BiNGO) plugin 92 was used to assess DEG overrepresentation of GO categories and visualisation using EnrichmentMap plugin 93 .","wikidataId":"Q3699942","type":"software","confidence":0.8039,"software-name":{"wikipediaExternalRef":10921962,"normalizedForm":"Cytoscape","offsetStart":0,"wikidataId":"Q3699942","offsetEnd":9,"lang":"en","confidence":0.8039,"rawForm":"Cytoscape","boundingBoxes":[{"x":375.376,"h":9.099,"y":50.6408,"p":14,"w":36.9216}]},"lang":"en"},
  {"_key":"60c20e757723bebd86645870","_id":"annotations/60c20e757723bebd86645870","_rev":"_cfFmXV2---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"KEGG Automatic Annotation Server (KAAS)","offsetEnd":39,"rawForm":"KEGG Automatic Annotation Server (KAAS)","boundingBoxes":[{"x":167.641,"h":9.099000000000046,"y":570.761,"p":13,"w":162.53799999999998}]},"context":"KEGG Automatic Annotation Server (KAAS) was used to annotate the transcriptome with KEGG Orthology (KO) identifiers or K numbers that are associated with enzymatic functions 85 ."},
  {"_key":"60c20e757723bebd86645871","_id":"annotations/60c20e757723bebd86645871","_rev":"_cfFmXWC---","wikipediaExternalRef":363695,"document":{"$oid":"60c20e757723bebd86645868"},"context":"Local BLASTN analysis against Arabidopsis genes found 37,911 (23.9%) hits.","wikidataId":"Q286820","type":"software","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTN","offsetStart":6,"wikidataId":"Q286820","offsetEnd":12,"lang":"en","confidence":0.708,"rawForm":"BLASTN","boundingBoxes":[{"x":374.604,"h":9.099,"y":640.797,"p":2,"w":32.787}]},"lang":"en"},
  {"_key":"60c20e757723bebd86645872","_id":"annotations/60c20e757723bebd86645872","_rev":"_cfFmXWO---","wikipediaExternalRef":363695,"document":{"$oid":"60c20e757723bebd86645868"},"context":"Local BLASTN was performed against TAIR10 Arabidopsis sequence database (https://www.arabidopsis.org/)","wikidataId":"Q286820","type":"software","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTN","offsetStart":6,"wikidataId":"Q286820","offsetEnd":12,"lang":"en","confidence":0.708,"rawForm":"BLASTN","boundingBoxes":[{"x":291.716,"h":9.099,"y":530.762,"p":13,"w":33.0714}]},"lang":"en"},
  {"_key":"60c20e757723bebd86645873","_id":"annotations/60c20e757723bebd86645873","_rev":"_cfFmXWa---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":22,"normalizedForm":"SignalP","offsetEnd":29,"rawForm":"SignalP","boundingBoxes":[{"x":252.755,"h":9.099,"y":450.759,"p":13,"w":24.3282375}]},"context":"HMMSCAN against Pfam, SignalP, TMHMM, and RNAMMER."},
  {"_key":"60c20e757723bebd86645874","_id":"annotations/60c20e757723bebd86645874","_rev":"_cfFmXWm---","document":{"$oid":"60c20e757723bebd86645868"},"context":"visualised using online tool REViGO (http://revigo.irb.hr/) 91","type":"software","software-name":{"offsetStart":29,"normalizedForm":"REViGO","offsetEnd":35,"rawForm":"REViGO","boundingBoxes":[{"x":255.292,"h":9.099,"y":50.6408,"p":14,"w":32.0715}]},"url":{"offsetStart":37,"normalizedForm":"http://revigo.irb.hr","offsetEnd":57,"rawForm":"http://revigo.irb.hr","boundingBoxes":[{"x":292.62882173913044,"h":9.099000000000004,"y":50.6408,"p":14,"w":66.43643478260867}]}},
  {"_key":"60c20e757723bebd86645875","_id":"annotations/60c20e757723bebd86645875","_rev":"_cfFmXWu---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":31,"normalizedForm":"TMHMM","offsetEnd":36,"rawForm":"TMHMM","boundingBoxes":[{"x":282.259,"h":9.099,"y":450.759,"p":13,"w":32.00475}]},"context":"HMMSCAN against Pfam, SignalP, TMHMM, and RNAMMER."},
  {"_key":"60c20e757723bebd86645876","_id":"annotations/60c20e757723bebd86645876","_rev":"_cfFmXW6---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":33,"normalizedForm":"RSEM","offsetEnd":37,"rawForm":"RSEM","boundingBoxes":[{"x":270.472,"h":9.099,"y":665.149,"p":3,"w":22.7997}]},"context":"results for each sample based on RSEM analysis at the unigene level."},
  {"_key":"60c20e757723bebd86645877","_id":"annotations/60c20e757723bebd86645877","_rev":"_cfFmXXG---","document":{"$oid":"60c20e757723bebd86645868"},"context":"The primers were designed using Primer-BLAST 94 as listed in Table S1.","references":[{"offsetStart":56309,"normalizedForm":"94","refKey":92,"label":"94","reference_id":{"$oid":"60c20e757723bebd86645869"},"offsetEnd":56312,"boundingBoxes":[{"x":288.641,"h":5.9143,"y":130.352,"p":14,"w":5.692}]}],"type":"software","software-name":{"offsetStart":33,"normalizedForm":"Primer-BLAST","offsetEnd":45,"rawForm":"Primer-BLAST","boundingBoxes":[{"x":232.891,"h":9.09899999999999,"y":131.357,"p":14,"w":55.65150000000003}]}},
  {"_key":"60c20e757723bebd86645878","_id":"annotations/60c20e757723bebd86645878","_rev":"_cfFmXXW---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":35,"normalizedForm":"Network Gene Ontology (BiNGO)","offsetEnd":65,"rawForm":"Network Gene \nOntology (BiNGO)","boundingBoxes":[{"x":502.209,"h":9.099000000000004,"y":50.6408,"p":14,"w":52.40259999999995},{"x":155.641,"h":9.098999999999997,"y":60.6398,"p":14,"w":69.49800000000005}]},"context":"Cytoscape software with Biological Network Gene Ontology (BiNGO) plugin 92 was used to assess DEG overrepresentation of GO categories and visualisation using EnrichmentMap plugin 93 ."},
  {"_key":"60c20e757723bebd86645879","_id":"annotations/60c20e757723bebd86645879","_rev":"_cfFmXXi---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":42,"normalizedForm":"RNAMMER","offsetEnd":49,"rawForm":"RNAMMER","boundingBoxes":[{"x":337.545,"h":9.099,"y":450.759,"p":13,"w":41.07915}]},"context":"HMMSCAN against Pfam, SignalP, TMHMM, and RNAMMER."},
  {"_key":"60c20e757723bebd8664587a","_id":"annotations/60c20e757723bebd8664587a","_rev":"_cfFmXXu---","document":{"$oid":"60c20e757723bebd86645868"},"context":"The processe reads were assembled and analysed through the Trinity analysis pipeline (v2.0.6), using default parameters with k-mer size of 25 78 .","type":"software","software-name":{"offsetStart":59,"normalizedForm":"Trinity","offsetEnd":66,"rawForm":"Trinity","boundingBoxes":[{"x":466.193,"h":9.099,"y":360.721,"p":13,"w":25.3602}]},"version":{"offsetStart":88,"normalizedForm":"2.0.6","offsetEnd":93,"rawForm":"2.0.6","boundingBoxes":[{"x":158.89,"h":9.09899999999999,"y":370.72,"p":13,"w":19.53}]}},
  {"_key":"60c20e757723bebd8664587b","_id":"annotations/60c20e757723bebd8664587b","_rev":"_cfFmXX6---","wikipediaExternalRef":363695,"document":{"$oid":"60c20e757723bebd86645868"},"context":"Translated peptides were  generated using TransDecoder for BLASTP and other protein-based analyses in the Trinity pipeline.","wikidataId":"Q286820","type":"software","lang":"en","confidence":0.7063,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTP","offsetStart":60,"wikidataId":"Q286820","offsetEnd":66,"lang":"en","confidence":0.7063,"rawForm":"BLASTP","boundingBoxes":[{"x":281.647,"h":9.099,"y":430.761,"p":13,"w":31.4577}]},"version":{"offsetStart":14,"normalizedForm":"2.3.0","offsetEnd":19,"rawForm":"2.3.0","boundingBoxes":[{"x":525.588,"h":9.09899999999999,"y":440.76,"p":13,"w":21.786299999999983}]}},
  {"_key":"60c20e757723bebd8664587c","_id":"annotations/60c20e757723bebd8664587c","_rev":"_cfFmXYK---","document":{"$oid":"60c20e757723bebd86645868"},"context":"Transcription factor was annotated using standalone software iTAK v1.7 with database v18.10 82 and combined with Arabidopsis annotation 83 .","type":"software","software-name":{"offsetStart":61,"normalizedForm":"iTAK","offsetEnd":65,"rawForm":"iTAK","boundingBoxes":[{"x":385.787,"h":9.099,"y":520.76,"p":13,"w":19.4742}]},"version":{"offsetStart":86,"normalizedForm":"18.10","offsetEnd":91,"rawForm":"18.10","boundingBoxes":[{"x":473.374,"h":9.099000000000046,"y":520.76,"p":13,"w":23.319000000000017}]}},
  {"_key":"60c20e757723bebd8664587d","_id":"annotations/60c20e757723bebd8664587d","_rev":"_cfFmXYa---","wikipediaExternalRef":363695,"document":{"$oid":"60c20e757723bebd86645868"},"context":"Functional annotation of unigenes through Trinotate pipeline with BLAST searches found hits against dif- ferent public databases (Table 1), including nr (35,346, 22.3%), Swiss-Prot (19,053, 12.0%), PFAM (18,377, 11.6%), eggNOG (15,577), and KEGG (25,512, 16.1%).","wikidataId":"Q286820","type":"software","confidence":0.2835,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":66,"wikidataId":"Q286820","offsetEnd":71,"lang":"en","confidence":0.2835,"rawForm":"BLAST","boundingBoxes":[{"x":413.109,"h":9.099,"y":620.799,"p":2,"w":26.3727}]},"lang":"en"},
  {"_key":"60c20e757723bebd8664587e","_id":"annotations/60c20e757723bebd8664587e","_rev":"_cfFmXYq---","wikipediaExternalRef":363695,"document":{"$oid":"60c20e757723bebd86645868"},"context":"Trinotate annotation suite provides multiple homology searches, including BLASTX (vers.","wikidataId":"Q286820","type":"software","lang":"en","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTX","offsetStart":75,"wikidataId":"Q286820","offsetEnd":81,"lang":"en","confidence":0.708,"rawForm":"BLASTX","boundingBoxes":[{"x":385.928,"h":9.099,"y":440.76,"p":13,"w":32.0796}]},"version":{"offsetStart":89,"normalizedForm":"2.3.0","offsetEnd":94,"rawForm":"2.3.0","boundingBoxes":[{"x":440.914,"h":9.09899999999999,"y":440.76,"p":13,"w":21.787649999999985}]}},
  {"_key":"60c20e757723bebd8664587f","_id":"annotations/60c20e757723bebd8664587f","_rev":"_cfFmXY2---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":75,"normalizedForm":"Bowtie","offsetEnd":81,"rawForm":"Bowtie","boundingBoxes":[{"x":433.868,"h":9.099,"y":650.802,"p":13,"w":25.731}]},"context":"for all samples were aligned to the reference transcriptome assembly using Bowtie 87 as part of Trinity work- flow."},
  {"_key":"60c20e757723bebd86645880","_id":"annotations/60c20e757723bebd86645880","_rev":"_cfFmXZG---","document":{"$oid":"60c20e757723bebd86645868"},"context":"The estimation of transcript abundance from each sample was performed using RSEM (RNA-Seq by Expectation-Maximization) 88 by following default settings with the alignment results.","references":[{"offsetStart":54744,"normalizedForm":"88","refKey":86,"label":"88","reference_id":{"$oid":"60c20e757723bebd8664586a"},"offsetEnd":54747,"boundingBoxes":[{"x":257.881,"h":5.9143,"y":669.793,"p":13,"w":5.6774}]}],"type":"software","software-name":{"offsetStart":76,"normalizedForm":"RSEM (RNA-Seq by Expectation-Maximization)","offsetEnd":119,"rawForm":"RSEM (RNA-Seq by \nExpectation-Maximization)","boundingBoxes":[{"x":479.047,"h":9.099000000000046,"y":660.802,"p":13,"w":75.61519999999996},{"x":155.637,"h":9.099000000000046,"y":670.801,"p":13,"w":102.17000000000002}]}},
  {"_key":"60c20e757723bebd86645881","_id":"annotations/60c20e757723bebd86645881","_rev":"_cfFmXZS---","wikipediaExternalRef":363695,"document":{"$oid":"60c20e757723bebd86645868"},"context":"In total, 34,444 (21.7%) unigenes were annotated with gene ontology (GO) terms through BLAST and Pfam analyses, in which 27,646 unigenes categorised in cellular component (mainly cell, cell part, and organelle), 28,839 unigenes in molecular function (mainly binding and catalytic activity), and 26,926 unigenes in biological process (mainly cellular process and metabolic process) (Fig. S1).","wikidataId":"Q286820","type":"software","confidence":0.2835,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":88,"wikidataId":"Q286820","offsetEnd":93,"lang":"en","confidence":0.2835,"rawForm":"BLAST","boundingBoxes":[{"x":186.47,"h":9.099,"y":710.79,"p":2,"w":26.0568}]},"lang":"en"},
  {"_key":"60c20e757723bebd86645882","_id":"annotations/60c20e757723bebd86645882","_rev":"_cfFmXZe---","document":{"$oid":"60c20e757723bebd86645868"},"context":"Adapter sequences and raw reads with Phred score < 25 were removed from raw reads using Trimmomatic 77 .","references":[{"offsetStart":51834,"normalizedForm":"77","refKey":75,"label":"77","reference_id":{"$oid":"60c20e757723bebd8664586b"},"offsetEnd":51837,"boundingBoxes":[{"x":228.95,"h":5.9143,"y":359.712,"p":13,"w":5.6833}]}],"type":"software","software-name":{"offsetStart":89,"normalizedForm":"Trimmomatic","offsetEnd":100,"rawForm":"Trimmomatic","boundingBoxes":[{"x":177.878,"h":9.099,"y":360.718,"p":13,"w":50.9643}]}},
  {"_key":"60c20e757723bebd86645883","_id":"annotations/60c20e757723bebd86645883","_rev":"_cfFmXZq---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":93,"normalizedForm":"edgeR Bioconductor","offsetEnd":111,"rawForm":"edgeR Bioconductor","boundingBoxes":[{"x":404.437,"h":9.099000000000046,"y":680.802,"p":13,"w":73.05400000000003}]},"context":"Pairwise DEG analysis was performed at the unigene level based on the read counts using the edgeR Bioconductor package 89 with TMM normalisation."},
  {"_key":"60c20e757723bebd86645884","_id":"annotations/60c20e757723bebd86645884","_rev":"_cfFmXZ6---","document":{"$oid":"60c20e757723bebd86645868"},"context":"Unigenes with annotated KO numbers were mapped against KEGG PATHWAY database (May 1, 2019) with KEGG Mapper 86 and tabulated for enrichment analysis.","references":[{"offsetStart":54375,"normalizedForm":"86","refKey":84,"label":"86","reference_id":{"$oid":"60c20e757723bebd8664586c"},"offsetEnd":54379,"boundingBoxes":[{"x":548.993,"h":5.9143,"y":609.753,"p":13,"w":5.6452}]}],"type":"software","software-name":{"offsetStart":97,"normalizedForm":"KEGG Mapper","offsetEnd":108,"rawForm":"KEGG Mapper","boundingBoxes":[{"x":494.318,"h":9.099000000000046,"y":610.759,"p":13,"w":54.650699999999915}]}},
  {"_key":"60c20e757723bebd86645885","_id":"annotations/60c20e757723bebd86645885","_rev":"_cfFmXaG---","wikipediaExternalRef":3661251,"document":{"$oid":"60c20e757723bebd86645868"},"context":"In total, 34,444 (21.7%) unigenes were annotated with gene ontology (GO) terms through BLAST and Pfam analyses, in which 27,646 unigenes categorised in cellular component (mainly cell, cell part, and organelle), 28,839 unigenes in molecular function (mainly binding and catalytic activity), and 26,926 unigenes in biological process (mainly cellular process and metabolic process) (Fig. S1).","wikidataId":"Q906796","type":"software","confidence":0.7831,"software-name":{"wikipediaExternalRef":3661251,"normalizedForm":"Pfam","offsetStart":98,"wikidataId":"Q906796","offsetEnd":102,"lang":"en","confidence":0.7831,"rawForm":"Pfam","boundingBoxes":[{"x":229.452,"h":9.099,"y":710.79,"p":2,"w":18.8604}]},"lang":"en"},
  {"_key":"60c20e757723bebd86645886","_id":"annotations/60c20e757723bebd86645886","_rev":"_cfFmXaS---","document":{"$oid":"60c20e757723bebd86645868"},"context":"Reverse transcription quantitative real-time PCR (RT-qPCR) was performed using Eco TM Real-Time PCR System with Eco Study (v5.2.12) software using iTaq TM  Universal SYBR ® Green Supermix (Bio-Rad).","type":"software","software-name":{"offsetStart":113,"normalizedForm":"Eco Study","offsetEnd":122,"rawForm":"Eco Study","boundingBoxes":[{"x":404.563,"h":9.09899999999999,"y":141.361,"p":14,"w":35.97130000000004}]},"version":{"offsetStart":125,"normalizedForm":"5.2.12","offsetEnd":131,"rawForm":"5.2.12","boundingBoxes":[{"x":446.036,"h":9.09899999999999,"y":141.361,"p":14,"w":24.772999999999968}]}},
  {"_key":"60c20e757723bebd86645887","_id":"annotations/60c20e757723bebd86645887","_rev":"_cfFmXae---","wikipediaExternalRef":363695,"document":{"$oid":"60c20e757723bebd86645868"},"context":"All results were stored into the Trinotate SQLite database template and a spreadsheet-based summary report was generated from Trinotate using BLAST E-value cut-off of 1E −5 .","wikidataId":"Q286820","type":"software","confidence":0.2835,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":143,"wikidataId":"Q286820","offsetEnd":148,"lang":"en","confidence":0.2835,"rawForm":"BLAST","boundingBoxes":[{"x":499.379,"h":9.099,"y":460.758,"p":13,"w":26.1}]},"lang":"en"},
  {"_key":"60c20e757723bebd86645888","_id":"annotations/60c20e757723bebd86645888","_rev":"_cfFmXaq---","document":{"$oid":"60c20e757723bebd86645868"},"type":"software","software-name":{"offsetStart":160,"normalizedForm":"EnrichmentMap","offsetEnd":173,"rawForm":"EnrichmentMap","boundingBoxes":[{"x":155.636,"h":9.099,"y":70.6398,"p":14,"w":59.4171}]},"context":"Cytoscape software with Biological Network Gene Ontology (BiNGO) plugin 92 was used to assess DEG overrepresentation of GO categories and visualisation using EnrichmentMap plugin 93 ."},
  {"_key":"60c20e757723bebd8664588b","_id":"annotations/60c20e757723bebd8664588b","_rev":"_cfFmXa2---","document":{"$oid":"60c20e757723bebd86645889"},"context":"Solutions such as CovTracer [4] used in Cyprus collect GPS data to compute the proximity of devices.","references":[{"offsetStart":16655,"normalizedForm":"[4]","refKey":2,"label":"[4]","reference_id":{"$oid":"60c20e757723bebd8664588a"},"offsetEnd":16659,"boundingBoxes":[{"x":490.109,"h":8.966399999999993,"y":202.49,"p":3,"w":10.553499999999985}]}],"type":"software","software-name":{"offsetStart":18,"normalizedForm":"CovTracer","offsetEnd":27,"rawForm":"CovTracer","boundingBoxes":[{"x":449.734,"h":8.9664,"y":202.49,"p":3,"w":38.1431}]}},
  {"_key":"60c20e757723bebd8664588c","_id":"annotations/60c20e757723bebd8664588c","_rev":"_cfFmXbC---","wikipediaExternalRef":12610483,"document":{"$oid":"60c20e757723bebd86645889"},"context":"For eg., 25% of global Android users would be unable to use apps designed below Android 8.0 that was launched in 2017.","wikidataId":"Q94","type":"software","lang":"en","confidence":0.4481,"software-name":{"wikipediaExternalRef":12610483,"normalizedForm":"Android","offsetStart":23,"wikidataId":"Q94","offsetEnd":30,"lang":"en","confidence":0.4481,"rawForm":"Android","boundingBoxes":[{"x":443.794,"h":8.9664,"y":536.239,"p":2,"w":30.4085}]},"version":{"offsetStart":89,"normalizedForm":"8.0","offsetEnd":92,"rawForm":"8.0","boundingBoxes":[{"x":472.491,"h":8.966400000000021,"y":547.198,"p":2,"w":10.105099999999993}]}},
  {"_key":"60c20e757723bebd8664588d","_id":"annotations/60c20e757723bebd8664588d","_rev":"_cfFmXbO---","wikipediaExternalRef":12610483,"document":{"$oid":"60c20e757723bebd86645889"},"context":"For eg., 25% of global Android users would be unable to use apps designed below Android 8.0 that was launched in 2017.","wikidataId":"Q94","type":"software","lang":"en","confidence":0.4481,"software-name":{"wikipediaExternalRef":12610483,"normalizedForm":"Android","offsetStart":81,"wikidataId":"Q94","offsetEnd":88,"lang":"en","confidence":0.4481,"rawForm":"Android","boundingBoxes":[{"x":440.858,"h":8.9664,"y":547.198,"p":2,"w":29.7706}]},"version":{"offsetStart":89,"normalizedForm":"8.0","offsetEnd":92,"rawForm":"8.0","boundingBoxes":[{"x":472.491,"h":8.966400000000021,"y":547.198,"p":2,"w":10.105099999999993}]}},
  {"_key":"60c20e7d7723bebd8664588f","_id":"annotations/60c20e7d7723bebd8664588f","_rev":"_cfFmXba---","wikipediaExternalRef":1852564,"document":{"$oid":"60c20e7d7723bebd8664588e"},"publisher":{"offsetStart":66,"normalizedForm":"Thermo Scientific","offsetEnd":83,"rawForm":"Thermo Scientific","boundingBoxes":[{"x":126.38647142857144,"h":8.820999999999998,"y":207.518,"p":3,"w":64.88877857142856}]},"context":"Noncompartmental analysis was performed in Kinetica version 5.1 (Thermo Scientific).","wikidataId":"Q4117112","type":"software","lang":"en","confidence":0.3254,"software-name":{"wikipediaExternalRef":1852564,"normalizedForm":"Kinetica","offsetStart":44,"wikidataId":"Q4117112","offsetEnd":52,"lang":"en","confidence":0.3254,"rawForm":"Kinetica","boundingBoxes":[{"x":42.9718,"h":8.821,"y":207.518,"p":3,"w":31.2143}]},"version":{"offsetStart":61,"normalizedForm":"5.1","offsetEnd":64,"rawForm":"5.1","boundingBoxes":[{"x":107.487,"h":8.820999999999998,"y":207.518,"p":3,"w":11.130399999999995}]}},
  {"_key":"60c20e7d7723bebd86645890","_id":"annotations/60c20e7d7723bebd86645890","_rev":"_cfFmXbm---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20e7d7723bebd8664588e"},"publisher":{"offsetStart":76,"normalizedForm":"STATA Corp","offsetEnd":86,"rawForm":"STATA Corp","boundingBoxes":[{"x":37.86878333333333,"h":8.821000000000026,"y":263.584,"p":3,"w":46.51721666666666}]},"context":"Statistical and graphical analyses were performed using STATA version 13 (STATA Corp.) and GraphPad Prism version 6.0 (GraphPad Software, Inc.).","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7367,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"STATA","offsetStart":57,"wikidataId":"Q1204300","offsetEnd":62,"lang":"en","confidence":0.7367,"rawForm":"STATA","boundingBoxes":[{"x":98.8716,"h":8.821,"y":252.641,"p":3,"w":29.0563}]},"version":{"offsetStart":71,"normalizedForm":"13","offsetEnd":73,"rawForm":"13","boundingBoxes":[{"x":161.744,"h":8.821,"y":252.641,"p":3,"w":9.0671}]}},
  {"_key":"60c20e7d7723bebd86645891","_id":"annotations/60c20e7d7723bebd86645891","_rev":"_cfFmXbu---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20e7d7723bebd8664588e"},"publisher":{"offsetStart":122,"normalizedForm":"GraphPad Software, Inc","offsetEnd":144,"rawForm":"GraphPad Software, Inc","boundingBoxes":[{"x":82.03627777777777,"h":8.821000000000026,"y":274.526,"p":3,"w":88.13787222222223}]},"context":"Statistical and graphical analyses were performed using STATA version 13 (STATA Corp.) and GraphPad Prism version 6.0 (GraphPad Software, Inc.).","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":93,"wikidataId":"Q5597066","offsetEnd":107,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":113.101,"h":8.821000000000026,"y":263.584,"p":3,"w":64.13839999999999}]},"version":{"offsetStart":117,"normalizedForm":"6.0","offsetEnd":120,"rawForm":"6.0","boundingBoxes":[{"x":63.0992,"h":8.821000000000026,"y":274.526,"p":3,"w":11.130400000000002}]}},
  {"_key":"60c20e7e7723bebd86645893","_id":"annotations/60c20e7e7723bebd86645893","_rev":"_cfFmXb6---","wikipediaExternalRef":179088,"document":{"$oid":"60c20e7e7723bebd86645892"},"publisher":{"offsetStart":79,"normalizedForm":"IBM Corp","offsetEnd":87,"rawForm":"IBM Corp","boundingBoxes":[{"x":242.282,"h":11.480000000000018,"y":257.755,"p":3,"w":38.369999999999976}]},"context":"All analyses were performed with IBM SPSS Statistics for Windows (Version 24, IBM Corp., Armonk, NY).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":38,"wikidataId":"Q181596","offsetEnd":42,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":72.3936,"h":11.48,"y":257.755,"p":3,"w":22.4}]},"version":{"offsetStart":75,"normalizedForm":"24","offsetEnd":77,"rawForm":"24","boundingBoxes":[{"x":227.302,"h":11.48,"y":257.755,"p":3,"w":8.399999999999999}]}},
  {"_key":"60c20e807723bebd86645895","_id":"annotations/60c20e807723bebd86645895","_rev":"_cfFmXcG---","wikipediaExternalRef":3235536,"document":{"$oid":"60c20e807723bebd86645894"},"context":"There was no restriction based on language of study and Google  Translate was used to convert studies from Chinese journals to English.","wikidataId":"Q135622","type":"software","confidence":0.8887,"software-name":{"wikipediaExternalRef":3235536,"normalizedForm":"Google Translate","offsetStart":56,"wikidataId":"Q135622","offsetEnd":74,"lang":"en","confidence":0.8887,"rawForm":"Google \n\nTranslate","boundingBoxes":[{"x":499.968,"h":10.536,"y":68.259,"p":5,"w":35.328},{"x":60,"h":10.536,"y":88.957,"p":5,"w":44.64}]},"lang":"en"},
  {"_key":"60c20e857723bebd86645897","_id":"annotations/60c20e857723bebd86645897","_rev":"_cfFmXcS---","document":{"$oid":"60c20e857723bebd86645896"},"type":"software","software-name":{"offsetStart":234,"normalizedForm":"NOVA","offsetEnd":238,"rawForm":"NOVA","boundingBoxes":[{"x":535.406,"h":8.8468,"y":421.605,"p":3,"w":22.2525}]},"context":"Cyclic voltammetry (CV) and elec- trochemical impedance spectroscopy were employed to characterize the LbL films and to detect the biomarker with a PGSTAT 204, Autolab electrochemical system (Eco Chimie, Netherlands), controlled by NOVA software."},
  {"_key":"60c20e887723bebd86645899","_id":"annotations/60c20e887723bebd86645899","_rev":"_cfFmXce---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20e887723bebd86645898"},"context":"El análisis estadístico se hizo con el programa Stata 14.2™ de la siguiente manera.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":48,"wikidataId":"Q1204300","offsetEnd":53,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":443.426,"h":9.43,"y":455.034,"p":3,"w":23.15}]},"version":{"offsetStart":54,"normalizedForm":"14.2","offsetEnd":58,"rawForm":"14.2","boundingBoxes":[{"x":469.356,"h":9.430000000000007,"y":455.034,"p":3,"w":29.060000000000002}]}},
  {"_key":"60c20e8c7723bebd8664589c","_id":"annotations/60c20e8c7723bebd8664589c","_rev":"_cfFmXcq---","document":{"$oid":"60c20e8c7723bebd8664589a"},"type":"software","software-name":{"offsetStart":64,"normalizedForm":"GetOldTweets","offsetEnd":76,"rawForm":"GetOldTweets","boundingBoxes":[{"x":331.883,"h":9,"y":492.721,"p":1,"w":57.52}]},"context":"Methods: We collected tweets on COVID-19 and dementia using the GetOldTweets application in Python from February 15 to September 7, 2020."},
  {"_key":"60c20e8c7723bebd8664589d","_id":"annotations/60c20e8c7723bebd8664589d","_rev":"_cfFmXc2---","wikipediaExternalRef":20268,"document":{"$oid":"60c20e8c7723bebd8664589a"},"publisher":{"offsetStart":96,"normalizedForm":"Microsoft Corporation","offsetEnd":119,"rawForm":"Microsoft \n\nCorporation","boundingBoxes":[{"x":253.143,"h":9,"y":774.566,"p":2,"w":38.493},{"x":303.638,"h":9,"y":72.366,"p":2,"w":47.355}]},"context":"This filtering procedure resulted in a total of 5063 tweets that were extracted into an Excel (Microsoft  Corporation) spreadsheet for qualitative line-by-line coding as the basis for thematic analysis.","wikidataId":"Q11272","type":"software","confidence":0.378,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Excel","offsetStart":89,"wikidataId":"Q11272","offsetEnd":94,"lang":"en","confidence":0.378,"rawForm":"Excel","boundingBoxes":[{"x":220.834,"h":9,"y":774.566,"p":2,"w":22.77}]},"lang":"en"},
  {"_key":"60c20e8c7723bebd8664589e","_id":"annotations/60c20e8c7723bebd8664589e","_rev":"_cfFmXdC---","wikipediaExternalRef":23862,"document":{"$oid":"60c20e8c7723bebd8664589a"},"context":"Methods: We collected tweets on COVID-19 and dementia using the GetOldTweets application in Python from February 15 to September 7, 2020.","wikidataId":"Q28865","references":[{"offsetStart":5116,"normalizedForm":"[14]","refKey":12,"label":"[14]","reference_id":{"$oid":"60c20e8c7723bebd8664589b"},"offsetEnd":5120,"boundingBoxes":[{"x":42.52,"h":9,"y":494.366,"p":2,"w":15.328000000000003}]}],"type":"software","confidence":0.6138,"software-name":{"wikipediaExternalRef":23862,"normalizedForm":"Python","offsetStart":92,"wikidataId":"Q28865","offsetEnd":98,"lang":"en","confidence":0.6138,"rawForm":"Python","boundingBoxes":[{"x":450.242,"h":9,"y":492.721,"p":1,"w":28.34}]},"lang":"en"},
  {"_key":"60c20e8c7723bebd8664589f","_id":"annotations/60c20e8c7723bebd8664589f","_rev":"_cfFmXdK---","document":{"$oid":"60c20e8c7723bebd8664589a"},"type":"software","software-name":{"offsetStart":295,"normalizedForm":"GetOldTweets","offsetEnd":307,"rawForm":"GetOldTweets","boundingBoxes":[{"x":42.52,"h":9,"y":482.366,"p":2,"w":57.52}]},"context":"We scraped tweets posted in the English language containing synonyms for dementia (eg, \"Alzheimer's disease\" and \"Lewy Body disease\") and synonyms for COVID-19 (including nontechnical phrases such as \"Corona\") during the period from February 15 to September 7, 2020, from Twitter using the GetOldTweets application programming interface in Python [14]."},
  {"_key":"60c20e8c7723bebd866458a0","_id":"annotations/60c20e8c7723bebd866458a0","_rev":"_cfFmXdW---","wikipediaExternalRef":23862,"document":{"$oid":"60c20e8c7723bebd8664589a"},"context":"We scraped tweets posted in the English language containing synonyms for dementia (eg, \"Alzheimer's disease\" and \"Lewy Body disease\") and synonyms for COVID-19 (including nontechnical phrases such as \"Corona\") during the period from February 15 to September 7, 2020, from Twitter using the GetOldTweets application programming interface in Python [14].","wikidataId":"Q28865","references":[{"offsetStart":5116,"normalizedForm":"[14]","refKey":12,"label":"[14]","reference_id":{"$oid":"60c20e8c7723bebd8664589b"},"offsetEnd":5120,"boundingBoxes":[{"x":42.52,"h":9,"y":494.366,"p":2,"w":15.328000000000003}]}],"type":"software","confidence":0.6138,"software-name":{"wikipediaExternalRef":23862,"normalizedForm":"Python","offsetStart":345,"wikidataId":"Q28865","offsetEnd":351,"lang":"en","confidence":0.6138,"rawForm":"Python","boundingBoxes":[{"x":263.295,"h":9,"y":482.366,"p":2,"w":28.34}]},"lang":"en"},
  {"_key":"60c20e8c7723bebd866458a2","_id":"annotations/60c20e8c7723bebd866458a2","_rev":"_cfFmXdi---","wikipediaExternalRef":16161443,"document":{"$oid":"60c20e8c7723bebd866458a1"},"context":"Apple and Google recently announced the joint development of a tool to track COVID-19 infection in a partnership aimed at ensuring in- teroperability between iOS and Android operat- ing systems.","wikidataId":"Q48493","type":"software","confidence":0.7161,"software-name":{"wikipediaExternalRef":16161443,"normalizedForm":"iOS","offsetStart":160,"wikidataId":"Q48493","offsetEnd":163,"lang":"en","confidence":0.7161,"rawForm":"iOS","boundingBoxes":[{"x":414.633,"h":8.73,"y":182.02,"p":2,"w":14.4239}]},"lang":"en"},
  {"_key":"60c20e8c7723bebd866458a3","_id":"annotations/60c20e8c7723bebd866458a3","_rev":"_cfFmXdu---","wikipediaExternalRef":12610483,"document":{"$oid":"60c20e8c7723bebd866458a1"},"context":"Apple and Google recently announced the joint development of a tool to track COVID-19 infection in a partnership aimed at ensuring in- teroperability between iOS and Android operat- ing systems.","wikidataId":"Q94","type":"software","confidence":0.4457,"software-name":{"wikipediaExternalRef":12610483,"normalizedForm":"Android","offsetStart":168,"wikidataId":"Q94","offsetEnd":175,"lang":"en","confidence":0.4457,"rawForm":"Android","boundingBoxes":[{"x":449.023,"h":8.73,"y":182.02,"p":2,"w":32.7181}]},"lang":"en"},
  {"_key":"60c20ea07723bebd866458a5","_id":"annotations/60c20ea07723bebd866458a5","_rev":"_cfFmXd6---","document":{"$oid":"60c20ea07723bebd866458a4"},"context":"We will use Review Manager 5 (RevMan5) soft- ware to assist with this process.","type":"software","software-name":{"offsetStart":12,"normalizedForm":"Review Manager","offsetEnd":26,"rawForm":"Review Manager","boundingBoxes":[{"x":144.398,"h":8.976699999999994,"y":244.722,"p":5,"w":67.68119999999999}]},"version":{"offsetStart":27,"normalizedForm":"5","offsetEnd":28,"rawForm":"5","boundingBoxes":[{"x":215.775,"h":8.9767,"y":244.722,"p":5,"w":4.8999}]}},
  {"_key":"60c20ea07723bebd866458a6","_id":"annotations/60c20ea07723bebd866458a6","_rev":"_cfFmXeC---","wikipediaExternalRef":1092923,"document":{"$oid":"60c20ea07723bebd866458a4"},"context":"We will carry out searches in Google/Google Scholar, and contact experts in the field, to access grey literature and other relevant work not retrieved through database searches.","wikidataId":"Q95","type":"software","confidence":0.3335,"software-name":{"wikipediaExternalRef":1092923,"normalizedForm":"Google","offsetStart":30,"wikidataId":"Q95","offsetEnd":36,"lang":"en","confidence":0.3335,"rawForm":"Google","boundingBoxes":[{"x":191.679,"h":8.9767,"y":316.724,"p":4,"w":28.50369230769231}]},"lang":"en"},
  {"_key":"60c20ea07723bebd866458a7","_id":"annotations/60c20ea07723bebd866458a7","_rev":"_cfFmXeO---","document":{"$oid":"60c20ea07723bebd866458a4"},"context":"We will use Review Manager 5 (RevMan5) soft- ware to assist with this process.","type":"software","software-name":{"offsetStart":30,"normalizedForm":"RevMan","offsetEnd":36,"rawForm":"RevMan","boundingBoxes":[{"x":229.33474444444445,"h":8.9767,"y":244.722,"p":5,"w":34.59921111111111}]},"version":{"offsetStart":36,"normalizedForm":"5","offsetEnd":37,"rawForm":"5","boundingBoxes":[{"x":229.33474444444445,"h":8.9767,"y":244.722,"p":5,"w":34.59921111111111}]}},
  {"_key":"60c20ea07723bebd866458a8","_id":"annotations/60c20ea07723bebd866458a8","_rev":"_cfFmXea---","document":{"$oid":"60c20ea07723bebd866458a4"},"type":"software","software-name":{"offsetStart":44,"normalizedForm":"Scholar","offsetEnd":51,"rawForm":"Scholar","boundingBoxes":[{"x":258.52,"h":8.9767,"y":316.724,"p":4,"w":28.0125125}]},"context":"We will carry out searches in Google/Google Scholar, and contact experts in the field, to access grey literature and other relevant work not retrieved through database searches."},
  {"_key":"60c20eac7723bebd866458aa","_id":"annotations/60c20eac7723bebd866458aa","_rev":"_cfFmXem---","wikipediaExternalRef":3524766,"document":{"$oid":"60c20eac7723bebd866458a9"},"context":"Cast/1YqKDLjXrzQKV); • YouTube (https://www.youtube.com/channel/","wikidataId":"Q866","type":"software","confidence":0.4534,"software-name":{"wikipediaExternalRef":3524766,"normalizedForm":"YouTube","offsetStart":24,"wikidataId":"Q866","offsetEnd":31,"lang":"en","confidence":0.4534,"rawForm":"YouTube","boundingBoxes":[{"x":320.308,"h":9.43,"y":281.074,"p":3,"w":37.98}]},"lang":"en"},
  {"_key":"60c20eac7723bebd866458ab","_id":"annotations/60c20eac7723bebd866458ab","_rev":"_cfFmXey---","wikipediaExternalRef":1092923,"document":{"$oid":"60c20eac7723bebd866458a9"},"context":"The lectures can be searched directly on Google or YouTube by typing the name of the lecture or of the speaker of interest followed by the word \"pathCast\" .","wikidataId":"Q95","type":"software","confidence":0.3333,"software-name":{"wikipediaExternalRef":1092923,"normalizedForm":"Google","offsetStart":41,"wikidataId":"Q95","offsetEnd":47,"lang":"en","confidence":0.3333,"rawForm":"Google","boundingBoxes":[{"x":244.038,"h":9.43,"y":496.114,"p":4,"w":32.24}]},"lang":"en"},
  {"_key":"60c20eac7723bebd866458ac","_id":"annotations/60c20eac7723bebd866458ac","_rev":"_cfFmXe6---","wikipediaExternalRef":3524766,"document":{"$oid":"60c20eac7723bebd866458a9"},"context":"The lectures can be searched directly on Google or YouTube by typing the name of the lecture or of the speaker of interest followed by the word \"pathCast\" .","wikidataId":"Q866","type":"software","confidence":0.4534,"software-name":{"wikipediaExternalRef":3524766,"normalizedForm":"YouTube","offsetStart":52,"wikidataId":"Q866","offsetEnd":59,"lang":"en","confidence":0.4534,"rawForm":"YouTube","boundingBoxes":[{"x":53.8583,"h":9.43,"y":508.154,"p":4,"w":37.98}]},"lang":"en"},
  {"_key":"60c20eae7723bebd866458ae","_id":"annotations/60c20eae7723bebd866458ae","_rev":"_cfFmXfG---","document":{"$oid":"60c20eae7723bebd866458ad"},"context":"The Parmap article describes a specific version of the Parmap library, the one that was used for the experiments reported in the article, so in order to support reproducibility of these results, we need to be able to pinpoint precisely the state(s) of the source code used in the article.","type":"software","software-name":{"offsetStart":4,"normalizedForm":"Parmap","offsetEnd":10,"rawForm":"Parmap","boundingBoxes":[{"x":74.4456,"h":8.9365,"y":433.385,"p":6,"w":34.2046}]},"url":{"offsetStart":130,"normalizedForm":".","offsetEnd":131,"rawForm":".","boundingBoxes":[{"x":322.4053846153846,"h":8.9365,"y":335.743,"p":6,"w":4.180153846153846}]}},
  {"_key":"60c20eae7723bebd866458af","_id":"annotations/60c20eae7723bebd866458af","_rev":"_cfFmXfS---","document":{"$oid":"60c20eae7723bebd866458ad"},"context":"This article introduced Parmap [12], an elegant library for multicore parallel programming that was distributed via the gitorious.org","type":"software","software-name":{"offsetStart":24,"normalizedForm":"Parmap","offsetEnd":30,"rawForm":"Parmap","boundingBoxes":[{"x":199.988,"h":8.4981,"y":324.458,"p":6,"w":31.3772}]},"url":{"offsetStart":130,"normalizedForm":".","offsetEnd":131,"rawForm":".","boundingBoxes":[{"x":322.4053846153846,"h":8.9365,"y":335.743,"p":6,"w":4.180153846153846}]}},
  {"_key":"60c20eae7723bebd866458b0","_id":"annotations/60c20eae7723bebd866458b0","_rev":"_cfFmXfe---","document":{"$oid":"60c20eae7723bebd866458ad"},"type":"software","software-name":{"offsetStart":29,"normalizedForm":"resarch","offsetEnd":36,"rawForm":"resarch","boundingBoxes":[{"x":329.48,"h":8.9365,"y":172.355,"p":2,"w":30.8243}]},"context":"Also, as remarked in [3,20], resarch software is often a thin layer on top of a large number of software dependencies that are developed and maintained outside of academia, so the usual approach based on institutional archives is not sufficient to cover all the software that is relevant for reproducibility of research."},
  {"_key":"60c20eae7723bebd866458b1","_id":"annotations/60c20eae7723bebd866458b1","_rev":"_cfFmXfq---","wikipediaExternalRef":29792844,"document":{"$oid":"60c20eae7723bebd866458ad"},"context":"Since April 2020, users of the BibLaTeX package can leverage the biblatex-software package [10], available on CTAN [8], to produce rich soft- ware bibliographies.","wikidataId":"Q4902993","type":"software","confidence":0.5102,"software-name":{"wikipediaExternalRef":29792844,"normalizedForm":"BibLaTeX","offsetStart":31,"wikidataId":"Q4902993","offsetEnd":39,"lang":"en","confidence":0.5102,"rawForm":"BibLaTeX","boundingBoxes":[{"x":226.267,"h":8.9365,"y":514.454,"p":8,"w":44.8207}]},"lang":"en"},
  {"_key":"60c20eae7723bebd866458b2","_id":"annotations/60c20eae7723bebd866458b2","_rev":"_cfFmXf2---","document":{"$oid":"60c20eae7723bebd866458ad"},"context":"The Parmap article describes a specific version of the Parmap library, the one that was used for the experiments reported in the article, so in order to support reproducibility of these results, we need to be able to pinpoint precisely the state(s) of the source code used in the article.","type":"software","software-name":{"offsetStart":55,"normalizedForm":"Parmap","offsetEnd":61,"rawForm":"Parmap","boundingBoxes":[{"x":294.238,"h":8.9365,"y":433.385,"p":6,"w":34.2046}]},"url":{"offsetStart":130,"normalizedForm":".","offsetEnd":131,"rawForm":".","boundingBoxes":[{"x":322.4053846153846,"h":8.9365,"y":335.743,"p":6,"w":4.180153846153846}]}},
  {"_key":"60c20eae7723bebd866458b3","_id":"annotations/60c20eae7723bebd866458b3","_rev":"_cfFmXg----","document":{"$oid":"60c20eae7723bebd866458ad"},"type":"software","software-name":{"offsetStart":66,"normalizedForm":"biblatex","offsetEnd":74,"rawForm":"biblatex","boundingBoxes":[{"x":53.5781,"h":8.4981,"y":527.074,"p":8,"w":41.835435294117644}]},"context":"Since April 2020, users of the BibLaTeX package can leverage the biblatex-software package [10], available on CTAN [8], to produce rich soft- ware bibliographies."},
  {"_key":"60c20eae7723bebd866458b4","_id":"annotations/60c20eae7723bebd866458b4","_rev":"_cfFmXgK---","document":{"$oid":"60c20eae7723bebd866458ad"},"context":"While practices in this area are still evolving, one can use the CodeMeta generator available at https:// codemeta.github.io/codemeta-generator/ to produces metadata conformant to the CodeMeta schema: the JSON-LD output can be put at the root of the project in a codemeta.json","type":"software","software-name":{"offsetStart":66,"normalizedForm":"CodeMeta generator","offsetEnd":84,"rawForm":"CodeMeta generator","boundingBoxes":[{"x":198.504,"h":8.936499999999995,"y":172.202,"p":5,"w":90.61610000000005}]},"url":{"offsetStart":98,"normalizedForm":"https:// codemeta.github.io/codemeta-generator","offsetEnd":145,"rawForm":"https:// \ncodemeta.github.io/codemeta-generator","boundingBoxes":[{"x":350.025,"h":8.936499999999995,"y":172.202,"p":5,"w":35.195899999999995},{"x":39.401,"h":8.936499999999995,"y":184.154,"p":5,"w":173.77731578947368}]}},
