PMC:7560789 / 8176-9438 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T11","span":{"begin":399,"end":407},"obj":"Body_part"},{"id":"T12","span":{"begin":678,"end":682},"obj":"Body_part"},{"id":"T13","span":{"begin":747,"end":751},"obj":"Body_part"}],"attributes":[{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A13","pred":"fma_id","subj":"T13","obj":"http://purl.org/sig/ont/fma/fma7195"}],"text":"A bronchoscopy with BAL is the preferred diagnostic approach because GM antigen detection and culture have a good sensitivity in influenza-associated IPA. However, given the risk of aerosolization, The American Association for Bronchology and Interventional Pulmonology issued a statement providing a limited role for bronchoscopy in patients with COVID-19, advocating the use of a nonbronchoscopic alveolar lavage (10). The technique we used in this study minimizes the risk for care providers while providing a diagnostic tool for our patients. However, the nondirected BAL technique is not validated for GM detection. As all patients had consolidations in all regions of the lung, the chances that a nondirected BAL may result in sampling of a lung region that was not affected by IPA may be low, although it is unclear to which extent consolidations are caused by the virus or by the fungus. More importantly, we cannot rule out overdiagnosis, as a nondirected sample may not always reflect microbiology of the lower airways. Therefore, instead of 0.5, a cutoff GM index of 1.0 was applied in this study. Nevertheless, sampling error cannot be ruled out. Of note, however, concordance between GM index \u003e1.0 and positive Aspergillus cultures was high (77.8%)."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T3","span":{"begin":678,"end":682},"obj":"Body_part"},{"id":"T4","span":{"begin":747,"end":751},"obj":"Body_part"}],"attributes":[{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"}],"text":"A bronchoscopy with BAL is the preferred diagnostic approach because GM antigen detection and culture have a good sensitivity in influenza-associated IPA. However, given the risk of aerosolization, The American Association for Bronchology and Interventional Pulmonology issued a statement providing a limited role for bronchoscopy in patients with COVID-19, advocating the use of a nonbronchoscopic alveolar lavage (10). The technique we used in this study minimizes the risk for care providers while providing a diagnostic tool for our patients. However, the nondirected BAL technique is not validated for GM detection. As all patients had consolidations in all regions of the lung, the chances that a nondirected BAL may result in sampling of a lung region that was not affected by IPA may be low, although it is unclear to which extent consolidations are caused by the virus or by the fungus. More importantly, we cannot rule out overdiagnosis, as a nondirected sample may not always reflect microbiology of the lower airways. Therefore, instead of 0.5, a cutoff GM index of 1.0 was applied in this study. Nevertheless, sampling error cannot be ruled out. Of note, however, concordance between GM index \u003e1.0 and positive Aspergillus cultures was high (77.8%)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T53","span":{"begin":129,"end":138},"obj":"Disease"},{"id":"T54","span":{"begin":348,"end":356},"obj":"Disease"}],"attributes":[{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0005812"},{"id":"A54","pred":"mondo_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"A bronchoscopy with BAL is the preferred diagnostic approach because GM antigen detection and culture have a good sensitivity in influenza-associated IPA. However, given the risk of aerosolization, The American Association for Bronchology and Interventional Pulmonology issued a statement providing a limited role for bronchoscopy in patients with COVID-19, advocating the use of a nonbronchoscopic alveolar lavage (10). The technique we used in this study minimizes the risk for care providers while providing a diagnostic tool for our patients. However, the nondirected BAL technique is not validated for GM detection. As all patients had consolidations in all regions of the lung, the chances that a nondirected BAL may result in sampling of a lung region that was not affected by IPA may be low, although it is unclear to which extent consolidations are caused by the virus or by the fungus. More importantly, we cannot rule out overdiagnosis, as a nondirected sample may not always reflect microbiology of the lower airways. Therefore, instead of 0.5, a cutoff GM index of 1.0 was applied in this study. Nevertheless, sampling error cannot be ruled out. Of note, however, concordance