PMC:7340597 / 543-1293 JSONTXT

{"project":"LitCovid_Glycan-Motif-Structure","denotations":[{"id":"T1","span":{"begin":260,"end":273},"obj":"https://glytoucan.org/Structures/Glycans/G93424OB"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T2","span":{"begin":379,"end":384},"obj":"Body_part"},{"id":"T3","span":{"begin":592,"end":600},"obj":"Body_part"}],"attributes":[{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma9576"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma264783"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T2","span":{"begin":379,"end":384},"obj":"Body_part"}],"attributes":[{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-PubTator","denotations":[{"id":"32","span":{"begin":0,"end":8},"obj":"Species"},{"id":"33","span":{"begin":238,"end":246},"obj":"Species"},{"id":"34","span":{"begin":313,"end":321},"obj":"Species"},{"id":"35","span":{"begin":395,"end":403},"obj":"Species"},{"id":"36","span":{"begin":644,"end":652},"obj":"Species"},{"id":"37","span":{"begin":260,"end":273},"obj":"Chemical"},{"id":"38","span":{"begin":211,"end":229},"obj":"Disease"},{"id":"39","span":{"begin":334,"end":342},"obj":"Disease"},{"id":"40","span":{"begin":354,"end":377},"obj":"Disease"},{"id":"41","span":{"begin":573,"end":582},"obj":"Disease"},{"id":"42","span":{"begin":592,"end":607},"obj":"Disease"},{"id":"43","span":{"begin":609,"end":617},"obj":"Disease"},{"id":"44","span":{"begin":667,"end":676},"obj":"Disease"},{"id":"45","span":{"begin":727,"end":749},"obj":"Disease"}],"attributes":[{"id":"A32","pred":"tao:has_database_id","subj":"32","obj":"Tax:9606"},{"id":"A33","pred":"tao:has_database_id","subj":"33","obj":"Tax:9606"},{"id":"A34","pred":"tao:has_database_id","subj":"34","obj":"Tax:9606"},{"id":"A35","pred":"tao:has_database_id","subj":"35","obj":"Tax:9606"},{"id":"A36","pred":"tao:has_database_id","subj":"36","obj":"Tax:9606"},{"id":"A37","pred":"tao:has_database_id","subj":"37","obj":"MESH:C012990"},{"id":"A38","pred":"tao:has_database_id","subj":"38","obj":"MESH:D011655"},{"id":"A39","pred":"tao:has_database_id","subj":"39","obj":"MESH:C000657245"},{"id":"A40","pred":"tao:has_database_id","subj":"40","obj":"MESH:D055732"},{"id":"A41","pred":"tao:has_database_id","subj":"41","obj":"MESH:D011014"},{"id":"A42","pred":"tao:has_database_id","subj":"42","obj":"MESH:D055370"},{"id":"A43","pred":"tao:has_database_id","subj":"43","obj":"MESH:D005355"},{"id":"A44","pred":"tao:has_database_id","subj":"44","obj":"MESH:D011014"},{"id":"A45","pred":"tao:has_database_id","subj":"45","obj":"MESH:D055744"}],"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":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T7","span":{"begin":211,"end":229},"obj":"Disease"},{"id":"T8","span":{"begin":334,"end":342},"obj":"Disease"},{"id":"T9","span":{"begin":364,"end":377},"obj":"Disease"},{"id":"T10","span":{"begin":562,"end":582},"obj":"Disease"},{"id":"T12","span":{"begin":573,"end":582},"obj":"Disease"},{"id":"T13","span":{"begin":656,"end":676},"obj":"Disease"},{"id":"T15","span":{"begin":667,"end":676},"obj":"Disease"},{"id":"T16","span":{"begin":727,"end":749},"obj":"Disease"},{"id":"T17","span":{"begin":736,"end":749},"obj":"Disease"}],"attributes":[{"id":"A7","pred":"mondo_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/MONDO_0005279"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/MONDO_0005657"},{"id":"A10","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0015265"},{"id":"A11","pred":"mondo_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/MONDO_0056821"},{"id":"A12","pred":"mondo_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A13","pred":"mondo_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/MONDO_0015265"},{"id":"A14","pred":"mondo_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/MONDO_0056821"},{"id":"A15","pred":"mondo_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A16","pred":"mondo_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A