PMC:7306567 / 30257-32058
Annnotations
LitCovid-PD-FMA-UBERON
{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T46","span":{"begin":312,"end":321},"obj":"Body_part"},{"id":"T47","span":{"begin":332,"end":340},"obj":"Body_part"},{"id":"T48","span":{"begin":356,"end":367},"obj":"Body_part"},{"id":"T49","span":{"begin":405,"end":409},"obj":"Body_part"},{"id":"T50","span":{"begin":465,"end":469},"obj":"Body_part"},{"id":"T51","span":{"begin":500,"end":504},"obj":"Body_part"},{"id":"T52","span":{"begin":525,"end":543},"obj":"Body_part"},{"id":"T53","span":{"begin":557,"end":562},"obj":"Body_part"},{"id":"T54","span":{"begin":1187,"end":1192},"obj":"Body_part"},{"id":"T55","span":{"begin":1218,"end":1223},"obj":"Body_part"}],"attributes":[{"id":"A46","pred":"fma_id","subj":"T46","obj":"http://purl.org/sig/ont/fma/fma241981"},{"id":"A47","pred":"fma_id","subj":"T47","obj":"http://purl.org/sig/ont/fma/fma62864"},{"id":"A48","pred":"fma_id","subj":"T48","obj":"http://purl.org/sig/ont/fma/fma63261"},{"id":"A49","pred":"fma_id","subj":"T49","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A50","pred":"fma_id","subj":"T50","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A51","pred":"fma_id","subj":"T51","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A52","pred":"fma_id","subj":"T52","obj":"http://purl.org/sig/ont/fma/fma62501"},{"id":"A53","pred":"fma_id","subj":"T53","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A54","pred":"fma_id","subj":"T54","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A55","pred":"fma_id","subj":"T55","obj":"http://purl.org/sig/ont/fma/fma63083"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
LitCovid-PD-UBERON
{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T41","span":{"begin":465,"end":469},"obj":"Body_part"},{"id":"T42","span":{"begin":1187,"end":1192},"obj":"Body_part"},{"id":"T43","span":{"begin":1218,"end":1223},"obj":"Body_part"}],"attributes":[{"id":"A41","pred":"uberon_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A42","pred":"uberon_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A43","pred":"uberon_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
LitCovid-PubTator
{"project":"LitCovid-PubTator","denotations":[{"id":"282","span":{"begin":237,"end":255},"obj":"Disease"},{"id":"283","span":{"begin":275,"end":307},"obj":"Disease"},{"id":"284","span":{"begin":771,"end":826},"obj":"Disease"},{"id":"285","span":{"begin":858,"end":896},"obj":"Disease"},{"id":"286","span":{"begin":1253,"end":1261},"obj":"Disease"},{"id":"287","span":{"begin":1280,"end":1300},"obj":"Disease"},{"id":"288","span":{"begin":1484,"end":1493},"obj":"Disease"},{"id":"289","span":{"begin":1606,"end":1614},"obj":"Disease"},{"id":"290","span":{"begin":1653,"end":1662},"obj":"Disease"},{"id":"291","span":{"begin":1676,"end":1684},"obj":"Disease"},{"id":"292","span":{"begin":1772,"end":1781},"obj":"Disease"},{"id":"293","span":{"begin":1792,"end":1800},"obj":"Disease"}],"attributes":[{"id":"A282","pred":"tao:has_database_id","subj":"282","obj":"MESH:D045169"},{"id":"A283","pred":"tao:has_database_id","subj":"283","obj":"MESH:D008231"},{"id":"A284","pred":"tao:has_database_id","subj":"284","obj":"MESH:D000072742"},{"id":"A285","pred":"tao:has_database_id","subj":"285","obj":"MESH:D001228"},{"id":"A286","pred":"tao:has_database_id","subj":"286","obj":"MESH:C000657245"},{"id":"A287","pred":"tao:has_database_id","subj":"287","obj":"MESH:D060085"},{"id":"A288","pred":"tao:has_database_id","subj":"288","obj":"MESH:D003643"},{"id":"A289","pred":"tao:has_database_id","subj":"289","obj":"MESH:C000657245"},{"id":"A290","pred":"tao:has_database_id","subj":"290","obj":"MESH:D003643"},{"id":"A291","pred":"tao:has_database_id","subj":"291","obj":"MESH:C000657245"},{"id":"A292","pred":"tao:has_database_id","subj":"292","obj":"MESH:D003643"},{"id":"A293","pred":"tao:has_database_id","subj":"293","obj":"MESH:C000657245"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
