PMC:7239617 / 2403-5116 JSONTXT

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Clinical characteristics of nine critically ill patients with COVID-19 probable (n=1) and putative invasive pulmonary aspergillosis (n=8)\nPutative invasive pulmonary aspergillosis patients (sex, age) Probable IPA patient (sex, age)\nPatient 1 (male, 53 years) Patient 2 (female, 59 years) Patient3 (female, 69 years) Patient 4 (female, 63 years) Patient 5 (male, 43 years) Patient 6 (male, 79 years) Patient 7 (male, 77 years) Patient 8 (female, 75 years) Patient 9 (male, 47 years)\nRisk factors of severe COVID-19 Hypertension, obesity, ischaemic heart disease Hypertension, diabetes, obesity Hypertension, obesity Hypertension, diabetes, ischaemic heart disease Asthma Hypertension Hypertension, asthma Hypertension, diabetes None\nEORTC risk factors None None None None Steroids None None None Myeloma, steroids\nAPACHE II score 26 16 11 20 8 16 25 21 10\nThoracic CT-scan/x-ray* Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19, segmental lung atelectasis Typical COVID-19, emphysema Typical COVID-19 Typical COVID-19 + one peripheral nodule\nAnti-COVID-19 therapies LPV–RTV LPV–RTV, AZI LPV–RTV LPV–RTV AZI LPV–RTV, HCQ, AZI LPV–RTV, HCQ, AZI LPV–RTV, AZI No\nSteroids to treat pneumonia† Yes No Yes Yes No Yes Yes Yes No\nRenal replacement therapy Yes No No Yes No No Yes No No\nVasopressor Yes Yes Yes Yes No Yes Yes Yes Yes\nPulmonary specimen‡ BAL BAL BA BAL BAL BAL BAL BAL BA\nInvasive pulmonary aspergillosis diagnosis\nBAL culture§ − + + − + + + + +\nBAL/BA qPCR¶ − − 23·9 − − 34·5 29·0 31·7 −\nBAL galactomannan index 0·89 0·03 ND 0·15 0·12 0·05 3·91 0·36 ND\nSerum qPCR¶ − − − ND − − − − −\nβ-D-glucan, pg/mL 523 ND 7·8 105 7 23 135 450 14\nSerum galactomannan index 0·13 0·04 0·03 0·51 0·04 0·02 0·37 0·37 0·09\nNumber of mycological criteria 2 1 2 2 1 2 3 3 1\nAntifungal therapy None None None None None None VRC CSP None\nOutcome Alive Alive Alive Death (day 0) Alive Alive Death (day 18) Death (day 11) Death day 3)\nEORTC=European Organization for Research and Treatment of Cancer. APACHE= Acute Physiology and Chronic Health Enquiry. LPV–RTV=lopnavir–ritonavir combination. AZI=azithromycin. HCQ=hydroxychloroquine. BAL=Bronchoalveolar lavage. BA=bronchial aspiration. ND=not done. VRC=voriconazole. CSP=caspofungin.\n* Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.\n† Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;\n‡ No endotracheal or endobronchial lesion was observed.\n§ −=negative; +=positive with Aspergillus fumigatus identification.\n¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles)."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T7","span":{"begin":553,"end":558},"obj":"Body_part"},{"id":"T8","span":{"begin":655,"end":660},"obj":"Body_part"},{"id":"T9","span":{"begin":998,"end":1002},"obj":"Body_part"},{"id":"T10","span":{"begin":1619,"end":1624},"obj":"Body_part"},{"id":"T11","span":{"begin":1699,"end":1704},"obj":"Body_part"}],"attributes":[{"id":"A7","pred":"fma_id","subj":"T7","obj":"http://purl.org/sig/ont/fma/fma7088"},{"id":"A8","pred":"fma_id","subj":"T8","obj":"http://purl.org/sig/ont/fma/fma7088"},{"id":"A9","pred":"fma_id","subj":"T9","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma63083"}],"text":"Table Clinical characteristics of nine critically ill patients with COVID-19 probable (n=1) and putative invasive pulmonary aspergillosis (n=8)\nPutative invasive pulmonary aspergillosis patients (sex, age) Probable IPA patient (sex, age)\nPatient 1 (male, 53 years) Patient 2 (female, 59 years) Patient3 (female, 69 years) Patient 4 (female, 63 years) Patient 5 (male, 43 years) Patient 6 (male, 79 years) Patient 7 (male, 77 years) Patient 8 (female, 75 years) Patient 9 (male, 47 years)\nRisk factors of severe COVID-19 Hypertension, obesity, ischaemic heart disease Hypertension, diabetes, obesity Hypertension, obesity Hypertension, diabetes, ischaemic heart disease Asthma Hypertension Hypertension, asthma Hypertension, diabetes None\nEORTC risk factors None None None None Steroids None None None Myeloma, steroids\nAPACHE II score 26 16 11 20 8 16 25 21 10\nThoracic CT-scan/x-ray* Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19, segmental lung atelectasis Typical COVID-19, emphysema Typical COVID-19 Typical COVID-19 + one peripheral