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LitCovid_Glycan-Motif-Structure

{"project":"LitCovid_Glycan-Motif-Structure","denotations":[{"id":"T1","span":{"begin":640,"end":653},"obj":"https://glytoucan.org/Structures/Glycans/G93424OB"}],"text":"Purpose\nPathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.\n\nMaterial and methods\nWe performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS. Clinical, radiological and microbiological characteristics are reported together with histopathological findings.\n\nMeasurement and main results\nPatients 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.\n\nConclusions\nIn this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia. Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis."}

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1","span":{"begin":176,"end":180},"obj":"Body_part"},{"id":"T2","span":{"begin":759,"end":764},"obj":"Body_part"},{"id":"T3","span":{"begin":972,"end":980},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma7195"},{"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":"Purpose\nPathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.\n\nMaterial and methods\nWe performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS. Clinical, radiological and microbiological characteristics are reported together with histopathological findings.\n\nMeasurement and main results\nPatients 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.\n\nConclusions\nIn this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia. Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T1","span":{"begin":176,"end":180},"obj":"Body_part"},{"id":"T2","span":{"begin":759,"end":764},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"uberon_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"}],"text":"Purpose\nPathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.\n\nMaterial and methods\nWe performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS. Clinical, radiological and microbiological characteristics are reported together with histopathological findings.\n\nMeasurement and main results\nPatients 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.\n\nConclusions\nIn this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia. Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis."}

LitCovid-PubTator

LitCovid-PD-MONDO

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T2","span":{"begin":176,"end":180},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T3","span":{"begin":176,"end":180},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T4","span":{"begin":426,"end":431},"obj":"http://purl.obolibrary.org/obo/UBERON_0003101"},{"id":"T5","span":{"begin":426,"end":431},"obj":"http://www.ebi.ac.uk/efo/EFO_0000970"},{"id":"T6","span":{"begin":440,"end":447},"obj":"http://purl.obolibrary.org/obo/UBERON_0003100"},{"id":"T7","span":{"begin":519,"end":521},"obj":"http://purl.obolibrary.org/obo/CLO_0001313"},{"id":"T8","span":{"begin":533,"end":534},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T9","span":{"begin":759,"end":764},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T10","span":{"begin":942,"end":952},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T11","span":{"begin":1036,"end":1046},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T12","span":{"begin":1289,"end":1299},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"}],"text":"Purpose\nPathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.\n\nMaterial and methods\nWe performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS. Clinical, radiological and microbiological characteristics are reported together with histopathological findings.\n\nMeasurement and main results\nPatients 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.\n\nConclusions\nIn this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia. Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T1","span":{"begin":640,"end":653},"obj":"Chemical"}],"attributes":[{"id":"A1","pred":"chebi_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"}],"text":"Purpose\nPathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.\n\nMaterial and methods\nWe performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS. Clinical, radiological and microbiological characteristics are reported together with histopathological findings.\n\nMeasurement and main results\nPatients 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.\n\nConclusions\nIn this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia. Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T1","span":{"begin":591,"end":609},"obj":"Phenotype"},{"id":"T2","span":{"begin":953,"end":962},"obj":"Phenotype"},{"id":"T3","span":{"begin":964,"end":987},"obj":"Phenotype"},{"id":"T4","span":{"begin":1047,"end":1056},"obj":"Phenotype"},{"id":"T5","span":{"begin":1300,"end":1309},"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"},{"id":"A5","pred":"hp_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"Purpose\nPathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.\n\nMaterial and methods\nWe performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS. Clinical, radiological and microbiological characteristics are reported together with histopathological findings.\n\nMeasurement and main results\nPatients 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.\n\nConclusions\nIn this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia. Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":640,"end":653},"obj":"GlycoEpitope"}],"attributes":[{"id":"A1","pred":"glyco_epitope_db_id","subj":"T1","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Purpose\nPathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.\n\nMaterial and methods\nWe performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS. Clinical, radiological and microbiological characteristics are reported together with histopathological findings.\n\nMeasurement and main results\nPatients 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.\n\nConclusions\nIn this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia. Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T4","span":{"begin":0,"end":7},"obj":"Sentence"},{"id":"T5","span":{"begin":8,"end":117},"obj":"Sentence"},{"id":"T6","span":{"begin":119,"end":139},"obj":"Sentence"},{"id":"T7","span":{"begin":140,"end":235},"obj":"Sentence"},{"id":"T8","span":{"begin":236,"end":349},"obj":"Sentence"},{"id":"T9","span":{"begin":351,"end":379},"obj":"Sentence"},{"id":"T10","span":{"begin":380,"end":462},"obj":"Sentence"},{"id":"T11","span":{"begin":463,"end":562},"obj":"Sentence"},{"id":"T12","span":{"begin":563,"end":758},"obj":"Sentence"},{"id":"T13","span":{"begin":759,"end":867},"obj":"Sentence"},{"id":"T14","span":{"begin":868,"end":1057},"obj":"Sentence"},{"id":"T15","span":{"begin":1058,"end":1130},"obj":"Sentence"},{"id":"T16","span":{"begin":1132,"end":1143},"obj":"Sentence"},{"id":"T17","span":{"begin":1144,"end":1310},"obj":"Sentence"},{"id":"T18","span":{"begin":1311,"end":1482},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Purpose\nPathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.\n\nMaterial and methods\nWe performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS. Clinical, radiological and microbiological characteristics are reported together with histopathological findings.\n\nMeasurement and main results\nPatients 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.\n\nConclusions\nIn this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia. Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis."}