LitCovid-PD-MONDO
{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T145","span":{"begin":55,"end":59},"obj":"Disease"},{"id":"T146","span":{"begin":72,"end":76},"obj":"Disease"},{"id":"T147","span":{"begin":237,"end":241},"obj":"Disease"},{"id":"T148","span":{"begin":296,"end":307},"obj":"Disease"},{"id":"T149","span":{"begin":771,"end":787},"obj":"Disease"},{"id":"T150","span":{"begin":778,"end":787},"obj":"Disease"},{"id":"T151","span":{"begin":809,"end":826},"obj":"Disease"},{"id":"T152","span":{"begin":879,"end":896},"obj":"Disease"},{"id":"T153","span":{"begin":1029,"end":1033},"obj":"Disease"},{"id":"T154","span":{"begin":1253,"end":1261},"obj":"Disease"},{"id":"T155","span":{"begin":1290,"end":1303},"obj":"Disease"},{"id":"T156","span":{"begin":1363,"end":1373},"obj":"Disease"},{"id":"T157","span":{"begin":1527,"end":1536},"obj":"Disease"},{"id":"T158","span":{"begin":1574,"end":1578},"obj":"Disease"},{"id":"T159","span":{"begin":1606,"end":1614},"obj":"Disease"},{"id":"T160","span":{"begin":1623,"end":1627},"obj":"Disease"},{"id":"T161","span":{"begin":1676,"end":1684},"obj":"Disease"},{"id":"T162","span":{"begin":1693,"end":1697},"obj":"Disease"},{"id":"T163","span":{"begin":1792,"end":1800},"obj":"Disease"}],"attributes":[{"id":"A145","pred":"mondo_id","subj":"T145","obj":"http://purl.obolibrary.org/obo/MONDO_0007163"},{"id":"A146","pred":"mondo_id","subj":"T146","obj":"http://purl.obolibrary.org/obo/MONDO_0007163"},{"id":"A147","pred":"mondo_id","subj":"T147","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A148","pred":"mondo_id","subj":"T148","obj":"http://purl.obolibrary.org/obo/MONDO_0003783"},{"id":"A149","pred":"mondo_id","subj":"T149","obj":"http://purl.obolibrary.org/obo/MONDO_0002041"},{"id":"A150","pred":"mondo_id","subj":"T150","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A151","pred":"mondo_id","subj":"T151","obj":"http://purl.obolibrary.org/obo/MONDO_0021925"},{"id":"A152","pred":"mondo_id","subj":"T152","obj":"http://purl.obolibrary.org/obo/MONDO_0021925"},{"id":"A153","pred":"mondo_id","subj":"T153","obj":"http://purl.obolibrary.org/obo/MONDO_0007163"},{"id":"A154","pred":"mondo_id","subj":"T154","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A155","pred":"mondo_id","subj":"T155","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A156","pred":"mondo_id","subj":"T156","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A157","pred":"mondo_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A158","pred":"mondo_id","subj":"T158","obj":"http://purl.obolibrary.org/obo/MONDO_0007163"},{"id":"A159","pred":"mondo_id","subj":"T159","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A160","pred":"mondo_id","subj":"T160","obj":"http://purl.obolibrary.org/obo/MONDO_0007163"},{"id":"A161","pred":"mondo_id","subj":"T161","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A162","pred":"mondo_id","subj":"T162","obj":"http://purl.obolibrary.org/obo/MONDO_0007163"},{"id":"A163","pred":"mondo_id","subj":"T163","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
LitCovid-PD-CLO