nodule\nAnti-COVID-19 therapies LPV–RTV LPV–RTV, AZI LPV–RTV LPV–RTV AZI LPV–RTV, HCQ, AZI LPV–RTV, HCQ, AZI LPV–RTV, AZI No\nSteroids to treat pneumonia† Yes No Yes Yes No Yes Yes Yes No\nRenal replacement therapy Yes No No Yes No No Yes No No\nVasopressor Yes Yes Yes Yes No Yes Yes Yes Yes\nPulmonary specimen‡ BAL BAL BA BAL BAL BAL BAL BAL BA\nInvasive pulmonary aspergillosis diagnosis\nBAL culture§ − + + − + + + + +\nBAL/BA qPCR¶ − − 23·9 − − 34·5 29·0 31·7 −\nBAL galactomannan index 0·89 0·03 ND 0·15 0·12 0·05 3·91 0·36 ND\nSerum qPCR¶ − − − ND − − − − −\nβ-D-glucan, pg/mL 523 ND 7·8 105 7 23 135 450 14\nSerum galactomannan index 0·13 0·04 0·03 0·51 0·04 0·02 0·37 0·37 0·09\nNumber of mycological criteria 2 1 2 2 1 2 3 3 1\nAntifungal therapy None None None None None None VRC CSP None\nOutcome Alive Alive Alive Death (day 0) Alive Alive Death (day 18) Death (day 11) Death day 3)\nEORTC=European Organization for Research and Treatment of Cancer. APACHE= Acute Physiology and Chronic Health Enquiry. LPV–RTV=lopnavir–ritonavir combination. AZI=azithromycin. HCQ=hydroxychloroquine. BAL=Bronchoalveolar lavage. BA=bronchial aspiration. ND=not done. VRC=voriconazole. CSP=caspofungin.\n* Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.\n† Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;\n‡ No endotracheal or endobronchial lesion was observed.\n§ −=negative; +=positive with Aspergillus fumigatus identification.\n¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles)."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T7","span":{"begin":553,"end":558},"obj":"Body_part"},{"id":"T8","span":{"begin":655,"end":660},"obj":"Body_part"},{"id":"T9","span":{"begin":998,"end":1002},"obj":"Body_part"},{"id":"T10","span":{"begin":1619,"end":1624},"obj":"Body_part"},{"id":"T11","span":{"begin":1699,"end":1704},"obj":"Body_part"}],"attributes":[{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0000948"},{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_0000948"},{"id":"A9","pred":"uberon_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"}],"text":"Table Clinical characteristics of nine critically ill patients with COVID-19 probable (n=1) and putative invasive pulmonary aspergillosis (n=8)\nPutative invasive pulmonary aspergillosis patients (sex, age) Probable IPA patient (sex, age)\nPatient 1 (male, 53 years) Patient 2 (female, 59 years) Patient3 (female, 69 years) Patient 4 (female, 63 years) Patient 5 (male, 43 years) Patient 6 (male, 79 years) Patient 7 (male, 77 years) Patient 8 (female, 75 years) Patient 9 (male, 47 years)\nRisk factors of severe COVID-19 Hypertension, obesity, ischaemic heart disease Hypertension, diabetes, obesity Hypertension, obesity Hypertension, diabetes, ischaemic heart disease Asthma Hypertension Hypertension, asthma Hypertension, diabetes None\nEORTC risk factors None None None None Steroids None None None Myeloma, steroids\nAPACHE II score 26 16 11 20 8 16 25 21 10\nThoracic CT-scan/x-ray* Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19, segmental lung atelectasis Typical COVID-19, emphysema Typical COVID-19 Typical COVID-19 + one peripheral nodule\nAnti-COVID-19 therapies LPV–RTV LPV–RTV, AZI LPV–RTV LPV–RTV AZI LPV–RTV, HCQ, AZI LPV–RTV, HCQ, AZI LPV–RTV, AZI No\nSteroids to treat pneumonia† Yes No Yes Yes No Yes Yes Yes No\nRenal replacement therapy Yes No No Yes No No Yes No No\nVasopressor Yes Yes Yes Yes No Yes Yes Yes Yes\nPulmonary specimen‡ BAL BAL BA BAL BAL BAL BAL BAL BA\nInvasive pulmonary aspergillosis diagnosis\nBAL culture§ − + + − + + + + +\nBAL/BA qPCR¶ − − 23·9 − − 34·5 29·0 31·7 −\nBAL galactomannan index 0·89 0·03 ND 0·15 0·12 0·05 3·91 0·36 ND\nSerum qPCR¶ − − − ND − − − − −\nβ-D-glucan, pg/mL 523 ND 7·8 105 7 23 135 450 14\nSerum galactomannan index 0·13 0·04 0·03 0·51 0·04 0·02 0·37 0·37 0·09\nNumber of mycological criteria 2 1 2 2 1 2 3 3 1\nAntifungal therapy None None None None None None VRC CSP None\nOutcome Alive Alive Alive Death (day 0) Alive Alive Death (day 18) Death (day 11) Death day 3)\nEORTC=European Organization for Research and Treatment of Cancer. APACHE= Acute Physiology and Chronic Health Enquiry. LPV–RTV=lopnavir–ritonavir combination. AZI=azithromycin. HCQ=hydroxychloroquine. BAL=Bronchoalveolar lavage. BA=bronchial aspiration. ND=not done. VRC=voriconazole. CSP=caspofungin.