PMC:7234792 / 8836-9944 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"183","span":{"begin":3,"end":13},"obj":"Species"},{"id":"184","span":{"begin":755,"end":762},"obj":"Species"},{"id":"185","span":{"begin":878,"end":885},"obj":"Species"},{"id":"186","span":{"begin":1013,"end":1023},"obj":"Species"},{"id":"187","span":{"begin":543,"end":554},"obj":"Disease"},{"id":"188","span":{"begin":624,"end":632},"obj":"Disease"},{"id":"189","span":{"begin":666,"end":677},"obj":"Disease"},{"id":"190","span":{"begin":689,"end":704},"obj":"Disease"},{"id":"191","span":{"begin":768,"end":776},"obj":"Disease"},{"id":"192","span":{"begin":913,"end":924},"obj":"Disease"},{"id":"193","span":{"begin":1061,"end":1069},"obj":"Disease"}],"attributes":[{"id":"A183","pred":"tao:has_database_id","subj":"183","obj":"Tax:2697049"},{"id":"A184","pred":"tao:has_database_id","subj":"184","obj":"Tax:9606"},{"id":"A185","pred":"tao:has_database_id","subj":"185","obj":"Tax:9606"},{"id":"A186","pred":"tao:has_database_id","subj":"186","obj":"Tax:2697049"},{"id":"A187","pred":"tao:has_database_id","subj":"187","obj":"MESH:D055370"},{"id":"A188","pred":"tao:has_database_id","subj":"188","obj":"MESH:C000657245"},{"id":"A189","pred":"tao:has_database_id","subj":"189","obj":"MESH:D055370"},{"id":"A190","pred":"tao:has_database_id","subj":"190","obj":"MESH:D055370"},{"id":"A191","pred":"tao:has_database_id","subj":"191","obj":"MESH:C000657245"},{"id":"A192","pred":"tao:has_database_id","subj":"192","obj":"MESH:D055370"},{"id":"A193","pred":"tao:has_database_id","subj":"193","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":"If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives. In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases. The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury. The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T63","span":{"begin":22,"end":26},"obj":"Body_part"},{"id":"T64","span":{"begin":386,"end":390},"obj":"Body_part"},{"id":"T65","span":{"begin":438,"end":454},"obj":"Body_part"},{"id":"T66","span":{"begin":494,"end":499},"obj":"Body_part"},{"id":"T67","span":{"begin":543,"end":547},"obj":"Body_part"},{"id":"T68","span":{"begin":666,"end":670},"obj":"Body_part"},{"id":"T69","span":{"begin":689,"end":697},"obj":"Body_part"},{"id":"T70","span":{"begin":819,"end":831},"obj":"Body_part"},{"id":"T71","span":{"begin":819,"end":825},"obj":"Body_part"},{"id":"T72","span":{"begin":826,"end":831},"obj":"Body_part"},{"id":"T73","span":{"begin":913,"end":917},"obj":"Body_part"},{"id":"T74","span":{"begin":940,"end":944},"obj":"Body_part"}],"attributes":[{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma25000"},{"id":"A64","pred":"fma_id","subj":"T64","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A65","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma7337"},{"id":"A66","pred":"fma_id","subj":"T66","obj":"http://purl.org/sig/ont/fma/fma9576"},{"id":"A67","pred":"fma_id","subj":"T67","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A68","pred":"fma_id","subj":"T68","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A69","pred":"fma_id","subj":"T69","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A70","pred":"fma_id","subj":"T70","obj":"http://purl.org/sig/ont/fma/fma70574"},{"id":"A71","pred":"fma_id","subj":"T71","obj":"http://purl.org/sig/ont/fma/fma62970"},{"id":"A72","pred":"fma_id","subj":"T72","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A73","pred":"fma_id","subj":"T73","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A74","pred":"fma_id","subj":"T74","obj":"http://purl.org/sig/ont/fma/fma7195"}],"text":"If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives. In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases. The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury. The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T38","span":{"begin":386,"end":390},"obj":"Body_part"},{"id":"T39","span":{"begin":450,"end":454},"obj":"Body_part"},{"id":"T40","span":{"begin":494,"end":499},"obj":"Body_part"},{"id":"T41","span":{"begin":543,"end":547},"obj":"Body_part"},{"id":"T42","span":{"begin":666,"end":670},"obj":"Body_part"},{"id":"T43","span":{"begin":913,"end":917},"obj":"Body_part"},{"id":"T44","span":{"begin":940,"end":944},"obj":"Body_part"}],"attributes":[{"id":"A38","pred":"uberon_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A39","pred":"uberon_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/UBERON_3010752"},{"id":"A40","pred":"uberon_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"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_0002048"},{"id":"A43","pred":"uberon_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A44","pred":"uberon_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"}],"text":"If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives. In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases. The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury. The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T44","span":{"begin":3,"end":11},"obj":"Disease"},{"id":"T45","span":{"begin":537,"end":554},"obj":"Disease"},{"id":"T47","span":{"begin":548,"end":554},"obj":"Disease"},{"id":"T48","span":{"begin":624,"end":632},"obj":"Disease"},{"id":"T49","span":{"begin":660,"end":677},"obj":"Disease"},{"id":"T51","span":{"begin":671,"end":677},"obj":"Disease"},{"id":"T52","span":{"begin":768,"end":776},"obj":"Disease"},{"id":"T53","span":{"begin":907,"end":924},"obj":"Disease"},{"id":"T55","span":{"begin":918,"end":924},"obj":"Disease"},{"id":"T56","span":{"begin":1013,"end":1021},"obj":"Disease"},{"id":"T57","span":{"begin":1061,"end":1069},"obj":"Disease"}],"attributes":[{"id":"A44","pred":"mondo_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A45","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0006502"},{"id":"A46","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0015796"},{"id":"A47","pred":"mondo_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"},{"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_0006502"},{"id":"A50","pred":"mondo_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