{"project":"LitCovid-PD-CLO","denotations":[{"id":"T201","span":{"begin":332,"end":340},"obj":"http://purl.obolibrary.org/obo/CL_0000576"},{"id":"T202","span":{"begin":399,"end":404},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T203","span":{"begin":405,"end":409},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T204","span":{"begin":445,"end":455},"obj":"http://purl.obolibrary.org/obo/CL_0000066"},{"id":"T205","span":{"begin":465,"end":469},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T206","span":{"begin":465,"end":469},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T207","span":{"begin":487,"end":494},"obj":"http://purl.obolibrary.org/obo/UBERON_0001005"},{"id":"T208","span":{"begin":500,"end":504},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T209","span":{"begin":557,"end":562},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T210","span":{"begin":734,"end":737},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T211","span":{"begin":1494,"end":1496},"obj":"http://purl.obolibrary.org/obo/CLO_0053799"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
LitCovid-PD-CHEBI
{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T212","span":{"begin":197,"end":211},"obj":"Chemical"},{"id":"T213","span":{"begin":220,"end":223},"obj":"Chemical"},{"id":"T215","span":{"begin":275,"end":290},"obj":"Chemical"},{"id":"T216","span":{"begin":424,"end":436},"obj":"Chemical"},{"id":"T217","span":{"begin":431,"end":436},"obj":"Chemical"},{"id":"T218","span":{"begin":608,"end":613},"obj":"Chemical"},{"id":"T220","span":{"begin":684,"end":694},"obj":"Chemical"},{"id":"T221","span":{"begin":1080,"end":1083},"obj":"Chemical"},{"id":"T222","span":{"begin":1084,"end":1086},"obj":"Chemical"},{"id":"T224","span":{"begin":1111,"end":1114},"obj":"Chemical"},{"id":"T225","span":{"begin":1115,"end":1117},"obj":"Chemical"},{"id":"T227","span":{"begin":1193,"end":1195},"obj":"Chemical"},{"id":"T229","span":{"begin":1224,"end":1226},"obj":"Chemical"}],"attributes":[{"id":"A212","pred":"chebi_id","subj":"T212","obj":"http://purl.obolibrary.org/obo/CHEBI_50858"},{"id":"A213","pred":"chebi_id","subj":"T213","obj":"http://purl.obolibrary.org/obo/CHEBI_17824"},{"id":"A214","pred":"chebi_id","subj":"T213","obj":"http://purl.obolibrary.org/obo/CHEBI_30802"},{"id":"A215","pred":"chebi_id","subj":"T215","obj":"http://purl.obolibrary.org/obo/CHEBI_50858"},{"id":"A216","pred":"chebi_id","subj":"T216","obj":"http://purl.obolibrary.org/obo/CHEBI_26667"},{"id":"A217","pred":"chebi_id","subj":"T217","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A218","pred":"chebi_id","subj":"T218","obj":"http://purl.obolibrary.org/obo/CHEBI_16474"},{"id":"A219","pred":"chebi_id","subj":"T218","obj":"http://purl.obolibrary.org/obo/CHEBI_57783"},{"id":"A220","pred":"chebi_id","subj":"T220","obj":"http://purl.obolibrary.org/obo/CHEBI_35718"},{"id":"A221","pred":"chebi_id","subj":"T221","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A222","pred":"chebi_id","subj":"T222","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A223","pred":"chebi_id","subj":"T222","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A224","pred":"chebi_id","subj":"T224","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A225","pred":"chebi_id","subj":"T225","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A226","pred":"chebi_id","subj":"T225","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A227","pred":"chebi_id","subj":"T227","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A228","pred":"chebi_id","subj":"T227","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A229","pred":"chebi_id","subj":"T229","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A230","pred":"chebi_id","subj":"T229","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