\n* Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.\n† Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;\n‡ No endotracheal or endobronchial lesion was observed.\n§ −=negative; +=positive with Aspergillus fumigatus identification.\n¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles)."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T12","span":{"begin":105,"end":137},"obj":"Phenotype"},{"id":"T13","span":{"begin":153,"end":185},"obj":"Phenotype"},{"id":"T14","span":{"begin":215,"end":218},"obj":"Phenotype"},{"id":"T15","span":{"begin":520,"end":532},"obj":"Phenotype"},{"id":"T16","span":{"begin":534,"end":541},"obj":"Phenotype"},{"id":"T17","span":{"begin":567,"end":579},"obj":"Phenotype"},{"id":"T18","span":{"begin":591,"end":598},"obj":"Phenotype"},{"id":"T19","span":{"begin":599,"end":611},"obj":"Phenotype"},{"id":"T20","span":{"begin":613,"end":620},"obj":"Phenotype"},{"id":"T21","span":{"begin":621,"end":633},"obj":"Phenotype"},{"id":"T22","span":{"begin":669,"end":675},"obj":"Phenotype"},{"id":"T23","span":{"begin":676,"end":688},"obj":"Phenotype"},{"id":"T24","span":{"begin":689,"end":701},"obj":"Phenotype"},{"id":"T25","span":{"begin":703,"end":709},"obj":"Phenotype"},{"id":"T26","span":{"begin":710,"end":722},"obj":"Phenotype"},{"id":"T27","span":{"begin":1003,"end":1014},"obj":"Phenotype"},{"id":"T28","span":{"begin":1033,"end":1042},"obj":"Phenotype"},{"id":"T29","span":{"begin":1236,"end":1245},"obj":"Phenotype"},{"id":"T30","span":{"begin":1437,"end":1469},"obj":"Phenotype"},{"id":"T31","span":{"begin":2034,"end":2040},"obj":"Phenotype"},{"id":"T32","span":{"begin":2218,"end":2228},"obj":"Phenotype"}],"attributes":[{"id":"A12","pred":"hp_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/HP_0020103"},{"id":"A13","pred":"hp_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/HP_0020103"},{"id":"A14","pred":"hp_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/HP_0020103"},{"id":"A15","pred":"hp_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A16","pred":"hp_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/HP_0001513"},{"id":"A17","pred":"hp_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A18","pred":"hp_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/HP_0001513"},{"id":"A19","pred":"hp_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A20","pred":"hp_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/HP_0001513"},{"id":"A21","pred":"hp_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A22","pred":"hp_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/HP_0002099"},{"id":"A23","pred":"hp_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A24","pred":"hp_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A25","pred":"hp_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/HP_0002099"},{"id":"A26","pred":"hp_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A27","pred":"hp_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/HP_0100750"},{"id":"A28","pred":"hp_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/HP_0002097"},{"id":"A29","pred":"hp_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A30","pred":"hp_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/HP_0020103"},{"id":"A31","pred":"hp_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/HP_0002664"},{"id":"A32","pred":"hp_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/HP_0002835"}],"text":"Table Clinical characteristics of nine critically ill patients with COVID-19 probable (n=1) and putative invasive pulmonary aspergillosis (n=8)\nPutative invasive pulmonary aspergillosis patients (sex, age) Probable IPA patient (sex, age)\nPatient 1 (male, 53 years) Patient 2 (female, 59 years) Patient3 (female, 69 years) Patient 4 (female, 63 years) Patient 5 (male, 43 years) Patient 6 (male, 79 years) Patient 7 (male, 77 years) Patient 8 (female, 75 years) Patient 9 (male, 47 years)\nRisk factors of severe COVID-19 Hypertension, obesity, ischaemic heart disease Hypertension, diabetes, obesity Hypertension, obesity Hypertension, diabetes, ischaemic heart disease Asthma Hypertension Hypertension, asthma Hypertension, diabetes None\nEORTC risk factors None None None None Steroids None None None Myeloma, steroids\nAPACHE II score 26 16 11 20 8 16 25 21 10\nThoracic CT-scan/x-ray* Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19, segmental