  {"_key":"60c20eae7723bebd866458b5","_id":"annotations/60c20eae7723bebd866458b5","_rev":"_cfFmXgW---","document":{"$oid":"60c20eae7723bebd866458ad"},"context":"Simple implementation of the distribution, fork, and recollection phases in Parmap (slightly  simplified from the the actual code in the version of Parmap used for this article)  Fig. 5.","type":"software","software-name":{"offsetStart":76,"normalizedForm":"Parmap","offsetEnd":82,"rawForm":"Parmap","boundingBoxes":[{"x":330.522,"h":6.9738,"y":303.897,"p":8,"w":22.236}]},"url":{"offsetStart":130,"normalizedForm":".","offsetEnd":131,"rawForm":".","boundingBoxes":[{"x":322.4053846153846,"h":8.9365,"y":335.743,"p":6,"w":4.180153846153846}]}},
  {"_key":"60c20eae7723bebd866458b6","_id":"annotations/60c20eae7723bebd866458b6","_rev":"_cfFmXgi---","wikipediaExternalRef":239392,"document":{"$oid":"60c20eae7723bebd866458ad"},"context":"Unfortunately, standard bibliography styles do not treat software as a first class citizen, and for example BibTeX users often resort to the @misc entry to this end, which is really unsatisfactory.","wikidataId":"Q8029","type":"software","confidence":0.7931,"software-name":{"wikipediaExternalRef":239392,"normalizedForm":"BibTeX","offsetStart":109,"wikidataId":"Q8029","offsetEnd":115,"lang":"en","confidence":0.7931,"rawForm":"BibTeX","boundingBoxes":[{"x":341.285,"h":8.9365,"y":490.541,"p":8,"w":33.6148}]},"lang":"en"},
  {"_key":"60c20eae7723bebd866458b7","_id":"annotations/60c20eae7723bebd866458b7","_rev":"_cfFmXgu---","document":{"$oid":"60c20eae7723bebd866458ad"},"context":"In our case, the article presented 29 lines of code, slightly edited from the 43 actual lines of code in the Parmap library: looking at Fig. 4a, one can easily see that some lines have been dropped (102-103, 118-121), one line has been split (117) and several lines simplified (127, 132-133, 137-142).","type":"software","software-name":{"offsetStart":110,"normalizedForm":"Parmap","offsetEnd":116,"rawForm":"Parmap","boundingBoxes":[{"x":154.643,"h":8.9365,"y":543.471,"p":7,"w":34.2006}]},"url":{"offsetStart":130,"normalizedForm":".","offsetEnd":131,"rawForm":".","boundingBoxes":[{"x":322.4053846153846,"h":8.9365,"y":335.743,"p":6,"w":4.180153846153846}]}},
  {"_key":"60c20eae7723bebd866458b8","_id":"annotations/60c20eae7723bebd866458b8","_rev":"_cfFmXg6---","document":{"$oid":"60c20eae7723bebd866458ad"},"context":"Simple implementation of the distribution, fork, and recollection phases in Parmap (slightly  simplified from the the actual code in the version of Parmap used for this article)  Fig. 5.","type":"software","software-name":{"offsetStart":149,"normalizedForm":"Parmap","offsetEnd":155,"rawForm":"Parmap","boundingBoxes":[{"x":252.995,"h":6.3671,"y":315.173,"p":8,"w":27.1316}]},"url":{"offsetStart":130,"normalizedForm":".","offsetEnd":131,"rawForm":".","boundingBoxes":[{"x":322.4053846153846,"h":8.9365,"y":335.743,"p":6,"w":4.180153846153846}]}},
  {"_key":"60c20eae7723bebd866458b9","_id":"annotations/60c20eae7723bebd866458b9","_rev":"_cfFmXhG---","document":{"$oid":"60c20eae7723bebd866458ad"},"publisher":{"offsetStart":210,"normalizedForm":"Software Heritage","offsetEnd":227,"rawForm":"Software Heritage","boundingBoxes":[{"x":299.26,"h":8.936500000000024,"y":368.771,"p":10,"w":76.15013333333337}]},"context":"An important consequence of the fact that SWH-IDs are intrinsic identifiers is that they can be generated and verified independently of Software Heritage, using swh-identify, an open source tool developed by Software Heritage, and distributed via PyPI as swh.model, with the stable version at the time of writing being this one.","type":"software","software-name":{"offsetStart":163,"normalizedForm":"swh-identify","offsetEnd":175,"rawForm":"swh-identify","boundingBoxes":[{"x":80.0187,"h":8.498100000000022,"y":369.438,"p":10,"w":60.478153846153845}]}},
  {"_key":"60c20eae7723bebd866458ba","_id":"annotations/60c20eae7723bebd866458ba","_rev":"_cfFmXhW---","document":{"$oid":"60c20eae7723bebd866458ad"},"context":"Among the initial collaborations that have been already established, we are happy to mention the cross linking with the curated mathematical software descriptions maintained by the swMath.org","type":"software","software-name":{"offsetStart":183,"normalizedForm":"swMath","offsetEnd":189,"rawForm":"swMath","boundingBoxes":[{"x":178.048,"h":8.4981,"y":93.3276,"p":11,"w":31.37682}]},"url":{"offsetStart":189,"normalizedForm":".org","offsetEnd":193,"rawForm":".org","boundingBoxes":[{"x":209.42482,"h":8.498100000000008,"y":93.3276,"p":11,"w":20.917879999999997}]}},
  {"_key":"60c20eae7723bebd866458bb","_id":"annotations/60c20eae7723bebd866458bb","_rev":"_cfFmXhi---","document":{"$oid":"60c20eae7723bebd866458ad"},"type":"software","software-name":{"offsetStart":187,"normalizedForm":"CodeMeta","offsetEnd":195,"rawForm":"CodeMeta","boundingBoxes":[{"x":58.1785,"h":8.9365,"y":196.106,"p":5,"w":44.8187}]},"context":"While practices in this area are still evolving, one can use the CodeMeta generator available at https:// codemeta.github.io/codemeta-generator/ to produces metadata conformant to the CodeMeta schema: the JSON-LD output can be put at the root of the project in a codemeta.json"},
  {"_key":"60c20eae7723bebd866458bc","_id":"annotations/60c20eae7723bebd866458bc","_rev":"_cfFmXhy---","wikipediaExternalRef":24193668,"document":{"$oid":"60c20eae7723bebd866458ad"},"context":"An important consequence of the fact that SWH-IDs are intrinsic identifiers is that they can be generated and verified independently of Software Heritage, using swh-identify, an open source tool developed by Software Heritage, and distributed via PyPI as swh.model, with the stable version at the time of writing being this one.","wikidataId":"Q2984686","type":"software","confidence":0.7339,"software-name":{"wikipediaExternalRef":24193668,"normalizedForm":"PyPI","offsetStart":250,"wikidataId":"Q2984686","offsetEnd":254,"lang":"en","confidence":0.7339,"rawForm":"PyPI","boundingBoxes":[{"x":119.464,"h":8.9365,"y":380.723,"p":10,"w":22.4208}]},"lang":"en"},
  {"_key":"60c20eae7723bebd866458bd","_id":"annotations/60c20eae7723bebd866458bd","_rev":"_cfFmXi----","document":{"$oid":"60c20eae7723bebd866458ad"},"type":"software","software-name":{"offsetStart":409,"normalizedForm":"Artifact Review and Badging","offsetEnd":436,"rawForm":"Artifact Review and Badging","boundingBoxes":[{"x":56.3145,"h":9.095899999999972,"y":445.075,"p":1,"w":124.73709999999997}]},"context":"Many research communities focus on the issue of scientific reproducibility and strongly encourage making the source code of the artefact available by archiving it in publicly-accessible long-term archives; some have even put in place mecha- nisms to assess research software, like the Artefact Evaluation process introduced in 2011 and now widely adopted by many computer science conferences [7], and the Artifact Review and Badging program of the ACM [4]."},
  {"_key":"60c20eb37723bebd866458bf","_id":"annotations/60c20eb37723bebd866458bf","_rev":"_cfFmXiK---","wikipediaExternalRef":179088,"document":{"$oid":"60c20eb37723bebd866458be"},"publisher":{"offsetStart":17,"normalizedForm":"IBM","offsetEnd":20,"rawForm":"IBM","boundingBoxes":[{"x":268.94,"h":12.4978,"y":67.1008,"p":5,"w":21.3239}]},"context":"(2020-06-22) and IBM ® SPSS ® Statistics for Windows ® ver 20 were  used for data analysis.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":23,"wikidataId":"Q181596","offsetEnd":27,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":298.818,"h":12.4978,"y":67.1008,"p":5,"w":25.1017}]},"version":{"offsetStart":59,"normalizedForm":"20","offsetEnd":61,"rawForm":"20","boundingBoxes":[{"x":461.099,"h":12.4978,"y":67.1008,"p":5,"w":11.2853}]}},
  {"_key":"60c20eb77723bebd866458c1","_id":"annotations/60c20eb77723bebd866458c1","_rev":"_cfFmXiW---","document":{"$oid":"60c20eb77723bebd866458c0"},"context":"The tree was drawn using the neighbor joining program with the HKY distance formula using PAUP 4.0.","type":"software","software-name":{"offsetStart":91,"normalizedForm":"PAUP","offsetEnd":95,"rawForm":"PAUP","boundingBoxes":[{"x":187.912,"h":8.2891,"y":582.769,"p":4,"w":20.9252}]},"version":{"offsetStart":96,"normalizedForm":"4.0","offsetEnd":99,"rawForm":"4.0","boundingBoxes":[{"x":211.582,"h":8.289099999999962,"y":582.769,"p":4,"w":9.618825000000015}]}},
  {"_key":"60c20ec27723bebd866458c3","_id":"annotations/60c20ec27723bebd866458c3","_rev":"_cfFmXii---","wikipediaExternalRef":4294204,"document":{"$oid":"60c20ec27723bebd866458c2"},"publisher":{"offsetStart":17,"normalizedForm":"MedCalc","offsetEnd":24,"rawForm":"MedCalc","boundingBoxes":[{"x":272.4996625,"h":9.584,"y":375.142,"p":11,"w":36.845637499999995}]},"context":"MedCalc package (MedCalc ® version 16.8.4;","wikidataId":"Q4272521","type":"software","lang":"en","confidence":0.7574,"software-name":{"wikipediaExternalRef":4294204,"normalizedForm":"MedCalc","offsetStart":0,"wikidataId":"Q4272521","offsetEnd":7,"lang":"en","confidence":0.7574,"rawForm":"MedCalc","boundingBoxes":[{"x":188.524,"h":9.584,"y":375.142,"p":11,"w":38.8581}]},"version":{"offsetStart":35,"normalizedForm":"16.8.4","offsetEnd":41,"rawForm":"16.8.4","boundingBoxes":[{"x":351.902,"h":9.584000000000003,"y":375.142,"p":11,"w":23.013599999999997}]}},
  {"_key":"60c20ec27723bebd866458c4","_id":"annotations/60c20ec27723bebd866458c4","_rev":"_cfFmXiu---","document":{"$oid":"60c20ec27723bebd866458c2"},"publisher":{"offsetStart":67,"normalizedForm":"Becton Dickinson","offsetEnd":83,"rawForm":"Becton Dickinson","boundingBoxes":[{"x":442.8111,"h":9.584000000000003,"y":261.866,"p":11,"w":72.41681999999992}]},"context":"Flow cytometry data were analyzed using FacsDiva software v6.1.3","type":"software","software-name":{"offsetStart":41,"normalizedForm":"FacsDiva","offsetEnd":49,"rawForm":"FacsDiva","boundingBoxes":[{"x":328.065,"h":9.584,"y":261.866,"p":11,"w":39.8633}]},"version":{"offsetStart":60,"normalizedForm":"6.1.3","offsetEnd":65,"rawForm":"6.1.3","boundingBoxes":[{"x":410.437,"h":9.584000000000003,"y":261.866,"p":11,"w":25.221900000000005}]}},
  {"_key":"60c20ec67723bebd866458c6","_id":"annotations/60c20ec67723bebd866458c6","_rev":"_cfFmXi6---","wikipediaExternalRef":179088,"document":{"$oid":"60c20ec67723bebd866458c5"},"publisher":{"offsetStart":25,"normalizedForm":"IBM","offsetEnd":28,"rawForm":"IBM","boundingBoxes":[{"x":419.31744,"h":8.8468,"y":400.683,"p":3,"w":11.79732}]},"context":"SPSS version 26 for MAC (IBM, Armonk, NY, USA) was used for statistical analysis.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":0,"wikidataId":"Q181596","offsetEnd":4,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":318.554,"h":8.8468,"y":400.683,"p":3,"w":17.072}]},"version":{"offsetStart":13,"normalizedForm":"26","offsetEnd":15,"rawForm":"26","boundingBoxes":[{"x":368.387,"h":8.8468,"y":400.683,"p":3,"w":8.9743}]}},
  {"_key":"60c20ed47723bebd866458c8","_id":"annotations/60c20ed47723bebd866458c8","_rev":"_cfFmXjG---","document":{"$oid":"60c20ed47723bebd866458c7"},"publisher":{"offsetStart":194,"normalizedForm":"Alpinion Medical Systems","offsetEnd":219,"rawForm":"Alpinion Medical \nSystems","boundingBoxes":[{"x":461.7841555555555,"h":8.97670000000005,"y":688.742,"p":2,"w":76.7257444444445},{"x":304.724,"h":8.9767,"y":700.76,"p":2,"w":30.415174999999998}]},"context":"The instrument set of included a needle (16 G), a blunt dissector, an ultrasound device (Alpinion ECube15) with an 8-to 17-MHz linear transducer and the Needle Vision Plus™ software package (Alpinion Medical Systems, Bothell, WA, USA) (Fig. 2).","type":"software","software-name":{"offsetStart":155,"normalizedForm":"Needle Vision Plus™","offsetEnd":175,"rawForm":"Needle \nVision Plus™","boundingBoxes":[{"x":510.181,"h":8.9767,"y":676.723,"p":2,"w":28.3413},{"x":304.724,"h":8.97670000000005,"y":688.742,"p":2,"w":57.48059999999998}]}},
  {"_key":"60c20ed57723bebd866458ca","_id":"annotations/60c20ed57723bebd866458ca","_rev":"_cfFmXjS---","document":{"$oid":"60c20ed57723bebd866458c9"},"context":"All analyses were conducted using statistical software SPPS version 17.0.","type":"software","software-name":{"offsetStart":56,"normalizedForm":"SPPS","offsetEnd":60,"rawForm":"SPPS","boundingBoxes":[{"x":353.025,"h":9.2296,"y":559.24,"p":3,"w":23.1842}]},"version":{"offsetStart":69,"normalizedForm":"17.0","offsetEnd":73,"rawForm":"17.0","boundingBoxes":[{"x":419.015,"h":9.229600000000005,"y":559.24,"p":3,"w":16.800160000000005}]}},
  {"_key":"60c20edc7723bebd866458d1","_id":"annotations/60c20edc7723bebd866458d1","_rev":"_cfFmXje---","document":{"$oid":"60c20edc7723bebd866458cb"},"context":"Primers were designed using PerlPrimer v1.21 (Smp_089320_ qF1 ATTGGATGGTTACATAGCAACTAC, qR1 CCATGGATCATTTGATTTGGGT) and assayed for efficiency at 1:0, 1:5, 1:25, and 1:100 cDNA concentrations.","type":"software","software-name":{"offsetStart":28,"normalizedForm":"PerlPrimer","offsetEnd":38,"rawForm":"PerlPrimer","boundingBoxes":[{"x":432.622,"h":8.5,"y":129.873,"p":5,"w":44.09}]},"version":{"offsetStart":40,"normalizedForm":"1.21","offsetEnd":44,"rawForm":"1.21","boundingBoxes":[{"x":478.94,"h":8.5,"y":129.873,"p":5,"w":21.08000000000004}]}},
  {"_key":"60c20edc7723bebd866458d2","_id":"annotations/60c20edc7723bebd866458d2","_rev":"_cfFmXjq---","document":{"$oid":"60c20edc7723bebd866458cb"},"type":"software","software-name":{"offsetStart":44,"normalizedForm":"Chimera","offsetEnd":51,"rawForm":"Chimera","boundingBoxes":[{"x":334.089,"h":8.5,"y":318.603,"p":5,"w":32.62875}]},"context":"Molecular visualization was performed with Chimera, Maestro and VMD [38, 40, 41]."},
  {"_key":"60c20edc7723bebd866458d3","_id":"annotations/60c20edc7723bebd866458d3","_rev":"_cfFmXj2---","document":{"$oid":"60c20edc7723bebd866458cb"},"context":"All modeling studies were performed with the Schro ¨dinger suite (version 2015-4) [38] except molecular dynamics simulations that were performed using GROMACS 5.1.2","references":[{"offsetStart":17545,"normalizedForm":"[38]","refKey":38,"label":"[38]","reference_id":{"$oid":"60c20edc7723bebd866458cc"},"offsetEnd":17550,"boundingBoxes":[{"x":526.391,"h":8.5,"y":292.582,"p":5,"w":16.32000000000005}]}],"type":"software","software-name":{"offsetStart":45,"normalizedForm":"Schro ¨dinger suite","offsetEnd":64,"rawForm":"Schro ¨dinger suite","boundingBoxes":[{"x":384.659,"h":8.5,"y":292.582,"p":5,"w":70.08699999999999}]},"version":{"offsetStart":74,"normalizedForm":"2015-4","offsetEnd":80,"rawForm":"2015-4","boundingBoxes":[{"x":491.865,"h":8.5,"y":292.582,"p":5,"w":27.720000000000027}]}},
  {"_key":"60c20edc7723bebd866458d4","_id":"annotations/60c20edc7723bebd866458d4","_rev":"_cfFmXkC---","document":{"$oid":"60c20edc7723bebd866458cb"},"type":"software","software-name":{"offsetStart":53,"normalizedForm":"Maestro","offsetEnd":60,"rawForm":"Maestro","boundingBoxes":[{"x":373.604,"h":8.5,"y":318.603,"p":5,"w":32.86}]},"context":"Molecular visualization was performed with Chimera, Maestro and VMD [38, 40, 41]."},
  {"_key":"60c20edc7723bebd866458d5","_id":"annotations/60c20edc7723bebd866458d5","_rev":"_cfFmXkK---","document":{"$oid":"60c20edc7723bebd866458cb"},"type":"software","software-name":{"offsetStart":56,"normalizedForm":"R script","offsetEnd":64,"rawForm":"R script","boundingBoxes":[{"x":423.834,"h":8.5,"y":187.757,"p":6,"w":30.826999999999998}]},"context":"Survival tests and curves were generated using a custom R script implementing the survival package [44] or Prism (version 8)."},
  {"_key":"60c20edc7723bebd866458d6","_id":"annotations/60c20edc7723bebd866458d6","_rev":"_cfFmXkW---","wikipediaExternalRef":633423,"document":{"$oid":"60c20edc7723bebd866458cb"},"context":"Molecular visualization was performed with Chimera, Maestro and VMD [38, 40, 41].","wikidataId":"Q7936565","references":[{"offsetStart":17704,"normalizedForm":"[38","refKey":38,"label":"[38,","reference_id":{"$oid":"60c20edc7723bebd866458cc"},"offsetEnd":17716,"boundingBoxes":[{"x":451.443,"h":8.5,"y":318.603,"p":5,"w":42.73599999999999}]},{"offsetStart":17704,"normalizedForm":"40","refKey":40,"label":"40,","reference_id":{"$oid":"60c20edc7723bebd866458cd"},"offsetEnd":17716,"boundingBoxes":[{"x":451.443,"h":8.5,"y":318.603,"p":5,"w":42.73599999999999}]},{"offsetStart":17704,"normalizedForm":"41]","refKey":41,"label":"41]","reference_id":{"$oid":"60c20edc7723bebd866458ce"},"offsetEnd":17716,"boundingBoxes":[{"x":451.443,"h":8.5,"y":318.603,"p":5,"w":42.73599999999999}]}],"type":"software","confidence":0.558,"software-name":{"wikipediaExternalRef":633423,"normalizedForm":"VMD","offsetStart":65,"wikidataId":"Q7936565","offsetEnd":68,"lang":"en","confidence":0.558,"rawForm":"VMD","boundingBoxes":[{"x":425.988,"h":8.5,"y":318.603,"p":5,"w":23.23}]},"lang":"en"},
  {"_key":"60c20edc7723bebd866458d7","_id":"annotations/60c20edc7723bebd866458d7","_rev":"_cfFmXki---","document":{"$oid":"60c20edc7723bebd866458cb"},"context":"The plausible complexes were generated using the docking engine Glide [43].","references":[{"offsetStart":18504,"normalizedForm":"[43]","refKey":43,"label":"[43]","reference_id":{"$oid":"60c20edc7723bebd866458cf"},"offsetEnd":18508,"boundingBoxes":[{"x":326.096,"h":8.5,"y":468.272,"p":5,"w":14.855999999999995}]}],"type":"software","software-name":{"offsetStart":65,"normalizedForm":"Glide","offsetEnd":70,"rawForm":"Glide","boundingBoxes":[{"x":302.115,"h":8.5,"y":468.272,"p":5,"w":21.8}]}},
  {"_key":"60c20edc7723bebd866458d8","_id":"annotations/60c20edc7723bebd866458d8","_rev":"_cfFmXku---","document":{"$oid":"60c20edc7723bebd866458cb"},"type":"software","software-name":{"offsetStart":79,"normalizedForm":"ConfGen","offsetEnd":86,"rawForm":"ConfGen","boundingBoxes":[{"x":538.353,"h":8.5,"y":676.277,"p":5,"w":36.92}]},"context":"To enumerate possible biologically relevant conformations of CIDD-0072229, the ConfGen utility from the Schro ¨dinger suite was applied [43]."},
  {"_key":"60c20edc7723bebd866458d9","_id":"annotations/60c20edc7723bebd866458d9","_rev":"_cfFmXk6---","document":{"$oid":"60c20edc7723bebd866458cb"},"type":"software","software-name":{"offsetStart":84,"normalizedForm":"ConfGen","offsetEnd":91,"rawForm":"ConfGen","boundingBoxes":[{"x":279.438,"h":8.5,"y":529.16,"p":9,"w":36.92}]},"context":"Superposition of the docking conformation with the lowest energy conformation from ConfGen returned a root-mean-square-deviation of 1.2 Å which supports the model (Fig 5C)."},
  {"_key":"60c20edc7723bebd866458da","_id":"annotations/60c20edc7723bebd866458da","_rev":"_cfFmXlG---","document":{"$oid":"60c20edc7723bebd866458cb"},"context":"Survival tests and curves were generated using a custom R script implementing the survival package [44] or Prism (version 8).","type":"software","software-name":{"offsetStart":108,"normalizedForm":"Prism","offsetEnd":113,"rawForm":"Prism","boundingBoxes":[{"x":263.621,"h":8.5,"y":200.739,"p":6,"w":23.77}]},"version":{"offsetStart":123,"normalizedForm":"8","offsetEnd":124,"rawForm":"8","boundingBoxes":[{"x":324.565,"h":8.5,"y":200.739,"p":6,"w":3.4766666666666666}]}},
  {"_key":"60c20edc7723bebd866458db","_id":"annotations/60c20edc7723bebd866458db","_rev":"_cfFmXlS---","document":{"$oid":"60c20edc7723bebd866458cb"},"type":"software","software-name":{"offsetStart":142,"normalizedForm":"ConfGen","offsetEnd":149,"rawForm":"ConfGen","boundingBoxes":[{"x":219.967,"h":8.5,"y":516.121,"p":9,"w":36.92}]},"context":"To validate the docking pose of CIDD-0072229, we compared its conformation against a set of conformations generated without a receptor with ConfGen tool [46]."},
  {"_key":"60c20edc7723bebd866458dc","_id":"annotations/60c20edc7723bebd866458dc","_rev":"_cfFmXle---","wikipediaExternalRef":306766,"document":{"$oid":"60c20edc7723bebd866458cb"},"context":"All modeling studies were performed with the Schro ¨dinger suite (version 2015-4) [38] except molecular dynamics simulations that were performed using GROMACS 5.1.2","wikidataId":"Q905302","references":[{"offsetStart":17629,"normalizedForm":"[39]","refKey":39,"label":"[39]","reference_id":{"$oid":"60c20edc7723bebd866458d0"},"offsetEnd":17633,"boundingBoxes":[{"x":510.12,"h":8.5,"y":305.621,"p":5,"w":14.856000000000108}]}],"type":"software","lang":"en","confidence":0.8007,"software-name":{"wikipediaExternalRef":306766,"normalizedForm":"GROMACS","offsetStart":152,"wikidataId":"Q905302","offsetEnd":159,"lang":"en","confidence":0.8007,"rawForm":"GROMACS","boundingBoxes":[{"x":438.914,"h":8.5,"y":305.621,"p":5,"w":47.96}]},"version":{"offsetStart":160,"normalizedForm":"5.1.2","offsetEnd":165,"rawForm":"5.1.2","boundingBoxes":[{"x":489.144,"h":8.5,"y":305.621,"p":5,"w":18.789999999999964}]}},
  {"_key":"60c20ee27723bebd866458e6","_id":"annotations/60c20ee27723bebd866458e6","_rev":"_cfFmXlq---","wikipediaExternalRef":3867229,"document":{"$oid":"60c20ee27723bebd866458dd"},"context":"These include RePast 3.1/Simphony (North and Macal 2007 ) , MASON (Luke et al. 2005 ) , NetLogo (Wilensky and Rand in press ) and Swarm (Minar et al. 1996 ) .","wikidataId":"Q7313917","type":"software","lang":"en","confidence":0.5345,"software-name":{"wikipediaExternalRef":3867229,"normalizedForm":"RePast","offsetStart":14,"wikidataId":"Q7313917","offsetEnd":20,"lang":"en","confidence":0.5345,"rawForm":"RePast","boundingBoxes":[{"x":298.196,"h":9,"y":266.138,"p":9,"w":27.63}]},"version":{"offsetStart":21,"normalizedForm":"3.1","offsetEnd":24,"rawForm":"3.1","boundingBoxes":[{"x":329.267,"h":9,"y":266.138,"p":9,"w":14.0625}]}},
  {"_key":"60c20ee27723bebd866458e7","_id":"annotations/60c20ee27723bebd866458e7","_rev":"_cfFmXl2---","document":{"$oid":"60c20ee27723bebd866458dd"},"context":"These include RePast 3.1/Simphony (North and Macal 2007 ) , MASON (Luke et al. 2005 ) , NetLogo (Wilensky and Rand in press ) and Swarm (Minar et al. 1996 ) .","references":[{"offsetStart":25697,"normalizedForm":"North and Macal 2007","refKey":59,"label":"(North and Macal 2007 )","reference_id":{"$oid":"60c20ee27723bebd866458de"},"offsetEnd":25721,"boundingBoxes":[{"x":53.858,"h":9,"y":278.138,"p":9,"w":95.636}]}],"type":"software","software-name":{"offsetStart":25,"normalizedForm":"Simphony","offsetEnd":33,"rawForm":"Simphony","boundingBoxes":[{"x":348.017,"h":9,"y":266.138,"p":9,"w":37.5}]}},
  {"_key":"60c20ee27723bebd866458e8","_id":"annotations/60c20ee27723bebd866458e8","_rev":"_cfFmXm----","wikipediaExternalRef":30526821,"document":{"$oid":"60c20ee27723bebd866458dd"},"context":"These include RePast 3.1/Simphony (North and Macal 2007 ) , MASON (Luke et al. 2005 ) , NetLogo (Wilensky and Rand in press ) and Swarm (Minar et al. 1996 ) .","wikidataId":"Q6714517","references":[{"offsetStart":25729,"normalizedForm":"Luke et al. 2005","refKey":47,"label":"(Luke et al. 2005 )","reference_id":{"$oid":"60c20ee27723bebd866458df"},"offsetEnd":25749,"boundingBoxes":[{"x":192.248,"h":9,"y":278.138,"p":9,"w":70.26600000000002}]}],"type":"software","confidence":0.389,"software-name":{"wikipediaExternalRef":30526821,"normalizedForm":"MASON","offsetStart":61,"wikidataId":"Q6714517","offsetEnd":66,"lang":"en","confidence":0.389,"rawForm":"MASON","boundingBoxes":[{"x":154.066,"h":9,"y":278.138,"p":9,"w":36.11}]},"lang":"en"},
  {"_key":"60c20ee27723bebd866458e9","_id":"annotations/60c20ee27723bebd866458e9","_rev":"_cfFmXmK---","document":{"$oid":"60c20ee27723bebd866458dd"},"context":"Widely-used software includes Pajek (de Nooy et al. 2005 ) , ORA (Carley et al. 2007 ) , StOCNET (Boer et al. 2006 ) and UCINet (Borgatti et al. 2004 ) (for a list of social network analysis software, see for example Wikipedia's entry under \"Social network analysis software\").","references":[{"offsetStart":25331,"normalizedForm":"Carley et al. 2007","refKey":20,"label":"(Carley et al. 2007 )","reference_id":{"$oid":"60c20ee27723bebd866458e0"},"offsetEnd":25353,"boundingBoxes":[{"x":232.912,"h":9,"y":218.138,"p":9,"w":79.43999999999997}]}],"type":"software","software-name":{"offsetStart":62,"normalizedForm":"ORA","offsetEnd":65,"rawForm":"ORA","boundingBoxes":[{"x":208.691,"h":9,"y":218.138,"p":9,"w":21.11}]}},
  {"_key":"60c20ee27723bebd866458ea","_id":"annotations/60c20ee27723bebd866458ea","_rev":"_cfFmXmW---","document":{"$oid":"60c20ee27723bebd866458dd"},"context":"Dedicated net- work modeling and analysis libraries such as the Java Universal Network/Graph library (JUNG) (O'Madadhain et al. 2005 ) ; the R Project packages statnet, sna, and igraph are to be used for more computationally-extensive handling of network data generated by ABMs.","references":[{"offsetStart":26121,"normalizedForm":"O'Madadhain et al. 2005","refKey":60,"label":"(O'Madadhain et al. 2005 )","reference_id":{"$oid":"60c20ee27723bebd866458e1"},"offsetEnd":26148,"boundingBoxes":[{"x":117.414,"h":9,"y":338.138,"p":9,"w":106.16800000000002}]}],"type":"software","software-name":{"offsetStart":64,"normalizedForm":"Java Universal Network/Graph library (JUNG)","offsetEnd":108,"rawForm":"Java Universal Network/Graph \nlibrary (JUNG)","boundingBoxes":[{"x":259.726,"h":9,"y":326.138,"p":9,"w":125.79200000000003},{"x":53.858,"h":9,"y":338.138,"p":9,"w":61.213000000000015}]}},
  {"_key":"60c20ee27723bebd866458eb","_id":"annotations/60c20ee27723bebd866458eb","_rev":"_cfFmXmi---","wikipediaExternalRef":593757,"document":{"$oid":"60c20ee27723bebd866458dd"},"context":"These include RePast 3.1/Simphony (North and Macal 2007 ) , MASON (Luke et al. 2005 ) , NetLogo (Wilensky and Rand in press ) and Swarm (Minar et al. 1996 ) .","wikidataId":"Q672307","type":"software","confidence":0.8018,"software-name":{"wikipediaExternalRef":593757,"normalizedForm":"NetLogo","offsetStart":89,"wikidataId":"Q672307","offsetEnd":96,"lang":"en","confidence":0.8018,"rawForm":"NetLogo","boundingBoxes":[{"x":267.086,"h":9,"y":278.138,"p":9,"w":35.55}]},"lang":"en"},
  {"_key":"60c20ee27723bebd866458ec","_id":"annotations/60c20ee27723bebd866458ec","_rev":"_cfFmXmu---","document":{"$oid":"60c20ee27723bebd866458dd"},"context":"Widely-used software includes Pajek (de Nooy et al. 2005 ) , ORA (Carley et al. 2007 ) , StOCNET (Boer et al. 2006 ) and UCINet (Borgatti et al. 2004 ) (for a list of social network analysis software, see for example Wikipedia's entry under \"Social network analysis software\").","references":[{"offsetStart":25363,"normalizedForm":"Boer et al. 2006","refKey":12,"label":"(Boer et al. 2006 )","reference_id":{"$oid":"60c20ee27723bebd866458e2"},"offsetEnd":25384,"boundingBoxes":[{"x":362.744,"h":9,"y":218.138,"p":9,"w":22.769999999999982},{"x":53.858,"h":9,"y":230.138,"p":9,"w":45.72690000000001}]}],"type":"software","software-name":{"offsetStart":90,"normalizedForm":"StOCNET","offsetEnd":97,"rawForm":"StOCNET","boundingBoxes":[{"x":317.963,"h":9,"y":218.138,"p":9,"w":41.67}]}},
  {"_key":"60c20ee27723bebd866458ed","_id":"annotations/60c20ee27723bebd866458ed","_rev":"_cfFmXm6---","document":{"$oid":"60c20ee27723bebd866458dd"},"type":"software","software-name":{"offsetStart":109,"normalizedForm":"DyNetML","offsetEnd":116,"rawForm":"DyNetML","boundingBoxes":[{"x":251.315,"h":9,"y":122.138,"p":9,"w":41.66}]},"context":"Two of the most widely adopted data formats used for social networks are GraphML (Brandes et al. 2004 ) and DyNetML (Tsvetovat 2005 ) , both based on XML."},
  {"_key":"60c20ee27723bebd866458ee","_id":"annotations/60c20ee27723bebd866458ee","_rev":"_cfFmXnG---","document":{"$oid":"60c20ee27723bebd866458dd"},"context":"Widely-used software includes Pajek (de Nooy et al. 2005 ) , ORA (Carley et al. 2007 ) , StOCNET (Boer et al. 2006 ) and UCINet (Borgatti et al. 2004 ) (for a list of social network analysis software, see for example Wikipedia's entry under \"Social network analysis software\").","references":[{"offsetStart":25395,"normalizedForm":"(Borgatti et al. 2004","refKey":13,"label":"(Borgatti et al. 2004","reference_id":{"$oid":"60c20ee27723bebd866458e3"},"offsetEnd":25417,"boundingBoxes":[{"x":153.848,"h":9,"y":230.138,"p":9,"w":81.02599999999998}]}],"type":"software","software-name":{"offsetStart":123,"normalizedForm":"UCINet","offsetEnd":129,"rawForm":"UCINet","boundingBoxes":[{"x":119.472,"h":9,"y":230.138,"p":9,"w":31.65}]}},
  {"_key":"60c20ee27723bebd866458ef","_id":"annotations/60c20ee27723bebd866458ef","_rev":"_cfFmXnS---","document":{"$oid":"60c20ee27723bebd866458dd"},"context":"These include RePast 3.1/Simphony (North and Macal 2007 ) , MASON (Luke et al. 2005 ) , NetLogo (Wilensky and Rand in press ) and Swarm (Minar et al. 1996 ) .","references":[{"offsetStart":25800,"normalizedForm":"Minar et al. 1996","refKey":51,"label":"(Minar et al. 1996 )","reference_id":{"$oid":"60c20ee27723bebd866458e4"},"offsetEnd":25821,"boundingBoxes":[{"x":140.512,"h":9,"y":290.138,"p":9,"w":76.983}]}],"type":"software","software-name":{"offsetStart":132,"normalizedForm":"Swarm","offsetEnd":137,"rawForm":"Swarm","boundingBoxes":[{"x":109.301,"h":9,"y":290.138,"p":9,"w":28.23}]}},
  {"_key":"60c20ee27723bebd866458f0","_id":"annotations/60c20ee27723bebd866458f0","_rev":"_cfFmXne---","document":{"$oid":"60c20ee27723bebd866458dd"},"type":"software","software-name":{"offsetStart":134,"normalizedForm":"DyNetML","offsetEnd":141,"rawForm":"DyNetML","boundingBoxes":[{"x":341.352,"h":9,"y":374.138,"p":9,"w":38.64}]},"context":"Social network analysis software and APIs provide an inter- face to read/write social network data in data formats such as GraphML or DyNetML."},
  {"_key":"60c20ee27723bebd866458f1","_id":"annotations/60c20ee27723bebd866458f1","_rev":"_cfFmXnq---","wikipediaExternalRef":376707,"document":{"$oid":"60c20ee27723bebd866458dd"},"context":"Dedicated net- work modeling and analysis libraries such as the Java Universal Network/Graph library (JUNG) (O'Madadhain et al. 2005 ) ; the R Project packages statnet, sna, and igraph are to be used for more computationally-extensive handling of network data generated by ABMs.","wikidataId":"Q206904","type":"software","confidence":0.511,"software-name":{"wikipediaExternalRef":376707,"normalizedForm":"R Project","offsetStart":142,"wikidataId":"Q206904","offsetEnd":151,"lang":"en","confidence":0.511,"rawForm":"R Project","boundingBoxes":[{"x":243.268,"h":9,"y":338.138,"p":9,"w":37.34299999999999}]},"lang":"en"},
  {"_key":"60c20ee27723bebd866458f2","_id":"annotations/60c20ee27723bebd866458f2","_rev":"_cfFmXn2---","wikipediaExternalRef":30526821,"document":{"$oid":"60c20ee27723bebd866458dd"},"context":"Dunham ( 2005 ) demonstrated an implementation of the spread of three viruses using a spatially-explicit agent-based epidemiological model developed in MASON.","wikidataId":"Q6714517","references":[{"offsetStart":33279,"normalizedForm":"Huang et al. ( 2010 )","refKey":42,"label":"Huang et al. ( 2010 )","reference_id":{"$oid":"60c20ee27723bebd866458e5"},"offsetEnd":33301,"boundingBoxes":[{"x":53.858,"h":9,"y":470.158,"p":11,"w":79.91300000000001}]}],"type":"software","confidence":0.389,"software-name":{"wikipediaExternalRef":30526821,"normalizedForm":"MASON","offsetStart":153,"wikidataId":"Q6714517","offsetEnd":158,"lang":"en","confidence":0.389,"rawForm":"MASON","boundingBoxes":[{"x":347.214,"h":9,"y":458.158,"p":11,"w":31.970833333333335}]},"lang":"en"},
  {"_key":"60c20ee27723bebd866458f3","_id":"annotations/60c20ee27723bebd866458f3","_rev":"_cfFmXoC---","document":{"$oid":"60c20ee27723bebd866458dd"},"type":"software","software-name":{"offsetStart":161,"normalizedForm":"statnet","offsetEnd":168,"rawForm":"statnet","boundingBoxes":[{"x":321.947,"h":9,"y":338.138,"p":9,"w":25.033749999999998}]},"context":"Dedicated net- work modeling and analysis libraries such as the Java Universal Network/Graph library (JUNG) (O'Madadhain et al. 2005 ) ; the R Project packages statnet, sna, and igraph are to be used for more computationally-extensive handling of network data generated by ABMs."},
  {"_key":"60c20ee27723bebd866458f4","_id":"annotations/60c20ee27723bebd866458f4","_rev":"_cfFmXoO---","document":{"$oid":"60c20ee27723bebd866458dd"},"type":"software","software-name":{"offsetStart":170,"normalizedForm":"sna","offsetEnd":173,"rawForm":"sna","boundingBoxes":[{"x":352.9,"h":9,"y":338.138,"p":9,"w":11.8725}]},"context":"Dedicated net- work modeling and analysis libraries such as the Java Universal Network/Graph library (JUNG) (O'Madadhain et al. 2005 ) ; the R Project packages statnet, sna, and igraph are to be used for more computationally-extensive handling of network data generated by ABMs."},
  {"_key":"60c20ee27723bebd866458f5","_id":"annotations/60c20ee27723bebd866458f5","_rev":"_cfFmXoa---","document":{"$oid":"60c20ee27723bebd866458dd"},"type":"software","software-name":{"offsetStart":180,"normalizedForm":"igraph","offsetEnd":186,"rawForm":"igraph","boundingBoxes":[{"x":53.858,"h":9,"y":350.138,"p":9,"w":25.55}]},"context":"Dedicated net- work modeling and analysis libraries such as the Java Universal Network/Graph library (JUNG) (O'Madadhain et al. 2005 ) ; the R Project packages statnet, sna, and igraph are to be used for more computationally-extensive handling of network data generated by ABMs."},
  {"_key":"60c20ee57723bebd866458f7","_id":"annotations/60c20ee57723bebd866458f7","_rev":"_cfFmXom---","wikipediaExternalRef":3524766,"document":{"$oid":"60c20ee57723bebd866458f6"},"context":"These results mimicked other studies on school websites, which have generally shown that schools link to free, generic, non-pedagogical tools, like YouTube, much more than fee-based or education-specific tools, like SchoolTube (Kimmons 2015; Kimmons et al. 2019).","wikidataId":"Q866","type":"software","confidence":0.4534,"software-name":{"wikipediaExternalRef":3524766,"normalizedForm":"YouTube","offsetStart":150,"wikidataId":"Q866","offsetEnd":157,"lang":"en","confidence":0.4534,"rawForm":"YouTube","boundingBoxes":[{"x":478.029,"h":8.7472,"y":434.926,"p":3,"w":35.2177875}]},"lang":"en"},
  {"_key":"60c20ee57723bebd866458f8","_id":"annotations/60c20ee57723bebd866458f8","_rev":"_cfFmXoy---","wikipediaExternalRef":1520204,"document":{"$oid":"60c20ee57723bebd866458f6"},"context":"To understand the topics educational technology researchers have been studying over the past 5 years, I used the Elsevier Scopus (n.d.) API to collect all articles from the most-highly- cited journals in the field of educational technology as identi- fied by Google Scholar (n.d.), which included TechTrends, Computers & Education, Educational Technology Research & Development, and 13 others.","wikidataId":"Q494817","type":"software","confidence":0.9596,"software-name":{"wikipediaExternalRef":1520204,"normalizedForm":"Google Scholar","offsetStart":261,"wikidataId":"Q494817","offsetEnd":275,"lang":"en","confidence":0.9596,"rawForm":"Google Scholar","boundingBoxes":[{"x":83.2247,"h":8.74720000000002,"y":532.95,"p":2,"w":62.055099999999996}]},"lang":"en"},
  {"_key":"60c20eed7723bebd866458fa","_id":"annotations/60c20eed7723bebd866458fa","_rev":"_cfFmXp----","wikipediaExternalRef":21572326,"document":{"$oid":"60c20eed7723bebd866458f9"},"context":"All statistical analyses were performed in GraphPad Prism version 6, as defined in the text and figure legends.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":43,"wikidataId":"Q5597066","offsetEnd":57,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":459.44,"h":7.91719999999998,"y":268.395,"p":9,"w":60.56819999999999}]},"version":{"offsetStart":67,"normalizedForm":"6","offsetEnd":68,"rawForm":"6","boundingBoxes":[{"x":301.89,"h":7.9172,"y":278.373,"p":9,"w":3.1696}]}},
  {"_key":"60c20ef57723bebd866458fe","_id":"annotations/60c20ef57723bebd866458fe","_rev":"_cfFmXpK---","document":{"$oid":"60c20ef57723bebd866458fb"},"context":"dplyr (0.8.3), tidyr  (1.0.2) and lubridate (1.7.4).","type":"software","software-name":{"offsetStart":0,"normalizedForm":"dplyr","offsetEnd":5,"rawForm":"dplyr","boundingBoxes":[{"x":442.99,"h":11.04,"y":396.41,"p":33,"w":22.9191}]},"version":{"offsetStart":7,"normalizedForm":"0.8.3","offsetEnd":12,"rawForm":"0.8.3","boundingBoxes":[{"x":472.43025,"h":11.04000000000002,"y":396.41,"p":33,"w":19.851249999999993}]}},
  {"_key":"60c20ef57723bebd866458ff","_id":"annotations/60c20ef57723bebd866458ff","_rev":"_cfFmXpW---","document":{"$oid":"60c20ef57723bebd866458fb"},"context":"openxlsx (4.1.4),","type":"software","software-name":{"offsetStart":0,"normalizedForm":"openxlsx","offsetEnd":8,"rawForm":"openxlsx","boundingBoxes":[{"x":367.03,"h":11.04,"y":396.41,"p":33,"w":39.3466}]},"version":{"offsetStart":10,"normalizedForm":"4.1.4","offsetEnd":15,"rawForm":"4.1.4","boundingBoxes":[{"x":412.74645000000004,"h":11.04000000000002,"y":396.41,"p":33,"w":19.782249999999976}]}},
  {"_key":"60c20ef57723bebd86645900","_id":"annotations/60c20ef57723bebd86645900","_rev":"_cfFmXpi---","document":{"$oid":"60c20ef57723bebd866458fb"},"context":"dplyr (0.8.3), tidyr  (1.0.2) and lubridate (1.7.4).","type":"software","software-name":{"offsetStart":15,"normalizedForm":"tidyr","offsetEnd":22,"rawForm":"tidyr","boundingBoxes":[{"x":502.66,"h":11.04,"y":396.41,"p":33,"w":20.8901}]},"version":{"offsetStart":24,"normalizedForm":"1.0.2","offsetEnd":29,"rawForm":"1.0.2","boundingBoxes":[{"x":76.16714285714286,"h":11.04000000000002,"y":423.17,"p":33,"w":20.715714285714284}]}},
  {"_key":"60c20ef57723bebd86645901","_id":"annotations/60c20ef57723bebd86645901","_rev":"_cfFmXpu---","wikipediaExternalRef":24666773,"document":{"$oid":"60c20ef57723bebd866458fb"},"publisher":{"offsetStart":36,"normalizedForm":"Becton Dickinson","offsetEnd":52,"rawForm":"Becton Dickinson","boundingBoxes":[{"x":386.97354285714283,"h":11.039999999999964,"y":635.83,"p":37,"w":73.10411714285715}]},"context":"Data were analysed with FlowJo v10 (Becton Dickinson, Wokingham,  UK).","wikidataId":"Q5462055","type":"software","lang":"en","confidence":0.4725,"software-name":{"wikipediaExternalRef":24666773,"normalizedForm":"FlowJo","offsetStart":24,"wikidataId":"Q5462055","offsetEnd":30,"lang":"en","confidence":0.4725,"rawForm":"FlowJo","boundingBoxes":[{"x":331.154,"h":11.04,"y":635.83,"p":37,"w":30.5366}]},"version":{"offsetStart":32,"normalizedForm":"10","offsetEnd":34,"rawForm":"10","boundingBoxes":[{"x":363.788,"h":11.04,"y":635.83,"p":37,"w":16.1515}]}},
  {"_key":"60c20ef57723bebd86645902","_id":"annotations/60c20ef57723bebd86645902","_rev":"_cfFmXp6---","document":{"$oid":"60c20ef57723bebd866458fb"},"publisher":{"offsetStart":43,"normalizedForm":"EdgeR","offsetEnd":48,"rawForm":"EdgeR","boundingBoxes":[{"x":131.5351,"h":11.04,"y":181.46,"p":39,"w":24.5955}]},"context":"Counts were filtered using  filterByExpr (EdgeR) with a gene count threshold of 10 CPM and the minimum number of samples set  at the size of the smallest disease group.","type":"software","software-name":{"offsetStart":29,"normalizedForm":"filterByExpr","offsetEnd":41,"rawForm":"filterByExpr","boundingBoxes":[{"x":72.024,"h":11.04,"y":181.46,"p":39,"w":52.2082}]}},
  {"_key":"60c20ef57723bebd86645903","_id":"annotations/60c20ef57723bebd86645903","_rev":"_cfFmXqG---","document":{"$oid":"60c20ef57723bebd866458fb"},"context":"Alignment was performed using HISAT2 v.2.1.0","references":[{"offsetStart":95013,"normalizedForm":"Kim et al., 2019","refKey":17,"label":"(Kim et al., 2019)","reference_id":{"$oid":"60c20ef57723bebd866458fd"},"offsetEnd":95034,"boundingBoxes":[{"x":503.26,"h":11.039999999999964,"y":701.86,"p":38,"w":20.21429999999998},{"x":72.024,"h":11.039999999999964,"y":728.62,"p":38,"w":52.52820000000001}]}],"type":"software","software-name":{"offsetStart":30,"normalizedForm":"HISAT2","offsetEnd":36,"rawForm":"HISAT2","boundingBoxes":[{"x":436.92,"h":11.039999999999964,"y":701.86,"p":38,"w":32.016099999999994}]},"version":{"offsetStart":39,"normalizedForm":"2.1.0","offsetEnd":44,"rawForm":"2.1.0","boundingBoxes":[{"x":479.59542857142856,"h":11.039999999999964,"y":701.86,"p":38,"w":21.488571428571447}]}},