LitCovid-PD-GlycoEpitope
{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T29","span":{"begin":1084,"end":1086},"obj":"GlycoEpitope"},{"id":"T30","span":{"begin":1115,"end":1117},"obj":"GlycoEpitope"},{"id":"T31","span":{"begin":1193,"end":1195},"obj":"GlycoEpitope"},{"id":"T32","span":{"begin":1224,"end":1226},"obj":"GlycoEpitope"}],"attributes":[{"id":"A29","pred":"glyco_epitope_db_id","subj":"T29","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A30","pred":"glyco_epitope_db_id","subj":"T30","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A31","pred":"glyco_epitope_db_id","subj":"T31","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A32","pred":"glyco_epitope_db_id","subj":"T32","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
LitCovid-PD-HP
{"project":"LitCovid-PD-HP","denotations":[{"id":"T41","span":{"begin":220,"end":223},"obj":"Phenotype"},{"id":"T42","span":{"begin":296,"end":307},"obj":"Phenotype"},{"id":"T43","span":{"begin":1363,"end":1373},"obj":"Phenotype"}],"attributes":[{"id":"A41","pred":"hp_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/HP_0020103"},{"id":"A42","pred":"hp_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/HP_0001888"},{"id":"A43","pred":"hp_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
LitCovid-sentences
{"project":"LitCovid-sentences","denotations":[{"id":"T218","span":{"begin":0,"end":59},"obj":"Sentence"},{"id":"T219","span":{"begin":60,"end":76},"obj":"Sentence"},{"id":"T220","span":{"begin":77,"end":175},"obj":"Sentence"},{"id":"T221","span":{"begin":176,"end":295},"obj":"Sentence"},{"id":"T222","span":{"begin":296,"end":398},"obj":"Sentence"},{"id":"T223","span":{"begin":399,"end":567},"obj":"Sentence"},{"id":"T224","span":{"begin":568,"end":770},"obj":"Sentence"},{"id":"T225","span":{"begin":771,"end":922},"obj":"Sentence"},{"id":"T226","span":{"begin":923,"end":1055},"obj":"Sentence"},{"id":"T227","span":{"begin":1056,"end":1186},"obj":"Sentence"},{"id":"T228","span":{"begin":1187,"end":1279},"obj":"Sentence"},{"id":"T229","span":{"begin":1280,"end":1479},"obj":"Sentence"},{"id":"T230","span":{"begin":1480,"end":1801},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
LitCovid-PMC-OGER-BB
{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T288","span":{"begin":146,"end":150},"obj":"GO:0018995"},{"id":"T289","span":{"begin":197,"end":211},"obj":"CHEBI:50858;CHEBI:50858"},{"id":"T290","span":{"begin":237,"end":241},"obj":"SP_10"},{"id":"T291","span":{"begin":275,"end":290},"obj":"CHEBI:50858;CHEBI:50858"},{"id":"T292","span":{"begin":332,"end":340},"obj":"CL:0000576"},{"id":"T293","span":{"begin":349,"end":353},"obj":"PR:000007437"},{"id":"T294","span":{"begin":356,"end":367},"obj":"CL:0000235"},{"id":"T295","span":{"begin":424,"end":430},"obj":"CHEBI:30563;CHEBI:30563"},{"id":"T296","span":{"begin":431,"end":436},"obj":"CHEBI:41865;CHEBI:41865"},{"id":"T297","span":{"begin":445,"end":455},"obj":"UBERON:0000483"},{"id":"T298","span":{"begin":456,"end":461},"obj":"UBERON:0000115"},{"id":"T299","span":{"begin":465,"end":469},"obj":"UBERON:0002048"},{"id":"T300","span":{"begin":487,"end":494},"obj":"UBERON:0001005"},{"id":"T301","span":{"begin":500,"end":510},"obj":"GO:0035376"},{"id":"T302","span":{"begin":519,"end":523},"obj":"PR:000003622;G_3;PG_10"},{"id":"T303","span":{"begin":525,"end":543},"obj":"CL:0002063"},{"id":"T304","span":{"begin":548,"end":562},"obj":"CL:0000064"},{"id":"T305","span":{"begin":575,