between GM index \u003e1.0 and positive Aspergillus cultures was high (77.8%)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T60","span":{"begin":0,"end":1},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T61","span":{"begin":107,"end":108},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T62","span":{"begin":277,"end":278},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T63","span":{"begin":299,"end":300},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T64","span":{"begin":380,"end":381},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T65","span":{"begin":511,"end":512},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T66","span":{"begin":678,"end":682},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T67","span":{"begin":678,"end":682},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T68","span":{"begin":701,"end":702},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T69","span":{"begin":745,"end":746},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T70","span":{"begin":747,"end":751},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T71","span":{"begin":747,"end":751},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T72","span":{"begin":872,"end":877},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T73","span":{"begin":951,"end":952},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T74","span":{"begin":1021,"end":1028},"obj":"http://purl.obolibrary.org/obo/UBERON_0001005"},{"id":"T75","span":{"begin":1057,"end":1058},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"A bronchoscopy with BAL is the preferred diagnostic approach because GM antigen detection and culture have a good sensitivity in influenza-associated IPA. However, given the risk of aerosolization, The American Association for Bronchology and Interventional Pulmonology issued a statement providing a limited role for bronchoscopy in patients with COVID-19, advocating the use of a nonbronchoscopic alveolar lavage (10). The technique we used in this study minimizes the risk for care providers while providing a diagnostic tool for our patients. However, the nondirected BAL technique is not validated for GM detection. As all patients had consolidations in all regions of the lung, the chances that a nondirected BAL may result in sampling of a lung region that was not affected by IPA may be low, although it is unclear to which extent consolidations are caused by the virus or by the fungus. More importantly, we cannot rule out overdiagnosis, as a nondirected sample may not always reflect microbiology of the lower airways. Therefore, instead of 0.5, a cutoff GM index of 1.0 was applied in this study. Nevertheless, sampling error cannot be ruled out. Of note, however, concordance between GM index \u003e1.0 and positive Aspergillus cultures was high (77.8%)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T128","span":{"begin":20,"end":23},"obj":"Chemical"},{"id":"T129","span":{"begin":69,"end":71},"obj":"Chemical"},{"id":"T131","span":{"begin":72,"end":79},"obj":"Chemical"},{"id":"T132","span":{"begin":150,"end":153},"obj":"Chemical"},{"id":"T134","span":{"begin":572,"end":575},"obj":"Chemical"},{"id":"T135","span":{"begin":607,"end":609},"obj":"Chemical"},{"id":"T137","span":{"begin":715,"end":718},"obj":"Chemical"},{"id":"T138","span":{"begin":784,"end":787},"obj":"Chemical"},{"id":"T140","span":{"begin":1066,"end":1068},"obj":"Chemical"},{"id":"T142","span":{"begin":1197,"end":1199},"obj":"Chemical"}],"attributes":[{"id":"A128","pred":"chebi_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A129","pred":"chebi_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A130","pred":"chebi_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A131","pred":"chebi_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/CHEBI_59132"},{"id":"A132","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_17824"},{"id":"A133","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_30802"},{"id":"A134","pred":"chebi_id","subj":"T134","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A135","pred":"chebi_id","subj":"T135","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A136","pred":"chebi_id","subj":"T135","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A137","pred":"chebi_id","subj":"T137","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A138","pred":"chebi_id","subj":"T138","obj":"http://purl.obolibrary.org/obo/CHEBI_17824"},{"id":"A139","pred":"chebi_id","subj":"T138","obj":"http://purl.obolibrary.org/obo/CHEBI_30802"},{"id":"A140","pred":"chebi_id","subj":"T140","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A141","pred":"chebi_id","subj":"T140","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A142","pred":"chebi_id","subj":"T142","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A143","pred":"chebi_id","subj":"T142","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"}],"text":"A