  {"_key":"60c20ef57723bebd86645904","_id":"annotations/60c20ef57723bebd86645904","_rev":"_cfFmXqS---","document":{"$oid":"60c20ef57723bebd866458fb"},"publisher":{"offsetStart":49,"normalizedForm":"Babraham Bioinformatics","offsetEnd":72,"rawForm":"Babraham Bioinformatics","boundingBoxes":[{"x":409.5749111111111,"h":11.039999999999964,"y":621.19,"p":38,"w":109.37831555555567}]},"context":"Read quality was assessed using FastQC v.0.11.8 (Babraham Bioinformatics,  UK), and SMARTer adaptors trimmed and residual rRNA reads depleted in silico using Trim_galore  v.0.6.4 (Babraham Bioinformatics, UK) and BBSplit (BBMap v.38.67(BBMap -Bushnell B. - sourceforge.net/projects/bbmap/)),","type":"software","software-name":{"offsetStart":32,"normalizedForm":"FastQC","offsetEnd":38,"rawForm":"FastQC","boundingBoxes":[{"x":332.016,"h":11.04,"y":621.19,"p":38,"w":31.6737}]},"version":{"offsetStart":41,"normalizedForm":"0.11.8","offsetEnd":47,"rawForm":"0.11.8","boundingBoxes":[{"x":374.97769999999997,"h":11.039999999999964,"y":621.19,"p":38,"w":26.67810000000003}]}},
  {"_key":"60c20ef57723bebd86645905","_id":"annotations/60c20ef57723bebd86645905","_rev":"_cfFmXqa---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":33,"normalizedForm":"ComplexHeatmap","offsetEnd":47,"rawForm":"ComplexHeatmap","boundingBoxes":[{"x":229.489,"h":11.04,"y":590.35,"p":41,"w":80.1835}]},"context":"Heat maps were created using the ComplexHeatmap package (Gu et al., 2016), with data scaled and  centred prior to visualisation."},
  {"_key":"60c20ef57723bebd86645906","_id":"annotations/60c20ef57723bebd86645906","_rev":"_cfFmXqm---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":35,"normalizedForm":"lubridate","offsetEnd":44,"rawForm":"lubridate","boundingBoxes":[{"x":122.9,"h":11.04,"y":423.17,"p":33,"w":40.6492}]},"context":"dplyr (0.8.3), tidyr  (1.0.2) and lubridate (1.7.4)."},
  {"_key":"60c20ef57723bebd86645907","_id":"annotations/60c20ef57723bebd86645907","_rev":"_cfFmXqy---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":37,"normalizedForm":"sPLS-DA","offsetEnd":44,"rawForm":"sPLS-DA","boundingBoxes":[{"x":125.137,"h":11.039999999999992,"y":100.94,"p":30,"w":36.308599999999984}]},"context":"D) Thirteen cell types  selected by sPLS-DA as most informative in predictive models discriminating patients in clusters 1  and 2. Bars indicate loading coefficient weights of selected features (ranked from most to least  informative in cluster prediction, from bottom to top)."},
  {"_key":"60c20ef57723bebd86645908","_id":"annotations/60c20ef57723bebd86645908","_rev":"_cfFmXr----","document":{"$oid":"60c20ef57723bebd866458fb"},"publisher":{"offsetStart":56,"normalizedForm":"EdgeR","offsetEnd":61,"rawForm":"EdgeR","boundingBoxes":[{"x":76.9557142857143,"h":11.04,"y":235.22,"p":39,"w":24.658571428571427}]},"context":"Library counts were normalised using calcNormFactors  (EdgeR) using the method 'weighted trimmed mean of M-values'.","type":"software","software-name":{"offsetStart":37,"normalizedForm":"calcNormFactors","offsetEnd":54,"rawForm":"calcNormFactors","boundingBoxes":[{"x":448.038,"h":11.04,"y":208.34,"p":39,"w":75.2156}]}},
  {"_key":"60c20ef57723bebd86645909","_id":"annotations/60c20ef57723bebd86645909","_rev":"_cfFmXrK---","document":{"$oid":"60c20ef57723bebd866458fb"},"publisher":{"offsetStart":82,"normalizedForm":"Verity Software House","offsetEnd":105,"rawForm":"Verity Software \n\nHouse","boundingBoxes":[{"x":454.9201428571429,"h":11.04000000000002,"y":454.01,"p":36,"w":68.56595714285709},{"x":72.024,"h":11.04,"y":480.79,"p":36,"w":25.879666666666665}]},"context":"FCS files generated were analysed using the Maxpar Pathsetter software v2.0.45 (Verity Software  House, Topsham, ME).","type":"software","software-name":{"offsetStart":44,"normalizedForm":"Maxpar Pathsetter","offsetEnd":63,"rawForm":"Maxpar Pathsetter","boundingBoxes":[{"x":269.838,"h":11.04000000000002,"y":454.01,"p":36,"w":101.18939999999998}]},"version":{"offsetStart":74,"normalizedForm":"2.0.45","offsetEnd":80,"rawForm":"2.0.45","boundingBoxes":[{"x":415.344,"h":11.04000000000002,"y":454.01,"p":36,"w":32.85509999999999}]}},
  {"_key":"60c20ef57723bebd8664590a","_id":"annotations/60c20ef57723bebd8664590a","_rev":"_cfFmXrW---","document":{"$oid":"60c20ef57723bebd866458fb"},"context":"Data were merged from the various  data sources using R version 3.6 and the R packages readr (1.3.1),","type":"software","software-name":{"offsetStart":77,"normalizedForm":"R packages readr","offsetEnd":93,"rawForm":"R packages readr","boundingBoxes":[{"x":254.21,"h":11.04000000000002,"y":396.41,"p":33,"w":76.0934}]},"version":{"offsetStart":95,"normalizedForm":"1.3.1","offsetEnd":100,"rawForm":"1.3.1","boundingBoxes":[{"x":336.80025,"h":11.04000000000002,"y":396.41,"p":33,"w":19.851249999999993}]}},
  {"_key":"60c20ef57723bebd8664590b","_id":"annotations/60c20ef57723bebd8664590b","_rev":"_cfFmXri---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":79,"normalizedForm":"plsda","offsetEnd":84,"rawForm":"plsda","boundingBoxes":[{"x":324.53,"h":11.04,"y":321.77,"p":41,"w":21.766571428571428}]},"context":"Partial least squares  discriminant analysis (PLS-DA) was conducted using the plsda() function from the package mixOmics  (Rohart et al., 2017), a supervised method of sample discrimination whereby sample clustering is  informed by group membership (here patient clusters 1 and 2)."},
  {"_key":"60c20ef57723bebd8664590c","_id":"annotations/60c20ef57723bebd8664590c","_rev":"_cfFmXru---","document":{"$oid":"60c20ef57723bebd866458fb"},"context":"Samples were  acquired using a Fluidigm Helios mass cytometer and normalised using the CyTOF Software v6.7.1016.","type":"software","software-name":{"offsetStart":88,"normalizedForm":"CyTOF","offsetEnd":93,"rawForm":"CyTOF","boundingBoxes":[{"x":403.577,"h":11.04,"y":426.41,"p":36,"w":28.5715}]},"version":{"offsetStart":104,"normalizedForm":"6.7.1016","offsetEnd":112,"rawForm":"6.7.1016","boundingBoxes":[{"x":476.617,"h":11.04000000000002,"y":426.41,"p":36,"w":42.09885000000003}]}},
  {"_key":"60c20ef57723bebd8664590d","_id":"annotations/60c20ef57723bebd8664590d","_rev":"_cfFmXr6---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":97,"normalizedForm":"nlme","offsetEnd":103,"rawForm":"nlme","boundingBoxes":[{"x":501.34,"h":11.04,"y":235.22,"p":40,"w":22.08}]},"context":"Longitudinal mixed modelling of gene module changes over time (𝑦 𝑖𝑗 ) was conducted using the nlme  package in R (Pinheiro J et al., 2020), including time (𝑡 𝑖𝑗 ) with a quadratic trend and disease severity  category or unsupervised cluster ids (𝑋 𝑗 ) as fixed effects, and sampled individuals as random effects  (𝑢 𝑗 ):  Gene set enrichment analysis (GSEA) (Subramanian et al., 2005) was used to identify biological  pathways enriched in COVID-19 severity groups relative to healthy controls."},
  {"_key":"60c20ef57723bebd8664590e","_id":"annotations/60c20ef57723bebd8664590e","_rev":"_cfFmXsG---","document":{"$oid":"60c20ef57723bebd866458fb"},"publisher":{"offsetStart":132,"normalizedForm":"Autoimmun Diagnostika GmbH","offsetEnd":158,"rawForm":"Autoimmun Diagnostika GmbH","boundingBoxes":[{"x":77.69967,"h":11.039999999999992,"y":181.46,"p":38,"w":134.32241}]},"context":"Developed plates were read using an  AID iSpot reader (Oxford Biosystems, Oxford, UK) and counted using AID EliSpot v7 software  (Autoimmun Diagnostika GmbH, Strasberg, Germany).","type":"software","software-name":{"offsetStart":105,"normalizedForm":"AID EliSpot","offsetEnd":116,"rawForm":"AID EliSpot","boundingBoxes":[{"x":409.637,"h":11.039999999999992,"y":154.58,"p":38,"w":52.274699999999996}]},"version":{"offsetStart":118,"normalizedForm":"7","offsetEnd":119,"rawForm":"7","boundingBoxes":[{"x":467.442,"h":11.04,"y":154.58,"p":38,"w":10.5212}]}},
  {"_key":"60c20ef57723bebd8664590f","_id":"annotations/60c20ef57723bebd8664590f","_rev":"_cfFmXsS---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":113,"normalizedForm":"mixOmics","offsetEnd":123,"rawForm":"mixOmics","boundingBoxes":[{"x":480.1,"h":11.04,"y":321.77,"p":41,"w":43.3983}]},"context":"Partial least squares  discriminant analysis (PLS-DA) was conducted using the plsda() function from the package mixOmics  (Rohart et al., 2017), a supervised method of sample discrimination whereby sample clustering is  informed by group membership (here patient clusters 1 and 2)."},
  {"_key":"60c20ef57723bebd86645910","_id":"annotations/60c20ef57723bebd86645910","_rev":"_cfFmXsa---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":153,"normalizedForm":"Hmisc","offsetEnd":158,"rawForm":"Hmisc","boundingBoxes":[{"x":359.32396666666665,"h":11.04,"y":275.512,"p":42,"w":25.474833333333336}]},"context":"The relationships between immunophenotyping and transcriptional data in the form of gene  expression modules were assessed using Pearson's correlation (Hmisc package) and visualized with  corrplot."},
  {"_key":"60c20ef57723bebd86645911","_id":"annotations/60c20ef57723bebd86645911","_rev":"_cfFmXsm---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":154,"normalizedForm":"mixOmics","offsetEnd":162,"rawForm":"mixOmics","boundingBoxes":[{"x":316.49,"h":11.04,"y":187.46,"p":41,"w":43.3983}]},"context":"Principal component analysis (PCA) of centred and scaled absolute counts for 24 major cell types was  conducted using the pca()function from the package mixOmics (Rohart et al., 2017)."},
  {"_key":"60c20ef57723bebd86645912","_id":"annotations/60c20ef57723bebd86645912","_rev":"_cfFmXsy---","wikipediaExternalRef":24666773,"document":{"$oid":"60c20ef57723bebd866458fb"},"publisher":{"offsetStart":36,"normalizedForm":"Becton Dickinson","offsetEnd":52,"rawForm":"Becton Dickinson","boundingBoxes":[{"x":386.97354285714283,"h":11.039999999999964,"y":635.83,"p":37,"w":73.10411714285715}]},"context":"is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Samples were gated in FlowJo v10.2 according to the schema set out in Figure S8.","wikidataId":"Q5462055","type":"software","lang":"en","confidence":0.4725,"software-name":{"wikipediaExternalRef":24666773,"normalizedForm":"FlowJo","offsetStart":158,"wikidataId":"Q5462055","offsetEnd":164,"lang":"en","confidence":0.4725,"rawForm":"FlowJo","boundingBoxes":[{"x":174.707,"h":11.04,"y":100.94,"p":36,"w":30.5588}]},"version":{"offsetStart":166,"normalizedForm":"10.2","offsetEnd":170,"rawForm":"10.2","boundingBoxes":[{"x":207.584,"h":11.039999999999992,"y":100.94,"p":36,"w":24.453599999999994}]}},
  {"_key":"60c20ef57723bebd86645913","_id":"annotations/60c20ef57723bebd86645913","_rev":"_cfFmXt----","document":{"$oid":"60c20ef57723bebd866458fb"},"publisher":{"offsetStart":182,"normalizedForm":"Babraham Bioinformatics","offsetEnd":205,"rawForm":"Babraham Bioinformatics","boundingBoxes":[{"x":115.05338888888889,"h":11.039999999999964,"y":674.98,"p":38,"w":114.39333111111111}]},"context":"Read quality was assessed using FastQC v.0.11.8 (Babraham Bioinformatics,  UK), and SMARTer adaptors trimmed and residual rRNA reads depleted in silico using Trim_galore  v.0.6.4 (Babraham Bioinformatics, UK) and BBSplit (BBMap v.38.67(BBMap -Bushnell B. - sourceforge.net/projects/bbmap/)),","type":"software","software-name":{"offsetStart":159,"normalizedForm":"Trim_galore","offsetEnd":172,"rawForm":"Trim_galore","boundingBoxes":[{"x":469.177,"h":11.04,"y":648.07,"p":38,"w":54.096}]},"version":{"offsetStart":175,"normalizedForm":"0.6.4","offsetEnd":180,"rawForm":"0.6.4","boundingBoxes":[{"x":80.61314285714286,"h":11.039999999999964,"y":674.98,"p":38,"w":21.47285714285715}]}},
  {"_key":"60c20ef57723bebd86645914","_id":"annotations/60c20ef57723bebd86645914","_rev":"_cfFmXtK---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":172,"normalizedForm":"Rsubreads","offsetEnd":181,"rawForm":"Rsubreads","boundingBoxes":[{"x":244.13929,"h":11.04,"y":74.04,"p":39,"w":44.93061}]},"context":"is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint were generated using featureCounts (Rsubreads package -(Liao et al., 2019) and stored as a DGEList  object (EdgeR package (Robinson et al., 2010) for further analysis."},
  {"_key":"60c20ef57723bebd86645915","_id":"annotations/60c20ef57723bebd86645915","_rev":"_cfFmXtW---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":190,"normalizedForm":"corrplot","offsetEnd":198,"rawForm":"corrplot","boundingBoxes":[{"x":72.024,"h":11.04,"y":302.364,"p":42,"w":34.51351111111111}]},"context":"The relationships between immunophenotyping and transcriptional data in the form of gene  expression modules were assessed using Pearson's correlation (Hmisc package) and visualized with  corrplot."},
  {"_key":"60c20ef57723bebd86645916","_id":"annotations/60c20ef57723bebd86645916","_rev":"_cfFmXti---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":215,"normalizedForm":"BBSplit","offsetEnd":222,"rawForm":"BBSplit","boundingBoxes":[{"x":289.228,"h":11.04,"y":674.98,"p":38,"w":31.5413}]},"context":"Read quality was assessed using FastQC v.0.11.8 (Babraham Bioinformatics,  UK), and SMARTer adaptors trimmed and residual rRNA reads depleted in silico using Trim_galore  v.0.6.4 (Babraham Bioinformatics, UK) and BBSplit (BBMap v.38.67(BBMap -Bushnell B. - sourceforge.net/projects/bbmap/)),"},
  {"_key":"60c20ef57723bebd86645917","_id":"annotations/60c20ef57723bebd86645917","_rev":"_cfFmXtu---","document":{"$oid":"60c20ef57723bebd866458fb"},"type":"software","software-name":{"offsetStart":245,"normalizedForm":"EdgeR","offsetEnd":250,"rawForm":"EdgeR","boundingBoxes":[{"x":107.78318333333333,"h":11.04,"y":100.94,"p":39,"w":26.005916666666668}]},"context":"is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint were generated using featureCounts (Rsubreads package -(Liao et al., 2019) and stored as a DGEList  object (EdgeR package (Robinson et al., 2010) for further analysis."},
  {"_key":"60c20ef57723bebd86645918","_id":"annotations/60c20ef57723bebd86645918","_rev":"_cfFmXt6---","document":{"$oid":"60c20ef57723bebd866458fb"},"context":"Latent factors were generated by  leveraging off pre-existing knowledge of cell specific pathways.To better understand the relationship  between gene expression and clinical severity, weighted gene co-expression network analysis was  carried out using the WGCNA package (Langfelder and Horvath, 2008) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint matrix was generated and a soft thresholding power was chosen to impose approximate scale-free  topology.","type":"software","software-name":{"offsetStart":259,"normalizedForm":"WGCNA","offsetEnd":264,"rawForm":"WGCNA","boundingBoxes":[{"x":166.338,"h":11.04,"y":751.536,"p":39,"w":36.0235}]},"url":{"offsetStart":-34,"normalizedForm":"http://gobie.csb.pitt.edu/PLIER","offsetEnd":-3,"rawForm":"http://gobie.csb.pitt.edu/PLIER","boundingBoxes":[{"x":215.9900588235294,"h":11.039999999999964,"y":671.02,"p":39,"w":136.02982352941171}]}},
  {"_key":"60c20ef67723bebd8664591a","_id":"annotations/60c20ef67723bebd8664591a","_rev":"_cfFmXuG---","document":{"$oid":"60c20ef67723bebd86645919"},"type":"software","software-name":{"offsetStart":40,"normalizedForm":"SimHe","offsetEnd":45,"rawForm":"SimHe","boundingBoxes":[{"x":201.992,"h":7.5318,"y":340.702,"p":5,"w":24.7114}]},"context":"Step 1: outline the Jia-character using SimHe font, with its height (W2) approximately equal to 0.6 k 2.6G and set the length (Rb) of the R-patch roughly to 0.5 k 3.4G , where k 2.6G and k 3.4G are free-space wavelengths at 2.6 and 3.4 GHz, respectively."},
  {"_key":"60c20efa7723bebd8664591c","_id":"annotations/60c20efa7723bebd8664591c","_rev":"_cfFmXuS---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"ProtParam","offsetEnd":9,"rawForm":"ProtParam","boundingBoxes":[{"x":50.061,"h":8.8468,"y":572.348,"p":4,"w":37.3957}]},"context":"ProtParam tool [39] was applied for analyzing the physical and chemical properties of MEPVC such as amino acid composition, esti- mated half-life, instability index, extinction coefficient, theoretical pl, atomic composition, molecular weight, and grand average of hydro- pathicity (GRAVY) to assist experimental studies."},
  {"_key":"60c20efa7723bebd8664591d","_id":"annotations/60c20efa7723bebd8664591d","_rev":"_cfFmXue---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":4,"normalizedForm":"antechamber","offsetEnd":15,"rawForm":"antechamber","boundingBoxes":[{"x":392.368,"h":8.8468,"y":436.342,"p":4,"w":45.7563}]},"context":"The antechamber program [49] was used to build the libraries and parameters for the TLR4 and vaccine construct."},
  {"_key":"60c20efa7723bebd8664591e","_id":"annotations/60c20efa7723bebd8664591e","_rev":"_cfFmXuq---","wikipediaExternalRef":363695,"document":{"$oid":"60c20efa7723bebd8664591b"},"context":"Again, a BLASTp search against the Mouse (Mus musculus, taxonomy id: 10090) was performed using host non- similar proteins keeping the input parameters E score cut-off 0.005, bit score > 100, and identity < 30% [11].","wikidataId":"Q286820","type":"software","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTp","offsetStart":9,"wikidataId":"Q286820","offsetEnd":15,"lang":"en","confidence":0.708,"rawForm":"BLASTp","boundingBoxes":[{"x":435.174,"h":8.8468,"y":132.982,"p":3,"w":27.8077}]},"lang":"en"},
  {"_key":"60c20efa7723bebd8664591f","_id":"annotations/60c20efa7723bebd8664591f","_rev":"_cfFmXu2---","document":{"$oid":"60c20efa7723bebd8664591b"},"context":"module [56] of AMBER16 was castoff.","type":"software","software-name":{"offsetStart":15,"normalizedForm":"AMBER","offsetEnd":20,"rawForm":"AMBER","boundingBoxes":[{"x":92.4655,"h":8.8468,"y":101.63,"p":5,"w":35.9691}]},"version":{"offsetStart":20,"normalizedForm":"16","offsetEnd":22,"rawForm":"16","boundingBoxes":[{"x":92.4655,"h":8.8468,"y":101.63,"p":5,"w":35.9691}]}},
  {"_key":"60c20efa7723bebd86645920","_id":"annotations/60c20efa7723bebd86645920","_rev":"_cfFmXvC---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":25,"normalizedForm":"MMPBSA","offsetEnd":31,"rawForm":"MMPBSA","boundingBoxes":[{"x":138.272,"h":8.8468,"y":80.7112,"p":5,"w":32.9245}]},"context":"In order to estimate the MMPBSA binding free energies for the re- ceptors and multi-epitope peptide vaccine construct, the MMPBSA.py"},
  {"_key":"60c20efa7723bebd86645921","_id":"annotations/60c20efa7723bebd86645921","_rev":"_cfFmXvO---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":31,"normalizedForm":"FireDock","offsetEnd":39,"rawForm":"FireDock","boundingBoxes":[{"x":186.518,"h":8.8468,"y":656.539,"p":9,"w":31.6014}]},"context":"The selection was based on the FireDock analysis (S-Table 4) which is an efficient package for refinement and reassigning procedure of docking scores to rigid body docking solutions."},
  {"_key":"60c20efa7723bebd86645922","_id":"annotations/60c20efa7723bebd86645922","_rev":"_cfFmXva---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":44,"normalizedForm":"Java Codon Adaptation Tool (JCat)","offsetEnd":77,"rawForm":"Java Codon Adaptation Tool (JCat)","boundingBoxes":[{"x":158.796,"h":8.846799999999973,"y":415.423,"p":4,"w":129.84790000000004}]},"context":"The entire activity was accomplished using Java Codon Adaptation Tool (JCat) server [36]."},
  {"_key":"60c20efa7723bebd86645923","_id":"annotations/60c20efa7723bebd86645923","_rev":"_cfFmXvm---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":47,"normalizedForm":"GalaxyLoop","offsetEnd":57,"rawForm":"GalaxyLoop","boundingBoxes":[{"x":212.993,"h":8.8468,"y":342.176,"p":4,"w":41.6677}]},"context":"The best model was further loop modelled using GalaxyLoop [31] and refined using GalaxyRefine [32] of GalaxyWeb."},
  {"_key":"60c20efa7723bebd86645924","_id":"annotations/60c20efa7723bebd86645924","_rev":"_cfFmXvy---","wikipediaExternalRef":363695,"document":{"$oid":"60c20efa7723bebd8664591b"},"context":"Selected vaccine candi- dates were then used in BLASTp tool to align the selected adhesive protein candidates with the probiotic bacteria proteome including three Lactobacillus species: L. rhamnosus (tax id: 47715), L. johnsonii (tax id: 33959), and Lactobacillus casei (tax id: 1582) to avoid accidental in- hibition of the useful gut bacteria [11].","wikidataId":"Q286820","type":"software","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTp","offsetStart":48,"wikidataId":"Q286820","offsetEnd":54,"lang":"en","confidence":0.708,"rawForm":"BLASTp","boundingBoxes":[{"x":399.288,"h":8.8468,"y":227.148,"p":3,"w":27.8077}]},"lang":"en"},
  {"_key":"60c20efa7723bebd86645925","_id":"annotations/60c20efa7723bebd86645925","_rev":"_cfFmXw----","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":56,"normalizedForm":"Fast Interaction Refinement in Molecular Docking (FireDock)","offsetEnd":116,"rawForm":"Fast Interaction \nRefinement in Molecular Docking (FireDock)","boundingBoxes":[{"x":502.294,"h":8.846799999999973,"y":248.067,"p":4,"w":55.35610000000008},{"x":306.593,"h":8.846799999999973,"y":258.498,"p":4,"w":166.627}]},"context":"The resulting structures were further refined using the Fast Interaction Refinement in Molecular Docking (FireDock) [43]."},
  {"_key":"60c20efa7723bebd86645926","_id":"annotations/60c20efa7723bebd86645926","_rev":"_cfFmXwK---","document":{"$oid":"60c20efa7723bebd8664591b"},"context":"The screened mouse non-si- milar proteins were then subjected to TMHMM 2.0 [12] and HMMTOP 2.0 [13] for observing the number of transmembrane helices.","type":"software","software-name":{"offsetStart":65,"normalizedForm":"TMHMM","offsetEnd":70,"rawForm":"TMHMM","boundingBoxes":[{"x":441.41,"h":8.8468,"y":174.821,"p":3,"w":31.6413}]},"version":{"offsetStart":71,"normalizedForm":"2.0","offsetEnd":74,"rawForm":"2.0","boundingBoxes":[{"x":475.425,"h":8.846800000000002,"y":174.821,"p":3,"w":11.206000000000017}]}},
  {"_key":"60c20efa7723bebd86645927","_id":"annotations/60c20efa7723bebd86645927","_rev":"_cfFmXwW---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":82,"normalizedForm":"GalaxyRefine","offsetEnd":94,"rawForm":"GalaxyRefine","boundingBoxes":[{"x":88.2713,"h":8.8468,"y":352.665,"p":4,"w":46.8243}]},"context":"The best model was further loop modelled using GalaxyLoop [31] and refined using GalaxyRefine [32] of GalaxyWeb."},
  {"_key":"60c20efa7723bebd86645928","_id":"annotations/60c20efa7723bebd86645928","_rev":"_cfFmXwi---","document":{"$oid":"60c20efa7723bebd8664591b"},"context":"The screened mouse non-si- milar proteins were then subjected to TMHMM 2.0 [12] and HMMTOP 2.0 [13] for observing the number of transmembrane helices.","type":"software","software-name":{"offsetStart":84,"normalizedForm":"HMMTOP","offsetEnd":90,"rawForm":"HMMTOP","boundingBoxes":[{"x":522.536,"h":8.8468,"y":174.821,"p":3,"w":35.1003}]},"version":{"offsetStart":92,"normalizedForm":"2.0","offsetEnd":95,"rawForm":"2.0","boundingBoxes":[{"x":306.596,"h":8.846800000000002,"y":185.309,"p":3,"w":11.206000000000017}]}},
  {"_key":"60c20efa7723bebd86645929","_id":"annotations/60c20efa7723bebd86645929","_rev":"_cfFmXwq---","wikipediaExternalRef":9236158,"document":{"$oid":"60c20efa7723bebd8664591b"},"context":"The tertiary structure of the MEPVC was created through a software called 3Dpro of SCRATCH protein predictor [28], I-tasser [29], and Swiss-Model [30].","wikidataId":"Q275131","type":"software","confidence":0.2958,"software-name":{"wikipediaExternalRef":9236158,"normalizedForm":"SCRATCH","offsetStart":85,"wikidataId":"Q275131","offsetEnd":92,"lang":"en","confidence":0.2958,"rawForm":"SCRATCH","boundingBoxes":[{"x":37.5886,"h":8.8468,"y":331.745,"p":4,"w":35.3872}]},"lang":"en"},
  {"_key":"60c20efa7723bebd8664592a","_id":"annotations/60c20efa7723bebd8664592a","_rev":"_cfFmXw2---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":94,"normalizedForm":"ante- MMPBSA.py","offsetEnd":109,"rawForm":"ante-\nMMPBSA.py","boundingBoxes":[{"x":270.932,"h":8.846800000000002,"y":112.062,"p":5,"w":17.7414},{"x":37.5874,"h":8.846799999999988,"y":122.55,"p":5,"w":43.8356}]},"context":"The program generated the input files for the complex, receptor and MEPVC molecule using the ante- MMPBSA.py"},
  {"_key":"60c20efa7723bebd8664592b","_id":"annotations/60c20efa7723bebd8664592b","_rev":"_cfFmXxC---","wikipediaExternalRef":62887627,"document":{"$oid":"60c20efa7723bebd8664591b"},"context":"In order to predict the immune epitopes, a po- sition-specific scoring matrix (PSSM) employed by C-ImmSim was used.","wikidataId":"Q85850299","type":"software","confidence":0.2114,"software-name":{"wikipediaExternalRef":62887627,"normalizedForm":"C-ImmSim","offsetStart":97,"wikidataId":"Q85850299","offsetEnd":105,"lang":"en","confidence":0.2114,"rawForm":"C-ImmSim","boundingBoxes":[{"x":215.772,"h":8.84680000000003,"y":718.784,"p":4,"w":37.068899999999985}]},"lang":"en"},
  {"_key":"60c20efa7723bebd8664592c","_id":"annotations/60c20efa7723bebd8664592c","_rev":"_cfFmXxS---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":103,"normalizedForm":"GalaxyWeb","offsetEnd":112,"rawForm":"GalaxyWeb","boundingBoxes":[{"x":168.036,"h":8.8468,"y":352.665,"p":4,"w":38.06046}]},"context":"The best model was further loop modelled using GalaxyLoop [31] and refined using GalaxyRefine [32] of GalaxyWeb."},
  {"_key":"60c20efa7723bebd8664592d","_id":"annotations/60c20efa7723bebd8664592d","_rev":"_cfFmXxe---","wikipediaExternalRef":41452308,"document":{"$oid":"60c20efa7723bebd8664591b"},"context":"The tertiary structure of the MEPVC was created through a software called 3Dpro of SCRATCH protein predictor [28], I-tasser [29], and Swiss-Model [30].","wikidataId":"Q17029600","type":"software","confidence":0.7047,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-tasser","offsetStart":117,"wikidataId":"Q17029600","offsetEnd":125,"lang":"en","confidence":0.7047,"rawForm":"I-tasser","boundingBoxes":[{"x":159.646,"h":8.846799999999973,"y":331.745,"p":4,"w":25.312999999999988}]},"lang":"en"},
  {"_key":"60c20efa7723bebd8664592e","_id":"annotations/60c20efa7723bebd8664592e","_rev":"_cfFmXxq---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":122,"normalizedForm":"C-immsim","offsetEnd":130,"rawForm":"C-immsim","boundingBoxes":[{"x":252.791,"h":8.846799999999973,"y":465.541,"p":10,"w":35.873400000000004}]},"context":"The dynamic simulations of the human immune system in response to the designed vaccine construct were deciphered through C-immsim server [40]."},
  {"_key":"60c20efa7723bebd8664592f","_id":"annotations/60c20efa7723bebd8664592f","_rev":"_cfFmXx2---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":123,"normalizedForm":"MMPBSA.py","offsetEnd":132,"rawForm":"MMPBSA.py","boundingBoxes":[{"x":244.854,"h":8.846800000000002,"y":91.1425,"p":5,"w":43.835499999999996}]},"context":"In order to estimate the MMPBSA binding free energies for the re- ceptors and multi-epitope peptide vaccine construct, the MMPBSA.py"},
  {"_key":"60c20efa7723bebd86645930","_id":"annotations/60c20efa7723bebd86645930","_rev":"_cfFmXyC---","document":{"$oid":"60c20efa7723bebd8664591b"},"type":"software","software-name":{"offsetStart":125,"normalizedForm":"PATCHDOCK","offsetEnd":134,"rawForm":"PATCHDOCK","boundingBoxes":[{"x":467.145,"h":8.8468,"y":237.579,"p":4,"w":47.1352}]},"context":"Blind docking employed to calculate the regular pose of the vaccine construct with the mentioned receptors using an online PATCHDOCK server [42]."},
  {"_key":"60c20efa7723bebd86645931","_id":"annotations/60c20efa7723bebd86645931","_rev":"_cfFmXyO---","document":{"$oid":"60c20efa7723bebd8664591b"},"context":"As the final step of this phase, the cloning of the engineered construct was carried out into pET- 28a (+) expression vector using SnapGene (https://www.snapgene. com/).","type":"software","software-name":{"offsetStart":132,"normalizedForm":"SnapGene","offsetEnd":140,"rawForm":"SnapGene","boundingBoxes":[{"x":162.934,"h":8.8468,"y":520.02,"p":4,"w":35.0525}]},"url":{"offsetStart":142,"normalizedForm":"https://www.snapgene. com","offsetEnd":168,"rawForm":"https://www.snapgene. \ncom","boundingBoxes":[{"x":206.04369545454546,"h":8.84680000000003,"y":520.02,"p":4,"w":82.62860454545455},{"x":37.5886,"h":8.8468,"y":530.509,"p":4,"w":11.97905}]}},
  {"_key":"60c20efa7723bebd86645932","_id":"annotations/60c20efa7723bebd86645932","_rev":"_cfFmXye---","wikipediaExternalRef":62887627,"document":{"$oid":"60c20efa7723bebd8664591b"},"context":"In this step, the vaccine construct underwent immune response profiling and immunogenicity classification, which was done using the C-ImmSim server [40].","wikidataId":"Q85850299","type":"software","confidence":0.2114,"software-name":{"wikipediaExternalRef":62887627,"normalizedForm":"C-ImmSim","offsetStart":134,"wikidataId":"Q85850299","offsetEnd":142,"lang":"en","confidence":0.2114,"rawForm":"C-ImmSim","boundingBoxes":[{"x":37.5886,"h":8.84680000000003,"y":708.353,"p":4,"w":37.0689}]},"lang":"en"},
  {"_key":"60c20efa7723bebd86645933","_id":"annotations/60c20efa7723bebd86645933","_rev":"_cfFmXyq---","wikipediaExternalRef":34913748,"document":{"$oid":"60c20efa7723bebd8664591b"},"context":"The tertiary structure of the MEPVC was created through a software called 3Dpro of SCRATCH protein predictor [28], I-tasser [29], and Swiss-Model [30].","wikidataId":"Q7658835","type":"software","confidence":0.6163,"software-name":{"wikipediaExternalRef":34913748,"normalizedForm":"Swiss-Model","offsetStart":136,"wikidataId":"Q7658835","offsetEnd":147,"lang":"en","confidence":0.6163,"rawForm":"Swiss-Model","boundingBoxes":[{"x":224.162,"h":8.846799999999973,"y":331.745,"p":4,"w":43.7877}]},"lang":"en"},
  {"_key":"60c20efa7723bebd86645934","_id":"annotations/60c20efa7723bebd86645934","_rev":"_cfFmXy2---","wikipediaExternalRef":5269034,"document":{"$oid":"60c20efa7723bebd8664591b"},"context":"The top ranked complex with the minimum global energy was selected and used to analyse the binding pose and intermolecular connections using UCSF Chimera 1.13.","wikidataId":"Q7864121","type":"software","lang":"en","confidence":0.894,"software-name":{"wikipediaExternalRef":5269034,"normalizedForm":"UCSF Chimera","offsetStart":143,"wikidataId":"Q7864121","offsetEnd":156,"lang":"en","confidence":0.894,"rawForm":"UCSF \nChimera","boundingBoxes":[{"x":538.521,"h":8.8468,"y":279.418,"p":4,"w":19.1362},{"x":306.593,"h":8.8468,"y":289.906,"p":4,"w":29.8401}]},"version":{"offsetStart":157,"normalizedForm":"1.13","offsetEnd":161,"rawForm":"1.13","boundingBoxes":[{"x":343.67,"h":8.846799999999973,"y":289.906,"p":4,"w":14.941266666666706}]}},
  {"_key":"60c20efa7723bebd86645935","_id":"annotations/60c20efa7723bebd86645935","_rev":"_cfFmXzC---","document":{"$oid":"60c20efa7723bebd8664591b"},"context":"The MD simulations took place in three different phases: system preparation, pre-processing and pro- duction [47] with an Assistant model building with Energy Refinement (AMBER) 16 [48].","type":"software","software-name":{"offsetStart":153,"normalizedForm":"Energy Refinement (AMBER)","offsetEnd":179,"rawForm":"Energy Refinement \n(AMBER)","boundingBoxes":[{"x":490.333,"h":8.846799999999973,"y":425.911,"p":4,"w":67.29630000000003},{"x":306.593,"h":8.846799999999973,"y":436.342,"p":4,"w":32.988200000000006}]},"version":{"offsetStart":180,"normalizedForm":"16","offsetEnd":182,"rawForm":"16","boundingBoxes":[{"x":342.763,"h":8.8468,"y":436.342,"p":4,"w":8.9743}]}},
  {"_key":"60c20eff7723bebd86645937","_id":"annotations/60c20eff7723bebd86645937","_rev":"_cfFmXzO---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20eff7723bebd86645936"},"publisher":{"offsetStart":63,"normalizedForm":"GraphPad Software","offsetEnd":80,"rawForm":"GraphPad Software","boundingBoxes":[{"x":457.7017222222222,"h":8.966300000000047,"y":639.595,"p":3,"w":76.74350000000004}]},"context":"All statistical analyses were performed using GraphPad Prism (GraphPad Software, San Diego, CA).","wikidataId":"Q5597066","type":"software","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":47,"wikidataId":"Q5597066","offsetEnd":61,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":381.14,"h":8.966300000000047,"y":639.595,"p":3,"w":67.3637}]},"lang":"en"},
  {"_key":"60c20f017723bebd86645939","_id":"annotations/60c20f017723bebd86645939","_rev":"_cfFmXza---","document":{"$oid":"60c20f017723bebd86645938"},"publisher":{"offsetStart":103,"normalizedForm":"Invitrogen","offsetEnd":113,"rawForm":"Invitrogen","boundingBoxes":[{"x":360.35400833333335,"h":8.7571,"y":273.127,"p":6,"w":39.27008333333333}]},"context":"Primers for real-time PCR were designed using the web-based version of the Lux TM Designer software (Invitrogen, Melbourne, Australia).","type":"software","software-name":{"offsetStart":76,"normalizedForm":"Lux TM Designer","offsetEnd":92,"rawForm":"Lux TM \nDesigner","boundingBoxes":[{"x":469.47,"h":8.7571,"y":261.165,"p":6,"w":16.0796},{"x":485.574,"h":5.8374,"y":258.942,"p":6,"w":11.201},{"x":281.65,"h":8.7571,"y":273.127,"p":6,"w":35.9749}]}},
  {"_key":"60c20f087723bebd8664593b","_id":"annotations/60c20f087723bebd8664593b","_rev":"_cfFmXzq---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20f087723bebd8664593a"},"context":"IC 50 values were calculated by GraphPad Prism.","wikidataId":"Q5597066","type":"software","confidence":0.9835,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":33,"wikidataId":"Q5597066","offsetEnd":47,"lang":"en","confidence":0.9835,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":390.216,"h":5.731999999999999,"y":254.475,"p":4,"w":49.513000000000034}]},"lang":"en"},
  {"_key":"60c20f087723bebd8664593c","_id":"annotations/60c20f087723bebd8664593c","_rev":"_cfFmXz2---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20f087723bebd8664593a"},"context":"IC 50 values were determined with GraphPad Prism.","wikidataId":"Q5597066","type":"software","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":34,"wikidataId":"Q5597066","offsetEnd":48,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":510.295,"h":5.731999999999999,"y":109.908,"p":7,"w":44.352999999999895}]},"lang":"en"},
  {"_key":"60c20f107723bebd86645940","_id":"annotations/60c20f107723bebd86645940","_rev":"_cfFmX0C---","document":{"$oid":"60c20f107723bebd8664593f"},"publisher":{"offsetStart":77,"normalizedForm":"GraphPad Software","offsetEnd":94,"rawForm":"GraphPad Software","boundingBoxes":[{"x":311.7147555555556,"h":7.8799999999999955,"y":518.044,"p":2,"w":65.55696444444442}]},"context":"All  graphs and statistical testing were performed using Prism version 8  (GraphPad Software).","type":"software","software-name":{"offsetStart":58,"normalizedForm":"Prism","offsetEnd":63,"rawForm":"Prism","boundingBoxes":[{"x":494.958,"h":7.88,"y":505.044,"p":2,"w":20.0872}]},"version":{"offsetStart":72,"normalizedForm":"8","offsetEnd":75,"rawForm":"8","boundingBoxes":[{"x":545.84,"h":7.88,"y":505.044,"p":2,"w":4.64}]}},
  {"_key":"60c20f167723bebd86645947","_id":"annotations/60c20f167723bebd86645947","_rev":"_cfFmX0O---","document":{"$oid":"60c20f167723bebd86645941"},"context":"Nanopolish variants candidates were filtered directly with the ARTIC artic_vcf_filter tool, while Medaka candidates were evaluated by LongShot (0.4.1) 42 before filtering.","references":[{"offsetStart":30978,"normalizedForm":"41","refKey":40,"label":"41","reference_id":{"$oid":"60c20f167723bebd86645942"},"offsetEnd":30981,"boundingBoxes":[{"x":372.796,"h":7.5002,"y":315.328,"p":7,"w":8.853}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Nanopolish","offsetEnd":10,"rawForm":"Nanopolish","boundingBoxes":[{"x":115.765,"h":9.947,"y":331.069,"p":7,"w":50.6704}]}},
  {"_key":"60c20f167723bebd86645948","_id":"annotations/60c20f167723bebd86645948","_rev":"_cfFmX0a---","document":{"$oid":"60c20f167723bebd86645941"},"context":"The ARTIC tool align_trim was used to trim primer sequences from the termini of read alignments and cap sequencing depth at a maximum of 400-fold coverage.","type":"software","software-name":{"offsetStart":4,"normalizedForm":"ARTIC","offsetEnd":9,"rawForm":"ARTIC","boundingBoxes":[{"x":282.164,"h":9.947,"y":276.109,"p":7,"w":26.3525}]},"url":{"offsetStart":100,"normalizedForm":"https://github.com/artic-network/artic-ncov2019","offsetEnd":147,"rawForm":"https://github.com/artic-network/artic-ncov2019","boundingBoxes":[{"x":61.3857,"h":9.947000000000003,"y":317.629,"p":7,"w":217.0836}]}},
  {"_key":"60c20f167723bebd86645949","_id":"annotations/60c20f167723bebd86645949","_rev":"_cfFmX0m---","document":{"$oid":"60c20f167723bebd86645941"},"type":"software","software-name":{"offsetStart":4,"normalizedForm":"RAMPART","offsetEnd":11,"rawForm":"RAMPART","boundingBoxes":[{"x":449.675,"h":9.9581,"y":203.618,"p":7,"w":45.1315}]},"context":"The RAMPART software package 39 was used to monitor sequencing performance in real-time, with runs proceeding until a minimum ~200-fold coverage was achieved across all amplicons."},
  {"_key":"60c20f167723bebd8664594a","_id":"annotations/60c20f167723bebd8664594a","_rev":"_cfFmX0y---","document":{"$oid":"60c20f167723bebd86645941"},"context":"using bwa mem (0.7.12-r1039) 36 .","type":"software","software-name":{"offsetStart":6,"normalizedForm":"bwa","offsetEnd":9,"rawForm":"bwa","boundingBoxes":[{"x":301.728,"h":9.947,"y":675.469,"p":6,"w":18.9336}]},"version":{"offsetStart":16,"normalizedForm":".7.12","offsetEnd":21,"rawForm":".7.12","boundingBoxes":[{"x":360.5211142857143,"h":9.947000000000003,"y":675.469,"p":6,"w":22.865285714285733}]}},
  {"_key":"60c20f167723bebd8664594b","_id":"annotations/60c20f167723bebd8664594b","_rev":"_cfFmX1----","document":{"$oid":"60c20f167723bebd86645941"},"context":"Using Varscan2, we identified 154 sub-consensus SNV candidates in ONT sequencing libraries (Supplementary Table 5).","references":[{"offsetStart":31281,"normalizedForm":"43","refKey":42,"label":"43","reference_id":{"$oid":"60c20f167723bebd86645943"},"offsetEnd":31284,"boundingBoxes":[{"x":282.148,"h":7.5002,"y":358.048,"p":7,"w":8.853}]}],"type":"software","software-name":{"offsetStart":6,"normalizedForm":"Varscan2","offsetEnd":14,"rawForm":"Varscan2","boundingBoxes":[{"x":90.0174,"h":9.958099999999945,"y":540.818,"p":4,"w":39.2632}]},"version":{"offsetStart":73,"normalizedForm":"2.4.3","offsetEnd":78,"rawForm":"2.4.3","boundingBoxes":[{"x":252.470325,"h":9.947000000000003,"y":360.349,"p":7,"w":25.441949999999963}]}},
  {"_key":"60c20f167723bebd8664594c","_id":"annotations/60c20f167723bebd8664594c","_rev":"_cfFmX1K---","document":{"$oid":"60c20f167723bebd86645941"},"context":"using minimap2 (2.17-r941) 40 .","type":"software","software-name":{"offsetStart":6,"normalizedForm":"minimap2","offsetEnd":14,"rawForm":"minimap2","boundingBoxes":[{"x":150.697,"h":9.958100000000002,"y":276.098,"p":7,"w":45.017799999999994}]},"version":{"offsetStart":17,"normalizedForm":".17","offsetEnd":20,"rawForm":".17","boundingBoxes":[{"x":207.49759999999998,"h":9.947000000000003,"y":276.109,"p":7,"w":13.6704}]}},
  {"_key":"60c20f167723bebd8664594d","_id":"annotations/60c20f167723bebd8664594d","_rev":"_cfFmX1W---","document":{"$oid":"60c20f167723bebd86645941"},"context":"using Nanopolish 41 or Medaka (0.11.5) to variants, respectively.","references":[{"offsetStart":30978,"normalizedForm":"41","refKey":40,"label":"41","reference_id":{"$oid":"60c20f167723bebd86645942"},"offsetEnd":30981,"boundingBoxes":[{"x":372.796,"h":7.5002,"y":315.328,"p":7,"w":8.853}]}],"type":"software","software-name":{"offsetStart":6,"normalizedForm":"Nanopolish","offsetEnd":16,"rawForm":"Nanopolish","boundingBoxes":[{"x":322.464,"h":9.9581,"y":317.618,"p":7,"w":50.3613}]}},
