PMC:7558333 / 22183-23929 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T50","span":{"begin":577,"end":582},"obj":"Body_part"},{"id":"T51","span":{"begin":1313,"end":1321},"obj":"Body_part"},{"id":"T52","span":{"begin":1597,"end":1602},"obj":"Body_part"}],"attributes":[{"id":"A50","pred":"fma_id","subj":"T50","obj":"http://purl.org/sig/ont/fma/fma9670"},{"id":"A51","pred":"fma_id","subj":"T51","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A52","pred":"fma_id","subj":"T52","obj":"http://purl.org/sig/ont/fma/fma9670"}],"text":"Table 1 Diagnostic criteria of the AspICU clinical algorithm according to Blot et al., 2012, and proposal of a modified AspICU algorithm.\nClassification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology\nGM: galactomannan."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T35","span":{"begin":577,"end":582},"obj":"Body_part"},{"id":"T36","span":{"begin":1597,"end":1602},"obj":"Body_part"}],"attributes":[{"id":"A35","pred":"uberon_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"A36","pred":"uberon_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"}],"text":"Table 1 Diagnostic criteria of the AspICU clinical algorithm according to Blot et al., 2012, and proposal of a modified AspICU algorithm.\nClassification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology\nGM: galactomannan."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T126","span":{"begin":616,"end":618},"obj":"Disease"},{"id":"T127","span":{"begin":1560,"end":1562},"obj":"Disease"},{"id":"T128","span":{"begin":1579,"end":1581},"obj":"Disease"},{"id":"T129","span":{"begin":1650,"end":1652},"obj":"Disease"}],"attributes":[{"id":"A126","pred":"mondo_id","subj":"T126","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A127","pred":"mondo_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A128","pred":"mondo_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A129","pred":"mondo_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"}],"text":"Table 1 Diagnostic criteria of the AspICU clinical algorithm according to Blot et al., 2012, and proposal of a modified AspICU algorithm.\nClassification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology\nGM: galactomannan."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T159","span":{"begin":110,"end":111},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T160","span":{"begin":331,"end":343},"obj":"http://purl.obolibrary.org/obo/UBERON_0001155"},{"id":"T161","span":{"begin":552,"end":553},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T162","span":{"begin":577,"end":582},"obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"T163","span":{"begin":577,"end":582},"obj":"http://www.ebi.ac.uk/efo/EFO_0000296"},{"id":"T164","span":{"begin":1322,"end":1329},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T165","span":{"begin":1597,"end":1602},"obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"T166","span":{"begin":1597,"end":1602},"obj":"http://www.ebi.ac.uk/efo/EFO_0000296"}],"text":"Table 1 Diagnostic criteria of the AspICU clinical algorithm according to Blot et al., 2012, and proposal of a modified AspICU algorithm.\nClassification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology\nGM: galactomannan."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T19","span":{"begin":1614,"end":1616},"obj":"GlycoEpitope"},{"id":"T20","span":{"begin":1728,"end":1730},"obj":"GlycoEpitope"},{"id":"T21","span":{"begin":1732,"end":1745},"obj":"GlycoEpitope"}],"attributes":[{"id":"A19","pred":"glyco_epitope_db_id","subj":"T19","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A20","pred":"glyco_epitope_db_id","subj":"T20","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A21","pred":"glyco_epitope_db_id","subj":"T21","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Table 1 Diagnostic criteria of the AspICU clinical algorithm according to Blot et al., 2012, and proposal of a modified AspICU algorithm.\nClassification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology\nGM: galactomannan."}