"end":585},"obj":"GO:0065007"},{"id":"T306","span":{"begin":608,"end":629},"obj":"GO:0043020"},{"id":"T307","span":{"begin":700,"end":707},"obj":"GO:0006952"},{"id":"T308","span":{"begin":809,"end":826},"obj":"UBERON:0007196"},{"id":"T309","span":{"begin":1187,"end":1192},"obj":"UBERON:0001977"},{"id":"T310","span":{"begin":1218,"end":1223},"obj":"UBERON:0001977"},{"id":"T311","span":{"begin":1253,"end":1261},"obj":"SP_7"},{"id":"T312","span":{"begin":1360,"end":1362},"obj":"NCBITaxon:4896"},{"id":"T313","span":{"begin":1363,"end":1373},"obj":"NCBITaxon:31031"},{"id":"T314","span":{"begin":1375,"end":1386},"obj":"NCBITaxon:286"},{"id":"T315","span":{"begin":1387,"end":1397},"obj":"NCBITaxon:8296"},{"id":"T316","span":{"begin":1402,"end":1403},"obj":"NCBITaxon:4932"},{"id":"T317","span":{"begin":1403,"end":1404},"obj":"NCBITaxon:4896"},{"id":"T318","span":{"begin":1606,"end":1614},"obj":"SP_7"},{"id":"T319","span":{"begin":1676,"end":1684},"obj":"SP_7"},{"id":"T320","span":{"begin":1792,"end":1800},"obj":"SP_7"},{"id":"T342","span":{"begin":1360,"end":1362},"obj":"NCBITaxon:4896"},{"id":"T23407","span":{"begin":1363,"end":1373},"obj":"NCBITaxon:31031"},{"id":"T35842","span":{"begin":1375,"end":1386},"obj":"NCBITaxon:286"},{"id":"T24939","span":{"begin":1387,"end":1397},"obj":"NCBITaxon:8296"},{"id":"T27555","span":{"begin":1402,"end":1403},"obj":"NCBITaxon:4932"},{"id":"T55957","span":{"begin":1403,"end":1404},"obj":"NCBITaxon:4896"},{"id":"T31088","span":{"begin":1606,"end":1614},"obj":"SP_7"},{"id":"T66943","span":{"begin":1676,"end":1684},"obj":"SP_7"},{"id":"T66351","span":{"begin":1792,"end":1800},"obj":"SP_7"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}
2_test
{"project":"2_test","denotations":[{"id":"32572532-30076119-47963455","span":{"begin":126,"end":127},"obj":"30076119"},{"id":"32572532-32339350-47963456","span":{"begin":172,"end":174},"obj":"32339350"},{"id":"32572532-22895826-47963457","span":{"begin":217,"end":218},"obj":"22895826"},{"id":"32572532-12890854-47963458","span":{"begin":292,"end":294},"obj":"12890854"},{"id":"32572532-16554799-47963459","span":{"begin":496,"end":498},"obj":"16554799"},{"id":"32572532-24563256-47963460","span":{"begin":631,"end":633},"obj":"24563256"},{"id":"32572532-22895826-47963461","span":{"begin":853,"end":854},"obj":"22895826"},{"id":"32572532-28387526-47963461","span":{"begin":853,"end":854},"obj":"28387526"},{"id":"32572532-30076119-47963461","span":{"begin":853,"end":854},"obj":"30076119"},{"id":"32572532-32339350-47963462","span":{"begin":919,"end":921},"obj":"32339350"},{"id":"32572532-22895826-47963463","span":{"begin":986,"end":987},"obj":"22895826"},{"id":"32572532-28387526-47963463","span":{"begin":986,"end":987},"obj":"28387526"},{"id":"32572532-30076119-47963463","span":{"begin":986,"end":987},"obj":"30076119"},{"id":"32572532-22895826-47963464","span":{"begin":1106,"end":1107},"obj":"22895826"},{"id":"32572532-28387526-47963464","span":{"begin":1106,"end":1107},"obj":"28387526"},{"id":"32572532-30076119-47963464","span":{"begin":1106,"end":1107},"obj":"30076119"},{"id":"32572532-32339350-47963465","span":{"begin":1183,"end":1185},"obj":"32339350"},{"id":"32572532-22895826-47963466","span":{"begin":1213,"end":1214},"obj":"22895826"},{"id":"32572532-28387526-47963466","span":{"begin":1213,"end":1214},"obj":"28387526"},{"id":"32572532-30076119-47963466","span":{"begin":1213,"end":1214},"obj":"30076119"},{"id":"32572532-32339350-47963467","span":{"begin":1276,"end":1278},"obj":"32339350"},{"id":"32572532-27709265-47963468","span":{"begin":1413,"end":1415