  {"_key":"60c20f167723bebd8664594e","_id":"annotations/60c20f167723bebd8664594e","_rev":"_cfFmX1i---","document":{"$oid":"60c20f167723bebd86645941"},"type":"software","software-name":{"offsetStart":15,"normalizedForm":"align_trim","offsetEnd":25,"rawForm":"align_trim","boundingBoxes":[{"x":331.695,"h":9.9581,"y":276.098,"p":7,"w":46.189}]},"context":"The ARTIC tool align_trim was used to trim primer sequences from the termini of read alignments and cap sequencing depth at a maximum of 400-fold coverage."},
  {"_key":"60c20f167723bebd8664594f","_id":"annotations/60c20f167723bebd8664594f","_rev":"_cfFmX1u---","document":{"$oid":"60c20f167723bebd86645941"},"context":"using Nanopolish 41 or Medaka (0.11.5) to variants, respectively.","type":"software","software-name":{"offsetStart":23,"normalizedForm":"Medaka","offsetEnd":29,"rawForm":"Medaka","boundingBoxes":[{"x":402.54,"h":9.9581,"y":317.618,"p":7,"w":36.6362}]},"version":{"offsetStart":31,"normalizedForm":"0.11.5","offsetEnd":37,"rawForm":"0.11.5","boundingBoxes":[{"x":449.08687499999996,"h":9.947000000000003,"y":317.629,"p":7,"w":25.901250000000005}]}},
  {"_key":"60c20f167723bebd86645950","_id":"annotations/60c20f167723bebd86645950","_rev":"_cfFmX16---","document":{"$oid":"60c20f167723bebd86645941"},"context":"Variants were identified using bcftools call (v1.9) 38 , assuming a ploidy of 1 (--ploidy 1), then filtered for a minimum read depth of 30 and minimum quality of 20.","references":[{"offsetStart":28608,"normalizedForm":"38","refKey":37,"label":"38","reference_id":{"$oid":"60c20f167723bebd86645944"},"offsetEnd":28611,"boundingBoxes":[{"x":279.35,"h":7.5002,"y":730.528,"p":6,"w":8.853}]}],"type":"software","software-name":{"offsetStart":31,"normalizedForm":"bcftools call","offsetEnd":44,"rawForm":"bcftools call","boundingBoxes":[{"x":196.349,"h":9.958099999999945,"y":732.818,"p":6,"w":54.02660000000003}]},"version":{"offsetStart":47,"normalizedForm":"1.9","offsetEnd":50,"rawForm":"1.9","boundingBoxes":[{"x":258.04636666666664,"h":9.947000000000003,"y":732.829,"p":6,"w":17.04946666666666}]}},
  {"_key":"60c20f167723bebd86645951","_id":"annotations/60c20f167723bebd86645951","_rev":"_cfFmX2G---","document":{"$oid":"60c20f167723bebd86645941"},"context":"using the rearrangement-aware aligner NGMLR (v0.2.7) 44 .","references":[{"offsetStart":32921,"normalizedForm":"44","refKey":43,"label":"44","reference_id":{"$oid":"60c20f167723bebd86645945"},"offsetEnd":32924,"boundingBoxes":[{"x":373.542,"h":7.5002,"y":696.208,"p":7,"w":8.853}]}],"type":"software","software-name":{"offsetStart":38,"normalizedForm":"NGMLR","offsetEnd":43,"rawForm":"NGMLR","boundingBoxes":[{"x":302.923,"h":9.9581,"y":698.498,"p":7,"w":34.0558}]},"version":{"offsetStart":46,"normalizedForm":"0.2.7","offsetEnd":51,"rawForm":"0.2.7","boundingBoxes":[{"x":343.8640375,"h":9.947000000000003,"y":698.509,"p":7,"w":25.446225000000027}]}},
  {"_key":"60c20f167723bebd86645952","_id":"annotations/60c20f167723bebd86645952","_rev":"_cfFmX2S---","document":{"$oid":"60c20f167723bebd86645941"},"context":"The resulting reads were basecalled using Guppy (4.0.14) and aligned to the Wuhan-Hu-1 reference genome (MN908947.3)","type":"software","software-name":{"offsetStart":42,"normalizedForm":"Guppy","offsetEnd":47,"rawForm":"Guppy","boundingBoxes":[{"x":244.809,"h":9.9581,"y":261.458,"p":7,"w":28.8519}]},"version":{"offsetStart":49,"normalizedForm":"4.0.14","offsetEnd":55,"rawForm":"4.0.14","boundingBoxes":[{"x":280.35887499999995,"h":9.947000000000003,"y":261.469,"p":7,"w":25.90125000000006}]}},
  {"_key":"60c20f167723bebd86645953","_id":"annotations/60c20f167723bebd86645953","_rev":"_cfFmX2e---","document":{"$oid":"60c20f167723bebd86645941"},"context":"Trimmed alignments were converted to pileup format using samtools mpileup (v1.9) 38 , with anomalous read pairs retained (--count-orphans), base alignment quality disabled (--no-BAQ) and all bases considered, regardless of PHRED quality (--min-BQ 0).","references":[{"offsetStart":28384,"normalizedForm":"38","refKey":37,"label":"38","reference_id":{"$oid":"60c20f167723bebd86645944"},"offsetEnd":28387,"boundingBoxes":[{"x":255.134,"h":7.5002,"y":702.448,"p":6,"w":8.853}]}],"type":"software","software-name":{"offsetStart":58,"normalizedForm":"samtools mpileup","offsetEnd":74,"rawForm":"samtools mpileup","boundingBoxes":[{"x":147.477,"h":9.958099999999945,"y":704.738,"p":6,"w":79.27260000000001}]},"version":{"offsetStart":77,"normalizedForm":"1.9","offsetEnd":80,"rawForm":"1.9","boundingBoxes":[{"x":233.8293666666667,"h":9.947000000000003,"y":704.749,"p":6,"w":17.04946666666666}]}},
  {"_key":"60c20f167723bebd86645954","_id":"annotations/60c20f167723bebd86645954","_rev":"_cfFmX2q---","document":{"$oid":"60c20f167723bebd86645941"},"type":"software","software-name":{"offsetStart":61,"normalizedForm":"gatk","offsetEnd":65,"rawForm":"gatk","boundingBoxes":[{"x":138.282,"h":9.9581,"y":518.018,"p":7,"w":20.0188}]},"context":"and; (iii) indels at simple repeats were left-aligned using gatk LeftAlignAndTrimVariants (4.0.11.0)."},
  {"_key":"60c20f167723bebd86645955","_id":"annotations/60c20f167723bebd86645955","_rev":"_cfFmX22---","document":{"$oid":"60c20f167723bebd86645941"},"context":"Sub-consensus level variant candidates were identified using Varscan2 (v2.4.3) 43 .","references":[{"offsetStart":31281,"normalizedForm":"43","refKey":42,"label":"43","reference_id":{"$oid":"60c20f167723bebd86645943"},"offsetEnd":31284,"boundingBoxes":[{"x":282.148,"h":7.5002,"y":358.048,"p":7,"w":8.853}]}],"type":"software","software-name":{"offsetStart":62,"normalizedForm":"Varscan2","offsetEnd":70,"rawForm":"Varscan2","boundingBoxes":[{"x":204.332,"h":9.958100000000002,"y":360.338,"p":7,"w":41.42400000000001}]},"version":{"offsetStart":73,"normalizedForm":"2.4.3","offsetEnd":78,"rawForm":"2.4.3","boundingBoxes":[{"x":252.470325,"h":9.947000000000003,"y":360.349,"p":7,"w":25.441949999999963}]}},
  {"_key":"60c20f167723bebd86645956","_id":"annotations/60c20f167723bebd86645956","_rev":"_cfFmX3C---","document":{"$oid":"60c20f167723bebd86645941"},"type":"software","software-name":{"offsetStart":63,"normalizedForm":"ARTIC artic_vcf_filter","offsetEnd":85,"rawForm":"ARTIC artic_vcf_filter","boundingBoxes":[{"x":394.502,"h":9.958100000000002,"y":331.058,"p":7,"w":94.02909999999997}]},"context":"Nanopolish variants candidates were filtered directly with the ARTIC artic_vcf_filter tool, while Medaka candidates were evaluated by LongShot (0.4.1) 42 before filtering."},
  {"_key":"60c20f167723bebd86645957","_id":"annotations/60c20f167723bebd86645957","_rev":"_cfFmX3O---","document":{"$oid":"60c20f167723bebd86645941"},"context":"and; (iii) indels at simple repeats were left-aligned using gatk LeftAlignAndTrimVariants (4.0.11.0).","type":"software","software-name":{"offsetStart":66,"normalizedForm":"LeftAlignAndTrimVariants","offsetEnd":90,"rawForm":"LeftAlignAndTrimVariants","boundingBoxes":[{"x":161.788,"h":9.9581,"y":518.018,"p":7,"w":115.154}]},"version":{"offsetStart":92,"normalizedForm":"4.0.11.0","offsetEnd":100,"rawForm":"4.0.11.0","boundingBoxes":[{"x":284.5920363636364,"h":9.947000000000003,"y":518.029,"p":7,"w":33.20029090909088}]}},
  {"_key":"60c20f167723bebd86645958","_id":"annotations/60c20f167723bebd86645958","_rev":"_cfFmX3a---","document":{"$oid":"60c20f167723bebd86645941"},"context":"Primer sequences were trimmed from the termini of read alignments using iVar (1.0) 37 .","references":[{"offsetStart":28297,"normalizedForm":"37","refKey":36,"label":"37","reference_id":{"$oid":"60c20f167723bebd86645946"},"offsetEnd":28300,"boundingBoxes":[{"x":340.291,"h":7.5002,"y":687.808,"p":6,"w":8.853}]}],"type":"software","software-name":{"offsetStart":73,"normalizedForm":"iVar","offsetEnd":77,"rawForm":"iVar","boundingBoxes":[{"x":297.705,"h":9.9581,"y":690.098,"p":6,"w":18.2081}]},"version":{"offsetStart":79,"normalizedForm":"1.0","offsetEnd":82,"rawForm":"1.0","boundingBoxes":[{"x":323.81401999999997,"h":9.947000000000003,"y":690.109,"p":6,"w":12.363060000000019}]}},
  {"_key":"60c20f167723bebd86645959","_id":"annotations/60c20f167723bebd86645959","_rev":"_cfFmX3m---","document":{"$oid":"60c20f167723bebd86645941"},"context":"Consensus-level variant candidates were identified using each of two workflows developed by ARTIC (https://github.com/artic-network/artic-ncov2019),","type":"software","software-name":{"offsetStart":92,"normalizedForm":"ARTIC","offsetEnd":97,"rawForm":"ARTIC","boundingBoxes":[{"x":512.066,"h":9.947,"y":302.989,"p":7,"w":26.3547}]},"url":{"offsetStart":100,"normalizedForm":"https://github.com/artic-network/artic-ncov2019","offsetEnd":147,"rawForm":"https://github.com/artic-network/artic-ncov2019","boundingBoxes":[{"x":61.3857,"h":9.947000000000003,"y":317.629,"p":7,"w":217.0836}]}},
  {"_key":"60c20f167723bebd8664595a","_id":"annotations/60c20f167723bebd8664595a","_rev":"_cfFmX3y---","document":{"$oid":"60c20f167723bebd86645941"},"context":"Nanopolish variants candidates were filtered directly with the ARTIC artic_vcf_filter tool, while Medaka candidates were evaluated by LongShot (0.4.1) 42 before filtering.","type":"software","software-name":{"offsetStart":99,"normalizedForm":"Medaka","offsetEnd":105,"rawForm":"Medaka","boundingBoxes":[{"x":56.7669,"h":9.9581,"y":345.698,"p":7,"w":36.6362}]},"version":{"offsetStart":31,"normalizedForm":"0.11.5","offsetEnd":37,"rawForm":"0.11.5","boundingBoxes":[{"x":449.08687499999996,"h":9.947000000000003,"y":317.629,"p":7,"w":25.901250000000005}]}},
  {"_key":"60c20f167723bebd8664595b","_id":"annotations/60c20f167723bebd8664595b","_rev":"_cfFmX4----","document":{"$oid":"60c20f167723bebd86645941"},"type":"software","software-name":{"offsetStart":129,"normalizedForm":"pysamstats","offsetEnd":139,"rawForm":"pysamstats","boundingBoxes":[{"x":159.153,"h":9.9581,"y":419.858,"p":7,"w":48.69072727272727}]},"context":"For synthetic RNA controls, read-level quality metrics, such as sequencing error rates, were derived from read alignments using pysamstats, with any bases that differed from the Wuhan-Hu-1 reference sequence considered errors."},
  {"_key":"60c20f167723bebd8664595c","_id":"annotations/60c20f167723bebd8664595c","_rev":"_cfFmX4K---","document":{"$oid":"60c20f167723bebd86645941"},"context":"To ensure consistent representation of variants across calls generated by different programs: (i) multi-allelic variant candidates were separate into individual SNVs/indels using bcftools norm (1.9) 38 ; (ii) multi-nucleotide variants were decomposed into their simplest set of individual components using rtg-tools vcfdecompose (3.10.1)","type":"software","software-name":{"offsetStart":181,"normalizedForm":"bcftools norm","offsetEnd":194,"rawForm":"bcftools norm","boundingBoxes":[{"x":139.476,"h":9.958100000000002,"y":491.378,"p":7,"w":62.079499999999996}]},"version":{"offsetStart":196,"normalizedForm":"1.9","offsetEnd":199,"rawForm":"1.9","boundingBoxes":[{"x":208.55602,"h":9.947000000000003,"y":491.389,"p":7,"w":12.36305999999999}]}},
  {"_key":"60c20f167723bebd8664595d","_id":"annotations/60c20f167723bebd8664595d","_rev":"_cfFmX4W---","document":{"$oid":"60c20f167723bebd86645941"},"context":"To ensure consistent representation of variants across calls generated by different programs: (i) multi-allelic variant candidates were separate into individual SNVs/indels using bcftools norm (1.9) 38 ; (ii) multi-nucleotide variants were decomposed into their simplest set of individual components using rtg-tools vcfdecompose (3.10.1)","type":"software","software-name":{"offsetStart":309,"normalizedForm":"rtg-tools","offsetEnd":318,"rawForm":"rtg-tools","boundingBoxes":[{"x":218.18,"h":9.958099999999945,"y":504.578,"p":7,"w":38.28030000000001}]},"version":{"offsetStart":333,"normalizedForm":"3.10.1","offsetEnd":339,"rawForm":"3.10.1","boundingBoxes":[{"x":330.63422499999996,"h":9.946999999999946,"y":504.589,"p":7,"w":25.897350000000017}]}},
  {"_key":"60c20f1e7723bebd8664595f","_id":"annotations/60c20f1e7723bebd8664595f","_rev":"_cfFmX4i---","document":{"$oid":"60c20f1e7723bebd8664595e"},"type":"software","software-name":{"offsetStart":40,"normalizedForm":"UniDec","offsetEnd":46,"rawForm":"UniDec","boundingBoxes":[{"x":278.244,"h":10.8,"y":185.554,"p":37,"w":32.9592}]},"context":"Data were deconvolved and analyzed with UniDec.(5where"},
  {"_key":"60c20f1e7723bebd86645960","_id":"annotations/60c20f1e7723bebd86645960","_rev":"_cfFmX4u---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20f1e7723bebd8664595e"},"context":"The CC50 values were calculated  from best-fit dose−response curves using GraphPad Prism 5 software.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":75,"wikidataId":"Q5597066","offsetEnd":89,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":272.134,"h":10.799999999999955,"y":580.474,"p":39,"w":79.08000000000004}]},"version":{"offsetStart":90,"normalizedForm":"5","offsetEnd":91,"rawForm":"5","boundingBoxes":[{"x":354.106,"h":10.8,"y":580.474,"p":39,"w":6}]}},
  {"_key":"60c20f247723bebd86645962","_id":"annotations/60c20f247723bebd86645962","_rev":"_cfFmX46---","document":{"$oid":"60c20f247723bebd86645961"},"type":"software","software-name":{"offsetStart":91,"normalizedForm":"Covidence","offsetEnd":100,"rawForm":"Covidence","boundingBoxes":[{"x":252.572,"h":8.379,"y":701.538,"p":3,"w":39.024}]},"context":" Data were extracted in duplicate from eligible studies by two authors (CW and JSF) using Covidence systematic review software."},
  {"_key":"60c20f2c7723bebd86645964","_id":"annotations/60c20f2c7723bebd86645964","_rev":"_cfFmX5G---","document":{"$oid":"60c20f2c7723bebd86645963"},"publisher":{"offsetStart":264,"normalizedForm":"Graph","offsetEnd":269,"rawForm":"Graph","boundingBoxes":[{"x":377.799,"h":8.5,"y":547.188,"p":3,"w":23.25}]},"context":"We also evaluated the relationship between patient-reported complaint of blurred vision and ophthalmic variables of interest, which included at least moderate visual acuity impairment and presence of any ophthalmic complication with Fisher's exact test (Prism, Graph, San Diego, CA; Microsoft Excel, Seattle, WA).","type":"software","software-name":{"offsetStart":257,"normalizedForm":"Prism","offsetEnd":262,"rawForm":"Prism","boundingBoxes":[{"x":350.36642857142857,"h":8.5,"y":547.188,"p":3,"w":21.007142857142856}]}},
  {"_key":"60c20f2f7723bebd86645967","_id":"annotations/60c20f2f7723bebd86645967","_rev":"_cfFmX5S---","wikipediaExternalRef":43325101,"document":{"$oid":"60c20f2f7723bebd86645965"},"context":"The 199 Birman DNA samples were genotyped and genome- wide association (GWAS) studies were performed with PLINK (Purcell et al., 2007).","wikidataId":"Q18359288","references":[{"offsetStart":10038,"normalizedForm":"Purcell et al., 2007","refKey":25,"label":"(Purcell et al., 2007)","reference_id":{"$oid":"60c20f2f7723bebd86645966"},"offsetEnd":10060,"boundingBoxes":[{"x":311.411,"h":7.523799999999994,"y":343.699,"p":3,"w":73.27891666666665}]}],"type":"software","confidence":0.393,"software-name":{"wikipediaExternalRef":43325101,"normalizedForm":"PLINK","offsetStart":106,"wikidataId":"Q18359288","offsetEnd":111,"lang":"en","confidence":0.393,"rawForm":"PLINK","boundingBoxes":[{"x":540.099,"h":7.5238,"y":333.238,"p":3,"w":22.8582}]},"lang":"en"},
  {"_key":"60c20f2f7723bebd86645968","_id":"annotations/60c20f2f7723bebd86645968","_rev":"_cfFmX5e---","document":{"$oid":"60c20f2f7723bebd86645965"},"type":"software","software-name":{"offsetStart":165,"normalizedForm":"UCSC genome browser","offsetEnd":184,"rawForm":"UCSC genome browser","boundingBoxes":[{"x":311.411,"h":7.523799999999994,"y":275.67,"p":3,"w":84.27336249999996}]},"context":"The correct chromosome and position assignments for the 63K SNPs for this study was based upon the ICGSC Felis catus 6.2/felCat5 (September 2011) assembly on the UCSC genome browser."},
  {"_key":"60c20f2f7723bebd86645969","_id":"annotations/60c20f2f7723bebd86645969","_rev":"_cfFmX5q---","wikipediaExternalRef":43325101,"document":{"$oid":"60c20f2f7723bebd86645965"},"context":"Population stratification in case and control populations from each region were assessed by multidi- mensional scaling (MDS) and relatedness was confirmed by Pi-Hat test using the PLINK whole genome association analysis toolset (Purcell et al., 2007).","wikidataId":"Q18359288","references":[{"offsetStart":10038,"normalizedForm":"Purcell et al., 2007","refKey":25,"label":"(Purcell et al., 2007)","reference_id":{"$oid":"60c20f2f7723bebd86645966"},"offsetEnd":10060,"boundingBoxes":[{"x":311.411,"h":7.523799999999994,"y":343.699,"p":3,"w":73.27891666666665}]}],"type":"software","confidence":0.393,"software-name":{"wikipediaExternalRef":43325101,"normalizedForm":"PLINK","offsetStart":182,"wikidataId":"Q18359288","offsetEnd":187,"lang":"en","confidence":0.393,"rawForm":"PLINK","boundingBoxes":[{"x":369.272,"h":7.5238,"y":469.229,"p":3,"w":22.8582}]},"lang":"en"},
  {"_key":"60c20f307723bebd8664596b","_id":"annotations/60c20f307723bebd8664596b","_rev":"_cfFmX52---","wikipediaExternalRef":544733,"document":{"$oid":"60c20f307723bebd8664596a"},"publisher":{"offsetStart":104,"normalizedForm":"National Instruments Corporation","offsetEnd":136,"rawForm":"National Instruments Corporation","boundingBoxes":[{"x":146.9651777777778,"h":7.407900000000041,"y":683.775,"p":2,"w":129.7204722222222}]},"context":"The mucosal flow sensor recorded data using a software programme developed in- house based on Labview (National Instruments Corporation, Newbury, UK).","wikidataId":"Q746261","type":"software","confidence":0.8025,"software-name":{"wikipediaExternalRef":544733,"normalizedForm":"Labview","offsetStart":95,"wikidataId":"Q746261","offsetEnd":102,"lang":"en","confidence":0.8025,"rawForm":"Labview","boundingBoxes":[{"x":106.922,"h":7.4079,"y":683.775,"p":2,"w":31.2316}]},"lang":"en"},
  {"_key":"60c20f417723bebd8664596e","_id":"annotations/60c20f417723bebd8664596e","_rev":"_cfFmX6C---","document":{"$oid":"60c20f417723bebd8664596c"},"publisher":{"offsetStart":48,"normalizedForm":"Analyst","offsetEnd":55,"rawForm":"Analyst","boundingBoxes":[{"x":251.85282352941175,"h":11.48,"y":595.255,"p":3,"w":32.694529411764705}]},"context":"All data analyses were performed using OpenMeta[Analyst] [24] and comprehensive meta-analysis software version 3.0 [25].","references":[{"offsetStart":11244,"normalizedForm":"[24]","refKey":23,"label":"[24]","reference_id":{"$oid":"60c20f417723bebd8664596d"},"offsetEnd":11249,"boundingBoxes":[{"x":51.0236,"h":11.480000000000018,"y":607.755,"p":3,"w":16.810000000000002}]}],"type":"software","software-name":{"offsetStart":39,"normalizedForm":"OpenMeta[","offsetEnd":48,"rawForm":"OpenMeta[","boundingBoxes":[{"x":209.817,"h":11.480000000000018,"y":595.255,"p":3,"w":42.03582352941177}]},"version":{"offsetStart":112,"normalizedForm":"3.0","offsetEnd":115,"rawForm":"3.0","boundingBoxes":[{"x":276.638,"h":11.480000000000018,"y":607.755,"p":3,"w":12.599999999999966}]}},
  {"_key":"60c20f417723bebd8664596f","_id":"annotations/60c20f417723bebd8664596f","_rev":"_cfFmX6O---","wikipediaExternalRef":20268,"document":{"$oid":"60c20f417723bebd8664596c"},"context":"Information was extracted from eligible articles in a predesigned form in excel, including the last name of the first author, date and year of publication, journal name, study design, country of the population, and sample size.","wikidataId":"Q11272","type":"software","confidence":0.3909,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"excel","offsetStart":75,"wikidataId":"Q11272","offsetEnd":80,"lang":"en","confidence":0.3909,"rawForm":"excel","boundingBoxes":[{"x":190.002,"h":11.48,"y":470.255,"p":3,"w":19.913333333333334}]},"lang":"en"},
  {"_key":"60c20f417723bebd86645970","_id":"annotations/60c20f417723bebd86645970","_rev":"_cfFmX6a---","document":{"$oid":"60c20f417723bebd8664596c"},"type":"software","software-name":{"offsetStart":78,"normalizedForm":"Science","offsetEnd":85,"rawForm":"Science","boundingBoxes":[{"x":324.691,"h":11.48,"y":383.635,"p":2,"w":32.42}]},"context":"Relevant litera- ture was retrieved from Web of Science, PubMed, Scopus, and Science Direct search engines up to June 29, 2020."},
  {"_key":"60c20f417723bebd86645972","_id":"annotations/60c20f417723bebd86645972","_rev":"_cfFmX6m---","wikipediaExternalRef":179088,"document":{"$oid":"60c20f417723bebd86645971"},"context":"Data were calculated with SPSS Vs. 24 and plotted with Sigma plot Vs.13.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":26,"wikidataId":"Q181596","offsetEnd":30,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":158.055,"h":7.1652,"y":509.601,"p":4,"w":17.0483}]},"version":{"offsetStart":59,"normalizedForm":"24.0","offsetEnd":63,"rawForm":"24.0","boundingBoxes":[{"x":37.5877,"h":7.165200000000027,"y":666.468,"p":3,"w":13.915999999999997}]}},
  {"_key":"60c20f417723bebd86645973","_id":"annotations/60c20f417723bebd86645973","_rev":"_cfFmX6y---","wikipediaExternalRef":179088,"document":{"$oid":"60c20f417723bebd86645971"},"context":"In this case the minimal number of samples was 34 (SPSS v 24.0), following previously reported methodological recommendations [12].","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":51,"wikidataId":"Q181596","offsetEnd":55,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":266.37442000000004,"h":7.1652,"y":656.036,"p":3,"w":16.02968}]},"version":{"offsetStart":59,"normalizedForm":"24.0","offsetEnd":63,"rawForm":"24.0","boundingBoxes":[{"x":37.5877,"h":7.165200000000027,"y":666.468,"p":3,"w":13.915999999999997}]}},
  {"_key":"60c20f487723bebd86645975","_id":"annotations/60c20f487723bebd86645975","_rev":"_cfFmX7----","document":{"$oid":"60c20f487723bebd86645974"},"publisher":{"offsetStart":25,"normalizedForm":"NCBI","offsetEnd":29,"rawForm":"NCBI","boundingBoxes":[{"x":364.647,"h":8.1324,"y":125.931,"p":3,"w":21.8419}]},"context":"ORFs were identified by NCBI ORF Finder (http://www.ncbi.nlm.nih.gov/ gorf/gorf.html);","type":"software","software-name":{"offsetStart":30,"normalizedForm":"ORF Finder","offsetEnd":40,"rawForm":"ORF Finder","boundingBoxes":[{"x":390.045,"h":8.132400000000004,"y":125.931,"p":3,"w":46.189599999999984}]},"url":{"offsetStart":42,"normalizedForm":"http://www.ncbi.nlm.nih.gov/ gorf/gorf.html","offsetEnd":86,"rawForm":"http://www.ncbi.nlm.nih.gov/ \ngorf/gorf.html","boundingBoxes":[{"x":443.76237931034484,"h":8.132400000000004,"y":125.931,"p":3,"w":110.38662068965516},{"x":315.099,"h":8.13239999999999,"y":136.362,"p":3,"w":49.63069999999999}]}},
  {"_key":"60c20f487723bebd86645976","_id":"annotations/60c20f487723bebd86645976","_rev":"_cfFmX7K---","document":{"$oid":"60c20f487723bebd86645974"},"type":"software","software-name":{"offsetStart":48,"normalizedForm":"GAPipeline","offsetEnd":58,"rawForm":"GAPipeline","boundingBoxes":[{"x":58.0537,"h":8.1324,"y":362.402,"p":3,"w":41.8995}]},"context":"Base calling was conducted with the program of GAPipeline using default settings."},
  {"_key":"60c20f487723bebd86645977","_id":"annotations/60c20f487723bebd86645977","_rev":"_cfFmX7W---","document":{"$oid":"60c20f487723bebd86645974"},"context":"the secondary structure of circovirus genome was predicted with the mfold Web Server (http://mfold.rna.albany. edu/?q = mfold).","type":"software","software-name":{"offsetStart":69,"normalizedForm":"mfold Web Server","offsetEnd":85,"rawForm":"mfold Web Server","boundingBoxes":[{"x":388.174,"h":8.13239999999999,"y":146.85,"p":3,"w":69.58130000000006}]},"url":{"offsetStart":87,"normalizedForm":"http://mfold.rna.albany. edu/?q = mfold","offsetEnd":127,"rawForm":"http://mfold.rna.albany. \nedu/?q = mfold","boundingBoxes":[{"x":465.56352799999996,"h":8.13239999999999,"y":146.85,"p":3,"w":88.57267199999995},{"x":315.099,"h":8.13239999999999,"y":157.281,"p":3,"w":53.152714285714296}]}},
  {"_key":"60c20f487723bebd86645978","_id":"annotations/60c20f487723bebd86645978","_rev":"_cfFmX7i---","wikipediaExternalRef":363695,"document":{"$oid":"60c20f487723bebd86645974"},"context":"The significant data were aligned online against the nonredun- dant and viral reference databases of GenBank with BLASTx and BLASTn.","wikidataId":"Q286820","type":"software","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTx","offsetStart":114,"wikidataId":"Q286820","offsetEnd":120,"lang":"en","confidence":0.708,"rawForm":"BLASTx","boundingBoxes":[{"x":248.592,"h":8.1324,"y":459.4,"p":3,"w":32.3863}]},"lang":"en"},
  {"_key":"60c20f487723bebd86645979","_id":"annotations/60c20f487723bebd86645979","_rev":"_cfFmX7u---","wikipediaExternalRef":363695,"document":{"$oid":"60c20f487723bebd86645974"},"context":"The significant data were aligned online against the nonredun- dant and viral reference databases of GenBank with BLASTx and BLASTn.","wikidataId":"Q286820","type":"software","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTn","offsetStart":126,"wikidataId":"Q286820","offsetEnd":132,"lang":"en","confidence":0.708,"rawForm":"BLASTn","boundingBoxes":[{"x":58.0537,"h":8.1324,"y":469.945,"p":3,"w":30.080657142857138}]},"lang":"en"},
  {"_key":"60c20f487723bebd8664597a","_id":"annotations/60c20f487723bebd8664597a","_rev":"_cfFmX76---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20f487723bebd86645974"},"context":"Alignments of nucleotide (nt) and amino acid (aa) sequences with other representatives of known viruses were conducted using Clustal W version 2.0.","wikidataId":"Q866737","type":"software","lang":"en","confidence":0.8955,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"Clustal W","offsetStart":127,"wikidataId":"Q866737","offsetEnd":136,"lang":"en","confidence":0.8955,"rawForm":"Clustal W","boundingBoxes":[{"x":315.099,"h":8.132400000000004,"y":94.5238,"p":3,"w":36.042100000000005}]},"version":{"offsetStart":145,"normalizedForm":"2.0","offsetEnd":148,"rawForm":"2.0","boundingBoxes":[{"x":381.655,"h":8.132400000000004,"y":94.5238,"p":3,"w":10.087124999999958}]}},
  {"_key":"60c20f487723bebd8664597b","_id":"annotations/60c20f487723bebd8664597b","_rev":"_cfFmX8C---","document":{"$oid":"60c20f487723bebd86645974"},"publisher":{"offsetStart":191,"normalizedForm":"BGI","offsetEnd":194,"rawForm":"BGI","boundingBoxes":[{"x":205.0786,"h":8.1324,"y":394.038,"p":3,"w":11.9808}]},"context":"After removing the adaptor sequences and no-calling reads, the sequences of the four groups were differentiated by their barcodes and then assembled into contigs with SOAPdenove software (BGI, Shenzhen, China).","type":"software","software-name":{"offsetStart":170,"normalizedForm":"SOAPdenove","offsetEnd":180,"rawForm":"SOAPdenove","boundingBoxes":[{"x":110.38,"h":8.1324,"y":394.038,"p":3,"w":49.1802}]}},
  {"_key":"60c20f487723bebd8664597c","_id":"annotations/60c20f487723bebd8664597c","_rev":"_cfFmX8O---","document":{"$oid":"60c20f487723bebd86645974"},"publisher":{"offsetStart":221,"normalizedForm":"Premier Biosoft International","offsetEnd":250,"rawForm":"Premier Biosoft International","boundingBoxes":[{"x":145.885325,"h":8.132399999999961,"y":556.402,"p":3,"w":105.96549642857141}]},"context":"To validate the results of Solexa sequencing, primers to amplify identified viral sequences were synthesized according to publica- tions, or designed based on the Solexa sequences obtained in this study using Primer 5 (Premier Biosoft International, Palo Alto, CA) and Genefisher (http://bibiserv.techfak.uni-bielefeld.de/bibi/ Tools.html).","type":"software","software-name":{"offsetStart":211,"normalizedForm":"Primer","offsetEnd":217,"rawForm":"Primer","boundingBoxes":[{"x":104.257,"h":8.1324,"y":556.402,"p":3,"w":24.9173}]},"version":{"offsetStart":218,"normalizedForm":"5","offsetEnd":219,"rawForm":"5","boundingBoxes":[{"x":133.339,"h":8.1324,"y":556.402,"p":3,"w":4.4831}]}},
  {"_key":"60c20f487723bebd8664597d","_id":"annotations/60c20f487723bebd8664597d","_rev":"_cfFmX8a---","document":{"$oid":"60c20f487723bebd86645974"},"context":"To validate the results of Solexa sequencing, primers to amplify identified viral sequences were synthesized according to publica- tions, or designed based on the Solexa sequences obtained in this study using Primer 5 (Premier Biosoft International, Palo Alto, CA) and Genefisher (http://bibiserv.techfak.uni-bielefeld.de/bibi/ Tools.html).","type":"software","software-name":{"offsetStart":272,"normalizedForm":"Genefisher","offsetEnd":282,"rawForm":"Genefisher","boundingBoxes":[{"x":90.5942,"h":8.1324,"y":566.947,"p":3,"w":39.0931}]},"url":{"offsetStart":284,"normalizedForm":"http://bibiserv.techfak.uni-bielefeld.de/bibi/ Tools.html","offsetEnd":342,"rawForm":"http://bibiserv.techfak.uni-bielefeld.de/bibi/ \nTools.html","boundingBoxes":[{"x":135.32297872340425,"h":8.132399999999961,"y":566.947,"p":3,"w":161.6890212765958},{"x":58.0537,"h":8.132399999999961,"y":577.549,"p":3,"w":36.39566666666666}]}},
  {"_key":"60c20f497723bebd8664597f","_id":"annotations/60c20f497723bebd8664597f","_rev":"_cfFmX8m---","wikipediaExternalRef":21572326,"document":{"$oid":"60c20f497723bebd8664597e"},"context":"Statistical compari- son between the groups was performed by the Student t test, using GraphPad Prism 6. Differences were considered statisti- cally significant when the P value was <.05.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":88,"wikidataId":"Q5597066","offsetEnd":102,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":72.5676,"h":8.854000000000042,"y":598.501,"p":3,"w":64.1094}]},"version":{"offsetStart":103,"normalizedForm":"6","offsetEnd":104,"rawForm":"6","boundingBoxes":[{"x":139.92,"h":8.854,"y":598.501,"p":3,"w":3.31075}]}},
  {"_key":"60c20f537723bebd86645981","_id":"annotations/60c20f537723bebd86645981","_rev":"_cfFmX8y---","document":{"$oid":"60c20f537723bebd86645980"},"type":"software","software-name":{"offsetStart":92,"normalizedForm":"LINGO","offsetEnd":97,"rawForm":"LINGO","boundingBoxes":[{"x":51.0226,"h":11.48,"y":166.99,"p":19,"w":31}]},"context":"Meanwhile, we also presented the optimal solution by using nonlinear programming software LINGO in this table."},
  {"_key":"60c20f587723bebd86645983","_id":"annotations/60c20f587723bebd86645983","_rev":"_cfFmX9----","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"GOEA","offsetEnd":4,"rawForm":"GOEA","boundingBoxes":[{"x":235.209,"h":6.8908,"y":244.346,"p":7,"w":28.0908}]},"context":"GOEA on each of the modules identified associated gene signatures  displaying distinct functional characteristics, which distinguish the different sample groups G1-G6 (Fig.  2d+S3, Table S3)."},
  {"_key":"60c20f587723bebd86645984","_id":"annotations/60c20f587723bebd86645984","_rev":"_cfFmX9K---","document":{"$oid":"60c20f587723bebd86645982"},"context":"DESeq2 was used for the calculation of  normalized counts for each transcript using default parameters.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"DESeq","offsetEnd":5,"rawForm":"DESeq","boundingBoxes":[{"x":352.311,"h":6.8908,"y":517.634,"p":26,"w":36.2498}]},"version":{"offsetStart":5,"normalizedForm":"2","offsetEnd":6,"rawForm":"2","boundingBoxes":[{"x":352.311,"h":6.8908,"y":517.634,"p":26,"w":36.2498}]}},
  {"_key":"60c20f587723bebd86645985","_id":"annotations/60c20f587723bebd86645985","_rev":"_cfFmX9W---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"compareCluster","offsetEnd":14,"rawForm":"compareCluster","boundingBoxes":[{"x":70.052,"h":6.8908,"y":321.379,"p":23,"w":68.6758}]},"context":"compareCluster and enrichGo functions from the R package ClusterProfiler (v3.12.0) (90) were used to  determine significant enrichment (q-value<0.05) of biological processes."},
  {"_key":"60c20f587723bebd86645986","_id":"annotations/60c20f587723bebd86645986","_rev":"_cfFmX9i---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":4,"normalizedForm":"gsva","offsetEnd":8,"rawForm":"gsva","boundingBoxes":[{"x":243.427,"h":6.8713,"y":707.048,"p":27,"w":20.5549}]},"context":"The gsva method was used for the run and data were visualized in a  heat map with the pheatmap (v1.0.12) package."},
  {"_key":"60c20f587723bebd86645987","_id":"annotations/60c20f587723bebd86645987","_rev":"_cfFmX9u---","document":{"$oid":"60c20f587723bebd86645982"},"context":"The GSVA R package (v1.34.0) (103) was used to test the enrichment of neutrophil signatures (42) in the  normalized gene expression table.","type":"software","software-name":{"offsetStart":4,"normalizedForm":"GSVA R","offsetEnd":10,"rawForm":"GSVA R","boundingBoxes":[{"x":89.6731,"h":6.890800000000013,"y":690.273,"p":27,"w":36.89869999999999}]},"version":{"offsetStart":21,"normalizedForm":"1.34.0","offsetEnd":27,"rawForm":"1.34.0","boundingBoxes":[{"x":173.38254444444445,"h":6.890800000000013,"y":690.273,"p":27,"w":29.8658111111111}]}},
  {"_key":"60c20f587723bebd86645988","_id":"annotations/60c20f587723bebd86645988","_rev":"_cfFmX96---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":4,"normalizedForm":"CoCena 2","offsetEnd":12,"rawForm":"CoCena 2","boundingBoxes":[{"x":448.819,"h":6.8908,"y":323.128,"p":26,"w":35.6841},{"x":484.487,"h":4.4908,"y":321.349,"p":26,"w":3.5217}]},"context":"The CoCena 2 network  was visualized by using the ggplot function from the ggplot2 package."},
  {"_key":"60c20f587723bebd86645989","_id":"annotations/60c20f587723bebd86645989","_rev":"_cfFmY-C---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":10,"normalizedForm":"R-package pcaGoPromoter","offsetEnd":35,"rawForm":"R-package pcaGoPromoter","boundingBoxes":[{"x":406.787,"h":6.890800000000013,"y":683.557,"p":25,"w":118.62990000000008}]},"context":"Using the R-package pcaGoPromoter  (99) the genes are also analyzed for enrichment of transcription factor binding sides and if the predicted transcription factors are present in the data, their expression profile is visualized to facilitate evaluation of  their possible role."},
  {"_key":"60c20f587723bebd8664598a","_id":"annotations/60c20f587723bebd8664598a","_rev":"_cfFmY-O---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":14,"normalizedForm":"R-package clusterProfiler","offsetEnd":39,"rawForm":"R-package clusterProfiler","boundingBoxes":[{"x":124.054,"h":6.890800000000013,"y":650.017,"p":25,"w":108.53590625000001}]},"context":"Utilizing the R-package clusterProfiler, CoCena² automatically analyses the gene clusters with respect to  different kinds of gene set enrichments: The genes within each cluster are scanned for enrichment in KEGG  (95), Hallmark (96), Gene-Ontology terms (97) and Reactome (98)."},
  {"_key":"60c20f587723bebd8664598b","_id":"annotations/60c20f587723bebd8664598b","_rev":"_cfFmY-a---","wikipediaExternalRef":638429,"document":{"$oid":"60c20f587723bebd86645982"},"context":"from the package fpc (version 2.2-5).","wikidataId":"Q210295","type":"software","lang":"en","confidence":0.386,"software-name":{"wikipediaExternalRef":638429,"normalizedForm":"fpc","offsetStart":17,"wikidataId":"Q210295","offsetEnd":20,"lang":"en","confidence":0.386,"rawForm":"fpc","boundingBoxes":[{"x":257.597,"h":6.8908,"y":626.497,"p":23,"w":12.9665}]},"version":{"offsetStart":30,"normalizedForm":"2.2-5","offsetEnd":35,"rawForm":"2.2-5","boundingBoxes":[{"x":311.27,"h":6.890800000000013,"y":626.497,"p":23,"w":20.080857142857155}]}},
  {"_key":"60c20f587723bebd8664598c","_id":"annotations/60c20f587723bebd8664598c","_rev":"_cfFmY-m---","document":{"$oid":"60c20f587723bebd86645982"},"context":"Next, we used the CoCena 2 modules from the whole blood analysis (Fig. 2c) to identify modules that are  actually driven by alterations in neutrophil activation instead of a mere increase in the neutrophil population.","type":"software","software-name":{"offsetStart":18,"normalizedForm":"CoCena","offsetEnd":24,"rawForm":"CoCena","boundingBoxes":[{"x":151.952,"h":6.8908,"y":505.845,"p":9,"w":35.6841}]},"version":{"offsetStart":108,"normalizedForm":"2","offsetEnd":111,"rawForm":"2","boundingBoxes":[{"x":521.902,"h":4.4908,"y":252.492,"p":24,"w":3.5217}]}},
  {"_key":"60c20f587723bebd8664598d","_id":"annotations/60c20f587723bebd8664598d","_rev":"_cfFmY-y---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":19,"normalizedForm":"enrichGo","offsetEnd":27,"rawForm":"enrichGo","boundingBoxes":[{"x":162.276,"h":6.8908,"y":321.379,"p":23,"w":39.4924}]},"context":"compareCluster and enrichGo functions from the R package ClusterProfiler (v3.12.0) (90) were used to  determine significant enrichment (q-value<0.05) of biological processes."},
  {"_key":"60c20f587723bebd8664598e","_id":"annotations/60c20f587723bebd8664598e","_rev":"_cfFmY_----","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":33,"normalizedForm":"DESeqDataSetFromHTSeqCount","offsetEnd":59,"rawForm":"DESeqDataSetFromHTSeqCount","boundingBoxes":[{"x":70.052,"h":6.8908,"y":517.634,"p":26,"w":144.913}]},"context":"Raw counts were imported using  DESeqDataSetFromHTSeqCount function and rlog transformed."},
  {"_key":"60c20f587723bebd8664598f","_id":"annotations/60c20f587723bebd8664598f","_rev":"_cfFmY_K---","document":{"$oid":"60c20f587723bebd86645982"},"context":"compareCluster and enrichGo functions from the R package ClusterProfiler (v3.12.0) (90) were used to  determine significant enrichment (q-value<0.05) of biological processes.","type":"software","software-name":{"offsetStart":47,"normalizedForm":"R package ClusterProfiler","offsetEnd":72,"rawForm":"R package ClusterProfiler","boundingBoxes":[{"x":288.342,"h":6.890800000000013,"y":321.379,"p":23,"w":112.77200000000005}]},"version":{"offsetStart":75,"normalizedForm":"3.12.0","offsetEnd":81,"rawForm":"3.12.0","boundingBoxes":[{"x":409.0415111111111,"h":6.890800000000013,"y":321.379,"p":23,"w":29.844577777777772}]}},
  {"_key":"60c20f587723bebd86645990","_id":"annotations/60c20f587723bebd86645990","_rev":"_cfFmY_W---","document":{"$oid":"60c20f587723bebd86645982"},"context":"Sequenced reads were aligned and quantified using STAR: ultrafast universal RNA-seq aligner (v2.","type":"software","software-name":{"offsetStart":50,"normalizedForm":"STAR","offsetEnd":54,"rawForm":"STAR","boundingBoxes":[{"x":300.133,"h":6.8908,"y":652.272,"p":22,"w":22.90032}]},"version":{"offsetStart":94,"normalizedForm":"2","offsetEnd":95,"rawForm":"2","boundingBoxes":[{"x":491.24754444444443,"h":6.8908,"y":652.272,"p":22,"w":8.533088888888887}]}},
  {"_key":"60c20f587723bebd86645991","_id":"annotations/60c20f587723bebd86645991","_rev":"_cfFmY_e---","document":{"$oid":"60c20f587723bebd86645982"},"context":"Applying such an approach using our established  CoCena² pipeline [https://github.com/Ulas-lab/CoCena2]","type":"software","software-name":{"offsetStart":50,"normalizedForm":"CoCena² pipeline","offsetEnd":66,"rawForm":"CoCena² pipeline","boundingBoxes":[{"x":70.052,"h":6.890800000000013,"y":704.735,"p":6,"w":76.38770000000001}]},"url":{"offsetStart":68,"normalizedForm":"https://github.com/Ulas-lab/CoCena2","offsetEnd":103,"rawForm":"https://github.com/Ulas-lab/CoCena2","boundingBoxes":[{"x":154.8395945945946,"h":6.890800000000013,"y":704.735,"p":6,"w":155.52581081081087}]}},
  {"_key":"60c20f587723bebd86645992","_id":"annotations/60c20f587723bebd86645992","_rev":"_cfFmY_u---","document":{"$oid":"60c20f587723bebd86645982"},"context":"The CoCena 2 network  was visualized by using the ggplot function from the ggplot2 package.","type":"software","software-name":{"offsetStart":51,"normalizedForm":"ggplot","offsetEnd":57,"rawForm":"ggplot","boundingBoxes":[{"x":197.378,"h":6.8908,"y":339.893,"p":26,"w":26.4987}]},"version":{"offsetStart":122,"normalizedForm":"2","offsetEnd":125,"rawForm":"2","boundingBoxes":[{"x":493.494,"h":6.8908,"y":177.207,"p":24,"w":31.9253}]}},