lung atelectasis Typical COVID-19, emphysema Typical COVID-19 Typical COVID-19 + one peripheral nodule\nAnti-COVID-19 therapies LPV–RTV LPV–RTV, AZI LPV–RTV LPV–RTV AZI LPV–RTV, HCQ, AZI LPV–RTV, HCQ, AZI LPV–RTV, AZI No\nSteroids to treat pneumonia† Yes No Yes Yes No Yes Yes Yes No\nRenal replacement therapy Yes No No Yes No No Yes No No\nVasopressor Yes Yes Yes Yes No Yes Yes Yes Yes\nPulmonary specimen‡ BAL BAL BA BAL BAL BAL BAL BAL BA\nInvasive pulmonary aspergillosis diagnosis\nBAL culture§ − + + − + + + + +\nBAL/BA qPCR¶ − − 23·9 − − 34·5 29·0 31·7 −\nBAL galactomannan index 0·89 0·03 ND 0·15 0·12 0·05 3·91 0·36 ND\nSerum qPCR¶ − − − ND − − − − −\nβ-D-glucan, pg/mL 523 ND 7·8 105 7 23 135 450 14\nSerum galactomannan index 0·13 0·04 0·03 0·51 0·04 0·02 0·37 0·37 0·09\nNumber of mycological criteria 2 1 2 2 1 2 3 3 1\nAntifungal therapy None None None None None None VRC CSP None\nOutcome Alive Alive Alive Death (day 0) Alive Alive Death (day 18) Death (day 11) Death day 3)\nEORTC=European Organization for Research and Treatment of Cancer. APACHE= Acute Physiology and Chronic Health Enquiry. LPV–RTV=lopnavir–ritonavir combination. AZI=azithromycin. HCQ=hydroxychloroquine. BAL=Bronchoalveolar lavage. BA=bronchial aspiration. ND=not done. VRC=voriconazole. CSP=caspofungin.\n* Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.\n† Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;\n‡ No endotracheal or endobronchial lesion was observed.\n§ −=negative; +=positive with Aspergillus fumigatus identification.\n¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T17","span":{"begin":68,"end":76},"obj":"Disease"},{"id":"T18","span":{"begin":124,"end":137},"obj":"Disease"},{"id":"T19","span":{"begin":172,"end":185},"obj":"Disease"},{"id":"T20","span":{"begin":511,"end":519},"obj":"Disease"},{"id":"T21","span":{"begin":520,"end":532},"obj":"Disease"},{"id":"T22","span":{"begin":534,"end":541},"obj":"Disease"},{"id":"T23","span":{"begin":553,"end":566},"obj":"Disease"},{"id":"T24","span":{"begin":567,"end":579},"obj":"Disease"},{"id":"T25","span":{"begin":581,"end":589},"obj":"Disease"},{"id":"T26","span":{"begin":591,"end":598},"obj":"Disease"},{"id":"T27","span":{"begin":599,"end":611},"obj":"Disease"},{"id":"T28","span":{"begin":613,"end":620},"obj":"Disease"},{"id":"T29","span":{"begin":621,"end":633},"obj":"Disease"},{"id":"T30","span":{"begin":635,"end":643},"obj":"Disease"},{"id":"T31","span":{"begin":655,"end":668},"obj":"Disease"},{"id":"T32","span":{"begin":669,"end":675},"obj":"Disease"},{"id":"T33","span":{"begin":676,"end":688},"obj":"Disease"},{"id":"T34","span":{"begin":689,"end":701},"obj":"Disease"},{"id":"T35","span":{"begin":703,"end":709},"obj":"Disease"},{"id":"T36","span":{"begin":710,"end":722},"obj":"Disease"},{"id":"T37","span":{"begin":724,"end":732},"obj":"Disease"},{"id":"T38","span":{"begin":801,"end":808},"obj":"Disease"},{"id":"T40","span":{"begin":893,"end":901},"obj":"Disease"},{"id":"T41","span":{"begin":910,"end":918},"obj":"Disease"},{"id":"T42","span":{"begin":927,"end":935},"obj":"Disease"},{"id":"T43","span":{"begin":944,"end":952},"obj":"Disease"},{"id":"T44","span":{"begin":961,"end":969},"obj":"Disease"},{"id":"T45","span":{"begin":978,"end":986},"obj":"Disease"},{"id":"T46","span":{"begin":1023,"end":1031},"obj":"Disease"},{"id":"T47","span":{"begin":1033,"end":1042},"obj":"Disease"},{"id":"T48","span":{"begin":1051,"end":1059},"obj":"Disease"},{"id":"T49","span":{"begin":1068,"end":1076},"obj":"Disease"},{"id":"T50","span":{"begin":1106,"end":1114},"obj":"Disease"},{"id":"T51","span":{"begin":1236,"end":1245},"obj":"Disease"},{"id":"T52","span":{"begin":1456,"end":1469},"obj":"Disease"},{"id":"T53","span":{"begin":1872,"end":1875},"obj":"Disease"},{"id":"T54","span":{"begin":2034,"end":2040},"obj":"Disease"},{"id":"T55","span":{"begin":2261,"end":2264},"obj":"Disease"}],"attributes":[{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A18","pred":"mondo_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/MONDO_0005657"},{"id":"A19","pred":"mondo_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/MONDO_0005657"},{"id":"A20","pred":"mondo_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A21","pred":"mondo_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/MONDO_0005044"},{"id":"A22","