{"project":"LitCovid-sentences","denotations":[{"id":"T158","span":{"begin":0,"end":138},"obj":"Sentence"},{"id":"T159","span":{"begin":139,"end":316},"obj":"Sentence"},{"id":"T160","span":{"begin":317,"end":592},"obj":"Sentence"},{"id":"T161","span":{"begin":593,"end":639},"obj":"Sentence"},{"id":"T162","span":{"begin":640,"end":642},"obj":"Sentence"},{"id":"T163","span":{"begin":643,"end":696},"obj":"Sentence"},{"id":"T164","span":{"begin":697,"end":725},"obj":"Sentence"},{"id":"T165","span":{"begin":726,"end":783},"obj":"Sentence"},{"id":"T166","span":{"begin":784,"end":808},"obj":"Sentence"},{"id":"T167","span":{"begin":809,"end":917},"obj":"Sentence"},{"id":"T168","span":{"begin":918,"end":920},"obj":"Sentence"},{"id":"T169","span":{"begin":921,"end":978},"obj":"Sentence"},{"id":"T170","span":{"begin":979,"end":1007},"obj":"Sentence"},{"id":"T171","span":{"begin":1008,"end":1065},"obj":"Sentence"},{"id":"T172","span":{"begin":1066,"end":1090},"obj":"Sentence"},{"id":"T173","span":{"begin":1091,"end":1203},"obj":"Sentence"},{"id":"T174","span":{"begin":1204,"end":1206},"obj":"Sentence"},{"id":"T175","span":{"begin":1207,"end":1332},"obj":"Sentence"},{"id":"T176","span":{"begin":1333,"end":1361},"obj":"Sentence"},{"id":"T177","span":{"begin":1362,"end":1419},"obj":"Sentence"},{"id":"T178","span":{"begin":1420,"end":1444},"obj":"Sentence"},{"id":"T179","span":{"begin":1445,"end":1536},"obj":"Sentence"},{"id":"T180","span":{"begin":1537,"end":1628},"obj":"Sentence"},{"id":"T181","span":{"begin":1629,"end":1727},"obj":"Sentence"},{"id":"T182","span":{"begin":1728,"end":1746},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Table 1 Diagnostic criteria of the AspICU clinical algorithm according to Blot et al., 2012, and proposal of a modified AspICU algorithm.\nClassification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology\nGM: galactomannan."}

{"project":"LitCovid-PubTator","denotations":[{"id":"562","span":{"begin":345,"end":356},"obj":"Species"},{"id":"563","span":{"begin":403,"end":414},"obj":"Species"},{"id":"564","span":{"begin":465,"end":476},"obj":"Species"},{"id":"565","span":{"begin":643,"end":654},"obj":"Species"},{"id":"566","span":{"begin":826,"end":837},"obj":"Species"},{"id":"567","span":{"begin":921,"end":932},"obj":"Species"},{"id":"568","span":{"begin":1108,"end":1119},"obj":"Species"},{"id":"569","span":{"begin":1207,"end":1218},"obj":"Species"},{"id":"570","span":{"begin":1301,"end":1312},"obj":"Species"},{"id":"571","span":{"begin":1462,"end":1473},"obj":"Species"},{"id":"574","span":{"begin":1728,"end":1730},"obj":"Chemical"},{"id":"575","span":{"begin":1732,"end":1745},"obj":"Chemical"}],"attributes":[{"id":"A562","pred":"tao:has_database_id","subj":"562","obj":"Tax:746128"},{"id":"A563","pred":"tao:has_database_id","subj":"563","obj":"Tax:746128"},{"id":"A564","pred":"tao:has_database_id","subj":"564","obj":"Tax:746128"},{"id":"A565","pred":"tao:has_database_id","subj":"565","obj":"Tax:746128"},{"id":"A566","pred":"tao:has_database_id","subj":"566","obj":"Tax:746128"},{"id":"A567","pred":"tao:has_database_id","subj":"567","obj":"Tax:746128"},{"id":"A568","pred":"tao:has_database_id","subj":"568","obj":"Tax:746128"},{"id":"A569","pred":"tao:has_database_id","subj":"569","obj":"Tax:746128"},{"id":"A570","pred":"tao:has_database_id","subj":"570","obj":"Tax:746128"},{"id":"A571","pred":"tao:has_database_id","subj":"571","obj":"Tax:746128"},{"id":"A574","pred":"tao:has_database_id","subj":"574","obj":"MESH:C012990"},{"id":"A575","pred":"tao:has_database_id","subj":"575","obj":"MESH:C012990"}],"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 1 Diagnostic criteria of the AspICU clinical algorithm according to Blot et al., 2012, and proposal of a modified AspICU algorithm.\nClassification AspICU According to Blot et al., 2012 [3] AspICU Algorithm Incorporating PCR Modified AspICU Algorithm Incorporating PCR, Serology and Angioinvasion Biomarkers\nDefinition of colonization Aspergillus-positive culture endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate alone Aspergillus-positive culture/PCR endotracheal aspirate in one sample, not confirmed on a second sample or using blood biomarker\nDefinition of putative IA \u003e1 criterion among: 1. Aspergillus-positive culture endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy \u003e1 criterion among: 1. Aspergillus-positive culture/PCR endotracheal aspirate in repeated samples with negative anti-Aspergillus antibody testing 2. Compatible clinical signs 3. Abnormal thoracic medical imaging on CT scan or X-ray 4a. Host risk factors Or 4b. Semiquantitative Aspergillus-positive culture/PCR of BAL fluid + positive direct microscopy\nDefinition of probable IA - - Putative IA + one positive blood biomarker (GM and/or PCR)\nDefinition of proven IA Positive histopathology Positive histopathology Positive histopathology\nGM: galactomannan."}