  {"_key":"60c20f587723bebd86645993","_id":"annotations/60c20f587723bebd86645993","_rev":"_cfFmY_6---","document":{"$oid":"60c20f587723bebd86645982"},"context":"Granulocyte raw data was aligned and quantified using STAR (v2.7.3a) and the human reference genome,  GRCh38p13, from the Genome Reference Consortium.","type":"software","software-name":{"offsetStart":54,"normalizedForm":"STAR","offsetEnd":58,"rawForm":"STAR","boundingBoxes":[{"x":307.574,"h":6.8908,"y":484.094,"p":26,"w":25.9514}]},"version":{"offsetStart":61,"normalizedForm":"2.7.3a","offsetEnd":67,"rawForm":"2.7.3a","boundingBoxes":[{"x":340.3114,"h":6.890800000000013,"y":484.094,"p":26,"w":29.871800000000007}]}},
  {"_key":"60c20f587723bebd86645994","_id":"annotations/60c20f587723bebd86645994","_rev":"_cfFmYAG---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":60,"normalizedForm":"ssGSVA","offsetEnd":66,"rawForm":"ssGSVA","boundingBoxes":[{"x":341.29743333333334,"h":6.8908,"y":160.442,"p":12,"w":30.6206}]},"context":"A combination of single sample gene set variation analysis (ssGSVA), a non-parametric, unsupervised  approach to estimate variation of gene set enrichment within each single sample, and Hallmark enrichment  for each disease or inflammatory condition in the compiled dataset accentuated the findings on COVID-19  blood transcriptomes in context of the other diseases (Fig. 4c)."},
  {"_key":"60c20f587723bebd86645995","_id":"annotations/60c20f587723bebd86645995","_rev":"_cfFmYAO---","document":{"$oid":"60c20f587723bebd86645982"},"context":"Agglomerative  hierarchical clustering was performed by the hclust function (cluster package, version 2.1.0),","type":"software","software-name":{"offsetStart":61,"normalizedForm":"hclust","offsetEnd":67,"rawForm":"hclust","boundingBoxes":[{"x":274.572,"h":6.8908,"y":537.646,"p":25,"w":25.4149}]},"version":{"offsetStart":103,"normalizedForm":"2.1.0","offsetEnd":108,"rawForm":"2.1.0","boundingBoxes":[{"x":459.921,"h":6.890800000000013,"y":537.646,"p":25,"w":19.699642857142862}]}},
  {"_key":"60c20f587723bebd86645996","_id":"annotations/60c20f587723bebd86645996","_rev":"_cfFmYAa---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":72,"normalizedForm":"enrichGO","offsetEnd":80,"rawForm":"enrichGO","boundingBoxes":[{"x":134.415,"h":6.8908,"y":390.257,"p":26,"w":41.6094}]},"context":"GO enrichment analysis was performed on each cluster  by utilizing the enrichGO function from the clusterProfiler package to assess the overall functionality of the  cluster using the genes of each cluster as the input and all the in the network as background."},
  {"_key":"60c20f587723bebd86645997","_id":"annotations/60c20f587723bebd86645997","_rev":"_cfFmYAm---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":75,"normalizedForm":"GOEA","offsetEnd":79,"rawForm":"GOEA","boundingBoxes":[{"x":387.854,"h":6.8908,"y":271.044,"p":23,"w":28.119}]},"context":"To test for functional enrichment within all three scenarios, we performed GOEA for up-or downregulated  transcripts in the respective comparison using gene ontology set of biological processes."},
  {"_key":"60c20f587723bebd86645998","_id":"annotations/60c20f587723bebd86645998","_rev":"_cfFmYAy---","wikipediaExternalRef":32380922,"document":{"$oid":"60c20f587723bebd86645982"},"context":"The CoCena 2 network  was visualized by using the ggplot function from the ggplot2 package.","wikidataId":"Q326489","type":"software","confidence":0.4972,"software-name":{"wikipediaExternalRef":32380922,"normalizedForm":"ggplot2","offsetStart":76,"wikidataId":"Q326489","offsetEnd":83,"lang":"en","confidence":0.4972,"rawForm":"ggplot2","boundingBoxes":[{"x":307.153,"h":6.890800000000013,"y":339.893,"p":26,"w":31.903999999999996}]},"lang":"en"},
  {"_key":"60c20f587723bebd86645999","_id":"annotations/60c20f587723bebd86645999","_rev":"_cfFmYB----","document":{"$oid":"60c20f587723bebd86645982"},"context":"Unbiased clustering was performed using the \"label propagation\" algorithm in igraph (v1.2.1) [The igraph  software package for complex network research] and was repeated 1,000 times.","type":"software","software-name":{"offsetStart":77,"normalizedForm":"igraph","offsetEnd":83,"rawForm":"igraph","boundingBoxes":[{"x":409.278,"h":6.8908,"y":391.696,"p":25,"w":27.0119}]},"version":{"offsetStart":86,"normalizedForm":"1.2.1","offsetEnd":91,"rawForm":"1.2.1","boundingBoxes":[{"x":443.61905,"h":6.890800000000013,"y":391.696,"p":25,"w":24.774299999999982}]}},
  {"_key":"60c20f587723bebd8664599a","_id":"annotations/60c20f587723bebd8664599a","_rev":"_cfFmYBK---","document":{"$oid":"60c20f587723bebd86645982"},"context":"The counts were imported into R (v3.6.2) and were  modelled for each gene using DESeq2.","type":"software","software-name":{"offsetStart":81,"normalizedForm":"DESeq","offsetEnd":86,"rawForm":"DESeq","boundingBoxes":[{"x":207.819,"h":6.8908,"y":194.011,"p":27,"w":33.387342857142855}]},"version":{"offsetStart":86,"normalizedForm":"2","offsetEnd":87,"rawForm":"2","boundingBoxes":[{"x":207.819,"h":6.8908,"y":194.011,"p":27,"w":33.387342857142855}]}},
  {"_key":"60c20f587723bebd8664599b","_id":"annotations/60c20f587723bebd8664599b","_rev":"_cfFmYBW---","document":{"$oid":"60c20f587723bebd86645982"},"context":"The gsva method was used for the run and data were visualized in a  heat map with the pheatmap (v1.0.12) package.","type":"software","software-name":{"offsetStart":87,"normalizedForm":"pheatmap","offsetEnd":95,"rawForm":"pheatmap","boundingBoxes":[{"x":149.566,"h":6.8908,"y":723.813,"p":27,"w":43.2258}]},"version":{"offsetStart":98,"normalizedForm":"1.0.12","offsetEnd":104,"rawForm":"1.0.12","boundingBoxes":[{"x":199.7827,"h":6.890800000000013,"y":723.813,"p":27,"w":29.852900000000005}]}},
  {"_key":"60c20f587723bebd8664599c","_id":"annotations/60c20f587723bebd8664599c","_rev":"_cfFmYBi---","document":{"$oid":"60c20f587723bebd86645982"},"context":"Unbiased clustering was performed using the \"label propagation\" algorithm in igraph (v1.2.1) [The igraph  software package for complex network research] and was repeated 1,000 times.","type":"software","software-name":{"offsetStart":98,"normalizedForm":"igraph","offsetEnd":106,"rawForm":"igraph","boundingBoxes":[{"x":498.412,"h":6.8908,"y":391.696,"p":25,"w":27.0051}]},"version":{"offsetStart":86,"normalizedForm":"1.2.1","offsetEnd":91,"rawForm":"1.2.1","boundingBoxes":[{"x":443.61905,"h":6.890800000000013,"y":391.696,"p":25,"w":24.774299999999982}]}},
  {"_key":"60c20f587723bebd8664599d","_id":"annotations/60c20f587723bebd8664599d","_rev":"_cfFmYBu---","document":{"$oid":"60c20f587723bebd86645982"},"context":"To define differences and similarities in transcript expression patterns among the different groups, CoCena 2  (Construction of co-expression Network Analysis -automated) was performed based on Pearson  correlation.","type":"software","software-name":{"offsetStart":101,"normalizedForm":"CoCena","offsetEnd":107,"rawForm":"CoCena","boundingBoxes":[{"x":486.208,"h":6.8908,"y":254.279,"p":24,"w":35.6831}]},"version":{"offsetStart":108,"normalizedForm":"2","offsetEnd":111,"rawForm":"2","boundingBoxes":[{"x":521.902,"h":4.4908,"y":252.492,"p":24,"w":3.5217}]}},
  {"_key":"60c20f587723bebd8664599e","_id":"annotations/60c20f587723bebd8664599e","_rev":"_cfFmYB6---","document":{"$oid":"60c20f587723bebd86645982"},"context":"The algorithm  was subsequently run with 1,000 permutations and the proportions of cell types were visualized with ggplot2  (v3.2.1) (93).","type":"software","software-name":{"offsetStart":116,"normalizedForm":"ggplot","offsetEnd":122,"rawForm":"ggplot","boundingBoxes":[{"x":493.494,"h":6.8908,"y":177.207,"p":24,"w":31.9253}]},"version":{"offsetStart":122,"normalizedForm":"2","offsetEnd":125,"rawForm":"2","boundingBoxes":[{"x":493.494,"h":6.8908,"y":177.207,"p":24,"w":31.9253}]}},
  {"_key":"60c20f587723bebd8664599f","_id":"annotations/60c20f587723bebd8664599f","_rev":"_cfFmYCG---","document":{"$oid":"60c20f587723bebd86645982"},"context":"To identify genes whose expression patterns are highly similar across all tested samples, pairwise Pearson  correlation coefficients are calculated using the R package Hmisc (v4.1-1).","type":"software","software-name":{"offsetStart":159,"normalizedForm":"R package Hmisc","offsetEnd":174,"rawForm":"R package Hmisc","boundingBoxes":[{"x":277.302,"h":6.890800000000013,"y":383.386,"p":24,"w":77.01329999999996}]},"version":{"offsetStart":177,"normalizedForm":"4.1-1","offsetEnd":182,"rawForm":"4.1-1","boundingBoxes":[{"x":361.4233888888889,"h":6.890800000000013,"y":383.386,"p":24,"w":24.10433333333333}]}},
  {"_key":"60c20f587723bebd866459a0","_id":"annotations/60c20f587723bebd866459a0","_rev":"_cfFmYCS---","document":{"$oid":"60c20f587723bebd86645982"},"context":"The number drugs currently recommended or investigated, as well as the number of  clinical trials within the respective drug classes were visualized using the ggplot2 package (105, 106).","type":"software","software-name":{"offsetStart":160,"normalizedForm":"ggplot","offsetEnd":166,"rawForm":"ggplot","boundingBoxes":[{"x":384.778,"h":6.8908,"y":242.606,"p":28,"w":31.8884}]},"version":{"offsetStart":166,"normalizedForm":"2","offsetEnd":167,"rawForm":"2","boundingBoxes":[{"x":384.778,"h":6.8908,"y":242.606,"p":28,"w":31.8884}]}},
  {"_key":"60c20f587723bebd866459a1","_id":"annotations/60c20f587723bebd866459a1","_rev":"_cfFmYCa---","document":{"$oid":"60c20f587723bebd86645982"},"context":"High-throughput sequencing was carried out with a  NovaSeq™ 6000 Sequencing System S2 (50bp paired-end reads), and data was converted into fastq files  using bcl2fastq2 v2.20.","type":"software","software-name":{"offsetStart":160,"normalizedForm":"bcl2fastq2","offsetEnd":170,"rawForm":"bcl2fastq2","boundingBoxes":[{"x":96.0333,"h":6.890800000000013,"y":599.799,"p":22,"w":44.380499999999984}]},"version":{"offsetStart":172,"normalizedForm":"2.20","offsetEnd":176,"rawForm":"2.20","boundingBoxes":[{"x":143.116,"h":6.890800000000013,"y":599.799,"p":22,"w":22.05066666666667}]}},
  {"_key":"60c20f587723bebd866459a2","_id":"annotations/60c20f587723bebd866459a2","_rev":"_cfFmYCm---","document":{"$oid":"60c20f587723bebd86645982"},"context":"To identify drugs, which reverse the gene expression signature observed in the comparisons of the COVID- Patterns of differential gene expression of genes targeted by drugs which are currently approved or under  investigation for the treatment of COVID-19 patients were visualized using ggplot2.","type":"software","software-name":{"offsetStart":289,"normalizedForm":"ggplot","offsetEnd":295,"rawForm":"ggplot","boundingBoxes":[{"x":404.386,"h":6.8908,"y":172.114,"p":29,"w":30.280337499999998}]},"version":{"offsetStart":295,"normalizedForm":"2","offsetEnd":296,"rawForm":"2","boundingBoxes":[{"x":404.386,"h":6.8908,"y":172.114,"p":29,"w":30.280337499999998}]}},
  {"_key":"60c20f587723bebd866459a3","_id":"annotations/60c20f587723bebd866459a3","_rev":"_cfFmYCy---","document":{"$oid":"60c20f587723bebd86645982"},"type":"software","software-name":{"offsetStart":79647,"normalizedForm":"hclust","offsetEnd":79653,"rawForm":"hclust","boundingBoxes":[{"x":372.017,"h":6.8908,"y":592.957,"p":23,"w":25.4129}]},"version":{"offsetStart":103,"normalizedForm":"2.1.0","offsetEnd":108,"rawForm":"2.1.0","boundingBoxes":[{"x":459.921,"h":6.890800000000013,"y":537.646,"p":25,"w":19.699642857142862}]}},
  {"_key":"60c20f5a7723bebd866459a5","_id":"annotations/60c20f5a7723bebd866459a5","_rev":"_cfFmYDC---","wikipediaExternalRef":179088,"document":{"$oid":"60c20f5a7723bebd866459a4"},"publisher":{"offsetStart":70,"normalizedForm":"IBM Corp","offsetEnd":78,"rawForm":"IBM Corp","boundingBoxes":[{"x":109.07135000000001,"h":11.681600000000003,"y":535.208,"p":3,"w":38.47096999999998}]},"context":"The data were statistically analyzed using SPSS software version 25 (IBM Corp, Armonk, NY, USA).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":43,"wikidataId":"Q181596","offsetEnd":47,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":231.719,"h":11.6816,"y":523.213,"p":3,"w":20.6584}]},"version":{"offsetStart":66,"normalizedForm":"25","offsetEnd":68,"rawForm":"25","boundingBoxes":[{"x":90.1599,"h":11.6816,"y":535.208,"p":3,"w":9.8392}]}},
  {"_key":"60c20f627723bebd866459a7","_id":"annotations/60c20f627723bebd866459a7","_rev":"_cfFmYDK---","wikipediaExternalRef":1092923,"document":{"$oid":"60c20f627723bebd866459a6"},"context":"Google, Google Scholar, SCOPUS, Medline and Science Direct) which collate the scientific publications in the area.","wikidataId":"Q95","type":"software","confidence":0.3335,"software-name":{"wikipediaExternalRef":1092923,"normalizedForm":"Google","offsetStart":0,"wikidataId":"Q95","offsetEnd":6,"lang":"en","confidence":0.3335,"rawForm":"Google","boundingBoxes":[{"x":119.34,"h":7.5398,"y":357.942,"p":4,"w":24.603514285714283}]},"lang":"en"},
  {"_key":"60c20f627723bebd866459a8","_id":"annotations/60c20f627723bebd866459a8","_rev":"_cfFmYDW---","wikipediaExternalRef":1520204,"document":{"$oid":"60c20f627723bebd866459a6"},"context":"Google, Google Scholar, SCOPUS, Medline and Science Direct) which collate the scientific publications in the area.","wikidataId":"Q494817","type":"software","confidence":0.9596,"software-name":{"wikipediaExternalRef":1520204,"normalizedForm":"Google Scholar","offsetStart":8,"wikidataId":"Q494817","offsetEnd":22,"lang":"en","confidence":0.9596,"rawForm":"Google Scholar","boundingBoxes":[{"x":150.224,"h":7.539800000000014,"y":357.942,"p":4,"w":55.006225}]},"lang":"en"},
  {"_key":"60c20f637723bebd866459aa","_id":"annotations/60c20f637723bebd866459aa","_rev":"_cfFmYDi---","wikipediaExternalRef":20268,"document":{"$oid":"60c20f637723bebd866459a9"},"publisher":{"offsetStart":0,"normalizedForm":"Microsoft","offsetEnd":9,"rawForm":"Microsoft","boundingBoxes":[{"x":150,"h":9,"y":484.006,"p":3,"w":39.44}]},"context":"Microsoft Excel software was used for data analysis and for graphical representation.","wikidataId":"Q11272","type":"software","confidence":0.378,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Excel","offsetStart":10,"wikidataId":"Q11272","offsetEnd":15,"lang":"en","confidence":0.378,"rawForm":"Excel","boundingBoxes":[{"x":191.94,"h":9,"y":484.006,"p":3,"w":22.77}]},"lang":"en"},
  {"_key":"60c20f637723bebd866459ab","_id":"annotations/60c20f637723bebd866459ab","_rev":"_cfFmYDu---","document":{"$oid":"60c20f637723bebd866459a9"},"publisher":{"offsetStart":132,"normalizedForm":"Ted Pella, Inc","offsetEnd":146,"rawForm":"Ted Pella, Inc","boundingBoxes":[{"x":293.04,"h":9,"y":110.006,"p":3,"w":52.321999999999946}]},"context":"The wall thickness was measured in 2 different areas for each half catheter segment using Motic Images Plus 2.0 imaging software (Ted Pella, Inc., Redding, CA).","type":"software","software-name":{"offsetStart":91,"normalizedForm":"Motic Images Plus","offsetEnd":109,"rawForm":"Motic \nImages Plus","boundingBoxes":[{"x":493.24,"h":9,"y":98.0069,"p":3,"w":23.89},{"x":150,"h":9,"y":110.006,"p":3,"w":48.609999999999985}]},"version":{"offsetStart":110,"normalizedForm":"2.0","offsetEnd":113,"rawForm":"2.0","boundingBoxes":[{"x":201.11,"h":9,"y":110.006,"p":3,"w":12.5}]}},
  {"_key":"60c20f6d7723bebd866459ad","_id":"annotations/60c20f6d7723bebd866459ad","_rev":"_cfFmYD6---","wikipediaExternalRef":20935,"document":{"$oid":"60c20f6d7723bebd866459ac"},"publisher":{"offsetStart":6,"normalizedForm":"Microsoft","offsetEnd":15,"rawForm":"Microsoft","boundingBoxes":[{"x":426.141,"h":9.1806,"y":445.77,"p":2,"w":37.293}]},"context":"Using Microsoft Access, each dataset (SET-A and B) was compared (mapped) with the lung-protein database to select the proteins that are present in both datasets, which demonstrate the binding and regulatory events occur in Human lung tissue.","wikidataId":"Q80689","type":"software","confidence":0.2898,"software-name":{"wikipediaExternalRef":20935,"normalizedForm":"Access","offsetStart":16,"wikidataId":"Q80689","offsetEnd":22,"lang":"en","confidence":0.2898,"rawForm":"Access","boundingBoxes":[{"x":468.701,"h":9.1806,"y":445.77,"p":2,"w":23.472942857142858}]},"lang":"en"},
  {"_key":"60c20f6d7723bebd866459ae","_id":"annotations/60c20f6d7723bebd866459ae","_rev":"_cfFmYEG---","wikipediaExternalRef":20935,"document":{"$oid":"60c20f6d7723bebd866459ac"},"publisher":{"offsetStart":6,"normalizedForm":"Microsoft","offsetEnd":15,"rawForm":"Microsoft","boundingBoxes":[{"x":428.246,"h":9.1806,"y":569.438,"p":2,"w":37.293}]},"context":"Using Microsoft Access, all collected interactions were mapped to the lung-protein database to construct human lung protein-protein interactome, if both the interacting proteins neighbors were expressed in lung tissue.","wikidataId":"Q80689","type":"software","confidence":0.2898,"software-name":{"wikipediaExternalRef":20935,"normalizedForm":"Access","offsetStart":16,"wikidataId":"Q80689","offsetEnd":22,"lang":"en","confidence":0.2898,"rawForm":"Access","boundingBoxes":[{"x":470.537,"h":9.1806,"y":569.438,"p":2,"w":23.472942857142858}]},"lang":"en"},
  {"_key":"60c20f6d7723bebd866459af","_id":"annotations/60c20f6d7723bebd866459af","_rev":"_cfFmYES---","wikipediaExternalRef":20935,"document":{"$oid":"60c20f6d7723bebd866459ac"},"publisher":{"offsetStart":30,"normalizedForm":"Microsoft","offsetEnd":39,"rawForm":"Microsoft","boundingBoxes":[{"x":513.144,"h":9.1806,"y":422.857,"p":2,"w":37.293}]},"context":"database and integrated using Microsoft Access based on the common identifier to create an in-house lung-protein database.","wikidataId":"Q80689","type":"software","confidence":0.2898,"software-name":{"wikipediaExternalRef":20935,"normalizedForm":"Access","offsetStart":41,"wikidataId":"Q80689","offsetEnd":47,"lang":"en","confidence":0.2898,"rawForm":"Access","boundingBoxes":[{"x":305.109,"h":9.1806,"y":434.314,"p":2,"w":25.2266}]},"lang":"en"},
  {"_key":"60c20f6d7723bebd866459b0","_id":"annotations/60c20f6d7723bebd866459b0","_rev":"_cfFmYEe---","document":{"$oid":"60c20f6d7723bebd866459ac"},"type":"software","software-name":{"offsetStart":172,"normalizedForm":"DESeq","offsetEnd":177,"rawForm":"DESeq","boundingBoxes":[{"x":140.706,"h":9.1806,"y":621.822,"p":5,"w":25.6714}]},"context":"After quality assessment, the reads were aligned to the human genome (hg19) following the RNA-Seq analysis pipeline to determine the differential expression genes using DESeq with p-value < 0.05."},
  {"_key":"60c20f6d7723bebd866459b1","_id":"annotations/60c20f6d7723bebd866459b1","_rev":"_cfFmYEq---","wikipediaExternalRef":20935,"document":{"$oid":"60c20f6d7723bebd866459ac"},"publisher":{"offsetStart":223,"normalizedForm":"Microsoft","offsetEnd":232,"rawForm":"Microsoft","boundingBoxes":[{"x":175.204,"h":9.1806,"y":447.42,"p":5,"w":37.2935}]},"context":"Subsequently, in order to determine the involvement of each hub in viral pathogenesis, the expression data of SARS-CoV-2 infection was analyzed, and the differential expressed genes were mapped to the hub proteins using Microsoft Access.","wikidataId":"Q80689","type":"software","confidence":0.2898,"software-name":{"wikipediaExternalRef":20935,"normalizedForm":"Access","offsetStart":233,"wikidataId":"Q80689","offsetEnd":239,"lang":"en","confidence":0.2898,"rawForm":"Access","boundingBoxes":[{"x":214.651,"h":9.1806,"y":447.42,"p":5,"w":23.472857142857144}]},"lang":"en"},
  {"_key":"60c20f707723bebd866459b3","_id":"annotations/60c20f707723bebd866459b3","_rev":"_cfFmYE2---","wikipediaExternalRef":20412,"document":{"$oid":"60c20f707723bebd866459b2"},"context":"In this study, the ANN model was developed using the MATLAB software by applying the backpropagation method to model and predict the daily av- erage concentration of NO 2 , SO 2 , and PM 10 by feeding meteo- rological parameters as input to the model.","wikidataId":"Q169478","type":"software","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":54,"wikidataId":"Q169478","offsetEnd":60,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":168.722,"h":8.7472,"y":331.121,"p":5,"w":40.6125}]},"lang":"en"},
  {"_key":"60c20f737723bebd866459b5","_id":"annotations/60c20f737723bebd866459b5","_rev":"_cfFmYFC---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20f737723bebd866459b4"},"context":"The level of statistical significance was p<0.05 and the  analyses were performed using Stata 16 and R 3.6.2.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":89,"wikidataId":"Q1204300","offsetEnd":94,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":224.09,"h":10.8,"y":388.574,"p":3,"w":24.036}]},"version":{"offsetStart":95,"normalizedForm":"16","offsetEnd":97,"rawForm":"16","boundingBoxes":[{"x":251.078,"h":10.8,"y":388.574,"p":3,"w":12}]}},
  {"_key":"60c20f7f7723bebd866459b8","_id":"annotations/60c20f7f7723bebd866459b8","_rev":"_cfFmYFO---","document":{"$oid":"60c20f7f7723bebd866459b7"},"context":"OMS, MA and ADB removed duplicates using Mendeley Desktop v1.19.4.","type":"software","software-name":{"offsetStart":42,"normalizedForm":"Mendeley Desktop","offsetEnd":58,"rawForm":"Mendeley Desktop","boundingBoxes":[{"x":437.571,"h":7.4599999999999795,"y":506.089,"p":2,"w":65.97649999999999}]},"version":{"offsetStart":60,"normalizedForm":"1.19.4","offsetEnd":66,"rawForm":"1.19.4","boundingBoxes":[{"x":506.848,"h":7.4599999999999795,"y":506.089,"p":2,"w":25.27174999999994}]}},
  {"_key":"60c20f7f7723bebd866459b9","_id":"annotations/60c20f7f7723bebd866459b9","_rev":"_cfFmYFa---","wikipediaExternalRef":20268,"document":{"$oid":"60c20f7f7723bebd866459b7"},"context":"ADB, SK, OMS, MO, MA, and SN extracted data to an Excel sheet using the following headings:","wikidataId":"Q11272","type":"software","confidence":0.378,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Excel","offsetStart":50,"wikidataId":"Q11272","offsetEnd":55,"lang":"en","confidence":0.378,"rawForm":"Excel","boundingBoxes":[{"x":518.186,"h":7.46,"y":571.78,"p":2,"w":18.6851}]},"lang":"en"},
  {"_key":"60c20f7f7723bebd866459ba","_id":"annotations/60c20f7f7723bebd866459ba","_rev":"_cfFmYFm---","document":{"$oid":"60c20f7f7723bebd866459b7"},"context":"OMS, ADB, SK, MO and MA screened titles and abstracts against eligibility criteria using Covidence software ( www.covidence.org ).","type":"software","software-name":{"offsetStart":91,"normalizedForm":"Covidence","offsetEnd":100,"rawForm":"Covidence","boundingBoxes":[{"x":356.207,"h":7.46,"y":527.005,"p":2,"w":36.4967}]},"url":{"offsetStart":112,"normalizedForm":"www.covidence.org","offsetEnd":129,"rawForm":"www.covidence.org","boundingBoxes":[{"x":430.896,"h":7.460000000000036,"y":527.005,"p":2,"w":70.05399999999997}]}},
  {"_key":"60c20f8a7723bebd866459bc","_id":"annotations/60c20f8a7723bebd866459bc","_rev":"_cfFmYFy---","wikipediaExternalRef":2079997,"document":{"$oid":"60c20f8a7723bebd866459bb"},"context":"The statistical analysis was performed with STATISTICA software ver.","wikidataId":"Q1788435","type":"software","lang":"en","confidence":0.372,"software-name":{"wikipediaExternalRef":2079997,"normalizedForm":"STATISTICA","offsetStart":44,"wikidataId":"Q1788435","offsetEnd":54,"lang":"en","confidence":0.372,"rawForm":"STATISTICA","boundingBoxes":[{"x":202.728,"h":7.1652,"y":74.4265,"p":3,"w":43.1204}]},"version":{"offsetStart":69,"normalizedForm":"12","offsetEnd":71,"rawForm":"12","boundingBoxes":[{"x":295.19,"h":7.1652,"y":74.4265,"p":3,"w":7.407}]}},
  {"_key":"60c20f8c7723bebd866459be","_id":"annotations/60c20f8c7723bebd866459be","_rev":"_cfFmYG----","document":{"$oid":"60c20f8c7723bebd866459bd"},"context":"Basic Local Alignment Search Tool (BLAST; http://www.ncbi. nlm.nih.gov) and FASTA (http://www.ebi.ac.uk/fasta33) with default values were used to find homologous hits.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"Basic Local Alignment Search Tool (BLAST","offsetEnd":40,"rawForm":"Basic Local Alignment Search Tool (BLAST","boundingBoxes":[{"x":333.408,"h":7.539800000000014,"y":423.986,"p":3,"w":149.93939999999998}]},"url":{"offsetStart":42,"normalizedForm":"http://www.ncbi. nlm.nih.gov","offsetEnd":71,"rawForm":"http://www.ncbi. \nnlm.nih.gov","boundingBoxes":[{"x":489.656,"h":7.539800000000014,"y":423.986,"p":3,"w":63.115200000000016},{"x":301.719,"h":7.539800000000014,"y":434.417,"p":3,"w":42.792841666666675}]}},
  {"_key":"60c20f8c7723bebd866459bf","_id":"annotations/60c20f8c7723bebd866459bf","_rev":"_cfFmYGK---","wikipediaExternalRef":52292152,"document":{"$oid":"60c20f8c7723bebd866459bd"},"context":"Sequence editing and multiple alignments were carried out with the Geneious software pack- age version 9.1.6","wikidataId":"Q4915084","type":"software","confidence":0.2365,"software-name":{"wikipediaExternalRef":52292152,"normalizedForm":"Geneious","offsetStart":68,"wikidataId":"Q4915084","offsetEnd":76,"lang":"en","confidence":0.2365,"rawForm":"Geneious","boundingBoxes":[{"x":206.642,"h":7.5398,"y":162.405,"p":4,"w":32.9066}]},"lang":"en"},
  {"_key":"60c20f8c7723bebd866459c0","_id":"annotations/60c20f8c7723bebd866459c0","_rev":"_cfFmYGW---","wikipediaExternalRef":468001,"document":{"$oid":"60c20f8c7723bebd866459bd"},"context":"Basic Local Alignment Search Tool (BLAST; http://www.ncbi. nlm.nih.gov) and FASTA (http://www.ebi.ac.uk/fasta33) with default values were used to find homologous hits.","wikidataId":"Q1593782","type":"software","confidence":0.4942,"software-name":{"wikipediaExternalRef":468001,"normalizedForm":"FASTA","offsetStart":77,"wikidataId":"Q1593782","offsetEnd":82,"lang":"en","confidence":0.4942,"rawForm":"FASTA","boundingBoxes":[{"x":366.518,"h":7.5398,"y":434.417,"p":3,"w":22.9861}]},"url":{"offsetStart":84,"normalizedForm":"http://www.ebi.ac.uk/fasta","offsetEnd":110,"rawForm":"http://www.ebi.ac.uk/fasta","boundingBoxes":[{"x":395.6032,"h":7.539800000000014,"y":434.417,"p":3,"w":106.43360000000001}]},"lang":"en"},
  {"_key":"60c20f8c7723bebd866459c1","_id":"annotations/60c20f8c7723bebd866459c1","_rev":"_cfFmYGi---","wikipediaExternalRef":1976990,"document":{"$oid":"60c20f8c7723bebd866459bd"},"context":"Genome sequences of NoVs strains were retrieved from GenBank and aligned using Clustal W (Larkin et al., 2007).","wikidataId":"Q866737","type":"software","confidence":0.8933,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"Clustal W","offsetStart":80,"wikidataId":"Q866737","offsetEnd":89,"lang":"en","confidence":0.8933,"rawForm":"Clustal W","boundingBoxes":[{"x":259.536,"h":7.539800000000014,"y":183.324,"p":4,"w":34.036}]},"lang":"en"},
  {"_key":"60c20f8c7723bebd866459c2","_id":"annotations/60c20f8c7723bebd866459c2","_rev":"_cfFmYGu---","wikipediaExternalRef":47017,"document":{"$oid":"60c20f8c7723bebd866459bd"},"publisher":{"offsetStart":111,"normalizedForm":"Biomatters Ltd","offsetEnd":125,"rawForm":"Biomatters Ltd","boundingBoxes":[{"x":107.05805454545454,"h":7.539799999999985,"y":172.893,"p":4,"w":48.89134545454546}]},"context":"Sequence editing and multiple alignments were carried out with the Geneious software pack- age version 9.1.6","wikidataId":"Q891055","type":"software","lang":"en","confidence":0.3734,"software-name":{"wikipediaExternalRef":47017,"normalizedForm":"pack- age","offsetStart":86,"wikidataId":"Q891055","offsetEnd":95,"lang":"en","confidence":0.3734,"rawForm":"pack-\nage","boundingBoxes":[{"x":273.823,"h":7.539799999999985,"y":162.405,"p":4,"w":19.733400000000017},{"x":42.5197,"h":7.5398,"y":172.893,"p":4,"w":12.3084}]},"version":{"offsetStart":104,"normalizedForm":"9.1.6","offsetEnd":109,"rawForm":"9.1.6","boundingBoxes":[{"x":84.529,"h":7.539799999999985,"y":172.893,"p":4,"w":16.985299999999995}]}},
  {"_key":"60c20f927723bebd866459c4","_id":"annotations/60c20f927723bebd866459c4","_rev":"_cfFmYG2---","document":{"$oid":"60c20f927723bebd866459c3"},"context":"The data was checked for completeness, coded, recoded, and entered into Epi data version 3.1 software and exported to Stata version 14.2 for analysis.","type":"software","software-name":{"offsetStart":72,"normalizedForm":"Epi","offsetEnd":75,"rawForm":"Epi","boundingBoxes":[{"x":334.124,"h":9.69,"y":216.313,"p":6,"w":13.89}]},"version":{"offsetStart":90,"normalizedForm":"3.1","offsetEnd":93,"rawForm":"3.1","boundingBoxes":[{"x":92.614,"h":9.689999999999998,"y":228.313,"p":6,"w":12.5}]}},
  {"_key":"60c20f927723bebd866459c5","_id":"annotations/60c20f927723bebd866459c5","_rev":"_cfFmYHG---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20f927723bebd866459c3"},"context":"The data was checked for completeness, coded, recoded, and entered into Epi data version 3.1 software and exported to Stata version 14.2 for analysis.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7184,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":119,"wikidataId":"Q1204300","offsetEnd":124,"lang":"en","confidence":0.7184,"rawForm":"Stata","boundingBoxes":[{"x":208.049,"h":9.69,"y":228.313,"p":6,"w":20}]},"version":{"offsetStart":133,"normalizedForm":"14.2","offsetEnd":137,"rawForm":"14.2","boundingBoxes":[{"x":262.003,"h":9.689999999999998,"y":228.313,"p":6,"w":17.5}]}},
  {"_key":"60c20f927723bebd866459c6","_id":"annotations/60c20f927723bebd866459c6","_rev":"_cfFmYHS---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20f927723bebd866459c3"},"context":"A logistic regression analysis was used to identify the predictors of IPV among women and all statistical analyses were carried out using STATA 14.2.","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7367,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"STATA","offsetStart":140,"wikidataId":"Q1204300","offsetEnd":145,"lang":"en","confidence":0.7367,"rawForm":"STATA","boundingBoxes":[{"x":269.7,"h":9.32,"y":107.999,"p":2,"w":30}]},"version":{"offsetStart":146,"normalizedForm":"14.2","offsetEnd":150,"rawForm":"14.2","boundingBoxes":[{"x":302.05,"h":9.319999999999993,"y":107.999,"p":2,"w":15.503999999999962}]}},
  {"_key":"60c20f937723bebd866459c8","_id":"annotations/60c20f937723bebd866459c8","_rev":"_cfFmYHe---","wikipediaExternalRef":179088,"document":{"$oid":"60c20f937723bebd866459c7"},"context":"The data were analyzed by using SPSS 22.0.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":32,"wikidataId":"Q181596","offsetEnd":36,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":206.868,"h":8.7472,"y":369.842,"p":16,"w":21.9974}]},"version":{"offsetStart":37,"normalizedForm":"22.0","offsetEnd":41,"rawForm":"22.0","boundingBoxes":[{"x":233.4,"h":8.74720000000002,"y":369.842,"p":16,"w":15.940159999999992}]}},
  {"_key":"60c20f937723bebd866459c9","_id":"annotations/60c20f937723bebd866459c9","_rev":"_cfFmYHq---","wikipediaExternalRef":12610483,"document":{"$oid":"60c20f937723bebd866459c7"},"context":"It allows us to create an avatar in the Android and Ios operating systems without the need for an internet connection and voice an avatar in 25 languages.","wikidataId":"Q94","type":"software","confidence":0.4457,"software-name":{"wikipediaExternalRef":12610483,"normalizedForm":"Android","offsetStart":40,"wikidataId":"Q94","offsetEnd":47,"lang":"en","confidence":0.4457,"rawForm":"Android","boundingBoxes":[{"x":320.76,"h":8.7472,"y":106.847,"p":15,"w":32.5907}]},"lang":"en"},
  {"_key":"60c20f9c7723bebd866459cb","_id":"annotations/60c20f9c7723bebd866459cb","_rev":"_cfFmYHy---","document":{"$oid":"60c20f9c7723bebd866459ca"},"context":"The D' Agostino-Pearson normality test and Fisher's exact test were performed using Prism 7 for Mac IOS and all other tests were performed using SPSS software v.17.0 for Win- dows.","type":"software","software-name":{"offsetStart":86,"normalizedForm":"Prism","offsetEnd":91,"rawForm":"Prism","boundingBoxes":[{"x":397.971,"h":11.6816,"y":547.713,"p":4,"w":24.107}]},"version":{"offsetStart":92,"normalizedForm":"7","offsetEnd":93,"rawForm":"7","boundingBoxes":[{"x":424.783,"h":11.6816,"y":547.713,"p":4,"w":4.9196}]}},
  {"_key":"60c20f9c7723bebd866459cc","_id":"annotations/60c20f9c7723bebd866459cc","_rev":"_cfFmYIC---","document":{"$oid":"60c20f9c7723bebd866459ca"},"context":"The standard curve was calculated using a computer generat- ing four parameters logistic curve-fit with the program MyAssays (http://www.myass ays.com/).","type":"software","software-name":{"offsetStart":118,"normalizedForm":"MyAssays","offsetEnd":126,"rawForm":"MyAssays","boundingBoxes":[{"x":56.6929,"h":11.6816,"y":112.577,"p":4,"w":40.8268}]},"url":{"offsetStart":128,"normalizedForm":"http://www.myass ays.com","offsetEnd":152,"rawForm":"http://www.myass ays.com","boundingBoxes":[{"x":104.68723529411764,"h":11.681600000000003,"y":112.577,"p":4,"w":102.13940470588236}]}},
  {"_key":"60c20f9c7723bebd866459cd","_id":"annotations/60c20f9c7723bebd866459cd","_rev":"_cfFmYIO---","wikipediaExternalRef":179088,"document":{"$oid":"60c20f9c7723bebd866459ca"},"context":"The D' Agostino-Pearson normality test and Fisher's exact test were performed using Prism 7 for Mac IOS and all other tests were performed using SPSS software v.17.0 for Win- dows.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":148,"wikidataId":"Q181596","offsetEnd":152,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":417.599,"h":11.6816,"y":559.708,"p":4,"w":20.6584}]},"version":{"offsetStart":164,"normalizedForm":"17.0","offsetEnd":168,"rawForm":"17.0","boundingBoxes":[{"x":485.51259999999996,"h":11.681600000000003,"y":559.708,"p":4,"w":15.523200000000031}]}},
  {"_key":"60c20fa37723bebd866459d1","_id":"annotations/60c20fa37723bebd866459d1","_rev":"_cfFmYIa---","wikipediaExternalRef":15441720,"document":{"$oid":"60c20fa37723bebd866459ce"},"context":"A the- matic analysis will be conducted in NVivo 12 [42] using contextualizing and categorizing strategies.","wikidataId":"Q6955723","references":[{"offsetStart":42405,"normalizedForm":"[42]","refKey":41,"label":"[42]","reference_id":{"$oid":"60c20fa37723bebd866459cf"},"offsetEnd":42410,"boundingBoxes":[{"x":497.196,"h":8.97670000000005,"y":664.761,"p":9,"w":16.137499999999932}]}],"type":"software","lang":"en","confidence":0.498,"software-name":{"wikipediaExternalRef":15441720,"normalizedForm":"NVivo","offsetStart":43,"wikidataId":"Q6955723","offsetEnd":48,"lang":"en","confidence":0.498,"rawForm":"NVivo","boundingBoxes":[{"x":454.053,"h":8.9767,"y":664.761,"p":9,"w":26.4127}]},"version":{"offsetStart":49,"normalizedForm":"12","offsetEnd":51,"rawForm":"12","boundingBoxes":[{"x":483.93,"h":8.9767,"y":664.761,"p":9,"w":9.7999}]}},
  {"_key":"60c20fa37723bebd866459d2","_id":"annotations/60c20fa37723bebd866459d2","_rev":"_cfFmYIm---","wikipediaExternalRef":28309569,"document":{"$oid":"60c20fa37723bebd866459ce"},"context":"Once participants consent to participate, a unique identifier will be generated via REDCap, which will return the as- signment to the study arm.","wikidataId":"Q7305527","references":[{"offsetStart":27495,"normalizedForm":"[39]","refKey":38,"label":"[39]","reference_id":{"$oid":"60c20fa37723bebd866459d0"},"offsetEnd":27499,"boundingBoxes":[{"x":95.5279,"h":8.976699999999994,"y":460.72,"p":7,"w":14.61912000000001}]}],"type":"software","confidence":0.5036,"software-name":{"wikipediaExternalRef":28309569,"normalizedForm":"REDCap","offsetStart":86,"wikidataId":"Q7305527","offsetEnd":92,"lang":"en","confidence":0.5036,"rawForm":"REDCap","boundingBoxes":[{"x":146.266,"h":8.9767,"y":508.737,"p":7,"w":31.803771428571427}]},"lang":"en"},
  {"_key":"60c20fa37723bebd866459d3","_id":"annotations/60c20fa37723bebd866459d3","_rev":"_cfFmYIy---","wikipediaExternalRef":28309569,"document":{"$oid":"60c20fa37723bebd866459ce"},"context":"Participants who elect to participate and agree to be randomized will be assigned to the intervention or control with a 1:1 allocation ratio via a simple randomization procedure conducted by re- search coordinators at the study site and generated via REDCap [39].","wikidataId":"Q7305527","references":[{"offsetStart":27495,"normalizedForm":"[39]","refKey":38,"label":"[39]","reference_id":{"$oid":"60c20fa37723bebd866459d0"},"offsetEnd":27499,"boundingBoxes":[{"x":95.5279,"h":8.976699999999994,"y":460.72,"p":7,"w":14.61912000000001}]}],"type":"software","confidence":0.5036,"software-name":{"wikipediaExternalRef":28309569,"normalizedForm":"REDCap","offsetStart":255,"wikidataId":"Q7305527","offsetEnd":261,"lang":"en","confidence":0.5036,"rawForm":"REDCap","boundingBoxes":[{"x":56.6929,"h":8.9767,"y":460.72,"p":7,"w":34.968}]},"lang":"en"},
  {"_key":"60c20fa87723bebd866459d6","_id":"annotations/60c20fa87723bebd866459d6","_rev":"_cfFmYI6---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20fa87723bebd866459d4"},"context":"We used the STATA program and a user-contributed package 'simarwilson' (Tauchmann, 2016).","wikidataId":"Q1204300","type":"software","confidence":0.7367,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"STATA","offsetStart":12,"wikidataId":"Q1204300","offsetEnd":17,"lang":"en","confidence":0.7367,"rawForm":"STATA","boundingBoxes":[{"x":467.603,"h":7.5398,"y":546.557,"p":6,"w":23.4656}]},"lang":"en"},
  {"_key":"60c20fa87723bebd866459d7","_id":"annotations/60c20fa87723bebd866459d7","_rev":"_cfFmYJK---","document":{"$oid":"60c20fa87723bebd866459d4"},"context":"We used the STATA program and a user-contributed package 'simarwilson' (Tauchmann, 2016).","references":[{"offsetStart":32030,"normalizedForm":"Tauchmann, 2016","refKey":52,"label":"(Tauchmann, 2016)","reference_id":{"$oid":"60c20fa87723bebd866459d5"},"offsetEnd":32047,"boundingBoxes":[{"x":453.147,"h":7.539800000000014,"y":557.045,"p":6,"w":70.68116666666668}]}],"type":"software","software-name":{"offsetStart":59,"normalizedForm":"simarwilson","offsetEnd":70,"rawForm":"simarwilson","boundingBoxes":[{"x":404.3396230769231,"h":7.9702,"y":556.925,"p":6,"w":42.47785384615384}]}},
  {"_key":"60c20fac7723bebd866459dc","_id":"annotations/60c20fac7723bebd866459dc","_rev":"_cfFmYJW---","wikipediaExternalRef":3971631,"document":{"$oid":"60c20fac7723bebd866459d8"},"context":"KEGG [9] was used to perform pathway enrichment analysis of differentially expressed genes (DEGs), and expression pattern analysis was performed using Cluster [10] and JavaTreeView [11].","wikidataId":"Q909442","references":[{"offsetStart":8290,"normalizedForm":"[9]","refKey":8,"label":"[9]","reference_id":{"$oid":"60c20fac7723bebd866459d9"},"offsetEnd":8294,"boundingBoxes":[{"x":86.4021,"h":7.539800000000014,"y":545.306,"p":4,"w":10.609700000000004}]}],"type":"software","confidence":0.7486,"software-name":{"wikipediaExternalRef":3971631,"normalizedForm":"KEGG","offsetStart":0,"wikidataId":"Q909442","offsetEnd":4,"lang":"en","confidence":0.7486,"rawForm":"KEGG","boundingBoxes":[{"x":61.3442,"h":7.5398,"y":545.306,"p":4,"w":21.5592}]},"lang":"en"},
  {"_key":"60c20fac7723bebd866459dd","_id":"annotations/60c20fac7723bebd866459dd","_rev":"_cfFmYJi---","document":{"$oid":"60c20fac7723bebd866459d8"},"context":"Sequence alignment and quantification analysis of gene expression was done using SOAPaligner/SOAP2 [7].","references":[{"offsetStart":8227,"normalizedForm":"[7]","refKey":6,"label":"[7]","reference_id":{"$oid":"60c20fac7723bebd866459da"},"offsetEnd":8230,"boundingBoxes":[{"x":229.325,"h":7.539800000000014,"y":534.365,"p":4,"w":9.374625000000009}]}],"type":"software","software-name":{"offsetStart":82,"normalizedForm":"SOAPaligner/SOAP2","offsetEnd":99,"rawForm":"SOAPaligner/SOAP2","boundingBoxes":[{"x":152.333,"h":7.539800000000014,"y":534.365,"p":4,"w":73.85319999999999}]}},