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0011122"},{"id":"A23","pred":"mondo_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/MONDO_0005267"},{"id":"A24","pred":"mondo_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/MONDO_0005044"},{"id":"A25","pred":"mondo_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/MONDO_0005015"},{"id":"A26","pred":"mondo_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/MONDO_0011122"},{"id":"A27","pred":"mondo_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/MONDO_0005044"},{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0011122"},{"id":"A29","pred":"mondo_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/MONDO_0005044"},{"id":"A30","pred":"mondo_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/MONDO_0005015"},{"id":"A31","pred":"mondo_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/MONDO_0005267"},{"id":"A32","pred":"mondo_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/MONDO_0004979"},{"id":"A33","pred":"mondo_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/MONDO_0005044"},{"id":"A34","pred":"mondo_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/MONDO_0005044"},{"id":"A35","pred":"mondo_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/MONDO_0004979"},{"id":"A36","pred":"mondo_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/MONDO_0005044"},{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0005015"},{"id":"A38","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0005170"},{"id":"A39","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0009693"},{"id":"A40","pred":"mondo_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A41","pred":"mondo_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A42","pred":"mondo_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A44","pred":"mondo_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A45","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A46","pred":"mondo_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A47","pred":"mondo_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/MONDO_0004849"},{"id":"A48","pred":"mondo_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A49","pred":"mondo_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A50","pred":"mondo_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A52","pred":"mondo_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/MONDO_0005657"},{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0005078"},{"id":"A54","pred":"mondo_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/MONDO_0004992"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0005078"}],"text":"Table Clinical characteristics of nine critically ill patients with COVID-19 probable (n=1) and putative invasive pulmonary aspergillosis (n=8)\nPutative invasive pulmonary aspergillosis patients (sex, age) Probable IPA patient (sex, age)\nPatient 1 (male, 53 years) Patient 2 (female, 59 years) Patient3 (female, 69 years) Patient 4 (female, 63 years) Patient 5 (male, 43 years) Patient 6 (male, 79 years) Patient 7 (male, 77 years) Patient 8 (female, 75 years) Patient 9 (male, 47 years)\nRisk factors of severe COVID-19 Hypertension, obesity, ischaemic heart disease Hypertension, diabetes, obesity Hypertension, obesity Hypertension, diabetes, ischaemic heart disease Asthma Hypertension Hypertension, asthma Hypertension, diabetes None\nEORTC risk factors None None None None Steroids None None None Myeloma, steroids\nAPACHE II score 26 16 11 20 8 16 25 21 10\nThoracic CT-scan/x-ray* Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19, segmental lung atelectasis Typical COVID-19, emphysema Typical COVID-19 Typical COVID-19 + one peripheral nodule\nAnti-COVID-19 therapies LPV–RTV LPV–RTV, AZI LPV–RTV LPV–RTV AZI LPV–RTV, HCQ, AZI LPV–RTV, HCQ, AZI LPV–RTV, AZI No\nSteroids to treat pneumonia† Yes No Yes Yes No Yes Yes Yes No\nRenal replacement therapy Yes No No Yes No No Yes No No\nVasopressor Yes Yes Yes Yes No Yes Yes Yes Yes\nPulmonary specimen‡ BAL BAL BA BAL BAL BAL BAL BAL BA\nInvasive pulmonary aspergillosis diagnosis\nBAL culture§ − + + − + + + + +\nBAL/BA qPCR¶ − − 23·9 − − 34·5 29·0 31·7 −\nBAL galactomannan index 0·89 0·03 ND 0·15 0·12 0·05 3·91 0·36 ND\nSerum qPCR¶ − − − ND − − − − −\nβ-D-glucan, pg/mL 523 ND 7·8 105 7 23 135 450 14\nSerum galactomannan index 0·13 0·04 0·03 0·51 0·04 0·02 0·37 0·37 0·09\nNumber of mycological criteria 2 1 2 2 1 2 3 3 1\nAntifungal therapy None None None None None None VRC CSP None\nOutcome Alive Alive Alive Death (day 0) Alive Alive Death (day 18) Death (day 11) Death day 3)\nEORTC=European Organization for Research and Treatment of Cancer. APACHE= Acute Physiology and Chronic Health Enquiry. LPV–RTV=lopnavir–ritonavir combination. AZI=azithromycin. HCQ=hydroxychloroquine. BAL=Bronchoalveolar lavage. BA=bronchial aspiration. ND=not done. VRC=voriconazole. CSP=caspofungin.