bronchoscopy with BAL is the preferred diagnostic approach because GM antigen detection and culture have a good sensitivity in influenza-associated IPA. However, given the risk of aerosolization, The American Association for Bronchology and Interventional Pulmonology issued a statement providing a limited role for bronchoscopy in patients with COVID-19, advocating the use of a nonbronchoscopic alveolar lavage (10). The technique we used in this study minimizes the risk for care providers while providing a diagnostic tool for our patients. However, the nondirected BAL technique is not validated for GM detection. As all patients had consolidations in all regions of the lung, the chances that a nondirected BAL may result in sampling of a lung region that was not affected by IPA may be low, although it is unclear to which extent consolidations are caused by the virus or by the fungus. More importantly, we cannot rule out overdiagnosis, as a nondirected sample may not always reflect microbiology of the lower airways. Therefore, instead of 0.5, a cutoff GM index of 1.0 was applied in this study. Nevertheless, sampling error cannot be ruled out. Of note, however, concordance between GM index \u003e1.0 and positive Aspergillus cultures was high (77.8%)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T65","span":{"begin":0,"end":154},"obj":"Sentence"},{"id":"T66","span":{"begin":155,"end":420},"obj":"Sentence"},{"id":"T67","span":{"begin":421,"end":546},"obj":"Sentence"},{"id":"T68","span":{"begin":547,"end":620},"obj":"Sentence"},{"id":"T69","span":{"begin":621,"end":895},"obj":"Sentence"},{"id":"T70","span":{"begin":896,"end":1029},"obj":"Sentence"},{"id":"T71","span":{"begin":1030,"end":1108},"obj":"Sentence"},{"id":"T72","span":{"begin":1109,"end":1158},"obj":"Sentence"},{"id":"T73","span":{"begin":1159,"end":1262},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"A bronchoscopy with BAL is the preferred diagnostic approach because GM antigen detection and culture have a good sensitivity in influenza-associated IPA. However, given the risk of aerosolization, The American Association for Bronchology and Interventional Pulmonology issued a statement providing a limited role for bronchoscopy in patients with COVID-19, advocating the use of a nonbronchoscopic alveolar lavage (10). The technique we used in this study minimizes the risk for care providers while providing a diagnostic tool for our patients. However, the nondirected BAL technique is not validated for GM detection. As all patients had consolidations in all regions of the lung, the chances that a nondirected BAL may result in sampling of a lung region that was not affected by IPA may be low, although it is unclear to which extent consolidations are caused by the virus or by the fungus. More importantly, we cannot rule out overdiagnosis, as a nondirected sample may not always reflect microbiology of the lower airways. Therefore, instead of 0.5, a cutoff GM index of 1.0 was applied in this study. Nevertheless, sampling error cannot be ruled out. Of note, however, concordance between GM index \u003e1.0 and positive Aspergillus cultures was high (77.8%)."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T11","span":{"begin":69,"end":71},"obj":"GlycoEpitope"},{"id":"T12","span":{"begin":607,"end":609},"obj":"GlycoEpitope"},{"id":"T13","span":{"begin":1066,"end":1068},"obj":"GlycoEpitope"},{"id":"T14","span":{"begin":1197,"end":1199},"obj":"GlycoEpitope"}],"attributes":[{"id":"A11","pred":"glyco_epitope_db_id","subj":"T11","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A12","pred":"glyco_epitope_db_id","subj":"T12","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A13","pred":"glyco_epitope_db_id","subj":"T13","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A14","pred":"glyco_epitope_db_id","subj":"T14","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"A bronchoscopy with BAL is the preferred diagnostic approach because GM antigen detection and culture have a good sensitivity in influenza-associated IPA. However, given the risk of aerosolization, The American Association for Bronchology and Interventional Pulmonology issued a statement providing a limited role for bronchoscopy in patients with COVID-19, advocating the use of a nonbronchoscopic alveolar lavage (10). The technique we used in this study minimizes the risk for care providers while providing a diagnostic tool for our patients. However, the nondirected BAL technique is not validated for GM detection. As all patients had consolidations in all regions of the lung, the chances that a nondirected BAL may result in sampling of a lung region that was not affected by IPA may be low, although it is unclear to which extent consolidations are caused by the virus or by the fungus. More importantly, we cannot rule out overdiagnosis, as a nondirected sample may not always reflect microbiology of the lower airways. Therefore, instead of 0.5, a cutoff GM index of 1.0 was applied in this study. Nevertheless, sampling error cannot be ruled out. Of note, however, concordance between GM index \u003e1.0 and positive Aspergillus cultures was high (77.8%)."