  {"_key":"60c20fac7723bebd866459de","_id":"annotations/60c20fac7723bebd866459de","_rev":"_cfFmYJu---","document":{"$oid":"60c20fac7723bebd866459d8"},"context":"KEGG [9] was used to perform pathway enrichment analysis of differentially expressed genes (DEGs), and expression pattern analysis was performed using Cluster [10] and JavaTreeView [11].","references":[{"offsetStart":8467,"normalizedForm":"[11]","refKey":10,"label":"[11]","reference_id":{"$oid":"60c20fac7723bebd866459db"},"offsetEnd":8471,"boundingBoxes":[{"x":411.536,"h":7.539800000000014,"y":556.191,"p":4,"w":13.083680000000015}]}],"type":"software","software-name":{"offsetStart":169,"normalizedForm":"JavaTreeView","offsetEnd":181,"rawForm":"JavaTreeView","boundingBoxes":[{"x":357.224,"h":7.5398,"y":556.191,"p":4,"w":50.5617}]}},
  {"_key":"60c20fae7723bebd866459e0","_id":"annotations/60c20fae7723bebd866459e0","_rev":"_cfFmYJ6---","wikipediaExternalRef":20268,"document":{"$oid":"60c20fae7723bebd866459df"},"publisher":{"offsetStart":96,"normalizedForm":"Microsoft","offsetEnd":105,"rawForm":"Microsoft","boundingBoxes":[{"x":203.75,"h":11.48,"y":332.755,"p":3,"w":39.952}]},"context":"Each case that was triaged by the department was logged using a secure data collection tool in Microsoft Excel, and the data recorded were: patient age, referral source, reason for accessing the emergency service, and triage outcome.","wikidataId":"Q11272","type":"software","confidence":0.378,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Excel","offsetStart":106,"wikidataId":"Q11272","offsetEnd":111,"lang":"en","confidence":0.378,"rawForm":"Excel","boundingBoxes":[{"x":246.572,"h":11.48,"y":332.755,"p":3,"w":21.105}]},"lang":"en"},
  {"_key":"60c20fb07723bebd866459e2","_id":"annotations/60c20fb07723bebd866459e2","_rev":"_cfFmYKG---","document":{"$oid":"60c20fb07723bebd866459e1"},"context":"The pre-coded data were then trans- ferred to the Statistical Package of Social Science Soft- ware program, version 23 to be statistically analyzed.","type":"software","software-name":{"offsetStart":50,"normalizedForm":"Statistical Package of Social Science Soft- ware","offsetEnd":98,"rawForm":"Statistical Package of Social Science Soft-\nware","boundingBoxes":[{"x":114.917,"h":8.97670000000005,"y":508.741,"p":3,"w":175.57539999999997},{"x":56.6929,"h":8.9767,"y":520.76,"p":3,"w":19.2666}]},"version":{"offsetStart":116,"normalizedForm":"23","offsetEnd":118,"rawForm":"23","boundingBoxes":[{"x":151.427,"h":8.9767,"y":520.76,"p":3,"w":9.7999}]}},
  {"_key":"60c20fb07723bebd866459e3","_id":"annotations/60c20fb07723bebd866459e3","_rev":"_cfFmYKS---","document":{"$oid":"60c20fb07723bebd866459e1"},"context":"The performed studies were transferred to PACS system (PaxeraUltima version 6.0.0.Readers reported the presence of the following lung parenchymal findings: GGO, consolidation, crazy paving, peri-lobular fibrosis, reversed halo sign, vacuolar sign, pulmonary nodules, lobar pneumonia, and lung cavita- tion as well as associated traction bronchiectasis and vascular thickening.","type":"software","software-name":{"offsetStart":56,"normalizedForm":"PaxeraUltima","offsetEnd":68,"rawForm":"PaxeraUltima","boundingBoxes":[{"x":61.17959230769231,"h":8.9767,"y":112.742,"p":3,"w":53.8403076923077}]},"version":{"offsetStart":77,"normalizedForm":"6.0.0","offsetEnd":82,"rawForm":"6.0.0","boundingBoxes":[{"x":153.694,"h":8.976699999999994,"y":112.742,"p":3,"w":18.57778571428571}]}},
  {"_key":"60c20fb07723bebd866459e4","_id":"annotations/60c20fb07723bebd866459e4","_rev":"_cfFmYKe---","wikipediaExternalRef":20268,"document":{"$oid":"60c20fb07723bebd866459e1"},"publisher":{"offsetStart":109,"normalizedForm":"Microsoft","offsetEnd":118,"rawForm":"Microsoft","boundingBoxes":[{"x":61.02808,"h":9.7999,"y":484.006,"p":3,"w":39.016619999999996}]},"context":"The collected data were carefully revised, coded, tabu- lated, and introduced to a personal computer using \"Microsoft Office Excel Software\" program (2016) for windows by A.A.H.","wikidataId":"Q11272","type":"software","lang":"en","confidence":0.3543,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Office Excel","offsetStart":119,"wikidataId":"Q11272","offsetEnd":131,"lang":"en","confidence":0.3543,"rawForm":"Office Excel","boundingBoxes":[{"x":105.449,"h":8.976699999999994,"y":484.761,"p":3,"w":51.76980000000002}]},"version":{"offsetStart":151,"normalizedForm":"2016","offsetEnd":155,"rawForm":"2016","boundingBoxes":[{"x":251.8394833333333,"h":8.9767,"y":484.761,"p":3,"w":17.273933333333332}]}},
  {"_key":"60c20fbf7723bebd866459e6","_id":"annotations/60c20fbf7723bebd866459e6","_rev":"_cfFmYKq---","document":{"$oid":"60c20fbf7723bebd866459e5"},"context":"RdRp genes, were designed according to the SARS-CoV-2 genomic sequence, using the open access Primer Explorer V.5 software tool (http://primerexplorer.jp/).","type":"software","software-name":{"offsetStart":95,"normalizedForm":"Primer Explorer","offsetEnd":110,"rawForm":"Primer Explorer","boundingBoxes":[{"x":92.9179,"h":9.1533,"y":14.527,"p":3,"w":67.20000000000002}]},"url":{"offsetStart":130,"normalizedForm":"http://primerexplorer.jp","offsetEnd":154,"rawForm":"http://primerexplorer.jp","boundingBoxes":[{"x":247.99464285714288,"h":9.1533,"y":14.527,"p":3,"w":90.95142857142855}]},"version":{"offsetStart":113,"normalizedForm":"5","offsetEnd":114,"rawForm":"5","boundingBoxes":[{"x":174.19993333333332,"h":9.1533,"y":14.527,"p":3,"w":4.422466666666667}]}},
  {"_key":"60c20fbf7723bebd866459e7","_id":"annotations/60c20fbf7723bebd866459e7","_rev":"_cfFmYK2---","wikipediaExternalRef":179088,"document":{"$oid":"60c20fbf7723bebd866459e5"},"context":"The LOD was defined as a 95% probability of obtaining a positive result, using probit regression analysis with SPSS 17.0 software [26].","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":112,"wikidataId":"Q181596","offsetEnd":116,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":360.827,"h":9.584,"y":533.695,"p":7,"w":21.7085}]},"version":{"offsetStart":117,"normalizedForm":"17.0","offsetEnd":121,"rawForm":"17.0","boundingBoxes":[{"x":385.026,"h":9.583999999999946,"y":533.695,"p":7,"w":17.434500000000014}]}},
  {"_key":"60c20fbf7723bebd866459e8","_id":"annotations/60c20fbf7723bebd866459e8","_rev":"_cfFmYLC---","wikipediaExternalRef":363695,"document":{"$oid":"60c20fbf7723bebd866459e5"},"publisher":{"offsetStart":172,"normalizedForm":"NCBI","offsetEnd":176,"rawForm":"NCBI","boundingBoxes":[{"x":159.425,"h":9.584,"y":440.684,"p":2,"w":22.258560000000003}]},"context":"The primer specificity was first evaluated via sequence alignment with the other six human coronaviruses and the performance of a homology search using the BLAST tool in NCBI, and then by performing an RT-LAMP reaction with non-template control (NTC).","wikidataId":"Q286820","type":"software","confidence":0.2888,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":158,"wikidataId":"Q286820","offsetEnd":163,"lang":"en","confidence":0.2888,"rawForm":"BLAST","boundingBoxes":[{"x":93.3021,"h":9.584,"y":440.684,"p":2,"w":31.8879}]},"lang":"en"},
  {"_key":"60c20fbf7723bebd866459e9","_id":"annotations/60c20fbf7723bebd866459e9","_rev":"_cfFmYLO---","wikipediaExternalRef":363695,"document":{"$oid":"60c20fbf7723bebd866459e5"},"publisher":{"offsetStart":172,"normalizedForm":"NCBI","offsetEnd":176,"rawForm":"NCBI","boundingBoxes":[{"x":259.817,"h":9.1533,"y":38.7728,"p":3,"w":19.7516}]},"context":"The primer specificity was first evaluated via sequence alignment with the other six human coronaviruses and the performance of a homology search using the BLAST tool in NCBI, and then by performing an RT-LAMP reaction with non-template control (NTC).","wikidataId":"Q286820","type":"software","confidence":0.2888,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLAST","offsetStart":158,"wikidataId":"Q286820","offsetEnd":163,"lang":"en","confidence":0.2888,"rawForm":"BLAST","boundingBoxes":[{"x":202.02,"h":9.1533,"y":38.7728,"p":3,"w":28.2619}]},"lang":"en"},
  {"_key":"60c20fbf7723bebd866459ea","_id":"annotations/60c20fbf7723bebd866459ea","_rev":"_cfFmYLa---","document":{"$oid":"60c20fbf7723bebd866459e5"},"context":"Several sets of SARS-CoV-2-specific LAMP primers, targeting N, S and RdRp genes, were designed according to the SARS-CoV-2 genomic sequence, using the open access Primer Explorer V.5 software tool (http://primerexplorer.jp/).","type":"software","software-name":{"offsetStart":164,"normalizedForm":"Primer Explorer","offsetEnd":179,"rawForm":"Primer Explorer","boundingBoxes":[{"x":449.477,"h":9.584000000000003,"y":400.156,"p":2,"w":69.46590000000003}]},"url":{"offsetStart":200,"normalizedForm":"http://primerexplorer.jp","offsetEnd":224,"rawForm":"http://primerexplorer.jp","boundingBoxes":[{"x":157.39975,"h":9.584000000000003,"y":413.665,"p":2,"w":100.674}]},"version":{"offsetStart":183,"normalizedForm":"5","offsetEnd":184,"rawForm":"5","boundingBoxes":[{"x":85.25306666666667,"h":9.584,"y":413.665,"p":2,"w":4.538033333333333}]}},
  {"_key":"60c20fc37723bebd866459ef","_id":"annotations/60c20fc37723bebd866459ef","_rev":"_cfFmYLm---","document":{"$oid":"60c20fc37723bebd866459eb"},"context":"Molecular docking analysis was performed with Autodock Vina (Trott and Olson, 2009) as implemented in YASARA (Krieger and Vriend, 2014).","references":[{"offsetStart":19163,"normalizedForm":"Trott and Olson, 2009","refKey":29,"label":"(Trott and Olson, 2009)","reference_id":{"$oid":"60c20fc37723bebd866459ec"},"offsetEnd":19187,"boundingBoxes":[{"x":148.194,"h":8.846799999999973,"y":279.815,"p":5,"w":83.0804}]}],"type":"software","software-name":{"offsetStart":47,"normalizedForm":"Autodock Vina","offsetEnd":60,"rawForm":"Autodock Vina","boundingBoxes":[{"x":94.2246,"h":8.846799999999973,"y":279.815,"p":5,"w":52.01530000000001}]}},
  {"_key":"60c20fc37723bebd866459f0","_id":"annotations/60c20fc37723bebd866459f0","_rev":"_cfFmYLy---","document":{"$oid":"60c20fc37723bebd866459eb"},"publisher":{"offsetStart":54,"normalizedForm":"UCSF","offsetEnd":58,"rawForm":"UCSF","boundingBoxes":[{"x":498.496,"h":8.8468,"y":70.2251,"p":5,"w":19.1362}]},"context":"Molecular gra- phics and analyses were performed with UCSF Chimera (Pettersen et al., 2004).","references":[{"offsetStart":19746,"normalizedForm":"Pettersen et al., 2004","refKey":24,"label":"(Pettersen et al., 2004)","reference_id":{"$oid":"60c20fc37723bebd866459ed"},"offsetEnd":19770,"boundingBoxes":[{"x":306.593,"h":8.846800000000002,"y":80.7129,"p":5,"w":80.31524999999993}]}],"type":"software","software-name":{"offsetStart":59,"normalizedForm":"Chimera","offsetEnd":66,"rawForm":"Chimera","boundingBoxes":[{"x":527.806,"h":8.8468,"y":70.2251,"p":5,"w":29.8401}]}},
  {"_key":"60c20fc37723bebd866459f1","_id":"annotations/60c20fc37723bebd866459f1","_rev":"_cfFmYM----","document":{"$oid":"60c20fc37723bebd866459eb"},"type":"software","software-name":{"offsetStart":59,"normalizedForm":"ADME Predictor","offsetEnd":74,"rawForm":"ADME \nPredictor","boundingBoxes":[{"x":266.115,"h":8.8468,"y":712.043,"p":11,"w":22.5474},{"x":37.5891,"h":8.8468,"y":722.532,"p":11,"w":32.4224}]},"context":"Finally, the global parameter ADMET_Risk was calculated in ADME Predictor software, which concisely summarizes the information from other properties and descriptors predicted to identify important  liabilities in drug candidates."},
  {"_key":"60c20fc37723bebd866459f2","_id":"annotations/60c20fc37723bebd866459f2","_rev":"_cfFmYMK---","document":{"$oid":"60c20fc37723bebd866459eb"},"type":"software","software-name":{"offsetStart":80,"normalizedForm":"Protein-Ligand Interaction Profiler","offsetEnd":117,"rawForm":"Protein-Ligand \n\nInteraction Profiler","boundingBoxes":[{"x":236.578,"h":8.846799999999973,"y":342.631,"p":5,"w":52.06869999999995},{"x":306.593,"h":8.846799999999995,"y":59.7938,"p":5,"w":68.2507}]},"context":"The interactions of the best protein/ligand complexes were predicted using the Protein-Ligand  Interaction Profiler web server (Salentin et al., 2015)."},
  {"_key":"60c20fc37723bebd866459f3","_id":"annotations/60c20fc37723bebd866459f3","_rev":"_cfFmYMW---","wikipediaExternalRef":19391960,"document":{"$oid":"60c20fc37723bebd866459eb"},"context":"Molecular docking analysis was performed with Autodock Vina (Trott and Olson, 2009) as implemented in YASARA (Krieger and Vriend, 2014).","wikidataId":"Q8049645","references":[{"offsetStart":19213,"normalizedForm":"Krieger and Vriend, 2014","refKey":16,"label":"(Krieger and Vriend, 2014)","reference_id":{"$oid":"60c20fc37723bebd866459ee"},"offsetEnd":19239,"boundingBoxes":[{"x":80.2785,"h":8.846799999999973,"y":290.304,"p":5,"w":95.10975000000003}]}],"type":"software","confidence":0.8168,"software-name":{"wikipediaExternalRef":19391960,"normalizedForm":"YASARA","offsetStart":104,"wikidataId":"Q8049645","offsetEnd":110,"lang":"en","confidence":0.8168,"rawForm":"YASARA","boundingBoxes":[{"x":47.2265,"h":8.8468,"y":290.304,"p":5,"w":30.4298}]},"lang":"en"},
  {"_key":"60c20fd27723bebd866459f6","_id":"annotations/60c20fd27723bebd866459f6","_rev":"_cfFmYMi---","document":{"$oid":"60c20fd27723bebd866459f4"},"type":"software","software-name":{"offsetStart":12,"normalizedForm":"TreeAnnotator","offsetEnd":25,"rawForm":"TreeAnnotator","boundingBoxes":[{"x":246.046,"h":10.4847,"y":435.98,"p":5,"w":75.4325}]},"context":"We used the TreeAnnotator tool in BEAST to summarize trees in the form of maximum clade credibility (MCC) trees."},
  {"_key":"60c20fd27723bebd866459f7","_id":"annotations/60c20fd27723bebd866459f7","_rev":"_cfFmYMu---","wikipediaExternalRef":1527385,"document":{"$oid":"60c20fd27723bebd866459f4"},"context":"We capitalize on BEAGLE [10] in conjunction with BEAST to improve computational performance on our large data sets.","wikidataId":"Q791633","references":[{"offsetStart":13831,"normalizedForm":"[10]","refKey":9,"label":"[10]","reference_id":{"$oid":"60c20fd27723bebd866459f5"},"offsetEnd":13836,"boundingBoxes":[{"x":125.868,"h":10.484699999999975,"y":407.088,"p":5,"w":18.210199999999986}]}],"type":"software","confidence":0.3766,"software-name":{"wikipediaExternalRef":1527385,"normalizedForm":"BEAGLE","offsetStart":18,"wikidataId":"Q791633","offsetEnd":24,"lang":"en","confidence":0.3766,"rawForm":"BEAGLE","boundingBoxes":[{"x":72,"h":10.4847,"y":407.088,"p":5,"w":49.1705}]},"lang":"en"},
  {"_key":"60c20fd27723bebd866459f8","_id":"annotations/60c20fd27723bebd866459f8","_rev":"_cfFmYM6---","document":{"$oid":"60c20fd27723bebd866459f4"},"type":"software","software-name":{"offsetStart":85,"normalizedForm":"Tracer","offsetEnd":91,"rawForm":"Tracer","boundingBoxes":[{"x":135.838,"h":10.4847,"y":435.98,"p":5,"w":30.934628571428572}]},"context":"MCMC analyses were run sufficiently long to ensure stationarity as diag- nosed using Tracer."},
  {"_key":"60c20fd67723bebd866459fb","_id":"annotations/60c20fd67723bebd866459fb","_rev":"_cfFmYNG---","wikipediaExternalRef":2783580,"document":{"$oid":"60c20fd67723bebd866459f9"},"context":"We then used ArcGIS Pro 2.5 [7] to identify all COVID-19 deaths in nursing homes at facilities within a county's geographic boundaries for all US counties.","wikidataId":"Q513297","references":[{"offsetStart":6864,"normalizedForm":"[7]","refKey":6,"label":"[7]","reference_id":{"$oid":"60c20fd67723bebd866459fa"},"offsetEnd":6868,"boundingBoxes":[{"x":319.629,"h":8.999999999999986,"y":120.366,"p":2,"w":11.659999999999968}]}],"type":"software","lang":"en","confidence":0.9753,"software-name":{"wikipediaExternalRef":2783580,"normalizedForm":"ArcGIS Pro","offsetStart":13,"wikidataId":"Q513297","offsetEnd":23,"lang":"en","confidence":0.9753,"rawForm":"ArcGIS Pro","boundingBoxes":[{"x":505.83,"h":9,"y":108.366,"p":2,"w":46.934000000000026}]},"version":{"offsetStart":25,"normalizedForm":"2.5","offsetEnd":28,"rawForm":"2.5","boundingBoxes":[{"x":303.638,"h":8.999999999999986,"y":120.366,"p":2,"w":12.5}]}},
  {"_key":"60c20fd67723bebd866459fc","_id":"annotations/60c20fd67723bebd866459fc","_rev":"_cfFmYNS---","wikipediaExternalRef":1809002,"document":{"$oid":"60c20fd67723bebd866459f9"},"publisher":{"offsetStart":68,"normalizedForm":"StataCorp","offsetEnd":77,"rawForm":"StataCorp","boundingBoxes":[{"x":352.536,"h":9,"y":264.366,"p":3,"w":37.35}]},"context":"All statistical analyses were carried out using Stata (version 15, StataCorp), and results were considered significant when Cronbach α=.05 [20].","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7154,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":48,"wikidataId":"Q1204300","offsetEnd":53,"lang":"en","confidence":0.7154,"rawForm":"Stata","boundingBoxes":[{"x":533.023,"h":9,"y":252.366,"p":3,"w":19.748}]},"version":{"offsetStart":64,"normalizedForm":"15","offsetEnd":66,"rawForm":"15","boundingBoxes":[{"x":338.102,"h":9,"y":264.366,"p":3,"w":8.309333333333333}]}},
  {"_key":"60c20fdf7723bebd866459fe","_id":"annotations/60c20fdf7723bebd866459fe","_rev":"_cfFmYNe---","document":{"$oid":"60c20fdf7723bebd866459fd"},"context":"and  VIRsiRNApred (http://crdd.osdd.net/servers/virsirnapred/).","type":"software","software-name":{"offsetStart":7,"normalizedForm":"VIRsiRNApred","offsetEnd":19,"rawForm":"VIRsiRNApred","boundingBoxes":[{"x":94.1391,"h":10.2023,"y":564.838,"p":5,"w":70.821}]},"url":{"offsetStart":21,"normalizedForm":"http://crdd.osdd.net/servers/virsirnapred","offsetEnd":62,"rawForm":"http://crdd.osdd.net/servers/virsirnapred","boundingBoxes":[{"x":172.41815555555556,"h":10.202300000000037,"y":564.838,"p":5,"w":176.59337777777776}]}},
  {"_key":"60c20fdf7723bebd866459ff","_id":"annotations/60c20fdf7723bebd866459ff","_rev":"_cfFmYNq---","document":{"$oid":"60c20fdf7723bebd866459fd"},"context":"Potential siRNA sequences targeting  viral genes were predicted using the programs siDirect (http://sidirect2.rnai.jp/)","type":"software","software-name":{"offsetStart":85,"normalizedForm":"siDirect","offsetEnd":93,"rawForm":"siDirect","boundingBoxes":[{"x":341.789,"h":10.2023,"y":538.916,"p":5,"w":35.9005}]},"url":{"offsetStart":95,"normalizedForm":"http://sidirect2.rnai.jp","offsetEnd":119,"rawForm":"http://sidirect2.rnai.jp","boundingBoxes":[{"x":389.71933333333334,"h":10.202300000000037,"y":538.916,"p":5,"w":96.51199999999994}]}},
  {"_key":"60c20fe57723bebd86645a02","_id":"annotations/60c20fe57723bebd86645a02","_rev":"_cfFmYNy---","document":{"$oid":"60c20fe57723bebd86645a00"},"publisher":{"offsetStart":91,"normalizedForm":"Thermo Fisher Scientific","offsetEnd":115,"rawForm":"Thermo Fisher Scientific","boundingBoxes":[{"x":359.5857,"h":8.97670000000005,"y":700.752,"p":2,"w":98.33996666666667}]},"context":"Variant annotation and interpretation were performed with Ion Reporter Soft- ware v.5.10 (Thermo Fisher Scientific).","type":"software","software-name":{"offsetStart":59,"normalizedForm":"Ion Reporter Soft- ware","offsetEnd":82,"rawForm":"Ion Reporter Soft-\nware","boundingBoxes":[{"x":459.893,"h":8.97670000000005,"y":688.734,"p":2,"w":78.62940000000009},{"x":304.724,"h":8.9767,"y":700.752,"p":2,"w":19.2666}]},"version":{"offsetStart":85,"normalizedForm":"5.10","offsetEnd":89,"rawForm":"5.10","boundingBoxes":[{"x":335.27833333333336,"h":8.97670000000005,"y":700.752,"p":2,"w":15.640666666666675}]}},
  {"_key":"60c20fe57723bebd86645a03","_id":"annotations/60c20fe57723bebd86645a03","_rev":"_cfFmYO----","document":{"$oid":"60c20fe57723bebd86645a00"},"type":"software","software-name":{"offsetStart":81,"normalizedForm":"conumee","offsetEnd":88,"rawForm":"conumee","boundingBoxes":[{"x":350.1908555555556,"h":9.7999,"y":99.9693,"p":3,"w":34.52298888888889}]},"context":"Copy number  variation (CNV) profiles were calculated and displayed using the \"conumee\" package for R version 3.5.2"},
  {"_key":"60c20fe57723bebd86645a04","_id":"annotations/60c20fe57723bebd86645a04","_rev":"_cfFmYOK---","document":{"$oid":"60c20fe57723bebd86645a00"},"publisher":{"offsetStart":128,"normalizedForm":"Broad Institute","offsetEnd":143,"rawForm":"Broad Institute","boundingBoxes":[{"x":61.246583333333334,"h":8.976699999999994,"y":88.7622,"p":3,"w":60.601366666666664}]},"context":"All variants were manually reviewed by visualizing the raw sequencing read alignments using the Integrative Genomics Viewer (Broad Institute, Cambridge, MA).","type":"software","software-name":{"offsetStart":98,"normalizedForm":"Integrative Genomics Viewer","offsetEnd":125,"rawForm":"Integrative Genomics Viewer","boundingBoxes":[{"x":417.317,"h":8.97670000000005,"y":724.733,"p":2,"w":121.18409999999994}]}},
  {"_key":"60c20fe57723bebd86645a05","_id":"annotations/60c20fe57723bebd86645a05","_rev":"_cfFmYOW---","document":{"$oid":"60c20fe57723bebd86645a00"},"publisher":{"offsetStart":150,"normalizedForm":"Thermo Fisher Scientific","offsetEnd":174,"rawForm":"Thermo Fisher Scientific","boundingBoxes":[{"x":331.0687,"h":8.97670000000005,"y":676.715,"p":2,"w":99.24696666666671}]},"context":"Signal processing, base calling, and alignment to the GRCh37/hg19 human genome assem- bly were carried out using Torrent Suite™ software pack- ages (Thermo Fisher Scientific).","type":"software","software-name":{"offsetStart":114,"normalizedForm":"Torrent Suite™ software pack- ages","offsetEnd":148,"rawForm":"Torrent Suite™ software pack-\nages","boundingBoxes":[{"x":415.388,"h":8.97670000000005,"y":664.753,"p":2,"w":123.11900000000009},{"x":304.724,"h":8.9767,"y":676.715,"p":2,"w":17.2282}]}},
  {"_key":"60c20fe57723bebd86645a06","_id":"annotations/60c20fe57723bebd86645a06","_rev":"_cfFmYOi---","document":{"$oid":"60c20fe57723bebd86645a00"},"type":"software","software-name":{"offsetStart":15181,"normalizedForm":"conumee","offsetEnd":15188,"rawForm":"conumee","boundingBoxes":[{"x":380.6305444444444,"h":9.7999,"y":615.983,"p":3,"w":34.47881111111111}]}},
  {"_key":"60c20fe67723bebd86645a09","_id":"annotations/60c20fe67723bebd86645a09","_rev":"_cfFmYOu---","wikipediaExternalRef":15441720,"document":{"$oid":"60c20fe67723bebd86645a07"},"context":"Qualitative studies Qualitative data will be thematically analysed using the qualitative research software NVivo. 42","wikidataId":"Q6955723","references":[{"offsetStart":19561,"normalizedForm":"42","refKey":41,"label":"42","reference_id":{"$oid":"60c20fe67723bebd86645a08"},"offsetEnd":19564,"boundingBoxes":[{"x":209.455,"h":6.1792,"y":457.444,"p":4,"w":6.8952}]}],"type":"software","confidence":0.498,"software-name":{"wikipediaExternalRef":15441720,"normalizedForm":"NVivo","offsetStart":109,"wikidataId":"Q6955723","offsetEnd":114,"lang":"en","confidence":0.498,"rawForm":"NVivo","boundingBoxes":[{"x":180.259,"h":9.32,"y":459.72,"p":4,"w":24.333333333333332}]},"lang":"en"},
  {"_key":"60c20fe97723bebd86645a0b","_id":"annotations/60c20fe97723bebd86645a0b","_rev":"_cfFmYO6---","wikipediaExternalRef":20268,"document":{"$oid":"60c20fe97723bebd86645a0a"},"publisher":{"offsetStart":0,"normalizedForm":"Microsoft","offsetEnd":9,"rawForm":"Microsoft","boundingBoxes":[{"x":76.4162,"h":7.5238,"y":651.663,"p":5,"w":36.519}]},"context":"Microsoft Office Excel 2003 was used for processing the data, calculations and graphics.","wikidataId":"Q11272","type":"software","lang":"en","confidence":0.3543,"software-name":{"wikipediaExternalRef":20268,"normalizedForm":"Office Excel","offsetStart":10,"wikidataId":"Q11272","offsetEnd":22,"lang":"en","confidence":0.3543,"rawForm":"Office Excel","boundingBoxes":[{"x":114.441,"h":7.523800000000051,"y":651.663,"p":5,"w":43.6285}]},"version":{"offsetStart":23,"normalizedForm":"2003","offsetEnd":27,"rawForm":"2003","boundingBoxes":[{"x":159.576,"h":7.5238,"y":651.663,"p":5,"w":19.4391}]}},
  {"_key":"60c20fed7723bebd86645a0d","_id":"annotations/60c20fed7723bebd86645a0d","_rev":"_cfFmYPG---","wikipediaExternalRef":179088,"document":{"$oid":"60c20fed7723bebd86645a0c"},"publisher":{"offsetStart":96,"normalizedForm":"SPSS Inc","offsetEnd":104,"rawForm":"SPSS Inc","boundingBoxes":[{"x":155.639,"h":9.099000000000046,"y":702.129,"p":3,"w":29.02679999999998}]},"context":"All analyses were performed according to intention-to-treat using SPSS software (version 21.0, SPSS Inc., Chicago, IL).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.7466,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":66,"wikidataId":"Q181596","offsetEnd":70,"lang":"en","confidence":0.7466,"rawForm":"SPSS","boundingBoxes":[{"x":453.158,"h":9.099,"y":692.13,"p":3,"w":17.8695}]},"version":{"offsetStart":89,"normalizedForm":"21.0","offsetEnd":93,"rawForm":"21.0","boundingBoxes":[{"x":537.218,"h":9.099000000000046,"y":692.13,"p":3,"w":13.766399999999976}]}},
  {"_key":"60c20fff7723bebd86645a0f","_id":"annotations/60c20fff7723bebd86645a0f","_rev":"_cfFmYPS---","document":{"$oid":"60c20fff7723bebd86645a0e"},"context":"Statistical analysis was completed using the jamovi version 1.1 computer software (the jamovi project.","type":"software","software-name":{"offsetStart":45,"normalizedForm":"jamovi","offsetEnd":51,"rawForm":"jamovi","boundingBoxes":[{"x":510.908,"h":8.9767,"y":232.762,"p":2,"w":27.6543}]},"url":{"offsetStart":152,"normalizedForm":"/","offsetEnd":153,"rawForm":"/","boundingBoxes":[{"x":530.923,"h":8.9767,"y":256.742,"p":2,"w":3.826}]},"version":{"offsetStart":61,"normalizedForm":"1.1","offsetEnd":64,"rawForm":"1.1","boundingBoxes":[{"x":341.621,"h":8.976699999999994,"y":244.723,"p":2,"w":12.1284}]}},
  {"_key":"60c20fff7723bebd86645a10","_id":"annotations/60c20fff7723bebd86645a10","_rev":"_cfFmYPe---","document":{"$oid":"60c20fff7723bebd86645a0e"},"type":"software","software-name":{"offsetStart":7574,"normalizedForm":"jamovi","offsetEnd":7580,"rawForm":"jamovi","boundingBoxes":[{"x":472.777,"h":8.9767,"y":244.723,"p":2,"w":27.6014}]},"url":{"offsetStart":152,"normalizedForm":"/","offsetEnd":153,"rawForm":"/","boundingBoxes":[{"x":530.923,"h":8.9767,"y":256.742,"p":2,"w":3.826}]},"version":{"offsetStart":61,"normalizedForm":"1.1","offsetEnd":64,"rawForm":"1.1","boundingBoxes":[{"x":341.621,"h":8.976699999999994,"y":244.723,"p":2,"w":12.1284}]}},
  {"_key":"60c20fff7723bebd86645a11","_id":"annotations/60c20fff7723bebd86645a11","_rev":"_cfFmYPq---","document":{"$oid":"60c20fff7723bebd86645a0e"},"type":"software","software-name":{"offsetStart":7591,"normalizedForm":"jamovi","offsetEnd":7597,"rawForm":"jamovi","boundingBoxes":[{"x":304.724,"h":8.9767,"y":256.742,"p":2,"w":27.6553}]},"url":{"offsetStart":152,"normalizedForm":"/","offsetEnd":153,"rawForm":"/","boundingBoxes":[{"x":530.923,"h":8.9767,"y":256.742,"p":2,"w":3.826}]},"version":{"offsetStart":61,"normalizedForm":"1.1","offsetEnd":64,"rawForm":"1.1","boundingBoxes":[{"x":341.621,"h":8.976699999999994,"y":244.723,"p":2,"w":12.1284}]}},
  {"_key":"60c20fff7723bebd86645a12","_id":"annotations/60c20fff7723bebd86645a12","_rev":"_cfFmYP2---","document":{"$oid":"60c20fff7723bebd86645a0e"},"type":"software","software-name":{"offsetStart":7646,"normalizedForm":"jamovi","offsetEnd":7652,"rawForm":"jamovi","boundingBoxes":[{"x":322.77615,"h":8.9767,"y":268.761,"p":2,"w":27.078225000000003}]},"url":{"offsetStart":152,"normalizedForm":"/","offsetEnd":153,"rawForm":"/","boundingBoxes":[{"x":530.923,"h":8.9767,"y":256.742,"p":2,"w":3.826}]},"version":{"offsetStart":61,"normalizedForm":"1.1","offsetEnd":64,"rawForm":"1.1","boundingBoxes":[{"x":341.621,"h":8.976699999999994,"y":244.723,"p":2,"w":12.1284}]}},
  {"_key":"60c210097723bebd86645a15","_id":"annotations/60c210097723bebd86645a15","_rev":"_cfFmYQ----","wikipediaExternalRef":15183990,"document":{"$oid":"60c210097723bebd86645a13"},"context":"The FEA simulation is performed by the ABAQUS dynamic explicit solver, and the design results are elaborated by the following 2 subsections.","wikidataId":"Q728658","type":"software","confidence":0.7583,"software-name":{"wikipediaExternalRef":15183990,"normalizedForm":"ABAQUS","offsetStart":40,"wikidataId":"Q728658","offsetEnd":46,"lang":"en","confidence":0.7583,"rawForm":"ABAQUS","boundingBoxes":[{"x":38.34,"h":8.6861,"y":74.6321,"p":6,"w":36.9496}]},"lang":"en"},
  {"_key":"60c210097723bebd86645a16","_id":"annotations/60c210097723bebd86645a16","_rev":"_cfFmYQK---","wikipediaExternalRef":15183990,"document":{"$oid":"60c210097723bebd86645a13"},"context":"To meet demands from process design for CFRP thermoforming, a cutting-edge FEA modeling method for preforming has been developed based on the non-orthogonal material frame and realized as user-defined material subroutine in commercial software such as LS-DYNA [29] and Abaqus [30].","wikidataId":"Q728658","references":[{"offsetStart":20650,"normalizedForm":"[30]","refKey":29,"label":"[30]","reference_id":{"$oid":"60c210097723bebd86645a14"},"offsetEnd":20654,"boundingBoxes":[{"x":279.928,"h":8.68610000000001,"y":551.422,"p":3,"w":13.904960000000017}]}],"type":"software","confidence":0.8056,"software-name":{"wikipediaExternalRef":15183990,"normalizedForm":"Abaqus","offsetStart":273,"wikidataId":"Q728658","offsetEnd":279,"lang":"en","confidence":0.8056,"rawForm":"Abaqus","boundingBoxes":[{"x":477.942,"h":8.6861,"y":540.621,"p":3,"w":27.4478}]},"lang":"en"},
  {"_key":"60c210097723bebd86645a17","_id":"annotations/60c210097723bebd86645a17","_rev":"_cfFmYQW---","wikipediaExternalRef":20412,"document":{"$oid":"60c210097723bebd86645a13"},"context":"To form a whole design procedure and illustrate effectiveness of the new approach, basic trial-and-error optimization is applied in current work for preliminary analysis, and the flowchart of the blank geometry design loop is plotted in Fig. 4. Mesh adjustment operation is automated via Python scripts and MATLAB ® codes for user convenience.","wikidataId":"Q169478","type":"software","confidence":0.7721,"software-name":{"wikipediaExternalRef":20412,"normalizedForm":"MATLAB","offsetStart":312,"wikidataId":"Q169478","offsetEnd":318,"lang":"en","confidence":0.7721,"rawForm":"MATLAB","boundingBoxes":[{"x":298.5,"h":8.6861,"y":227.288,"p":4,"w":37.8998}]},"lang":"en"},
  {"_key":"60c210107723bebd86645a1a","_id":"annotations/60c210107723bebd86645a1a","_rev":"_cfFmYQm---","document":{"$oid":"60c210107723bebd86645a18"},"type":"software","software-name":{"offsetStart":6,"normalizedForm":"Basic Logic Alignment Search Tool (BLAST)","offsetEnd":47,"rawForm":"Basic Logic Alignment Search Tool (BLAST)","boundingBoxes":[{"x":173.312,"h":9.584000000000003,"y":484.366,"p":18,"w":190.24419999999998}]},"context":"After Basic Logic Alignment Search Tool (BLAST) sequence comparison, strain M-157 showed 100% identity to Streptomyceces cyaneofuscatus and was sequenced being designated as Streptomyceces cyaneofuscatus M-157."},
  {"_key":"60c210107723bebd86645a1b","_id":"annotations/60c210107723bebd86645a1b","_rev":"_cfFmYQy---","document":{"$oid":"60c210107723bebd86645a18"},"type":"software","software-name":{"offsetStart":33,"normalizedForm":"pdbqt","offsetEnd":38,"rawForm":"pdbqt","boundingBoxes":[{"x":421.796,"h":9.584,"y":566.074,"p":19,"w":25.8826}]},"context":"Compounds were then converted to pdbqt using Autodock tools."},
  {"_key":"60c210107723bebd86645a1c","_id":"annotations/60c210107723bebd86645a1c","_rev":"_cfFmYR----","document":{"$oid":"60c210107723bebd86645a18"},"type":"software","software-name":{"offsetStart":45,"normalizedForm":"Autodock","offsetEnd":53,"rawForm":"Autodock","boundingBoxes":[{"x":475.963,"h":9.584,"y":566.074,"p":19,"w":43.0564}]},"context":"Compounds were then converted to pdbqt using Autodock tools."},
  {"_key":"60c210107723bebd86645a1d","_id":"annotations/60c210107723bebd86645a1d","_rev":"_cfFmYRK---","document":{"$oid":"60c210107723bebd86645a18"},"type":"software","software-name":{"offsetStart":147,"normalizedForm":"DockRMSD","offsetEnd":155,"rawForm":"DockRMSD","boundingBoxes":[{"x":159.832,"h":9.584,"y":660.64,"p":19,"w":52.1343}]},"context":"Root mean square deviation (RMSD) between docked and crystallized ligand in the validation step was accepted when it was less than 2 Å using the DockRMSD server [75]."},
  {"_key":"60c210107723bebd86645a1e","_id":"annotations/60c210107723bebd86645a1e","_rev":"_cfFmYRW---","document":{"$oid":"60c210107723bebd86645a18"},"context":"Based on the ADME results, compounds were selected for further docking studies to investigate their potential effects on five SARS-COV-2 targets using Autodock Vina [73].","references":[{"offsetStart":55628,"normalizedForm":"[73]","refKey":76,"label":"[73]","reference_id":{"$oid":"60c210107723bebd86645a19"},"offsetEnd":55632,"boundingBoxes":[{"x":268.72,"h":9.584000000000003,"y":444.489,"p":19,"w":15.41288000000003}]}],"type":"software","software-name":{"offsetStart":153,"normalizedForm":"Autodock Vina","offsetEnd":166,"rawForm":"Autodock Vina","boundingBoxes":[{"x":198.246,"h":9.584000000000003,"y":444.489,"p":19,"w":67.97699999999995}]}},
  {"_key":"60c210137723bebd86645a20","_id":"annotations/60c210137723bebd86645a20","_rev":"_cfFmYRi---","wikipediaExternalRef":990677,"document":{"$oid":"60c210137723bebd86645a1f"},"publisher":{"offsetStart":69,"normalizedForm":"SAS Institute","offsetEnd":82,"rawForm":"SAS Institute","boundingBoxes":[{"x":440.24325,"h":9.60450000000003,"y":597.205,"p":1,"w":48.97444999999999}]},"context":"Statistical analyses were performed using SAS version 9.4 software (SAS Institute, Cary, North Carolina).","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":43,"wikidataId":"Q2003932","offsetEnd":46,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":331.103,"h":9.6045,"y":597.205,"p":1,"w":15.542}]},"version":{"offsetStart":55,"normalizedForm":"9.4","offsetEnd":58,"rawForm":"9.4","boundingBoxes":[{"x":383.4,"h":9.60450000000003,"y":597.205,"p":1,"w":11.286000000000001}]}},
  {"_key":"60c210187723bebd86645a22","_id":"annotations/60c210187723bebd86645a22","_rev":"_cfFmYRu---","wikipediaExternalRef":179088,"document":{"$oid":"60c210187723bebd86645a21"},"context":"Data analysis was done using SPSS-version 22. Frequency (percentage), mean (SD), and median (IQR) were used to describe the variables, as appropriate.","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":29,"wikidataId":"Q181596","offsetEnd":33,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":178.187,"h":8.9767,"y":232.762,"p":4,"w":17.526133333333334}]},"version":{"offsetStart":42,"normalizedForm":"22","offsetEnd":44,"rawForm":"22","boundingBoxes":[{"x":233.973,"h":8.9767,"y":232.762,"p":4,"w":7.849733333333333}]}},
  {"_key":"60c210187723bebd86645a23","_id":"annotations/60c210187723bebd86645a23","_rev":"_cfFmYR6---","document":{"$oid":"60c210187723bebd86645a21"},"context":"Furthermore, in order to minimize the data entry errors, an entry program developed with Census and Survey Processing System (CSPro, Version 7.0) software package, that automatically checks the data structure of the file using skip patterns and range of valid values, was used.","type":"software","software-name":{"offsetStart":91,"normalizedForm":"Census and Survey Processing System (CSPro","offsetEnd":134,"rawForm":"Census and Survey Processing System \n(CSPro","boundingBoxes":[{"x":126.028,"h":8.976699999999994,"y":160.76,"p":4,"w":164.59429999999998},{"x":56.6929,"h":8.976699999999994,"y":172.722,"p":4,"w":26.371542857142863}]},"version":{"offsetStart":144,"normalizedForm":"7.0","offsetEnd":147,"rawForm":"7.0","boundingBoxes":[{"x":125.349,"h":8.976699999999994,"y":172.722,"p":4,"w":11.186549999999997}]}},
  {"_key":"60c210187723bebd86645a24","_id":"annotations/60c210187723bebd86645a24","_rev":"_cfFmYSG---","wikipediaExternalRef":179088,"document":{"$oid":"60c210187723bebd86645a21"},"context":"Kruskal-Wallis, Mann-Whitney U tests and spearman rank correlation coefficient tools were performed to analyze the data using SPSS (Version 22).","wikidataId":"Q181596","type":"software","lang":"en","confidence":0.751,"software-name":{"wikipediaExternalRef":179088,"normalizedForm":"SPSS","offsetStart":127,"wikidataId":"Q181596","offsetEnd":131,"lang":"en","confidence":0.751,"rawForm":"SPSS","boundingBoxes":[{"x":410.86,"h":8.8301,"y":392.322,"p":1,"w":18.7402}]},"version":{"offsetStart":141,"normalizedForm":"22","offsetEnd":143,"rawForm":"22","boundingBoxes":[{"x":467.326,"h":8.8301,"y":392.322,"p":1,"w":6.92005}]}},
  {"_key":"60c210197723bebd86645a26","_id":"annotations/60c210197723bebd86645a26","_rev":"_cfFmYSS---","wikipediaExternalRef":990677,"document":{"$oid":"60c210197723bebd86645a25"},"publisher":{"offsetStart":62,"normalizedForm":"SAS Institute Inc","offsetEnd":79,"rawForm":"SAS Institute Inc","boundingBoxes":[{"x":134.97385,"h":8.816900000000032,"y":577.848,"p":4,"w":66.3355}]},"context":"Data was analyzed using the SAS system software version 9.4 (SAS Institute Inc, Cary, NC).","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4566,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":28,"wikidataId":"Q2003932","offsetEnd":31,"lang":"en","confidence":0.4566,"rawForm":"SAS","boundingBoxes":[{"x":245.718,"h":8.8169,"y":565.886,"p":4,"w":18.1538}]},"version":{"offsetStart":57,"normalizedForm":"9.4","offsetEnd":60,"rawForm":"9.4","boundingBoxes":[{"x":114.185,"h":8.816900000000032,"y":577.848,"p":4,"w":12.45519999999999}]}},
  {"_key":"60c210197723bebd86645a27","_id":"annotations/60c210197723bebd86645a27","_rev":"_cfFmYSe---","wikipediaExternalRef":990677,"document":{"$oid":"60c210197723bebd86645a25"},"publisher":{"offsetStart":62,"normalizedForm":"SAS Institute Inc","offsetEnd":79,"rawForm":"SAS Institute Inc","boundingBoxes":[{"x":134.97385,"h":8.816900000000032,"y":577.848,"p":4,"w":66.3355}]},"context":"Then, to correct for base- line factors, a mixed model approach was implemented, using the PROC MIXED procedure in SAS, to model changes in room entry and other outcome variables, adjusting for baseline covariates (e.g.","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4566,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":116,"wikidataId":"Q2003932","offsetEnd":119,"lang":"en","confidence":0.4566,"rawForm":"SAS","boundingBoxes":[{"x":447.687,"h":8.8169,"y":513.273,"p":3,"w":15.602924999999999}]},"version":{"offsetStart":57,"normalizedForm":"9.4","offsetEnd":60,"rawForm":"9.4","boundingBoxes":[{"x":114.185,"h":8.816900000000032,"y":577.848,"p":4,"w":12.45519999999999}]}},
  {"_key":"60c210197723bebd86645a29","_id":"annotations/60c210197723bebd86645a29","_rev":"_cfFmYSu---","wikipediaExternalRef":1809002,"document":{"$oid":"60c210197723bebd86645a28"},"publisher":{"offsetStart":72,"normalizedForm":"StataCorp","offsetEnd":81,"rawForm":"StataCorp","boundingBoxes":[{"x":77.5554,"h":8.821,"y":362.286,"p":2,"w":35.21086363636364}]},"context":"R Foundation for Statistical Computing) and Stata software (2019.R.16; StataCorp).","wikidataId":"Q1204300","type":"software","lang":"en","confidence":0.7154,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":44,"wikidataId":"Q1204300","offsetEnd":49,"lang":"en","confidence":0.7154,"rawForm":"Stata","boundingBoxes":[{"x":208.571,"h":8.821,"y":351.287,"p":2,"w":18.4181}]},"version":{"offsetStart":61,"normalizedForm":"2019.R.16","offsetEnd":70,"rawForm":"2019.R.16","boundingBoxes":[{"x":36.34397272727273,"h":8.821000000000026,"y":362.286,"p":2,"w":34.730754545454545}]}},
  {"_key":"60c210207723bebd86645a2b","_id":"annotations/60c210207723bebd86645a2b","_rev":"_cfFmYS6---","document":{"$oid":"60c210207723bebd86645a2a"},"context":"First, open the URL of web server idrp-server.herokuapp. com/and then see a top header menu which has four tabs i.e.","type":"software","software-name":{"offsetStart":34,"normalizedForm":"idrp","offsetEnd":38,"rawForm":"idrp","boundingBoxes":[{"x":450.951,"h":11.48,"y":512.159,"p":11,"w":16.96509090909091}]},"url":{"offsetStart":38,"normalizedForm":"-server.herokuapp. com","offsetEnd":61,"rawForm":"-server.herokuapp. \ncom","boundingBoxes":[{"x":467.91609090909094,"h":11.480000000000018,"y":512.159,"p":11,"w":76.34290909090919},{"x":306.141,"h":11.48,"y":524.659,"p":11,"w":15.17142857142857}]}},