17","pred":"mondo_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/MONDO_0005657"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T4","span":{"begin":46,"end":51},"obj":"http://purl.obolibrary.org/obo/UBERON_0003101"},{"id":"T5","span":{"begin":46,"end":51},"obj":"http://www.ebi.ac.uk/efo/EFO_0000970"},{"id":"T6","span":{"begin":60,"end":67},"obj":"http://purl.obolibrary.org/obo/UBERON_0003100"},{"id":"T7","span":{"begin":139,"end":141},"obj":"http://purl.obolibrary.org/obo/CLO_0001313"},{"id":"T8","span":{"begin":153,"end":154},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T9","span":{"begin":379,"end":384},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T10","span":{"begin":562,"end":572},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T11","span":{"begin":656,"end":666},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T1","span":{"begin":260,"end":273},"obj":"Chemical"}],"attributes":[{"id":"A1","pred":"chebi_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T1","span":{"begin":211,"end":229},"obj":"Phenotype"},{"id":"T2","span":{"begin":573,"end":582},"obj":"Phenotype"},{"id":"T3","span":{"begin":584,"end":607},"obj":"Phenotype"},{"id":"T4","span":{"begin":667,"end":676},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/HP_0002204"},{"id":"A2","pred":"hp_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A3","pred":"hp_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/HP_0033006"},{"id":"A4","pred":"hp_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":260,"end":273},"obj":"GlycoEpitope"}],"attributes":[{"id":"A1","pred":"glyco_epitope_db_id","subj":"T1","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-sentences","denotations":[{"id":"T10","span":{"begin":0,"end":82},"obj":"Sentence"},{"id":"T11","span":{"begin":83,"end":182},"obj":"Sentence"},{"id":"T12","span":{"begin":183,"end":378},"obj":"Sentence"},{"id":"T13","span":{"begin":379,"end":487},"obj":"Sentence"},{"id":"T14","span":{"begin":488,"end":677},"obj":"Sentence"},{"id":"T15","span":{"begin":678,"end":750},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T6","span":{"begin":115,"end":120},"obj":"GO:0016265"},{"id":"T7","span":{"begin":211,"end":220},"obj":"UBERON:0002048"},{"id":"T8","span":{"begin":260,"end":273},"obj":"CHEBI:27680;CHEBI:27680"},{"id":"T9","span":{"begin":277,"end":292},"obj":"UBERON:0002186;BV_4"},{"id":"T10","span":{"begin":293,"end":299},"obj":"BV_4"},{"id":"T11","span":{"begin":300,"end":305},"obj":"BV_4;UBERON:0006314"},{"id":"T12","span":{"begin":334,"end":342},"obj":"SP_7"},{"id":"T13","span":{"begin":354,"end":363},"obj":"UBERON:0002048"},{"id":"T14","span":{"begin":592,"end":600},"obj":"UBERON:0003215"},{"id":"T47338","span":{"begin":27,"end":35},"obj":"SP_7"},{"id":"T50253","span":{"begin":131,"end":135},"obj":"UBERON:0002048"},{"id":"T37393","span":{"begin":452,"end":466},"obj":"GO:0007596"},{"id":"T57275","span":{"begin":539,"end":545},"obj":"UBERON:0001638"},{"id":"T97784","span":{"begin":546,"end":561},"obj":"GO:0007596"},{"id":"T2103","span":{"begin":582,"end":590},"obj":"SP_7"},{"id":"T61739","span":{"begin":634,"end":643},"obj":"UBERON:0002048"},{"id":"T56562","span":{"begin":697,"end":705},"obj":"SP_7"}],"text":"Patients age ranged from 58 to 83 years, five males and two females were included. Time from hospital admission to death ranged from 12 to 36 days, with a mean of 20 ventilated days. ICU stay was complicated by pulmonary embolism in five patients and positive galactomannan on bronchoalveolar lavage fluid in six patients, suggesting COVID-19 associated pulmonary aspergillosis. Chest CT in all patients showed ground glass opacities, commonly progressing to nondependent consolidations. We observed four distinct histopathological patterns: acute fibrinous and organizing pneumonia, diffuse alveolar damage, fibrosis and, in four out of seven patients an organizing pneumonia. None of the biopsy specimens showed any signs of invasive aspergillosis."}