\n* Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.\n† Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;\n‡ No endotracheal or endobronchial lesion was observed.\n§ −=negative; +=positive with Aspergillus fumigatus identification.\n¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T12","span":{"begin":249,"end":253},"obj":"http://purl.obolibrary.org/obo/UBERON_0003101"},{"id":"T13","span":{"begin":249,"end":253},"obj":"http://www.ebi.ac.uk/efo/EFO_0000970"},{"id":"T14","span":{"begin":276,"end":282},"obj":"http://purl.obolibrary.org/obo/UBERON_0003100"},{"id":"T15","span":{"begin":304,"end":310},"obj":"http://purl.obolibrary.org/obo/UBERON_0003100"},{"id":"T16","span":{"begin":333,"end":339},"obj":"http://purl.obolibrary.org/obo/UBERON_0003100"},{"id":"T17","span":{"begin":362,"end":366},"obj":"http://purl.obolibrary.org/obo/UBERON_0003101"},{"id":"T18","span":{"begin":362,"end":366},"obj":"http://www.ebi.ac.uk/efo/EFO_0000970"},{"id":"T19","span":{"begin":389,"end":393},"obj":"http://purl.obolibrary.org/obo/UBERON_0003101"},{"id":"T20","span":{"begin":389,"end":393},"obj":"http://www.ebi.ac.uk/efo/EFO_0000970"},{"id":"T21","span":{"begin":416,"end":420},"obj":"http://purl.obolibrary.org/obo/UBERON_0003101"},{"id":"T22","span":{"begin":416,"end":420},"obj":"http://www.ebi.ac.uk/efo/EFO_0000970"},{"id":"T23","span":{"begin":443,"end":449},"obj":"http://purl.obolibrary.org/obo/UBERON_0003100"},{"id":"T24","span":{"begin":472,"end":476},"obj":"http://purl.obolibrary.org/obo/UBERON_0003101"},{"id":"T25","span":{"begin":472,"end":476},"obj":"http://www.ebi.ac.uk/efo/EFO_0000970"},{"id":"T26","span":{"begin":553,"end":558},"obj":"http://purl.obolibrary.org/obo/UBERON_0000948"},{"id":"T27","span":{"begin":553,"end":558},"obj":"http://purl.obolibrary.org/obo/UBERON_0007100"},{"id":"T28","span":{"begin":553,"end":558},"obj":"http://purl.obolibrary.org/obo/UBERON_0015228"},{"id":"T29","span":{"begin":553,"end":558},"obj":"http://www.ebi.ac.uk/efo/EFO_0000815"},{"id":"T30","span":{"begin":655,"end":660},"obj":"http://purl.obolibrary.org/obo/UBERON_0000948"},{"id":"T31","span":{"begin":655,"end":660},"obj":"http://purl.obolibrary.org/obo/UBERON_0007100"},{"id":"T32","span":{"begin":655,"end":660},"obj":"http://purl.obolibrary.org/obo/UBERON_0015228"},{"id":"T33","span":{"begin":655,"end":660},"obj":"http://www.ebi.ac.uk/efo/EFO_0000815"},{"id":"T34","span":{"begin":841,"end":843},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T35","span":{"begin":998,"end":1002},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T36","span":{"begin":998,"end":1002},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T37","span":{"begin":1537,"end":1539},"obj":"http://purl.obolibrary.org/obo/CLO_0001302"},{"id":"T38","span":{"begin":1613,"end":1615},"obj":"http://purl.obolibrary.org/obo/CLO_0001313"},{"id":"T39","span":{"begin":1662,"end":1664},"obj":"http://purl.obolibrary.org/obo/CLO_0008426"},{"id":"T40","span":{"begin":1805,"end":1808},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"},{"id":"T41","span":{"begin":1944,"end":1946},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T42","span":{"begin":1959,"end":1961},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T43","span":{"begin":1991,"end":2003},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"}],"text":"Table Clinical characteristics of nine critically ill patients with COVID-19 probable (n=1) and putative invasive pulmonary aspergillosis (n=8)\nPutative invasive pulmonary aspergillosis patients (sex, age) Probable IPA patient (sex, age)\nPatient 1 (male, 53 years) Patient 2 (female, 59 years) Patient3 (female, 69 years) Patient 4 (female, 63 years) Patient 5 (male, 43 years) Patient 6 (male, 79 years) Patient 7 (male, 77 years) Patient 8 (female, 75 years) Patient 9 (male, 