  {"_key":"60c210207723bebd86645a2c","_id":"annotations/60c210207723bebd86645a2c","_rev":"_cfFmYTG---","document":{"$oid":"60c210207723bebd86645a2a"},"context":"For a neural system, the sci-unit neural system was utilized with Theano 1.0.0 at the backend.","type":"software","software-name":{"offsetStart":67,"normalizedForm":"Theano","offsetEnd":73,"rawForm":"Theano","boundingBoxes":[{"x":514.239,"h":11.48,"y":428.661,"p":11,"w":30.185}]},"version":{"offsetStart":75,"normalizedForm":"1.0.0","offsetEnd":80,"rawForm":"1.0.0","boundingBoxes":[{"x":306.141,"h":11.480000000000018,"y":441.161,"p":11,"w":20.200000000000045}]}},
  {"_key":"60c210207723bebd86645a2d","_id":"annotations/60c210207723bebd86645a2d","_rev":"_cfFmYTS---","wikipediaExternalRef":2247376,"document":{"$oid":"60c210207723bebd86645a2a"},"context":"In this manner, one shall make efforts to develop a webserver for the expecta- tion technique detailed in this paper; until further notice, its independent code is accessible at idrp-server.herokuapp. com/which is created utilizing Django 2.0.7.","wikidataId":"Q842014","type":"software","lang":"en","confidence":0.3901,"software-name":{"wikipediaExternalRef":2247376,"normalizedForm":"Django","offsetStart":235,"wikidataId":"Q842014","offsetEnd":241,"lang":"en","confidence":0.3901,"rawForm":"Django","boundingBoxes":[{"x":434.477,"h":11.48,"y":416.161,"p":11,"w":30.09}]},"url":{"offsetStart":180,"normalizedForm":"idrp-server.herokuapp. com","offsetEnd":207,"rawForm":"idrp-server.herokuapp. \ncom","boundingBoxes":[{"x":452.661,"h":11.480000000000018,"y":403.661,"p":11,"w":91.6509999999999},{"x":306.141,"h":11.48,"y":416.161,"p":11,"w":15.107666666666667}]},"version":{"offsetStart":242,"normalizedForm":"2.0.7","offsetEnd":247,"rawForm":"2.0.7","boundingBoxes":[{"x":467.617,"h":11.480000000000018,"y":416.161,"p":11,"w":19.291666666666686}]}},
  {"_key":"60c210217723bebd86645a2f","_id":"annotations/60c210217723bebd86645a2f","_rev":"_cfFmYTa---","wikipediaExternalRef":77229,"document":{"$oid":"60c210217723bebd86645a2e"},"context":"Further, most of the students are able to use word processors, PowerPoint, email and search engines.","wikidataId":"Q11266","type":"software","confidence":0.6885,"software-name":{"wikipediaExternalRef":77229,"normalizedForm":"PowerPoint","offsetStart":64,"wikidataId":"Q11266","offsetEnd":74,"lang":"en","confidence":0.6885,"rawForm":"PowerPoint","boundingBoxes":[{"x":263.96,"h":8.7571,"y":565.605,"p":9,"w":44.19772727272727}]},"lang":"en"},
  {"_key":"60c210257723bebd86645a31","_id":"annotations/60c210257723bebd86645a31","_rev":"_cfFmYTm---","wikipediaExternalRef":3793613,"document":{"$oid":"60c210257723bebd86645a30"},"publisher":{"offsetStart":109,"normalizedForm":"NIH","offsetEnd":112,"rawForm":"NIH","boundingBoxes":[{"x":518.1612,"h":7.1652,"y":708.363,"p":3,"w":11.7066}]},"context":"The band density was quantified under appropriate UV exposure by video densitometry using Image J software (NIH, USA).","wikidataId":"Q1659584","type":"software","confidence":0.9507,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":91,"wikidataId":"Q1659584","offsetEnd":98,"lang":"en","confidence":0.9507,"rawForm":"Image J","boundingBoxes":[{"x":448.383,"h":7.165200000000027,"y":708.363,"p":3,"w":28.858600000000024}]},"lang":"en"},
  {"_key":"60c210337723bebd86645a33","_id":"annotations/60c210337723bebd86645a33","_rev":"_cfFmYT2---","document":{"$oid":"60c210337723bebd86645a32"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"MARRtino","offsetEnd":8,"rawForm":"MARRtino","boundingBoxes":[{"x":58.1147,"h":10.906,"y":104.704,"p":6,"w":42.7595}]},"context":"MARRtino is a robot based on the Robot Operating System (ROS) 2 , thus exploiting all the available open-source components developed by the ROS community."},
  {"_key":"60c210337723bebd86645a34","_id":"annotations/60c210337723bebd86645a34","_rev":"_cfFmYUC---","document":{"$oid":"60c210337723bebd86645a32"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"MARRtino","offsetEnd":8,"rawForm":"MARRtino","boundingBoxes":[{"x":328.817,"h":10.906,"y":380.722,"p":6,"w":42.7595}]},"context":"MARRtino soft- ware running in the Raspberry Pi board mounted on the robot is configured to start a wire- less access point and a web server at boot to allow users to directly connect to the robot without the need of any other network infrastructure or device."},
  {"_key":"60c210337723bebd86645a35","_id":"annotations/60c210337723bebd86645a35","_rev":"_cfFmYUO---","document":{"$oid":"60c210337723bebd86645a32"},"type":"software","software-name":{"offsetStart":13,"normalizedForm":"MARRtino","offsetEnd":21,"rawForm":"MARRtino","boundingBoxes":[{"x":349.821,"h":10.906,"y":150.704,"p":6,"w":42.7595}]},"context":"In this way, MARRtino is compatible with other similar ROS-based platforms (such as TurtleBot2, 3 for example), but it is available at a much lower price and comes in a construction kit so that the students can build it."},
  {"_key":"60c210337723bebd86645a36","_id":"annotations/60c210337723bebd86645a36","_rev":"_cfFmYUW---","document":{"$oid":"60c210337723bebd86645a32"},"type":"software","software-name":{"offsetStart":29,"normalizedForm":"MARRtino","offsetEnd":37,"rawForm":"MARRtino","boundingBoxes":[{"x":183.543,"h":10.906,"y":416.101,"p":5,"w":42.7595}]},"context":"The main advantages of using MARRtino are its full hardware and software open- source design and implementation and the use of standard development tools that are well- known and largely used by the robotics research and industrial communities."},
  {"_key":"60c210337723bebd86645a37","_id":"annotations/60c210337723bebd86645a37","_rev":"_cfFmYUi---","document":{"$oid":"60c210337723bebd86645a32"},"type":"software","software-name":{"offsetStart":29,"normalizedForm":"MARRtino","offsetEnd":37,"rawForm":"MARRtino","boundingBoxes":[{"x":178.655,"h":10.906,"y":196.699,"p":6,"w":42.7595}]},"context":"Although ROS is essential in MARRtino project, as it guarantees the integration of state-of-the-art components with minimal effort, it is in general too challenging to learn for high-school students in a short time."},
  {"_key":"60c210337723bebd86645a38","_id":"annotations/60c210337723bebd86645a38","_rev":"_cfFmYUy---","document":{"$oid":"60c210337723bebd86645a32"},"publisher":{"offsetStart":280,"normalizedForm":"Arduino","offsetEnd":287,"rawForm":"Arduino","boundingBoxes":[{"x":134.476,"h":10.906,"y":139.199,"p":6,"w":31.6436}]},"context":"MARRtino is a robot based on the Robot Operating System (ROS) 2 , thus exploiting all the available open-source components developed by the ROS community.","type":"software","software-name":{"offsetStart":33,"normalizedForm":"Robot Operating System (ROS)","offsetEnd":61,"rawForm":"Robot Operating System (ROS)","boundingBoxes":[{"x":193.447,"h":10.906000000000006,"y":104.704,"p":6,"w":121.49549999999999}]},"version":{"offsetStart":62,"normalizedForm":"2","offsetEnd":63,"rawForm":"2","boundingBoxes":[{"x":314.9,"h":7.6342,"y":102.773,"p":6,"w":3.325}]}},
  {"_key":"60c210337723bebd86645a39","_id":"annotations/60c210337723bebd86645a39","_rev":"_cfFmYU6---","document":{"$oid":"60c210337723bebd86645a32"},"type":"software","software-name":{"offsetStart":35,"normalizedForm":"MARRtino","offsetEnd":43,"rawForm":"MARRtino","boundingBoxes":[{"x":144.671,"h":10.906,"y":610.212,"p":7,"w":43.6905}]},"context":"Additional examples of the use of MARRtino in educational competitions aiming at integrating  artificial intelligence and robotics techniques can be found in the material used to run the European RoboCup@Home Education Challenge 2019 5 Tan et al. (2019)."},
  {"_key":"60c210337723bebd86645a3a","_id":"annotations/60c210337723bebd86645a3a","_rev":"_cfFmYVG---","document":{"$oid":"60c210337723bebd86645a32"},"type":"software","software-name":{"offsetStart":50,"normalizedForm":"MARRtino","offsetEnd":58,"rawForm":"MARRtino","boundingBoxes":[{"x":254.547,"h":10.906,"y":518.776,"p":6,"w":43.6905}]},"context":"The possibility of using all these features makes MARRtino an exceptionally suited educational robot, where students can properly combine advanced artificial intelli- gence and robotics techniques (such as navigation in dynamic environments, object rec- ognition through deep learning, speech recognition using cloud services, etc.) with a suitable setting considering their background."},
  {"_key":"60c210337723bebd86645a3b","_id":"annotations/60c210337723bebd86645a3b","_rev":"_cfFmYVS---","wikipediaExternalRef":44494473,"document":{"$oid":"60c210337723bebd86645a32"},"context":"The programming experience was made more user-friendly using Blockly, an open-source library that allows adding block-based visual programming to a web application Pasternak et al. (2017), Fraser (2015) (an example is shown in Fig. 1).","wikidataId":"Q18202981","type":"software","confidence":0.8098,"software-name":{"wikipediaExternalRef":44494473,"normalizedForm":"Blockly","offsetStart":62,"wikidataId":"Q18202981","offsetEnd":69,"lang":"en","confidence":0.8098,"rawForm":"Blockly","boundingBoxes":[{"x":46.7725,"h":10.906,"y":495.767,"p":6,"w":27.6058125}]},"lang":"en"},
  {"_key":"60c210337723bebd86645a3c","_id":"annotations/60c210337723bebd86645a3c","_rev":"_cfFmYVe---","wikipediaExternalRef":54267845,"document":{"$oid":"60c210337723bebd86645a32"},"context":"In this way, MARRtino is compatible with other similar ROS-based platforms (such as TurtleBot2, 3 for example), but it is available at a much lower price and comes in a construction kit so that the students can build it.","wikidataId":"Q30644434","type":"software","lang":"en","confidence":0.7354,"software-name":{"wikipediaExternalRef":54267845,"normalizedForm":"TurtleBot","offsetStart":85,"wikidataId":"Q30644434","offsetEnd":94,"lang":"en","confidence":0.7354,"rawForm":"TurtleBot","boundingBoxes":[{"x":291.579,"h":10.906,"y":162.208,"p":6,"w":39.86545454545454}]},"version":{"offsetStart":94,"normalizedForm":"2","offsetEnd":95,"rawForm":"2","boundingBoxes":[{"x":291.579,"h":10.906,"y":162.208,"p":6,"w":39.86545454545454}]}},
  {"_key":"60c210337723bebd86645a3d","_id":"annotations/60c210337723bebd86645a3d","_rev":"_cfFmYVq---","document":{"$oid":"60c210337723bebd86645a32"},"type":"software","software-name":{"offsetStart":121,"normalizedForm":"MARRtino","offsetEnd":129,"rawForm":"MARRtino","boundingBoxes":[{"x":74.4451,"h":10.906,"y":423.106,"p":9,"w":43.6905}]},"context":"Some examples of experi- ments arising from real-world observations are provided below and illustrated in Fig. 2, where MARRtino robot and other tools (including another mobile robot) are used to demonstrate different effects of Newtonian physics, such as inertia, friction, relative motions, etc. Experiment n1."},
  {"_key":"60c210377723bebd86645a3f","_id":"annotations/60c210377723bebd86645a3f","_rev":"_cfFmYV2---","document":{"$oid":"60c210377723bebd86645a3e"},"publisher":{"offsetStart":68,"normalizedForm":"Graphpad Software Inc","offsetEnd":90,"rawForm":"Graphpad Software \nInc","boundingBoxes":[{"x":435.2611111111111,"h":9,"y":218.05,"p":7,"w":76.60888888888888},{"x":150,"h":9,"y":230.05,"p":7,"w":10.661999999999999}]},"context":"The data analysis was performed using Graphpad Prism, version 5.00 (Graphpad Software Inc., La Jolla, CA, USA).","type":"software","software-name":{"offsetStart":38,"normalizedForm":"Graphpad Prism","offsetEnd":52,"rawForm":"Graphpad Prism","boundingBoxes":[{"x":308.3,"h":9,"y":218.05,"p":7,"w":63.46333333333337}]},"version":{"offsetStart":62,"normalizedForm":"5.00","offsetEnd":66,"rawForm":"5.00","boundingBoxes":[{"x":410.51,"h":9,"y":218.05,"p":7,"w":17.5}]}},
  {"_key":"60c2103c7723bebd86645a41","_id":"annotations/60c2103c7723bebd86645a41","_rev":"_cfFmYWC---","document":{"$oid":"60c2103c7723bebd86645a40"},"publisher":{"offsetStart":95,"normalizedForm":"OSIS","offsetEnd":99,"rawForm":"OSIS","boundingBoxes":[{"x":188.046,"h":9.6495,"y":577.382,"p":11,"w":19.380599999999998}]},"context":"The \"iTEM\" software used includes an automated image \"stitching\" module (MIA, multiple image alignment), but the usability for ultrastructural diagnostic purposes is very limited.","type":"software","software-name":{"offsetStart":5,"normalizedForm":"iTEM","offsetEnd":9,"rawForm":"iTEM","boundingBoxes":[{"x":128.3269,"h":9.6495,"y":153.85,"p":19,"w":21.915599999999998}]}},
  {"_key":"60c2103c7723bebd86645a42","_id":"annotations/60c2103c7723bebd86645a42","_rev":"_cfFmYWO---","document":{"$oid":"60c2103c7723bebd86645a40"},"type":"software","software-name":{"offsetStart":25,"normalizedForm":"analySIS","offsetEnd":33,"rawForm":"analySIS","boundingBoxes":[{"x":299.38186666666667,"h":9.6495,"y":127.85,"p":9,"w":35.57493333333333}]},"context":"The commercial software \"analySIS ® \" (EsiVision ® Ver."},
  {"_key":"60c2103c7723bebd86645a43","_id":"annotations/60c2103c7723bebd86645a43","_rev":"_cfFmYWa---","document":{"$oid":"60c2103c7723bebd86645a40"},"type":"software","software-name":{"offsetStart":30,"normalizedForm":"Windows- XP","offsetEnd":41,"rawForm":"Windows-\nXP","boundingBoxes":[{"x":359.903,"h":8.270999999999958,"y":553.317,"p":10,"w":36.964800000000025},{"x":65.1965,"h":8.271,"y":564.317,"p":10,"w":10.863}]},"context":"The system is controlled by a Windows- XP server running the \"iTEM\" software and handling the communication via standard LAN or WLAN links to the Internet."},
  {"_key":"60c2103c7723bebd86645a44","_id":"annotations/60c2103c7723bebd86645a44","_rev":"_cfFmYWm---","wikipediaExternalRef":21291483,"document":{"$oid":"60c2103c7723bebd86645a40"},"context":"The system was controlled by a Windows NT server and acquired the images from the camera by a frame grabber.","wikidataId":"Q486487","type":"software","confidence":0.9701,"software-name":{"wikipediaExternalRef":21291483,"normalizedForm":"Windows NT","offsetStart":32,"wikidataId":"Q486487","offsetEnd":42,"lang":"en","confidence":0.9701,"rawForm":"Windows NT","boundingBoxes":[{"x":148.832,"h":9.649500000000003,"y":114.85,"p":9,"w":58.88390000000001}]},"lang":"en"},
  {"_key":"60c2103c7723bebd86645a45","_id":"annotations/60c2103c7723bebd86645a45","_rev":"_cfFmYWy---","document":{"$oid":"60c2103c7723bebd86645a40"},"publisher":{"offsetStart":62,"normalizedForm":"SIS/Muenster","offsetEnd":74,"rawForm":"SIS/Muenster","boundingBoxes":[{"x":99.06,"h":9.649499999999989,"y":140.85,"p":9,"w":57.093507692307696}]},"context":"The commercial software \"analySIS ® \" (EsiVision ® Ver.","type":"software","software-name":{"offsetStart":39,"normalizedForm":"EsiVision","offsetEnd":48,"rawForm":"EsiVision","boundingBoxes":[{"x":349.00788,"h":9.6495,"y":127.85,"p":9,"w":40.10292}]},"version":{"offsetStart":57,"normalizedForm":"3.1","offsetEnd":60,"rawForm":"3.1","boundingBoxes":[{"x":80.0833,"h":9.649499999999989,"y":140.85,"p":9,"w":11.391975000000002}]}},
  {"_key":"60c2103c7723bebd86645a46","_id":"annotations/60c2103c7723bebd86645a46","_rev":"_cfFmYX----","document":{"$oid":"60c2103c7723bebd86645a40"},"publisher":{"offsetStart":95,"normalizedForm":"OSIS","offsetEnd":99,"rawForm":"OSIS","boundingBoxes":[{"x":188.046,"h":9.6495,"y":577.382,"p":11,"w":19.380599999999998}]},"context":"The system is controlled by a Windows- XP server running the \"iTEM\" software and handling the communication via standard LAN or WLAN links to the Internet.","type":"software","software-name":{"offsetStart":62,"normalizedForm":"iTEM","offsetEnd":66,"rawForm":"iTEM","boundingBoxes":[{"x":152.653,"h":8.271,"y":564.317,"p":10,"w":18.491999999999997}]}},
  {"_key":"60c2103c7723bebd86645a47","_id":"annotations/60c2103c7723bebd86645a47","_rev":"_cfFmYXK---","document":{"$oid":"60c2103c7723bebd86645a40"},"publisher":{"offsetStart":95,"normalizedForm":"OSIS","offsetEnd":99,"rawForm":"OSIS","boundingBoxes":[{"x":188.046,"h":9.6495,"y":577.382,"p":11,"w":19.380599999999998}]},"context":"In the meantime, the client \"analySIS\" software (now upgraded by the \"iTEM\" software package, OSIS/Muenster, Germany; www.olympus-sis. com) was installed on Windows-XP running desktops in different locations (Fig. 14.4): Pathology Innsbruck/Austria, Thomas Mairinger; Pathology Zurich/  Using the present system configuration, JPEG2000 data compression, and standard client LAN Internet access (10 Mbps), we obtained in the preview \"live- image\" mode (used for screening the sample; image size 1,024 × 1,024 pixel, 2 MHz pixel-clock at 16 bits, and 100 ms exposure time) at a frame rate of 1-3/s;  for the transfer of the uncompressed high-resolution (16 bits, 1,024 × 1,024 pixel) \"snapshot\" image to the local hard disk, we experienced a transfer time of 4-7 s (depending on date and time of day).","type":"software","software-name":{"offsetStart":71,"normalizedForm":"iTEM","offsetEnd":75,"rawForm":"iTEM","boundingBoxes":[{"x":65.09485,"h":9.6495,"y":577.382,"p":11,"w":22.2614}]}},
  {"_key":"60c2103c7723bebd86645a48","_id":"annotations/60c2103c7723bebd86645a48","_rev":"_cfFmYXW---","document":{"$oid":"60c2103c7723bebd86645a40"},"publisher":{"offsetStart":123,"normalizedForm":"ORNL","offsetEnd":127,"rawForm":"ORNL","boundingBoxes":[{"x":198.246,"h":9.6495,"y":419.85,"p":8,"w":24.43728}]},"context":"This software effectively mirrors the remote computer, in this case a Macintosh running the DigitalMicrograph program at ORNL, to a Windows computer at the Univer- sity of Regensburg, operated by the author, J. Schroeder.","type":"software","software-name":{"offsetStart":94,"normalizedForm":"DigitalMicrograph","offsetEnd":111,"rawForm":"DigitalMicrograph","boundingBoxes":[{"x":65.1958,"h":9.6495,"y":419.85,"p":8,"w":80.2935}]}},
  {"_key":"60c2103c7723bebd86645a49","_id":"annotations/60c2103c7723bebd86645a49","_rev":"_cfFmYXi---","document":{"$oid":"60c2103c7723bebd86645a40"},"type":"software","software-name":{"offsetStart":126,"normalizedForm":"analy- SIS","offsetEnd":136,"rawForm":"analy-\nSIS","boundingBoxes":[{"x":365.45709999999997,"h":9.649499999999989,"y":179.85,"p":9,"w":25.842600000000004},{"x":59.5296,"h":9.6495,"y":192.85,"p":9,"w":13.6185}]},"context":"At the \"client site\" in Bochum, a laptop equipped with an ISDN-PCMCIA card provided direct access to the Internet (a client \"analy- SIS ® \" software was installed on the laptop computer)."},
  {"_key":"60c2103c7723bebd86645a4a","_id":"annotations/60c2103c7723bebd86645a4a","_rev":"_cfFmYXu---","document":{"$oid":"60c2103c7723bebd86645a40"},"publisher":{"offsetStart":95,"normalizedForm":"OSIS","offsetEnd":99,"rawForm":"OSIS","boundingBoxes":[{"x":188.046,"h":9.6495,"y":577.382,"p":11,"w":19.380599999999998}]},"context":"It is worth noting that the Bundeswehr EM laboratory has similar server telepathology equipment (sibling Zeiss-TEM and TRS-camera, iTEM software) and can provide remote telepathology support (Fig. 14.10).","type":"software","software-name":{"offsetStart":133,"normalizedForm":"iTEM","offsetEnd":137,"rawForm":"iTEM","boundingBoxes":[{"x":141.947,"h":9.6495,"y":179.85,"p":17,"w":25.2451}]}},
  {"_key":"60c2103c7723bebd86645a4b","_id":"annotations/60c2103c7723bebd86645a4b","_rev":"_cfFmYX6---","wikipediaExternalRef":18890,"document":{"$oid":"60c2103c7723bebd86645a40"},"context":"This software effectively mirrors the remote computer, in this case a Macintosh running the DigitalMicrograph program at ORNL, to a Windows computer at the Univer- sity of Regensburg, operated by the author, J. Schroeder.","wikidataId":"Q1406","type":"software","confidence":0.275,"software-name":{"wikipediaExternalRef":18890,"normalizedForm":"Windows","offsetStart":134,"wikidataId":"Q1406","offsetEnd":141,"lang":"en","confidence":0.275,"rawForm":"Windows","boundingBoxes":[{"x":249.989,"h":9.6495,"y":419.85,"p":8,"w":40.7736}]},"lang":"en"},
  {"_key":"60c2103c7723bebd86645a4c","_id":"annotations/60c2103c7723bebd86645a4c","_rev":"_cfFmYYG---","document":{"$oid":"60c2103c7723bebd86645a40"},"context":"In the meantime, the client \"analySIS\" software (now upgraded by the \"iTEM\" software package, OSIS/Muenster, Germany; www.olympus-sis. com) was installed on Windows-XP running desktops in different locations (Fig. 14.4): Pathology Innsbruck/Austria, Thomas Mairinger; Pathology Zurich/  Using the present system configuration, JPEG2000 data compression, and standard client LAN Internet access (10 Mbps), we obtained in the preview \"live- image\" mode (used for screening the sample; image size 1,024 × 1,024 pixel, 2 MHz pixel-clock at 16 bits, and 100 ms exposure time) at a frame rate of 1-3/s;  for the transfer of the uncompressed high-resolution (16 bits, 1,024 × 1,024 pixel) \"snapshot\" image to the local hard disk, we experienced a transfer time of 4-7 s (depending on date and time of day).","type":"software","software-name":{"offsetStart":159,"normalizedForm":"Windows-XP","offsetEnd":169,"rawForm":"Windows-XP","boundingBoxes":[{"x":160.543,"h":9.649499999999989,"y":590.382,"p":11,"w":56.65379999999999}]},"url":{"offsetStart":119,"normalizedForm":"www.olympus-sis. com","offsetEnd":140,"rawForm":"www.olympus-sis. \ncom","boundingBoxes":[{"x":313.58,"h":9.649499999999989,"y":577.382,"p":11,"w":77.57190000000003},{"x":59.5295,"h":9.6495,"y":590.382,"p":11,"w":16.6635}]}},
  {"_key":"60c2103c7723bebd86645a4d","_id":"annotations/60c2103c7723bebd86645a4d","_rev":"_cfFmYYS---","document":{"$oid":"60c2103c7723bebd86645a40"},"context":"For the transatlantic sessions, the material science-oriented Hitachi HF-2000 TEM in Oak Ridge was operated remotely via the Internet using the commercial col- laborative software TimbuktuPro® (http://www.Netopia.com).","type":"software","software-name":{"offsetStart":182,"normalizedForm":"TimbuktuPro","offsetEnd":193,"rawForm":"TimbuktuPro","boundingBoxes":[{"x":151.799,"h":9.6495,"y":393.85,"p":8,"w":61.6287}]},"url":{"offsetStart":196,"normalizedForm":"http://www.Netopia.com","offsetEnd":218,"rawForm":"http://www.Netopia.com","boundingBoxes":[{"x":222.11004,"h":9.649499999999989,"y":393.85,"p":8,"w":102.10288}]}},
  {"_key":"60c2103d7723bebd86645a4f","_id":"annotations/60c2103d7723bebd86645a4f","_rev":"_cfFmYYe---","wikipediaExternalRef":990677,"document":{"$oid":"60c2103d7723bebd86645a4e"},"publisher":{"offsetStart":54,"normalizedForm":"SAS","offsetEnd":57,"rawForm":"SAS","boundingBoxes":[{"x":314.49496,"h":9.584,"y":379.114,"p":3,"w":14.41188}]},"context":"Statistical analyses were conducted using SAS ® v9.4 (SAS, Cary, NC, USA).","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4613,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":42,"wikidataId":"Q2003932","offsetEnd":45,"lang":"en","confidence":0.4613,"rawForm":"SAS","boundingBoxes":[{"x":261.052,"h":9.584,"y":379.114,"p":3,"w":18.2116}]},"version":{"offsetStart":49,"normalizedForm":"9.4","offsetEnd":52,"rawForm":"9.4","boundingBoxes":[{"x":289.119,"h":9.584000000000003,"y":379.114,"p":3,"w":18.082100000000025}]}},
  {"_key":"60c210457723bebd86645a51","_id":"annotations/60c210457723bebd86645a51","_rev":"_cfFmYYm---","wikipediaExternalRef":1809002,"document":{"$oid":"60c210457723bebd86645a50"},"publisher":{"offsetStart":32,"normalizedForm":"StataCorp","offsetEnd":41,"rawForm":"StataCorp","boundingBoxes":[{"x":331.5775,"h":9,"y":143.57,"p":5,"w":36.2475}]},"context":"Data were analyzed using Stata (StataCorp., College Station, Texas), with a 2- sided P value of 0.05 considered statistically significant.","wikidataId":"Q1204300","type":"software","confidence":0.7154,"software-name":{"wikipediaExternalRef":1809002,"normalizedForm":"Stata","offsetStart":25,"wikidataId":"Q1204300","offsetEnd":30,"lang":"en","confidence":0.7154,"rawForm":"Stata","boundingBoxes":[{"x":305.05,"h":9,"y":143.57,"p":5,"w":20}]},"lang":"en"},
  {"_key":"60c210457723bebd86645a52","_id":"annotations/60c210457723bebd86645a52","_rev":"_cfFmYYy---","wikipediaExternalRef":6664689,"document":{"$oid":"60c210457723bebd86645a50"},"publisher":{"offsetStart":43,"normalizedForm":"Clarivate Analytics","offsetEnd":62,"rawForm":"Clarivate Analytics","boundingBoxes":[{"x":333.66,"h":9,"y":559.574,"p":3,"w":74.78800000000001}]},"context":"Search results were downloaded to EndNote (Clarivate Analytics, Philadelphia, PA) and, after being deduplicated, were uploaded to Covidence (Veritas Health Innovation Ltd, Melbourne, Australia).","wikidataId":"Q1340244","type":"software","confidence":0.794,"software-name":{"wikipediaExternalRef":6664689,"normalizedForm":"EndNote","offsetStart":34,"wikidataId":"Q1340244","offsetEnd":41,"lang":"en","confidence":0.794,"rawForm":"EndNote","boundingBoxes":[{"x":291.661,"h":9,"y":559.574,"p":3,"w":35.55}]},"lang":"en"},
  {"_key":"60c2104a7723bebd86645a56","_id":"annotations/60c2104a7723bebd86645a56","_rev":"_cfFmYZ----","wikipediaExternalRef":2324407,"document":{"$oid":"60c2104a7723bebd86645a53"},"context":"Figures were generated using PyMOL (Delano, 2002).","wikidataId":"Q1373457","references":[{"offsetStart":17083,"normalizedForm":"Delano, 2002","refKey":3,"label":"(Delano, 2002)","reference_id":{"$oid":"60c2104a7723bebd86645a54"},"offsetEnd":17097,"boundingBoxes":[{"x":139.913,"h":8.398000000000025,"y":584.292,"p":4,"w":54.98916666666665}]}],"type":"software","confidence":0.8093,"software-name":{"wikipediaExternalRef":2324407,"normalizedForm":"PyMOL","offsetStart":30,"wikidataId":"Q1373457","offsetEnd":35,"lang":"en","confidence":0.8093,"rawForm":"PyMOL","boundingBoxes":[{"x":107.376,"h":8.398,"y":584.292,"p":4,"w":30.381}]},"lang":"en"},
  {"_key":"60c2104a7723bebd86645a57","_id":"annotations/60c2104a7723bebd86645a57","_rev":"_cfFmYZK---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2104a7723bebd86645a53"},"context":"The model of Nsp9 was predicted using the I-TASSER server and built onto the averaged molecular envelope obtained using CHIMERA (Pettersen et al., 2004).","wikidataId":"Q17029600","type":"software","confidence":0.7609,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":42,"wikidataId":"Q17029600","offsetEnd":50,"lang":"en","confidence":0.7609,"rawForm":"I-TASSER","boundingBoxes":[{"x":225.888,"h":8.398000000000025,"y":268.872,"p":7,"w":38.61749999999998}]},"lang":"en"},
  {"_key":"60c2104a7723bebd86645a58","_id":"annotations/60c2104a7723bebd86645a58","_rev":"_cfFmYZW---","wikipediaExternalRef":21572326,"document":{"$oid":"60c2104a7723bebd86645a53"},"context":"Statistical analysis was conducted using GraphPad Prism 6, with significance assessed using Student t-test.","wikidataId":"Q5597066","type":"software","lang":"en","confidence":0.9856,"software-name":{"wikipediaExternalRef":21572326,"normalizedForm":"GraphPad Prism","offsetStart":42,"wikidataId":"Q5597066","offsetEnd":56,"lang":"en","confidence":0.9856,"rawForm":"GraphPad Prism","boundingBoxes":[{"x":67.514,"h":8.398000000000025,"y":450.296,"p":6,"w":63.364999999999995}]},"version":{"offsetStart":57,"normalizedForm":"6","offsetEnd":58,"rawForm":"6","boundingBoxes":[{"x":132.693,"h":8.398,"y":450.296,"p":6,"w":3.363}]}},
  {"_key":"60c2104a7723bebd86645a59","_id":"annotations/60c2104a7723bebd86645a59","_rev":"_cfFmYZi---","document":{"$oid":"60c2104a7723bebd86645a53"},"type":"software","software-name":{"offsetStart":50,"normalizedForm":"DAMMIF","offsetEnd":56,"rawForm":"DAMMIF","boundingBoxes":[{"x":253.324,"h":8.398,"y":532.383,"p":7,"w":38.3895}]},"context":"The average molecular envelope was obtained using DAMMIF server results based on a one-fold symmetry constraint followed by analysis using the DAMAVER program."},
  {"_key":"60c2104a7723bebd86645a5a","_id":"annotations/60c2104a7723bebd86645a5a","_rev":"_cfFmYZu---","document":{"$oid":"60c2104a7723bebd86645a53"},"type":"software","software-name":{"offsetStart":53,"normalizedForm":"DAMMIF","offsetEnd":59,"rawForm":"DAMMIF","boundingBoxes":[{"x":44.98,"h":8.398,"y":234.5,"p":7,"w":38.3895}]},"context":"We first built the monomer molecular envelope using DAMMIF server (Franke and Svergun, 2009) by imposing a one-fold symmetry constraint onto Nsp9 then the DAMAVER program was used to generate an average molecular envelope."},
  {"_key":"60c2104a7723bebd86645a5b","_id":"annotations/60c2104a7723bebd86645a5b","_rev":"_cfFmYZ6---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2104a7723bebd86645a53"},"context":"Protein structure models of Nsp9 and Nb6 were predicted using the I-TASSER program 1 as previously described (Liu et al., 2016) then models were built onto the envelopes using the Chimera program (Pettersen et al., 2004).","wikidataId":"Q17029600","type":"software","confidence":0.7583,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":67,"wikidataId":"Q17029600","offsetEnd":75,"lang":"en","confidence":0.7583,"rawForm":"I-TASSER","boundingBoxes":[{"x":121.939,"h":8.398000000000025,"y":549.921,"p":4,"w":38.61749999999998}]},"lang":"en"},
  {"_key":"60c2104a7723bebd86645a5c","_id":"annotations/60c2104a7723bebd86645a5c","_rev":"_cfFmYaG---","document":{"$oid":"60c2104a7723bebd86645a53"},"type":"software","software-name":{"offsetStart":68,"normalizedForm":"DAMAVER","offsetEnd":75,"rawForm":"DAMAVER","boundingBoxes":[{"x":165.212,"h":8.398,"y":527.006,"p":4,"w":45.2865}]},"context":"Continuous and meaningful shapes were extracted and averaged using DAMAVER server (Volkov and Svergun, 2003)."},
  {"_key":"60c2104a7723bebd86645a5d","_id":"annotations/60c2104a7723bebd86645a5d","_rev":"_cfFmYaS---","document":{"$oid":"60c2104a7723bebd86645a53"},"context":"Quality scores of scattering curves were analyzed using the program PRIMUS (Konarev et al., 2003) to assure that no radiation damage and no obvious protein aggregation had occurred before selection of the best sample for use in further analyses.","references":[{"offsetStart":16186,"normalizedForm":"Konarev et al., 2003","refKey":16,"label":"(Konarev et al., 2003)","reference_id":{"$oid":"60c2104a7723bebd86645a55"},"offsetEnd":16209,"boundingBoxes":[{"x":44.98,"h":8.398000000000025,"y":423.893,"p":4,"w":82.393}]}],"type":"software","software-name":{"offsetStart":69,"normalizedForm":"PRIMUS","offsetEnd":75,"rawForm":"PRIMUS","boundingBoxes":[{"x":257.267,"h":8.398,"y":412.436,"p":4,"w":34.447}]}},
  {"_key":"60c2104a7723bebd86645a5e","_id":"annotations/60c2104a7723bebd86645a5e","_rev":"_cfFmYae---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2104a7723bebd86645a53"},"context":"Meanwhile, the Nsp9-Nb6 complex structure was predicted using the online I-TASSER server then the predicted structural models were built onto the averaged molecular envelope using CHIMERA.","wikidataId":"Q17029600","type":"software","confidence":0.7609,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":75,"wikidataId":"Q17029600","offsetEnd":83,"lang":"en","confidence":0.7609,"rawForm":"I-TASSER","boundingBoxes":[{"x":44.98,"h":8.398000000000025,"y":578.211,"p":7,"w":38.6175}]},"lang":"en"},
  {"_key":"60c2104a7723bebd86645a5f","_id":"annotations/60c2104a7723bebd86645a5f","_rev":"_cfFmYaq---","wikipediaExternalRef":3793613,"document":{"$oid":"60c2104a7723bebd86645a53"},"context":"The ratio of the gray value for PCR products of (−) gRNA/β-actin calculated using Image J software.","wikidataId":"Q1659584","type":"software","confidence":0.9507,"software-name":{"wikipediaExternalRef":3793613,"normalizedForm":"Image J","offsetStart":82,"wikidataId":"Q1659584","offsetEnd":89,"lang":"en","confidence":0.9507,"rawForm":"Image J","boundingBoxes":[{"x":448.357,"h":6.432999999999993,"y":493.955,"p":11,"w":23.988999999999976}]},"lang":"en"},
  {"_key":"60c2104a7723bebd86645a60","_id":"annotations/60c2104a7723bebd86645a60","_rev":"_cfFmYa2---","document":{"$oid":"60c2104a7723bebd86645a53"},"type":"software","software-name":{"offsetStart":87,"normalizedForm":"DAMMIF","offsetEnd":93,"rawForm":"DAMMIF","boundingBoxes":[{"x":253.324,"h":8.398,"y":492.635,"p":4,"w":38.3895}]},"context":"Low-resolution shapes of Nsp9 and the Nsp9-Nb6 complex in solution were modeled using DAMMIF server (Franke and Svergun, 2009) based on P1 symmetry and an asymmetric unit."},
  {"_key":"60c2104a7723bebd86645a61","_id":"annotations/60c2104a7723bebd86645a61","_rev":"_cfFmYbC---","document":{"$oid":"60c2104a7723bebd86645a53"},"type":"software","software-name":{"offsetStart":122,"normalizedForm":"CHIMERA","offsetEnd":129,"rawForm":"CHIMERA","boundingBoxes":[{"x":70.022,"h":8.398,"y":291.786,"p":7,"w":43.206}]},"context":"The model of Nsp9 was predicted using the I-TASSER server and built onto the averaged molecular envelope obtained using CHIMERA (Pettersen et al., 2004)."},
  {"_key":"60c2104a7723bebd86645a62","_id":"annotations/60c2104a7723bebd86645a62","_rev":"_cfFmYbW---","document":{"$oid":"60c2104a7723bebd86645a53"},"type":"software","software-name":{"offsetStart":145,"normalizedForm":"DAMAVER","offsetEnd":152,"rawForm":"DAMAVER","boundingBoxes":[{"x":138.222,"h":8.398,"y":555.297,"p":7,"w":45.2865}]},"context":"The average molecular envelope was obtained using DAMMIF server results based on a one-fold symmetry constraint followed by analysis using the DAMAVER program."},
  {"_key":"60c2104a7723bebd86645a63","_id":"annotations/60c2104a7723bebd86645a63","_rev":"_cfFmYbm---","document":{"$oid":"60c2104a7723bebd86645a53"},"type":"software","software-name":{"offsetStart":157,"normalizedForm":"DAMAVER","offsetEnd":164,"rawForm":"DAMAVER","boundingBoxes":[{"x":246.427,"h":8.398,"y":245.957,"p":7,"w":45.2865}]},"context":"We first built the monomer molecular envelope using DAMMIF server (Franke and Svergun, 2009) by imposing a one-fold symmetry constraint onto Nsp9 then the DAMAVER program was used to generate an average molecular envelope."},
  {"_key":"60c2104a7723bebd86645a64","_id":"annotations/60c2104a7723bebd86645a64","_rev":"_cfFmYby---","document":{"$oid":"60c2104a7723bebd86645a53"},"type":"software","software-name":{"offsetStart":183,"normalizedForm":"Chimera","offsetEnd":190,"rawForm":"Chimera","boundingBoxes":[{"x":82.3625,"h":8.398,"y":572.835,"p":4,"w":33.497}]},"context":"Protein structure models of Nsp9 and Nb6 were predicted using the I-TASSER program 1 as previously described (Liu et al., 2016) then models were built onto the envelopes using the Chimera program (Pettersen et al., 2004)."},
  {"_key":"60c2104a7723bebd86645a65","_id":"annotations/60c2104a7723bebd86645a65","_rev":"_cfFmYcC---","document":{"$oid":"60c2104a7723bebd86645a53"},"type":"software","software-name":{"offsetStart":183,"normalizedForm":"CHIMERA","offsetEnd":190,"rawForm":"CHIMERA","boundingBoxes":[{"x":246.342,"h":8.398,"y":589.669,"p":7,"w":39.7005}]},"context":"Meanwhile, the Nsp9-Nb6 complex structure was predicted using the online I-TASSER server then the predicted structural models were built onto the averaged molecular envelope using CHIMERA."},
  {"_key":"60c2104a7723bebd86645a66","_id":"annotations/60c2104a7723bebd86645a66","_rev":"_cfFmYcW---","wikipediaExternalRef":1976990,"document":{"$oid":"60c2104a7723bebd86645a53"},"context":"Due to the fact that our data suggested that Nsp9 amino acid resides 588 and 643 were crucial for PRRSV replication in cells, Nsp9 amino acid sequences for the aa561-689 region from 32 PRRSV strains (12 Betaarterivirus suid 1 isolates and 20 Betaarterivirus suid 2 isolates) were obtained from GenBank and aligned using the Clustal W module of Lasergene 7.1 (DNASTAR, Inc.).","wikidataId":"Q866737","type":"software","confidence":0.8955,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"Clustal W","offsetStart":329,"wikidataId":"Q866737","offsetEnd":338,"lang":"en","confidence":0.8955,"rawForm":"Clustal W","boundingBoxes":[{"x":110.938,"h":8.398000000000025,"y":498.369,"p":10,"w":37.800500000000014}]},"lang":"en"},
  {"_key":"60c2104a7723bebd86645a67","_id":"annotations/60c2104a7723bebd86645a67","_rev":"_cfFmYcm---","document":{"$oid":"60c2104a7723bebd86645a53"},"publisher":{"offsetStart":364,"normalizedForm":"DNASTAR, Inc","offsetEnd":377,"rawForm":"DNASTAR, \nInc","boundingBoxes":[{"x":249.1877777777778,"h":8.398000000000025,"y":498.369,"p":10,"w":42.5262222222222},{"x":44.98,"h":8.398,"y":509.826,"p":10,"w":10.03675}]},"context":"Due to the fact that our data suggested that Nsp9 amino acid resides 588 and 643 were crucial for PRRSV replication in cells, Nsp9 amino acid sequences for the aa561-689 region from 32 PRRSV strains (12 Betaarterivirus suid 1 isolates and 20 Betaarterivirus suid 2 isolates) were obtained from GenBank and aligned using the Clustal W module of Lasergene 7.1 (DNASTAR, Inc.).","type":"software","software-name":{"offsetStart":349,"normalizedForm":"Lasergene","offsetEnd":358,"rawForm":"Lasergene","boundingBoxes":[{"x":190.9,"h":8.398,"y":498.369,"p":10,"w":38.1045}]},"version":{"offsetStart":359,"normalizedForm":"7.1","offsetEnd":362,"rawForm":"7.1","boundingBoxes":[{"x":230.79,"h":8.398000000000025,"y":498.369,"p":10,"w":11.286000000000001}]}},
  {"_key":"60c210527723bebd86645a69","_id":"annotations/60c210527723bebd86645a69","_rev":"_cfFmYcy---","document":{"$oid":"60c210527723bebd86645a68"},"context":"For Bartonella spp., sequence of the ITS-1 fragment am- plified by standard PCR and phylogenetic analysis with maximum-likelihood method and 1,000 bootstrap repli- cates, performed using MEGA software version 6 (5), con- firmed the bacteria as B. quintana (GenBank accession no.","type":"software","software-name":{"offsetStart":188,"normalizedForm":"MEGA","offsetEnd":192,"rawForm":"MEGA","boundingBoxes":[{"x":376.192,"h":9.69,"y":643.273,"p":1,"w":29.44}]},"version":{"offsetStart":210,"normalizedForm":"6","offsetEnd":211,"rawForm":"6","boundingBoxes":[{"x":476.679,"h":9.69,"y":643.273,"p":1,"w":5}]}},
  {"_key":"60c210547723bebd86645a6b","_id":"annotations/60c210547723bebd86645a6b","_rev":"_cfFmYdC---","wikipediaExternalRef":990677,"document":{"$oid":"60c210547723bebd86645a6a"},"context":"All analyses were conducted using SAS 9.4.","wikidataId":"Q2003932","type":"software","lang":"en","confidence":0.4599,"software-name":{"wikipediaExternalRef":990677,"normalizedForm":"SAS","offsetStart":35,"wikidataId":"Q2003932","offsetEnd":38,"lang":"en","confidence":0.4599,"rawForm":"SAS","boundingBoxes":[{"x":141.506,"h":8.024,"y":312.772,"p":3,"w":14.7237}]},"version":{"offsetStart":39,"normalizedForm":"9.4","offsetEnd":42,"rawForm":"9.4","boundingBoxes":[{"x":158.798,"h":8.024000000000001,"y":312.772,"p":3,"w":10.416149999999988}]}},
  {"_key":"60c210547723bebd86645a6c","_id":"annotations/60c210547723bebd86645a6c","_rev":"_cfFmYdO---","document":{"$oid":"60c210547723bebd86645a6a"},"type":"software","software-name":{"offsetStart":104,"normalizedForm":"Research Electronic Data Capture (REDCap)","offsetEnd":146,"rawForm":"Research \nElectronic Data Capture (REDCap)","boundingBoxes":[{"x":516.588,"h":8.024,"y":672.772,"p":2,"w":35.0175},{"x":315.722,"h":8.024000000000001,"y":684.791,"p":2,"w":138.10510000000005}]},"context":"Demographic and clinical data were obtained from the electronic medical record and double entered in a Research Electronic Data Capture (REDCap) database."},
  {"_key":"60c210567723bebd86645a6e","_id":"annotations/60c210567723bebd86645a6e","_rev":"_cfFmYda---","wikipediaExternalRef":33835593,"document":{"$oid":"60c210567723bebd86645a6d"},"context":"Gephi 3 was used to graph the network.","wikidataId":"Q5548660","type":"software","lang":"en","confidence":0.798,"software-name":{"wikipediaExternalRef":33835593,"normalizedForm":"Gephi","offsetStart":0,"wikidataId":"Q5548660","offsetEnd":5,"lang":"en","confidence":0.798,"rawForm":"Gephi","boundingBoxes":[{"x":274.961,"h":8.9365,"y":260.033,"p":6,"w":26.0881}]},"version":{"offsetStart":6,"normalizedForm":"3","offsetEnd":7,"rawForm":"3","boundingBoxes":[{"x":301.005,"h":6.3671,"y":258.352,"p":6,"w":3.9681}]}},