LitCovid-PMC-OGER-BB

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T2","span":{"begin":42,"end":50},"obj":"SP_7"},{"id":"T3","span":{"begin":153,"end":163},"obj":"GO:0016265"},{"id":"T4","span":{"begin":176,"end":180},"obj":"UBERON:0002048"},{"id":"T5","span":{"begin":213,"end":221},"obj":"SP_7"},{"id":"T6","span":{"begin":495,"end":500},"obj":"GO:0016265"},{"id":"T7","span":{"begin":591,"end":600},"obj":"UBERON:0002048"},{"id":"T8","span":{"begin":640,"end":653},"obj":"CHEBI:27680;CHEBI:27680"},{"id":"T9","span":{"begin":657,"end":672},"obj":"UBERON:0002186;BV_4"},{"id":"T10","span":{"begin":673,"end":679},"obj":"BV_4"},{"id":"T11","span":{"begin":680,"end":685},"obj":"BV_4;UBERON:0006314"},{"id":"T12","span":{"begin":714,"end":722},"obj":"SP_7"},{"id":"T13","span":{"begin":734,"end":743},"obj":"UBERON:0002048"},{"id":"T14","span":{"begin":972,"end":980},"obj":"UBERON:0003215"},{"id":"T15","span":{"begin":1311,"end":1321},"obj":"GO:0016265"},{"id":"T16","span":{"begin":1358,"end":1366},"obj":"SP_7"},{"id":"T17","span":{"begin":1390,"end":1398},"obj":"SP_7"},{"id":"T18","span":{"begin":1410,"end":1419},"obj":"UBERON:0002048"},{"id":"T43630","span":{"begin":38,"end":42},"obj":"UBERON:0007221"},{"id":"T69896","span":{"begin":81,"end":91},"obj":"UBERON:0001004"},{"id":"T89860","span":{"begin":229,"end":235},"obj":"UBERON:0000915"},{"id":"T77448","span":{"begin":272,"end":282},"obj":"UBERON:0001004"},{"id":"T47338","span":{"begin":407,"end":415},"obj":"SP_7"},{"id":"T50253","span":{"begin":511,"end":515},"obj":"UBERON:0002048"},{"id":"T37393","span":{"begin":832,"end":846},"obj":"GO:0007596"},{"id":"T57275","span":{"begin":919,"end":925},"obj":"UBERON:0001638"},{"id":"T97784","span":{"begin":926,"end":941},"obj":"GO:0007596"},{"id":"T2103","span":{"begin":962,"end":970},"obj":"SP_7"},{"id":"T61739","span":{"begin":1014,"end":1023},"obj":"UBERON:0002048"},{"id":"T56562","span":{"begin":1077,"end":1085},"obj":"SP_7"},{"id":"T20701","span":{"begin":1124,"end":1133},"obj":"SP_7"},{"id":"T44207","span":{"begin":1232,"end":1241},"obj":"UBERON:0002048"},{"id":"T36528","span":{"begin":1242,"end":1248},"obj":"UBERON:0000479"},{"id":"T77817","span":{"begin":1363,"end":1371},"obj":"SP_7"},{"id":"T24460","span":{"begin":1394,"end":1402},"obj":"UBERON:0003215"}],"text":"Purpose\nPathological data of critical ill COVID-19 patients is essential in the search for optimal treatment options.\n\nMaterial and methods\nWe performed postmortem needle core lung biopsies in seven patients with COVID-19 related ARDS. Clinical, radiological and microbiological characteristics are reported together with histopathological findings.\n\nMeasurement and main results\nPatients 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.\n\nConclusions\nIn this case series common late histopathology in critically ill COVID patients is not classic DAD but heterogeneous with predominant pattern of organizing pneumonia. Postmortem biopsy investigations in critically COVID-19 patients with probable COVID-19 associated pulmonary aspergillosis obtained no evidence for invasive aspergillosis."}

PMC:7340597 / 163-1645 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7340597 / 163-1645 JSON TXT