47 years)\nRisk factors of severe COVID-19 Hypertension, obesity, ischaemic heart disease Hypertension, diabetes, obesity Hypertension, obesity Hypertension, diabetes, ischaemic heart disease Asthma Hypertension Hypertension, asthma Hypertension, diabetes None\nEORTC risk factors None None None None Steroids None None None Myeloma, steroids\nAPACHE II score 26 16 11 20 8 16 25 21 10\nThoracic CT-scan/x-ray* Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19, segmental lung atelectasis Typical COVID-19, emphysema Typical COVID-19 Typical COVID-19 + one peripheral nodule\nAnti-COVID-19 therapies LPV–RTV LPV–RTV, AZI LPV–RTV LPV–RTV AZI LPV–RTV, HCQ, AZI LPV–RTV, HCQ, AZI LPV–RTV, AZI No\nSteroids to treat pneumonia† Yes No Yes Yes No Yes Yes Yes No\nRenal replacement therapy Yes No No Yes No No Yes No No\nVasopressor Yes Yes Yes Yes No Yes Yes Yes Yes\nPulmonary specimen‡ BAL BAL BA BAL BAL BAL BAL BAL BA\nInvasive pulmonary aspergillosis diagnosis\nBAL culture§ − + + − + + + + +\nBAL/BA qPCR¶ − − 23·9 − − 34·5 29·0 31·7 −\nBAL galactomannan index 0·89 0·03 ND 0·15 0·12 0·05 3·91 0·36 ND\nSerum qPCR¶ − − − ND − − − − −\nβ-D-glucan, pg/mL 523 ND 7·8 105 7 23 135 450 14\nSerum galactomannan index 0·13 0·04 0·03 0·51 0·04 0·02 0·37 0·37 0·09\nNumber of mycological criteria 2 1 2 2 1 2 3 3 1\nAntifungal therapy None None None None None None VRC CSP None\nOutcome Alive Alive Alive Death (day 0) Alive Alive Death (day 18) Death (day 11) Death day 3)\nEORTC=European Organization for Research and Treatment of Cancer. APACHE= Acute Physiology and Chronic Health Enquiry. LPV–RTV=lopnavir–ritonavir combination. AZI=azithromycin. HCQ=hydroxychloroquine. BAL=Bronchoalveolar lavage. BA=bronchial aspiration. ND=not done. VRC=voriconazole. CSP=caspofungin.\n* Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.\n† Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;\n‡ No endotracheal or endobronchial lesion was observed.\n§ −=negative; +=positive with Aspergillus fumigatus identification.\n¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles)."}

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","subj":"T60","obj":"http://purl.obolibrary.org/obo/CHEBI_73419"},{"id":"A61","pred":"chebi_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/CHEBI_10023"},{"id":"A62","pred":"chebi_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/CHEBI_474180"},{"id":"A63","pred":"chebi_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/CHEBI_41879"}],"text":"Table Clinical characteristics of nine critically ill patients with COVID-19 probable (n=1) and putative invasive pulmonary aspergillosis (n=8)\nPutative invasive pulmonary aspergillosis patients (sex, age) Probable IPA patient (sex, age)\nPatient 1 (male, 53 years) Patient 2 (female, 59 years) Patient3 (female, 69 years) Patient 4 (female, 63 years) Patient 5 (male, 43 years) Patient 6 (male, 79 years) Patient 7 (male, 77 years) Patient 8 (female, 75 years) Patient 9 (male, 47 years)\nRisk factors of severe COVID-19 Hypertension, obesity, ischaemic heart disease Hypertension, diabetes, obesity Hypertension, obesity Hypertension, diabetes, ischaemic heart disease Asthma Hypertension Hypertension, asthma Hypertension, diabetes None\nEORTC risk factors None None None None Steroids None None None Myeloma, steroids\nAPACHE II score 26 16 11 20 8 16 25 21 10\nThoracic CT-scan/x-ray* Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19, segmental lung atelectasis Typical COVID-19, emphysema Typical COVID-19 Typical COVID-19 + one peripheral nodule\nAnti-COVID-19 therapies LPV–RTV LPV–RTV, AZI LPV–RTV LPV–RTV AZI LPV–RTV, HCQ, AZI LPV–RTV, HCQ, AZI LPV–RTV, AZI No\nSteroids to treat pneumonia† Yes No Yes Yes No Yes Yes Yes No\nRenal replacement therapy Yes No No Yes No No Yes No No\nVasopressor Yes Yes Yes Yes No Yes Yes Yes Yes\nPulmonary specimen‡ BAL BAL BA BAL BAL BAL BAL BAL BA\nInvasive pulmonary aspergillosis diagnosis\nBAL culture§ − + + − + + + + +\nBAL/BA qPCR¶ − − 23·9 − − 34·5 29·0 31·7 −\nBAL galactomannan index 0·89 0·03 ND 0·15 0·12 0·05 3·91 0·36 ND\nSerum qPCR¶ − − − ND − − − − −\nβ-D-glucan, pg/mL 523 ND 7·8 105 7 23 135 450 14\nSerum galactomannan index 0·13 0·04 0·03 0·51 0·04 0·02 0·37 0·37 0·09\nNumber of mycological criteria 2 1 2 2 1 2 3 3 1\nAntifungal therapy None None None None None None VRC CSP None\nOutcome Alive Alive Alive Death (day 0) Alive Alive Death (day 18) Death (day 11) Death day 3)\nEORTC=European Organization for Research and Treatment of Cancer. APACHE= Acute Physiology and Chronic Health Enquiry. LPV–RTV=lopnavir–ritonavir combination. AZI=azithromycin. HCQ=hydroxychloroquine. BAL=Bronchoalveolar lavage. BA=bronchial aspiration. ND=not done. VRC=voriconazole. CSP=caspofungin.