},"obj":"27709265"},{"id":"32572532-31986264-47963469","span":{"begin":1476,"end":1478},"obj":"31986264"},{"id":"32572532-30076119-47963470","span":{"begin":1564,"end":1565},"obj":"30076119"},{"id":"T1239","span":{"begin":126,"end":127},"obj":"30076119"},{"id":"T11993","span":{"begin":172,"end":174},"obj":"32339350"},{"id":"T58330","span":{"begin":217,"end":218},"obj":"22895826"},{"id":"T34258","span":{"begin":292,"end":294},"obj":"12890854"},{"id":"T40916","span":{"begin":496,"end":498},"obj":"16554799"},{"id":"T49447","span":{"begin":631,"end":633},"obj":"24563256"},{"id":"T76577","span":{"begin":853,"end":854},"obj":"22895826"},{"id":"T1286","span":{"begin":853,"end":854},"obj":"28387526"},{"id":"T13233","span":{"begin":853,"end":854},"obj":"30076119"},{"id":"T5897","span":{"begin":919,"end":921},"obj":"32339350"},{"id":"T37794","span":{"begin":986,"end":987},"obj":"22895826"},{"id":"T50031","span":{"begin":986,"end":987},"obj":"28387526"},{"id":"T83601","span":{"begin":986,"end":987},"obj":"30076119"},{"id":"T28555","span":{"begin":1106,"end":1107},"obj":"22895826"},{"id":"T74628","span":{"begin":1106,"end":1107},"obj":"28387526"},{"id":"T70095","span":{"begin":1106,"end":1107},"obj":"30076119"},{"id":"T97225","span":{"begin":1183,"end":1185},"obj":"32339350"},{"id":"T50555","span":{"begin":1213,"end":1214},"obj":"22895826"},{"id":"T89999","span":{"begin":1213,"end":1214},"obj":"28387526"},{"id":"T65385","span":{"begin":1213,"end":1214},"obj":"30076119"},{"id":"T41608","span":{"begin":1276,"end":1278},"obj":"32339350"},{"id":"T66653","span":{"begin":1413,"end":1415},"obj":"27709265"},{"id":"T99520","span":{"begin":1476,"end":1478},"obj":"31986264"},{"id":"T87804","span":{"begin":1564,"end":1565},"obj":"30076119"}],"text":"Table 2 Comparison between characteristics of IAPA and CAPA\nFactor IAPA CAPA\nHost/Risk 57% EORTC/MSGERC host factor negative [9] 85% EORTC/MSGERC host factor negative [59, 60]\nIAPA associated with corticosteroid use [7] IPA developed in SARS-2003-infected patients receiving corticosteroids [61]\nLymphopenia and chemokine-producing monocyte-derived FCN1 + macrophages causing hyperinflammation [62]\nVirus Cell entry through sialic acids-2,6Gal: epithelial layer in lung including larger airways [63] Cell entry through ACE2: type 2 pneumocytes and ciliated cells [64]\nImmune modulation by suppression of the NADPH oxidase complex [65] No evidence for immunomodulatory effect on known antifungal host defense mechanisms, although this has not been extensively studied yet\nFungal infection Invasive Aspergillus tracheobronchitis in up to 55% of patients [7–9] Invasive Aspergillus tracheobronchitis not yet reported [59, 60]\nMedian time between ICU admission and IAPA diagnosis 2–3 days [7–9] Median time between ICU admission and CAPA diagnosis 6 days [59]\nAspergillus diagnostics BAL GM positive in \u003e 88% [7–9] BAL GM commonly positive, diagnostic performance currently unknown [59, 60]\nSerum GM positive in 65% [7–9] Serum GM positive in 3 of 14 (21%) COVID-19 patients [59, 60]\nSecondary infections In 80 of 342 (23.4%) ICU patients, most frequent pathogens S. pneumoniae, Pseudomonas aeruginosa and S. aureus [66] In four of 13 (31%) ICU patients, pathogens not specified [67]\nICU mortality 45% in IAPA compared with 20% in influenza without IAPA (p \u003c 0.0001) [9] 33% in CAPA cases compared with 17% in COVID-19 without CAPA (p = 0.4) [59] (although mortality rates due to COVID-19 without CAPA vary enormous between countries and we have no clear data yet on the true mortality in ICU of COVID-19)"}