  {"_key":"60c2105e7723bebd86645a70","_id":"annotations/60c2105e7723bebd86645a70","_rev":"_cfFmYdm---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"SAVE v5.0 server used five different algorithms (ERRAT, Prove, Procheck, Ramachandran plot and whatcheck) to validate and check the stereochemical quality and atomic interaction of predicted 3D structure.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"SAVE","offsetEnd":4,"rawForm":"SAVE","boundingBoxes":[{"x":284.881,"h":8.7571,"y":59.7293,"p":3,"w":25.9227}]},"url":{"offsetStart":-42,"normalizedForm":"https://servicesn.mbi.ucla.edu/SAVES","offsetEnd":-6,"rawForm":"https://servicesn.mbi.ucla.edu/SAVES","boundingBoxes":[{"x":100.6898,"h":8.757100000000037,"y":657.44,"p":3,"w":149.0616}]},"version":{"offsetStart":6,"normalizedForm":"5.0","offsetEnd":9,"rawForm":"5.0","boundingBoxes":[{"x":317.025,"h":8.757100000000001,"y":59.7293,"p":3,"w":17.434500000000014}]}},
  {"_key":"60c2105e7723bebd86645a71","_id":"annotations/60c2105e7723bebd86645a71","_rev":"_cfFmYdy---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"ElliPro server used modified Thornton's method along with residue clus- tering algorithms.","type":"software","software-name":{"offsetStart":0,"normalizedForm":"ElliPro","offsetEnd":7,"rawForm":"ElliPro","boundingBoxes":[{"x":408.131,"h":8.7571,"y":196.696,"p":3,"w":28.3954}]},"url":{"offsetStart":-41,"normalizedForm":"https:// tools.iedb.org/ellipro/help","offsetEnd":-4,"rawForm":"https:// \ntools.iedb.org/ellipro/help","boundingBoxes":[{"x":472.5929,"h":8.757100000000008,"y":184.224,"p":3,"w":27.68720000000002},{"x":284.881,"h":8.757100000000008,"y":196.696,"p":3,"w":101.40659999999997}]}},
  {"_key":"60c2105e7723bebd86645a72","_id":"annotations/60c2105e7723bebd86645a72","_rev":"_cfFmYe----","wikipediaExternalRef":41452308,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"I-TASSER server used hierarchical approach for pre- diction of protein structure including (a) Identification of structural template from PDB by LOMETS, (b) Fragments assembly, (c) Model selection, and (d) Functional annotation (Yang et al. 2015).","wikidataId":"Q17029600","type":"software","confidence":0.7609,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":0,"wikidataId":"Q17029600","offsetEnd":8,"lang":"en","confidence":0.7609,"rawForm":"I-TASSER","boundingBoxes":[{"x":46.7721,"h":8.75709999999998,"y":346.145,"p":3,"w":43.7627}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a73","_id":"annotations/60c2105e7723bebd86645a73","_rev":"_cfFmYeK---","document":{"$oid":"60c2105e7723bebd86645a6f"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"GalaxyRefine2","offsetEnd":13,"rawForm":"GalaxyRefine2","boundingBoxes":[{"x":46.773,"h":8.75709999999998,"y":483.111,"p":3,"w":58.3111}]},"context":"GalaxyRefine2 performs iterative optimization with several geometric operators to increase accuracy of the initial model."},
  {"_key":"60c2105e7723bebd86645a74","_id":"annotations/60c2105e7723bebd86645a74","_rev":"_cfFmYea---","wikipediaExternalRef":9236158,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"and Scratch servers (https:// scratch.proteomics.ics.uci.edu/).","wikidataId":"Q275131","type":"software","confidence":0.2937,"software-name":{"wikipediaExternalRef":9236158,"normalizedForm":"Scratch","offsetStart":4,"wikidataId":"Q275131","offsetEnd":11,"lang":"en","confidence":0.2937,"rawForm":"Scratch","boundingBoxes":[{"x":392.773,"h":8.7571,"y":532.929,"p":2,"w":29.9575}]},"url":{"offsetStart":21,"normalizedForm":"https:// scratch.proteomics.ics.uci.edu","offsetEnd":61,"rawForm":"https:// \nscratch.proteomics.ics.uci.edu","boundingBoxes":[{"x":472.6021111111111,"h":8.757100000000037,"y":532.929,"p":2,"w":27.70488888888889},{"x":284.888,"h":8.757100000000037,"y":545.401,"p":2,"w":117.58272727272731}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a75","_id":"annotations/60c2105e7723bebd86645a75","_rev":"_cfFmYem---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"Herein, ProtParam, Predictprotein and Scratch servers evaluated physicochemical properties of these constructs.","type":"software","software-name":{"offsetStart":8,"normalizedForm":"ProtParam","offsetEnd":17,"rawForm":"ProtParam","boundingBoxes":[{"x":102.273,"h":8.7571,"y":183.947,"p":6,"w":40.21497}]},"url":{"offsetStart":243,"normalizedForm":"https://web.expasy. org/protparam","offsetEnd":277,"rawForm":"https://web.expasy. \norg/protparam","boundingBoxes":[{"x":423.78448499999996,"h":8.75709999999998,"y":508.041,"p":2,"w":76.50321500000001},{"x":284.886,"h":8.757100000000037,"y":520.457,"p":2,"w":54.95697999999999}]}},
  {"_key":"60c2105e7723bebd86645a76","_id":"annotations/60c2105e7723bebd86645a76","_rev":"_cfFmYey---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"Finally, I-TASSER reported the top five models which corre- spond to the five largest structure clusters.","wikidataId":"Q17029600","type":"software","confidence":0.7603,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":10,"wikidataId":"Q17029600","offsetEnd":18,"lang":"en","confidence":0.7603,"rawForm":"I-TASSER","boundingBoxes":[{"x":284.881,"h":8.757100000000008,"y":159.051,"p":6,"w":43.762699999999995}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a77","_id":"annotations/60c2105e7723bebd86645a77","_rev":"_cfFmYe6---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"At first, I-TASSER generated a structural conformation called decoys.","wikidataId":"Q17029600","type":"software","confidence":0.7603,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":11,"wikidataId":"Q17029600","offsetEnd":19,"lang":"en","confidence":0.7603,"rawForm":"I-TASSER","boundingBoxes":[{"x":284.881,"h":8.757099999999994,"y":109.219,"p":6,"w":43.762699999999995}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a78","_id":"annotations/60c2105e7723bebd86645a78","_rev":"_cfFmYfG---","wikipediaExternalRef":37922760,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"Herein, ProtParam, Predictprotein and Scratch servers evaluated physicochemical properties of these constructs.","wikidataId":"Q7239681","type":"software","confidence":0.4584,"software-name":{"wikipediaExternalRef":37922760,"normalizedForm":"Predictprotein","offsetStart":19,"wikidataId":"Q7239681","offsetEnd":33,"lang":"en","confidence":0.4584,"rawForm":"Predictprotein","boundingBoxes":[{"x":151.595,"h":8.7571,"y":183.947,"p":6,"w":56.7131}]},"url":{"offsetStart":303,"normalizedForm":"https://www. predictprotein.org","offsetEnd":335,"rawForm":"https://www. \npredictprotein.org","boundingBoxes":[{"x":449.34353076923077,"h":8.757100000000037,"y":520.457,"p":2,"w":50.93436923076922},{"x":284.887,"h":8.757100000000037,"y":532.929,"p":2,"w":71.40694736842107}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a79","_id":"annotations/60c2105e7723bebd86645a79","_rev":"_cfFmYfS---","document":{"$oid":"60c2105e7723bebd86645a6f"},"type":"software","software-name":{"offsetStart":21,"normalizedForm":"TASSER","offsetEnd":27,"rawForm":"TASSER","boundingBoxes":[{"x":145.6051,"h":8.7571,"y":308.785,"p":3,"w":28.238}]},"context":"ccmb.med.umich.edu/I-TASSER/)."},
  {"_key":"60c2105e7723bebd86645a7a","_id":"annotations/60c2105e7723bebd86645a7a","_rev":"_cfFmYfe---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"According to the results of SAVE5.0 server, E5-model No. 1 and E7-model No. 2 refined structures had the highest quality factors (95.94 and 90.32, respectively) which were selected for further analysis.","type":"software","software-name":{"offsetStart":29,"normalizedForm":"SAVE","offsetEnd":33,"rawForm":"SAVE","boundingBoxes":[{"x":349.111,"h":8.7571,"y":408.097,"p":6,"w":27.4875}]},"url":{"offsetStart":-42,"normalizedForm":"https://servicesn.mbi.ucla.edu/SAVES","offsetEnd":-6,"rawForm":"https://servicesn.mbi.ucla.edu/SAVES","boundingBoxes":[{"x":100.6898,"h":8.757100000000037,"y":657.44,"p":3,"w":149.0616}]},"version":{"offsetStart":33,"normalizedForm":"5.0","offsetEnd":36,"rawForm":"5.0","boundingBoxes":[{"x":349.111,"h":8.75709999999998,"y":408.097,"p":6,"w":38.482500000000016}]}},
  {"_key":"60c2105e7723bebd86645a7b","_id":"annotations/60c2105e7723bebd86645a7b","_rev":"_cfFmYfq---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"Based on CASP13 experiments, I-TASSER server was ranked as No 1 server for predicting 3D structure of proteins.","wikidataId":"Q17029600","type":"software","confidence":0.7609,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":31,"wikidataId":"Q17029600","offsetEnd":39,"lang":"en","confidence":0.7609,"rawForm":"I-TASSER","boundingBoxes":[{"x":140.369,"h":8.75709999999998,"y":321.257,"p":3,"w":43.65610000000001}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a7c","_id":"annotations/60c2105e7723bebd86645a7c","_rev":"_cfFmYf2---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"Then, to select the final models, I-TASSER used the SPICKER program to cluster all the decoys based on the pair-wise structure similarity.","wikidataId":"Q17029600","type":"software","confidence":0.7603,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":34,"wikidataId":"Q17029600","offsetEnd":42,"lang":"en","confidence":0.7603,"rawForm":"I-TASSER","boundingBoxes":[{"x":456.545,"h":8.757100000000008,"y":121.691,"p":6,"w":43.768700000000024}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a7d","_id":"annotations/60c2105e7723bebd86645a7d","_rev":"_cfFmYgC---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"Top 3D structure model obtained from I-TASSER was refined by GalaxyRefine 2 Server (https://galaxy. seoklab.org/cgi-bin/submit.cgi/type=REFINE2).","wikidataId":"Q17029600","type":"software","confidence":0.7583,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":37,"wikidataId":"Q17029600","offsetEnd":45,"lang":"en","confidence":0.7583,"rawForm":"I-TASSER","boundingBoxes":[{"x":201.628,"h":8.75709999999998,"y":445.752,"p":3,"w":42.66579999999999}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a7e","_id":"annotations/60c2105e7723bebd86645a7e","_rev":"_cfFmYgO---","wikipediaExternalRef":9236158,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"Herein, ProtParam, Predictprotein and Scratch servers evaluated physicochemical properties of these constructs.","wikidataId":"Q275131","type":"software","confidence":0.2958,"software-name":{"wikipediaExternalRef":9236158,"normalizedForm":"Scratch","offsetStart":38,"wikidataId":"Q275131","offsetEnd":45,"lang":"en","confidence":0.2958,"rawForm":"Scratch","boundingBoxes":[{"x":232.154,"h":8.7571,"y":183.947,"p":6,"w":29.9575}]},"url":{"offsetStart":21,"normalizedForm":"https:// scratch.proteomics.ics.uci.edu","offsetEnd":61,"rawForm":"https:// \nscratch.proteomics.ics.uci.edu","boundingBoxes":[{"x":472.6021111111111,"h":8.757100000000037,"y":532.929,"p":2,"w":27.70488888888889},{"x":284.888,"h":8.757100000000037,"y":545.401,"p":2,"w":117.58272727272731}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a7f","_id":"annotations/60c2105e7723bebd86645a7f","_rev":"_cfFmYga---","document":{"$oid":"60c2105e7723bebd86645a6f"},"type":"software","software-name":{"offsetStart":53,"normalizedForm":"SPICKER","offsetEnd":60,"rawForm":"SPICKER","boundingBoxes":[{"x":321.788,"h":8.7571,"y":134.107,"p":6,"w":40.9383}]},"context":"Then, to select the final models, I-TASSER used the SPICKER program to cluster all the decoys based on the pair-wise structure similarity."},
  {"_key":"60c2105e7723bebd86645a80","_id":"annotations/60c2105e7723bebd86645a80","_rev":"_cfFmYgm---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"The allergenicity of the selected epitopes was calculated by PA 3 P server (https://lpa.saogabriel. unipampa.edu.br:8080/pa3p/pa3p/pa3p.jsp) using AFDS-motif, Allergen online (6aa and 80 wordmatch) algorithms.","type":"software","software-name":{"offsetStart":62,"normalizedForm":"PA 3 P","offsetEnd":68,"rawForm":"PA 3 P","boundingBoxes":[{"x":111.855,"h":8.7571,"y":171.815,"p":3,"w":12.6525},{"x":124.554,"h":5.8374,"y":169.594,"p":3,"w":3.7359},{"x":128.296,"h":8.7571,"y":171.817,"p":3,"w":5.4994}]},"url":{"offsetStart":77,"normalizedForm":"https://lpa.saogabriel. unipampa.edu.br","offsetEnd":118,"rawForm":"https://lpa.saogabriel. \nunipampa.edu.br:","boundingBoxes":[{"x":176.30482083333334,"h":8.757100000000008,"y":171.817,"p":3,"w":85.8548791666667},{"x":46.7721,"h":8.757100000000008,"y":184.232,"p":3,"w":69.69800000000001}]}},
  {"_key":"60c2105e7723bebd86645a81","_id":"annotations/60c2105e7723bebd86645a81","_rev":"_cfFmYgy---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"For prediction of the 3D structure of the designed epitopes, I-TASSER server was used.","wikidataId":"Q17029600","type":"software","confidence":0.7603,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":62,"wikidataId":"Q17029600","offsetEnd":70,"lang":"en","confidence":0.7603,"rawForm":"I-TASSER","boundingBoxes":[{"x":328.59,"h":8.757099999999994,"y":96.7473,"p":6,"w":43.762699999999995}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a82","_id":"annotations/60c2105e7723bebd86645a82","_rev":"_cfFmYg6---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"For each construct, the best 3D structures obtained from the I-TASSER server were submitted separately to GalaxyRefine2 server.","wikidataId":"Q17029600","type":"software","confidence":0.7583,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":62,"wikidataId":"Q17029600","offsetEnd":70,"lang":"en","confidence":0.7583,"rawForm":"I-TASSER","boundingBoxes":[{"x":321.899,"h":8.75709999999998,"y":358.265,"p":6,"w":43.768700000000024}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a83","_id":"annotations/60c2105e7723bebd86645a83","_rev":"_cfFmYhG---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"Top 3D structure model obtained from I-TASSER was refined by GalaxyRefine 2 Server (https://galaxy. seoklab.org/cgi-bin/submit.cgi/type=REFINE2).","type":"software","software-name":{"offsetStart":62,"normalizedForm":"GalaxyRefine 2 Server","offsetEnd":83,"rawForm":"GalaxyRefine 2 Server","boundingBoxes":[{"x":98.2508,"h":8.75709999999998,"y":458.224,"p":3,"w":98.44719999999998}]},"url":{"offsetStart":85,"normalizedForm":"https://galaxy. seoklab.org/cgi-bin/submit.cgi/type=REFINE2","offsetEnd":145,"rawForm":"https://galaxy. \nseoklab.org/cgi-bin/submit.cgi/type=REFINE2","boundingBoxes":[{"x":207.67926875,"h":8.75709999999998,"y":458.224,"p":3,"w":54.619031250000035},{"x":46.773,"h":8.75709999999998,"y":470.696,"p":3,"w":178.9296888888889}]}},
  {"_key":"60c2105e7723bebd86645a84","_id":"annotations/60c2105e7723bebd86645a84","_rev":"_cfFmYhS---","wikipediaExternalRef":41452308,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"The 3D structures of the designed constructs were generated by I-TASSER server (https://zhanglab.","wikidataId":"Q17029600","type":"software","confidence":0.7609,"software-name":{"wikipediaExternalRef":41452308,"normalizedForm":"I-TASSER","offsetStart":64,"wikidataId":"Q17029600","offsetEnd":72,"lang":"en","confidence":0.7609,"rawForm":"I-TASSER","boundingBoxes":[{"x":109.926,"h":8.75709999999998,"y":296.313,"p":3,"w":43.76270000000001}]},"lang":"en"},
  {"_key":"60c2105e7723bebd86645a85","_id":"annotations/60c2105e7723bebd86645a85","_rev":"_cfFmYhe---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"To predict linear and discontinuous antibody epitopes, refined model was analyzed by ElliPro server (https:// tools.iedb.org/ellipro/help/).","type":"software","software-name":{"offsetStart":86,"normalizedForm":"ElliPro","offsetEnd":93,"rawForm":"ElliPro","boundingBoxes":[{"x":411.305,"h":8.7571,"y":184.224,"p":3,"w":28.3954}]},"url":{"offsetStart":-41,"normalizedForm":"https:// tools.iedb.org/ellipro/help","offsetEnd":-4,"rawForm":"https:// \ntools.iedb.org/ellipro/help","boundingBoxes":[{"x":472.5929,"h":8.757100000000008,"y":184.224,"p":3,"w":27.68720000000002},{"x":284.881,"h":8.757100000000008,"y":196.696,"p":3,"w":101.40659999999997}]}},
  {"_key":"60c2105e7723bebd86645a86","_id":"annotations/60c2105e7723bebd86645a86","_rev":"_cfFmYhq---","document":{"$oid":"60c2105e7723bebd86645a6f"},"publisher":{"offsetStart":110,"normalizedForm":"GraphPad Software","offsetEnd":127,"rawForm":"GraphPad Software","boundingBoxes":[{"x":330.52,"h":8.757100000000037,"y":532.948,"p":5,"w":77.07832000000002}]},"context":"The differences between the control and test groups were assessed using one-way ANONA (Graph-pad Prism 5.0, GraphPad Software).","type":"software","software-name":{"offsetStart":88,"normalizedForm":"Graph-pad Prism","offsetEnd":104,"rawForm":"Graph-pad \nPrism","boundingBoxes":[{"x":458.87175,"h":8.757100000000037,"y":520.476,"p":5,"w":41.34375},{"x":284.882,"h":8.7571,"y":532.948,"p":5,"w":23.2328}]},"version":{"offsetStart":105,"normalizedForm":"5.0","offsetEnd":108,"rawForm":"5.0","boundingBoxes":[{"x":311.868,"h":8.757100000000037,"y":532.948,"p":5,"w":11.207924999999989}]}},
  {"_key":"60c2105e7723bebd86645a87","_id":"annotations/60c2105e7723bebd86645a87","_rev":"_cfFmYh2---","document":{"$oid":"60c2105e7723bebd86645a6f"},"type":"software","software-name":{"offsetStart":102,"normalizedForm":"GalaxyRefine2","offsetEnd":115,"rawForm":"GalaxyRefine2","boundingBoxes":[{"x":46.773,"h":8.757100000000037,"y":645.025,"p":3,"w":59.91609999999999}]},"context":"To validate and select the best model of a refined structure, all models of E5 and E7 obtained from GalaxyRefine2 server were analyzed by SAVE v5.0 server (https://servicesn.mbi.ucla.edu/SAVES/)."},
  {"_key":"60c2105e7723bebd86645a88","_id":"annotations/60c2105e7723bebd86645a88","_rev":"_cfFmYiC---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"For each construct, the best 3D structures obtained from the I-TASSER server were submitted separately to GalaxyRefine2 server.","type":"software","software-name":{"offsetStart":108,"normalizedForm":"GalaxyRefine","offsetEnd":120,"rawForm":"GalaxyRefine","boundingBoxes":[{"x":297.068,"h":8.7571,"y":370.737,"p":6,"w":59.9968}]},"version":{"offsetStart":120,"normalizedForm":"2","offsetEnd":121,"rawForm":"2","boundingBoxes":[{"x":297.068,"h":8.7571,"y":370.737,"p":6,"w":59.9968}]}},
  {"_key":"60c2105e7723bebd86645a89","_id":"annotations/60c2105e7723bebd86645a89","_rev":"_cfFmYiO---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"To validate and select the best model of a refined structure, all models of E5 and E7 obtained from GalaxyRefine2 server were analyzed by SAVE v5.0 server (https://servicesn.mbi.ucla.edu/SAVES/).","type":"software","software-name":{"offsetStart":140,"normalizedForm":"SAVE","offsetEnd":144,"rawForm":"SAVE","boundingBoxes":[{"x":214.978,"h":8.7571,"y":645.025,"p":3,"w":26.0163}]},"url":{"offsetStart":-42,"normalizedForm":"https://servicesn.mbi.ucla.edu/SAVES","offsetEnd":-6,"rawForm":"https://servicesn.mbi.ucla.edu/SAVES","boundingBoxes":[{"x":100.6898,"h":8.757100000000037,"y":657.44,"p":3,"w":149.0616}]},"version":{"offsetStart":146,"normalizedForm":"5.0","offsetEnd":149,"rawForm":"5.0","boundingBoxes":[{"x":244.742,"h":8.757100000000037,"y":645.025,"p":3,"w":17.434500000000043}]}},
  {"_key":"60c2105e7723bebd86645a8a","_id":"annotations/60c2105e7723bebd86645a8a","_rev":"_cfFmYia---","document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"The physicochemical properties of the designed constructs such as molecular weight, theoretical pI, negatively and positively charged residues, estimated half-time, instability index and solvent accessibility were determined by ProtParam (https://web.expasy. org/protparam/) tools, Predictprotein (https://www. predictprotein.org)","type":"software","software-name":{"offsetStart":232,"normalizedForm":"ProtParam","offsetEnd":241,"rawForm":"ProtParam","boundingBoxes":[{"x":372.987,"h":8.7571,"y":508.041,"p":2,"w":42.1717}]},"url":{"offsetStart":243,"normalizedForm":"https://web.expasy. org/protparam","offsetEnd":277,"rawForm":"https://web.expasy. \norg/protparam","boundingBoxes":[{"x":423.78448499999996,"h":8.75709999999998,"y":508.041,"p":2,"w":76.50321500000001},{"x":284.886,"h":8.757100000000037,"y":520.457,"p":2,"w":54.95697999999999}]}},
  {"_key":"60c2105e7723bebd86645a8b","_id":"annotations/60c2105e7723bebd86645a8b","_rev":"_cfFmYim---","wikipediaExternalRef":37922760,"document":{"$oid":"60c2105e7723bebd86645a6f"},"context":"The physicochemical properties of the designed constructs such as molecular weight, theoretical pI, negatively and positively charged residues, estimated half-time, instability index and solvent accessibility were determined by ProtParam (https://web.expasy. org/protparam/) tools, Predictprotein (https://www. predictprotein.org)","wikidataId":"Q7239681","type":"software","confidence":0.4584,"software-name":{"wikipediaExternalRef":37922760,"normalizedForm":"Predictprotein","offsetStart":287,"wikidataId":"Q7239681","offsetEnd":301,"lang":"en","confidence":0.4584,"rawForm":"Predictprotein","boundingBoxes":[{"x":382.284,"h":8.7571,"y":520.457,"p":2,"w":56.7131}]},"url":{"offsetStart":303,"normalizedForm":"https://www. predictprotein.org","offsetEnd":335,"rawForm":"https://www. \npredictprotein.org","boundingBoxes":[{"x":449.34353076923077,"h":8.757100000000037,"y":520.457,"p":2,"w":50.93436923076922},{"x":284.887,"h":8.757100000000037,"y":532.929,"p":2,"w":71.40694736842107}]},"lang":"en"},
  {"_key":"60c210657723bebd86645a8f","_id":"annotations/60c210657723bebd86645a8f","_rev":"_cfFmYiy---","document":{"$oid":"60c210657723bebd86645a8c"},"context":"Other software such as Ingenuity Pathways Analysis [43,44] can further group the identified proteins into functionally different categories of proteins according to their  proportion in order to understand the correlations of the functional proteins from an additional dimension.","references":[{"offsetStart":26179,"normalizedForm":"[43","refKey":42,"label":"[43,","reference_id":{"$oid":"60c210657723bebd86645a8d"},"offsetEnd":26187,"boundingBoxes":[{"x":103.391,"h":7.523800000000051,"y":726.05,"p":5,"w":27.10629999999999}]},{"offsetStart":26179,"normalizedForm":"44]","refKey":43,"label":"44]","reference_id":{"$oid":"60c210657723bebd86645a8e"},"offsetEnd":26187,"boundingBoxes":[{"x":103.391,"h":7.523800000000051,"y":726.05,"p":5,"w":27.10629999999999}]}],"type":"software","software-name":{"offsetStart":23,"normalizedForm":"Ingenuity Pathways Analysis","offsetEnd":51,"rawForm":"Ingenuity \nPathways Analysis","boundingBoxes":[{"x":246.901,"h":7.5238,"y":715.589,"p":5,"w":36.5668},{"x":31.9226,"h":7.523800000000051,"y":726.05,"p":5,"w":69.9494}]}},
  {"_key":"60c210657723bebd86645a90","_id":"annotations/60c210657723bebd86645a90","_rev":"_cfFmYi6---","document":{"$oid":"60c210657723bebd86645a8c"},"type":"software","software-name":{"offsetStart":43,"normalizedForm":"FluTyper","offsetEnd":51,"rawForm":"FluTyper","boundingBoxes":[{"x":260.723,"h":7.5238,"y":579.599,"p":8,"w":33.5541}]},"context":"In addition, one developed-software called FluTyper enabled to incorporate signature peptides of four influenza anti- gens together, e.g."},
  {"_key":"60c210657723bebd86645a91","_id":"annotations/60c210657723bebd86645a91","_rev":"_cfFmYjG---","document":{"$oid":"60c210657723bebd86645a8c"},"type":"software","software-name":{"offsetStart":110,"normalizedForm":"FluAlign","offsetEnd":118,"rawForm":"FluAlign","boundingBoxes":[{"x":196.059,"h":7.5238,"y":558.678,"p":8,"w":31.6254}]},"context":"And both of the conserved sequences and the unique sequences of the digested M1 peptides were identified by FluAlign algorithm, which further contributed to the precise typing of the influenza virus sub- types [110]."},
  {"_key":"60c210787723bebd86645a93","_id":"annotations/60c210787723bebd86645a93","_rev":"_cfFmYjS---","document":{"$oid":"60c210787723bebd86645a92"},"publisher":{"offsetStart":83,"normalizedForm":"Covidence","offsetEnd":92,"rawForm":"Covidence","boundingBoxes":[{"x":431.432,"h":9.32,"y":306.176,"p":2,"w":43.2}]},"context":"Database search results will be uploaded to Covidence Systematic Review Software (Covidence, Melbourne, VIC, Australia).","type":"software","software-name":{"offsetStart":44,"normalizedForm":"Covidence Systematic Review","offsetEnd":72,"rawForm":"Covidence \nSystematic Review","boundingBoxes":[{"x":508.982,"h":9.32,"y":294.136,"p":2,"w":45.8},{"x":306.892,"h":9.319999999999993,"y":306.176,"p":2,"w":77.57999999999998}]}},
  {"_key":"60c2107c7723bebd86645a96","_id":"annotations/60c2107c7723bebd86645a96","_rev":"_cfFmYje---","document":{"$oid":"60c2107c7723bebd86645a94"},"type":"software","software-name":{"offsetStart":34,"normalizedForm":"RDP4","offsetEnd":38,"rawForm":"RDP4","boundingBoxes":[{"x":358.806,"h":7.165199999999999,"y":118.246,"p":2,"w":19.654499999999985}]},"context":"Recombination was assessed using RDP4 software (Muhire et al., 2015)."},
  {"_key":"60c2107c7723bebd86645a97","_id":"annotations/60c2107c7723bebd86645a97","_rev":"_cfFmYjq---","document":{"$oid":"60c2107c7723bebd86645a94"},"publisher":{"offsetStart":70,"normalizedForm":"Ibis Biosciences","offsetEnd":86,"rawForm":"Ibis Biosciences","boundingBoxes":[{"x":184.51500000000001,"h":7.165200000000027,"y":516.572,"p":2,"w":52.459316666666666}]},"context":"Positions with Phred scores !20 were assembled with BioEdit 7.0.5.3 (Ibis Biosciences, Carlsbad, CA,  USA), and the final sequences were aligned with homologous sequences from GenBank (accession numbers in Figures 1, 2, 3, and 4) using Clustal W in Bioedit 7.0.5.3.","type":"software","software-name":{"offsetStart":53,"normalizedForm":"BioEdit","offsetEnd":60,"rawForm":"BioEdit","boundingBoxes":[{"x":128.18,"h":7.1652,"y":516.572,"p":2,"w":25.6322}]},"version":{"offsetStart":61,"normalizedForm":"7.0.5.3","offsetEnd":68,"rawForm":"7.0.5.3","boundingBoxes":[{"x":155.392,"h":7.165200000000027,"y":516.572,"p":2,"w":24.372899999999987}]}},
  {"_key":"60c2107c7723bebd86645a98","_id":"annotations/60c2107c7723bebd86645a98","_rev":"_cfFmYj2---","document":{"$oid":"60c2107c7723bebd86645a94"},"context":"The nucleotide alignments were used to build a maximum likelihood tree (Tamura-Nei model) with 1,000 bootstrap replicates using MEGA 7 (Kumar et al., 2016), and CRCoV was used as a root for the trees because it is a Betacoronavirus.","references":[{"offsetStart":7425,"normalizedForm":"Kumar et al., 2016","refKey":16,"label":"(Kumar et al., 2016)","reference_id":{"$oid":"60c2107c7723bebd86645a95"},"offsetEnd":7445,"boundingBoxes":[{"x":393.954,"h":7.165199999999999,"y":97.3268,"p":2,"w":69.05016666666666}]}],"type":"software","software-name":{"offsetStart":130,"normalizedForm":"MEGA","offsetEnd":134,"rawForm":"MEGA","boundingBoxes":[{"x":362.888,"h":7.1652,"y":97.3268,"p":2,"w":22.3166}]},"version":{"offsetStart":135,"normalizedForm":"7","offsetEnd":136,"rawForm":"7","boundingBoxes":[{"x":387.321,"h":7.1652,"y":97.3268,"p":2,"w":4.4793}]}},
  {"_key":"60c2107c7723bebd86645a99","_id":"annotations/60c2107c7723bebd86645a99","_rev":"_cfFmYkC---","wikipediaExternalRef":1976990,"document":{"$oid":"60c2107c7723bebd86645a94"},"publisher":{"offsetStart":253,"normalizedForm":"Bioedit","offsetEnd":260,"rawForm":"Bioedit","boundingBoxes":[{"x":327.287,"h":7.1652,"y":76.4074,"p":2,"w":24.9706}]},"context":"Positions with Phred scores !20 were assembled with BioEdit 7.0.5.3 (Ibis Biosciences, Carlsbad, CA,  USA), and the final sequences were aligned with homologous sequences from GenBank (accession numbers in Figures 1, 2, 3, and 4) using Clustal W in Bioedit 7.0.5.3.","wikidataId":"Q866737","type":"software","lang":"en","confidence":0.8418,"software-name":{"wikipediaExternalRef":1976990,"normalizedForm":"Clustal W","offsetStart":239,"wikidataId":"Q866737","offsetEnd":249,"lang":"en","confidence":0.8418,"rawForm":"Clustal \nW","boundingBoxes":[{"x":533.82,"h":7.1652,"y":65.976,"p":2,"w":23.8867},{"x":306.594,"h":7.1652,"y":76.4074,"p":2,"w":7.3884}]},"version":{"offsetStart":261,"normalizedForm":"7.0.5.3","offsetEnd":268,"rawForm":"7.0.5.3","boundingBoxes":[{"x":355.463,"h":7.165199999999999,"y":76.4074,"p":2,"w":23.20920000000001}]}},
  {"_key":"60c2107d7723bebd86645aa2","_id":"annotations/60c2107d7723bebd86645aa2","_rev":"_cfFmYkO---","wikipediaExternalRef":16725900,"document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"MEGAN addresses am- biguous matches by assigning reads that have multiple possible assignments to several species, to the taxonomic group containing all these species, or else their lowest common ancestor (LCA).","wikidataId":"Q6715329","references":[{"offsetStart":5385,"normalizedForm":"Huson et al., 2007","refKey":13,"label":"(Huson et al., 2007)","reference_id":{"$oid":"60c2107d7723bebd86645a9b"},"offsetEnd":5405,"boundingBoxes":[{"x":136.572,"h":7.62390000000002,"y":235.361,"p":2,"w":70.55608333333333}]}],"type":"software","lang":"en","confidence":0.7525,"software-name":{"wikipediaExternalRef":16725900,"normalizedForm":"MEGAN","offsetStart":0,"wikidataId":"Q6715329","offsetEnd":5,"lang":"en","confidence":0.7525,"rawForm":"MEGAN","boundingBoxes":[{"x":213.958,"h":7.6239,"y":235.361,"p":2,"w":31.5676}]},"version":{"offsetStart":64,"normalizedForm":"5.3","offsetEnd":67,"rawForm":"5.3","boundingBoxes":[{"x":519.76,"h":7.623900000000049,"y":730.518,"p":4,"w":11.079900000000066}]}},
  {"_key":"60c2107d7723bebd86645aa3","_id":"annotations/60c2107d7723bebd86645aa3","_rev":"_cfFmYka---","wikipediaExternalRef":16725900,"document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"MEGAN has a 'Min Support' parameter which sets a threshold for the number of reads that must be assigned to a taxon so that it appears in the result.","wikidataId":"Q6715329","references":[{"offsetStart":5385,"normalizedForm":"Huson et al., 2007","refKey":13,"label":"(Huson et al., 2007)","reference_id":{"$oid":"60c2107d7723bebd86645a9b"},"offsetEnd":5405,"boundingBoxes":[{"x":136.572,"h":7.62390000000002,"y":235.361,"p":2,"w":70.55608333333333}]}],"type":"software","lang":"en","confidence":0.7545,"software-name":{"wikipediaExternalRef":16725900,"normalizedForm":"MEGAN","offsetStart":0,"wikidataId":"Q6715329","offsetEnd":5,"lang":"en","confidence":0.7545,"rawForm":"MEGAN","boundingBoxes":[{"x":75.1158,"h":7.6239,"y":620.47,"p":6,"w":31.5676}]},"version":{"offsetStart":64,"normalizedForm":"5.3","offsetEnd":67,"rawForm":"5.3","boundingBoxes":[{"x":519.76,"h":7.623900000000049,"y":730.518,"p":4,"w":11.079900000000066}]}},
  {"_key":"60c2107d7723bebd86645aa4","_id":"annotations/60c2107d7723bebd86645aa4","_rev":"_cfFmYkm---","wikipediaExternalRef":16725900,"document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"MEGAN assigned the reads to 30 taxa.","wikidataId":"Q6715329","references":[{"offsetStart":5385,"normalizedForm":"Huson et al., 2007","refKey":13,"label":"(Huson et al., 2007)","reference_id":{"$oid":"60c2107d7723bebd86645a9b"},"offsetEnd":5405,"boundingBoxes":[{"x":136.572,"h":7.62390000000002,"y":235.361,"p":2,"w":70.55608333333333}]}],"type":"software","lang":"en","confidence":0.7576,"software-name":{"wikipediaExternalRef":16725900,"normalizedForm":"MEGAN","offsetStart":0,"wikidataId":"Q6715329","offsetEnd":5,"lang":"en","confidence":0.7576,"rawForm":"MEGAN","boundingBoxes":[{"x":63.1567,"h":7.6239,"y":719.46,"p":8,"w":31.5676}]},"version":{"offsetStart":64,"normalizedForm":"5.3","offsetEnd":67,"rawForm":"5.3","boundingBoxes":[{"x":519.76,"h":7.623900000000049,"y":730.518,"p":4,"w":11.079900000000066}]}},
  {"_key":"60c2107d7723bebd86645aa5","_id":"annotations/60c2107d7723bebd86645aa5","_rev":"_cfFmYku---","document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"GRAMMy formulates the problem as a finite mixture model, using the Expectation- Maximization (EM) algorithm to estimate the relative genome abun- dances.","references":[{"offsetStart":6620,"normalizedForm":"Xia et al., 2011","refKey":28,"label":"(Xia et al., 2011)","reference_id":{"$oid":"60c2107d7723bebd86645a9c"},"offsetEnd":6638,"boundingBoxes":[{"x":166.451,"h":7.623899999999992,"y":444.385,"p":2,"w":70.83608333333333}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"GRAMMy","offsetEnd":6,"rawForm":"GRAMMy","boundingBoxes":[{"x":219.515,"h":7.6239,"y":455.383,"p":2,"w":37.6187}]}},
  {"_key":"60c2107d7723bebd86645aa6","_id":"annotations/60c2107d7723bebd86645aa6","_rev":"_cfFmYk6---","document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"GRAMMy also only considers unassembled reads and requires that these are of the same fixed length.","references":[{"offsetStart":6620,"normalizedForm":"Xia et al., 2011","refKey":28,"label":"(Xia et al., 2011)","reference_id":{"$oid":"60c2107d7723bebd86645a9c"},"offsetEnd":6638,"boundingBoxes":[{"x":166.451,"h":7.623899999999992,"y":444.385,"p":2,"w":70.83608333333333}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"GRAMMy","offsetEnd":6,"rawForm":"GRAMMy","boundingBoxes":[{"x":243.155,"h":7.6239,"y":147.375,"p":5,"w":37.7355}]}},
  {"_key":"60c2107d7723bebd86645aa7","_id":"annotations/60c2107d7723bebd86645aa7","_rev":"_cfFmYlG---","document":{"$oid":"60c2107d7723bebd86645a9a"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"metaMix","offsetEnd":7,"rawForm":"metaMix","boundingBoxes":[{"x":75.1184,"h":7.6239,"y":447.508,"p":4,"w":31.5676}]},"context":"metaMix outputs log-likelihood traceplots so that the user can visually inspect the mixing and the convergence of the chain."},
  {"_key":"60c2107d7723bebd86645aa8","_id":"annotations/60c2107d7723bebd86645aa8","_rev":"_cfFmYlS---","document":{"$oid":"60c2107d7723bebd86645a9a"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"metaMix","offsetEnd":7,"rawForm":"metaMix","boundingBoxes":[{"x":371.564,"h":7.6239,"y":240.633,"p":5,"w":31.5676}]},"context":"metaMix identified 116 species, detecting success- fully all the members of the metagenomic community."},
  {"_key":"60c2107d7723bebd86645aa9","_id":"annotations/60c2107d7723bebd86645aa9","_rev":"_cfFmYle---","document":{"$oid":"60c2107d7723bebd86645a9a"},"type":"software","software-name":{"offsetStart":0,"normalizedForm":"metaMix","offsetEnd":7,"rawForm":"metaMix","boundingBoxes":[{"x":327.118,"h":7.6239,"y":634.537,"p":8,"w":31.7988}]},"context":"metaMix is most useful for complex datasets for which the in- terpretation is challenging."},
  {"_key":"60c2107d7723bebd86645aaa","_id":"annotations/60c2107d7723bebd86645aaa","_rev":"_cfFmYlq---","document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"Pathoscope refines this process by penalizing reads with am- biguous matches in the presence of reads with unique matches and enforcing parsimony within a Bayesian context.","references":[{"offsetStart":6666,"normalizedForm":"Francis et al., 2013","refKey":10,"label":"(Francis et al., 2013)","reference_id":{"$oid":"60c2107d7723bebd86645a9d"},"offsetEnd":6688,"boundingBoxes":[{"x":107.944,"h":7.623900000000049,"y":455.383,"p":2,"w":73.28274999999998}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Pathoscope","offsetEnd":10,"rawForm":"Pathoscope","boundingBoxes":[{"x":90.5396,"h":7.6239,"y":488.378,"p":2,"w":38.9755}]},"version":{"offsetStart":85,"normalizedForm":"2.0","offsetEnd":88,"rawForm":"2.0","boundingBoxes":[{"x":105.392,"h":7.623899999999999,"y":59.389,"p":5,"w":9.995850000000004}]}},
  {"_key":"60c2107d7723bebd86645aab","_id":"annotations/60c2107d7723bebd86645aab","_rev":"_cfFmYl2---","document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"Pathoscope identified 47 species.","references":[{"offsetStart":6666,"normalizedForm":"Francis et al., 2013","refKey":10,"label":"(Francis et al., 2013)","reference_id":{"$oid":"60c2107d7723bebd86645a9d"},"offsetEnd":6688,"boundingBoxes":[{"x":107.944,"h":7.623900000000049,"y":455.383,"p":2,"w":73.28274999999998}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Pathoscope","offsetEnd":10,"rawForm":"Pathoscope","boundingBoxes":[{"x":315.155,"h":7.6239,"y":410.823,"p":5,"w":38.9755}]},"version":{"offsetStart":85,"normalizedForm":"2.0","offsetEnd":88,"rawForm":"2.0","boundingBoxes":[{"x":105.392,"h":7.623899999999999,"y":59.389,"p":5,"w":9.995850000000004}]}},
  {"_key":"60c2107d7723bebd86645aac","_id":"annotations/60c2107d7723bebd86645aac","_rev":"_cfFmYm----","document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"Pathoscope pro- duced the results in 1 min.","references":[{"offsetStart":6666,"normalizedForm":"Francis et al., 2013","refKey":10,"label":"(Francis et al., 2013)","reference_id":{"$oid":"60c2107d7723bebd86645a9d"},"offsetEnd":6688,"boundingBoxes":[{"x":107.944,"h":7.623900000000049,"y":455.383,"p":2,"w":73.28274999999998}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Pathoscope","offsetEnd":10,"rawForm":"Pathoscope","boundingBoxes":[{"x":492.602,"h":7.6239,"y":542.859,"p":5,"w":38.9755}]},"version":{"offsetStart":85,"normalizedForm":"2.0","offsetEnd":88,"rawForm":"2.0","boundingBoxes":[{"x":105.392,"h":7.623899999999999,"y":59.389,"p":5,"w":9.995850000000004}]}},
  {"_key":"60c2107d7723bebd86645aad","_id":"annotations/60c2107d7723bebd86645aad","_rev":"_cfFmYmK---","document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"Pathoscope has a thetaPrior param- eter that enforces a unique read penalty.","references":[{"offsetStart":6666,"normalizedForm":"Francis et al., 2013","refKey":10,"label":"(Francis et al., 2013)","reference_id":{"$oid":"60c2107d7723bebd86645a9d"},"offsetEnd":6688,"boundingBoxes":[{"x":107.944,"h":7.623900000000049,"y":455.383,"p":2,"w":73.28274999999998}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Pathoscope","offsetEnd":10,"rawForm":"Pathoscope","boundingBoxes":[{"x":172.741,"h":7.6239,"y":532.484,"p":6,"w":38.9755}]},"version":{"offsetStart":85,"normalizedForm":"2.0","offsetEnd":88,"rawForm":"2.0","boundingBoxes":[{"x":105.392,"h":7.623899999999999,"y":59.389,"p":5,"w":9.995850000000004}]}},
  {"_key":"60c2107d7723bebd86645aae","_id":"annotations/60c2107d7723bebd86645aae","_rev":"_cfFmYmW---","document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"Pathoscope finds $15 more false positives while MEGAN $40 more compared with metaMix at the same read sup- port level, except for the lowest r ¼ 10 where metaMix and Pathoscope achieve the same specificity.","references":[{"offsetStart":6666,"normalizedForm":"Francis et al., 2013","refKey":10,"label":"(Francis et al., 2013)","reference_id":{"$oid":"60c2107d7723bebd86645a9d"},"offsetEnd":6688,"boundingBoxes":[{"x":107.944,"h":7.623900000000049,"y":455.383,"p":2,"w":73.28274999999998}]}],"type":"software","software-name":{"offsetStart":0,"normalizedForm":"Pathoscope","offsetEnd":10,"rawForm":"Pathoscope","boundingBoxes":[{"x":382.843,"h":7.6239,"y":70.3805,"p":6,"w":38.9755}]},"version":{"offsetStart":85,"normalizedForm":"2.0","offsetEnd":88,"rawForm":"2.0","boundingBoxes":[{"x":105.392,"h":7.623899999999999,"y":59.389,"p":5,"w":9.995850000000004}]}},
  {"_key":"60c2107d7723bebd86645aaf","_id":"annotations/60c2107d7723bebd86645aaf","_rev":"_cfFmYmi---","wikipediaExternalRef":363695,"document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"We use BLASTx due to the higher level of conser- vation expected at the protein level compared with nucleotides.","wikidataId":"Q286820","type":"software","confidence":0.708,"software-name":{"wikipediaExternalRef":363695,"normalizedForm":"BLASTx","offsetStart":7,"wikidataId":"Q286820","offsetEnd":13,"lang":"en","confidence":0.708,"rawForm":"BLASTx","boundingBoxes":[{"x":404.902,"h":7.6239,"y":587.48,"p":2,"w":29.3116}]},"lang":"en"},
  {"_key":"60c2107d7723bebd86645ab0","_id":"annotations/60c2107d7723bebd86645ab0","_rev":"_cfFmYmu---","document":{"$oid":"60c2107d7723bebd86645a9a"},"context":"However, GRAMMy is designed for nucleotide-nucleotide comparisons (BLASTn), which is suboptimal for viral discovery.","references":[{"offsetStart":6620,"normalizedForm":"Xia et al., 2011","refKey":28,"label":"(Xia et al., 2011)","reference_id":{"$oid":"60c2107d7723bebd86645a9c"},"offsetEnd":6638,"boundingBoxes":[{"x":166.451,"h":7.623899999999992,"y":444.385,"p":2,"w":70.836083