\n* Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.\n† Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;\n‡ No endotracheal or endobronchial lesion was observed.\n§ −=negative; +=positive with Aspergillus fumigatus identification.\n¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles)."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T4","span":{"begin":1558,"end":1571},"obj":"GlycoEpitope"},{"id":"T5","span":{"begin":1705,"end":1718},"obj":"GlycoEpitope"}],"attributes":[{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A5","pred":"glyco_epitope_db_id","subj":"T5","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Table Clinical characteristics of nine critically ill patients with COVID-19 probable (n=1) and putative invasive pulmonary aspergillosis (n=8)\nPutative invasive pulmonary aspergillosis patients (sex, age) Probable IPA patient (sex, age)\nPatient 1 (male, 53 years) Patient 2 (female, 59 years) Patient3 (female, 69 years) Patient 4 (female, 63 years) Patient 5 (male, 43 years) Patient 6 (male, 79 years) Patient 7 (male, 77 years) Patient 8 (female, 75 years) Patient 9 (male, 47 years)\nRisk factors of severe COVID-19 Hypertension, obesity, ischaemic heart disease Hypertension, diabetes, obesity Hypertension, obesity Hypertension, diabetes, ischaemic heart disease Asthma Hypertension Hypertension, asthma Hypertension, diabetes None\nEORTC risk factors None None None None Steroids None None None Myeloma, steroids\nAPACHE II score 26 16 11 20 8 16 25 21 10\nThoracic CT-scan/x-ray* Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19 Typical COVID-19, segmental lung atelectasis Typical COVID-19, emphysema Typical COVID-19 Typical COVID-19 + one peripheral nodule\nAnti-COVID-19 therapies LPV–RTV LPV–RTV, AZI LPV–RTV LPV–RTV AZI LPV–RTV, HCQ, AZI LPV–RTV, HCQ, AZI LPV–RTV, AZI No\nSteroids to treat pneumonia† Yes No Yes Yes No Yes Yes Yes No\nRenal replacement therapy Yes No No Yes No No Yes No No\nVasopressor Yes Yes Yes Yes No Yes Yes Yes Yes\nPulmonary specimen‡ BAL BAL BA BAL BAL BAL BAL BAL BA\nInvasive pulmonary aspergillosis diagnosis\nBAL culture§ − + + − + + + + +\nBAL/BA qPCR¶ − − 23·9 − − 34·5 29·0 31·7 −\nBAL galactomannan index 0·89 0·03 ND 0·15 0·12 0·05 3·91 0·36 ND\nSerum qPCR¶ − − − ND − − − − −\nβ-D-glucan, pg/mL 523 ND 7·8 105 7 23 135 450 14\nSerum galactomannan index 0·13 0·04 0·03 0·51 0·04 0·02 0·37 0·37 0·09\nNumber of mycological criteria 2 1 2 2 1 2 3 3 1\nAntifungal therapy None None None None None None VRC CSP None\nOutcome Alive Alive Alive Death (day 0) Alive Alive Death (day 18) Death (day 11) Death day 3)\nEORTC=European Organization for Research and Treatment of Cancer. APACHE= Acute Physiology and Chronic Health Enquiry. LPV–RTV=lopnavir–ritonavir combination. AZI=azithromycin. HCQ=hydroxychloroquine. BAL=Bronchoalveolar lavage. BA=bronchial aspiration. ND=not done. VRC=voriconazole. CSP=caspofungin.\n* Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.\n† Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;\n‡ No endotracheal or endobronchial lesion was observed.\n§ −=negative; +=positive with Aspergillus fumigatus identification.\n¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles)."}

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APACHE= Acute Physiology and Chronic Health Enquiry. LPV–RTV=lopnavir–ritonavir combination. AZI=azithromycin. HCQ=hydroxychloroquine. BAL=Bronchoalveolar lavage. BA=bronchial aspiration. ND=not done. VRC=voriconazole. CSP=caspofungin.\n* Thoracic CT scan was done in Pt3, Pt4, Pt5, 5 days (median) before respiratory specimens.\n† Dexamethasone intravenous dose of 20 mg once daily from day 1 to day 5, followed by 10 mg once daily from day 6 to day 10;\n‡ No endotracheal or endobronchial lesion was observed.\n§ −=negative; +=positive with Aspergillus fumigatus identification.\n¶ qPCR=quantitative real-time PCR (−, negative; if positive, number of quantification cycles)."}