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T64","span":{"begin":150,"end":153},"obj":"Phenotype"},{"id":"T65","span":{"begin":784,"end":787},"obj":"Phenotype"}],"attributes":[{"id":"A64","pred":"hp_id","subj":"T64","obj":"http://purl.obolibrary.org/obo/HP_0020103"},{"id":"A65","pred":"hp_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/HP_0020103"}],"text":"A bronchoscopy with BAL is the preferred diagnostic approach because GM antigen detection and culture have a good sensitivity in influenza-associated IPA. However, given the risk of aerosolization, The American Association for Bronchology and Interventional Pulmonology issued a statement providing a limited role for bronchoscopy in patients with COVID-19, advocating the use of a nonbronchoscopic alveolar lavage (10). The technique we used in this study minimizes the risk for care providers while providing a diagnostic tool for our patients. However, the nondirected BAL technique is not validated for GM detection. As all patients had consolidations in all regions of the lung, the chances that a nondirected BAL may result in sampling of a lung region that was not affected by IPA may be low, although it is unclear to which extent consolidations are caused by the virus or by the fungus. More importantly, we cannot rule out overdiagnosis, as a nondirected sample may not always reflect microbiology of the lower airways. Therefore, instead of 0.5, a cutoff GM index of 1.0 was applied in this study. Nevertheless, sampling error cannot be ruled out. Of note, however, concordance between GM index \u003e1.0 and positive Aspergillus cultures was high (77.8%)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"246","span":{"begin":334,"end":342},"obj":"Species"},{"id":"247","span":{"begin":537,"end":545},"obj":"Species"},{"id":"248","span":{"begin":628,"end":636},"obj":"Species"},{"id":"249","span":{"begin":1224,"end":1235},"obj":"Species"},{"id":"250","span":{"begin":69,"end":79},"obj":"Chemical"},{"id":"251","span":{"begin":607,"end":609},"obj":"Chemical"},{"id":"252","span":{"begin":1197,"end":1199},"obj":"Chemical"},{"id":"253","span":{"begin":348,"end":356},"obj":"Disease"}],"attributes":[{"id":"A246","pred":"tao:has_database_id","subj":"246","obj":"Tax:9606"},{"id":"A247","pred":"tao:has_database_id","subj":"247","obj":"Tax:9606"},{"id":"A248","pred":"tao:has_database_id","subj":"248","obj":"Tax:9606"},{"id":"A249","pred":"tao:has_database_id","subj":"249","obj":"Tax:746128"},{"id":"A251","pred":"tao:has_database_id","subj":"251","obj":"MESH:C012990"},{"id":"A252","pred":"tao:has_database_id","subj":"252","obj":"MESH:C012990"},{"id":"A253","pred":"tao:has_database_id","subj":"253","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":"A bronchoscopy with BAL is the preferred diagnostic approach because GM antigen detection and culture have a good sensitivity in influenza-associated IPA. However, given the risk of aerosolization, The American Association for Bronchology and Interventional Pulmonology issued a statement providing a limited role for bronchoscopy in patients with COVID-19, advocating the use of a nonbronchoscopic alveolar lavage (10). The technique we used in this study minimizes the risk for care providers while providing a diagnostic tool for our patients. However, the nondirected BAL technique is not validated for GM detection. As all patients had consolidations in all regions of the lung, the chances that a nondirected BAL may result in sampling of a lung region that was not affected by IPA may be low, although it is unclear to which extent consolidations are caused by the virus or by the fungus. More importantly, we cannot rule out overdiagnosis, as a nondirected sample may not always reflect microbiology of the lower airways. Therefore, instead of 0.5, a cutoff GM index of 1.0 was applied in this study. Nevertheless, sampling error cannot be ruled out. Of note, however, concordance between GM index \u003e1.0 and positive Aspergillus cultures was high (77.8%)."}