/MONDO_0015796"},{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"},{"id":"A52","pred":"mondo_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0006502"},{"id":"A54","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0015796"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"},{"id":"A56","pred":"mondo_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A57","pred":"mondo_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives. In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases. The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury. The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T111","span":{"begin":111,"end":113},"obj":"http://purl.obolibrary.org/obo/CLO_0008192"},{"id":"T112","span":{"begin":114,"end":119},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T113","span":{"begin":145,"end":146},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T114","span":{"begin":386,"end":390},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T115","span":{"begin":386,"end":390},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T116","span":{"begin":494,"end":499},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T117","span":{"begin":511,"end":512},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T118","span":{"begin":543,"end":547},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T119","span":{"begin":543,"end":547},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T120","span":{"begin":564,"end":568},"obj":"http://purl.obolibrary.org/obo/CLO_0008416"},{"id":"T121","span":{"begin":564,"end":568},"obj":"http://purl.obolibrary.org/obo/CLO_0050081"},{"id":"T122","span":{"begin":666,"end":670},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T123","span":{"begin":666,"end":670},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T124","span":{"begin":709,"end":711},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T125","span":{"begin":753,"end":754},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T126","span":{"begin":787,"end":788},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T127","span":{"begin":819,"end":831},"obj":"http://purl.obolibrary.org/obo/CL_0000786"},{"id":"T128","span":{"begin":913,"end":917},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T129","span":{"begin":913,"end":917},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T130","span":{"begin":940,"end":944},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T131","span":{"begin":940,"end":944},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T132","span":{"begin":1004,"end":1008},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"text":"If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives. In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases. The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury. The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T80","span":{"begin":111,"end":113},"obj":"Chemical"},{"id":"T83","span":{"begin":178,"end":181},"obj":"Chemical"},{"id":"T84","span":{"begin":746,"end":749},"obj":"Chemical"},{"id":"T85","span":{"begin":1031,"end":1034},"obj":"Chemical"}],"attributes":[{"id":"A80","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_50803"},{"id":"A81","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_53793"},{"id":"A82","pred":"chebi_id","subj":"T80","obj":"http://purl.obolibrary.org/obo/CHEBI_73425"},{"id":"A83","pred":"chebi_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A85","pred":"chebi_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"}],"text":"If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives. In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases. The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury. The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T31","span":{"begin":537,"end":554},"obj":"Phenotype"},{"id":"T32","span":{"begin":660,"end":677},"obj":"Phenotype"},{"id":"T33","span":{"begin":681,"end":704},"obj":"Phenotype"},{"id":"T34","span":{"begin":907,"end":924},"obj":"Phenotype"}],"attributes":[{"id":"A31","pred":"hp_id","subj":"T31","obj":"http://www.orpha.net/ORDO/Orphanet_178320"},{"id":"A32","pred":"hp_id","subj":"T32","obj":"http://www.orpha.net/ORDO/Orphanet_178320"},{"id":"A33","pred":"hp_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/HP_0033006"},{"id":"A34","pred":"hp_id","subj":"T34","obj":"http://www.orpha.net/ORDO/Orphanet_178320"}],"text":"If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives. In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases. The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury. The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course."}

{"project":"LitCovid-sentences","denotations":[{"id":"T60","span":{"begin":0,"end":141},"obj":"Sentence"},{"id":"T61","span":{"begin":142,"end":351},"obj":"Sentence"},{"id":"T62","span":{"begin":352,"end":555},"obj":"Sentence"},{"id":"T63","span":{"begin":556,"end":886},"obj":"Sentence"},{"id":"T64","span":{"begin":887,"end":1108},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"If SARS-CoV-2 was the sole cause of this presentation, starting on the day of admission, then the two negative NP tests were false negatives. In a study by Wang and colleagues,5 BAL was positive in 14 (93%) of 15 positive cases, whereas nasal swabs were positive in 5 (63%) of 8 positive cases, and pharyngeal swabs in 126 (32%) of 398 positive cases. The pathology from transbronchial lung biopsy, which was targeted specifically at the right lower lobe rounded opacity present on the initial chest CT, showed a pattern consistent with acute lung injury. The few peer-reviewed publications reporting pulmonary pathology in COVID-19 to date have all described acute lung injury or diffuse alveolar damage.10, 11, 12, 13, 14, 15, 16 One report of BAL in a patient with COVID-19 described a large number of aggregates of plasma cells;17 this was not seen in the specimen from our patient. Both the finding of acute lung injury in the area of lung affected at the onset of symptoms, and the positive RT-PCR test for SARS-CoV-2 in the BAL, support the diagnosis of COVID-19 to explain the entire hospital course."}