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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

LitCovid-PubTator

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T82","span":{"begin":49,"end":53},"obj":"Chemical"},{"id":"T83","span":{"begin":133,"end":135},"obj":"Chemical"},{"id":"T84","span":{"begin":1734,"end":1737},"obj":"Chemical"}],"attributes":[{"id":"A82","pred":"chebi_id","subj":"T82","obj":"http://purl.obolibrary.org/obo/CHEBI_30780"},{"id":"A83","pred":"chebi_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/CHEBI_73503"},{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_27565"}],"text":"3.2 Case 1 – Organizing pneumonia\nA 77-year old male without significant medical history was evaluated in our emergency department (ED) with complaints of general weakness, fever and dyspnoea. Initial chest CT showed extensive bilateral areas of ground-glass opacity with both central and peripheral distribution, patchy subpleural non-dependant consolidations and areas with subpleural sparing (Fig. 1-1A). Soon after admission patient was in need of mechanical ventilatory support and developed acute renal failure for which renal replacement therapy was initiated. After six days of mechanical ventilation chest CT-angiography showed pulmonary emboli along with new areas of ground-glass opacity and progression of dens subpleural consolidations with air-bronchograms (Fig. 1-1B). A nosocomial infection was ruled out by bronchial culture. Patient's neurologic status deteriorated and CT head revealed brain ischemia due to infarction of the area supplied by the left and right posterior cerebral artery. The patient died 12 days after admission.\nPostmortem pathologic examination revealed that the overall architecture of the lung tissue remained intact. However, a prominent amount of fibromyxoid or fibroblastic bodies was present in the alveoli with surrounding histiocytes (Fig. 2A . The extent of involved lung tissue was estimated at around 25% (Table 2). No remnants of hyaline membranes or prominent alveolar fibrinous exudate were found. Microthrombi in small blood vessels of the alveolar septa were seen, as well as an organizing thrombus in a larger sized vessel (Fig. 2E). The histologic findings in this case point towards an epithelial, and vascular phenotype of a SARS-CoV2 infection. No fungi were present in de PAS-D stain. This histologic pattern is characteristic for an organizing pneumonia.\nFig. 2 Microscopic lung findings. A, case 1: intra-alveolar fibroblastic bodies, consistent with organizing pneumonia, (H\u0026E, 10×) B, case 2: loss of alveolar architecture with extensive fibrosis (H\u0026E; 10×) C, case 3: inflammatory infiltrate with neutrophils and lymphocytes, note the hyaline membranes (arrows), suggestive for diffuse alveolar damage. (H\u0026E, 20×) D, case 4: prominent fibrinous exudate in alveoli as seen in AFOP (H\u0026E; 10×) E: thrombus in larger vessel (H\u0026E, 5×) F: cytopathogenic changes in pneumocytes due to viral infection seen in all cases: hyperplasia, multinucleated giant cells (asterisks), intranuclear inclusion bodies (H\u0026E, 40×)."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T30","span":{"begin":25,"end":34},"obj":"Phenotype"},{"id":"T31","span":{"begin":156,"end":172},"obj":"Phenotype"},{"id":"T32","span":{"begin":174,"end":179},"obj":"Phenotype"},{"id":"T33","span":{"begin":184,"end":192},"obj":"Phenotype"},{"id":"T34","span":{"begin":498,"end":517},"obj":"Phenotype"},{"id":"T35","span":{"begin":906,"end":920},"obj":"Phenotype"},{"id":"T36","span":{"begin":1807,"end":1816},"obj":"Phenotype"},{"id":"T37","span":{"begin":1926,"end":1935},"obj":"Phenotype"},{"id":"T38","span":{"begin":2145,"end":2168},"obj":"Phenotype"}],"attributes":[{"id":"A30","pred":"hp_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A31","pred":"hp_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/HP_0003324"},{"id":"A32","pred":"hp_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/HP_0001945"},{"id":"A33","pred":"hp_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/HP_0002094"},{"id":"A34","pred":"hp_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/HP_0001919"},{"id":"A35","pred":"hp_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/HP_0002637"},{"id":"A36","pred":"hp_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A37","pred":"hp_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A38","pred":"hp_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/HP_0033006"}],"text":"3.2 Case 1 – Organizing pneumonia\nA 77-year old male without significant medical history was evaluated in our emergency department (ED) with complaints of general weakness, fever and dyspnoea. Initial chest CT showed extensive bilateral areas of ground-glass opacity with both central and peripheral distribution, patchy subpleural non-dependant consolidations and areas with subpleural sparing (Fig. 1-1A). Soon after admission patient was in need of mechanical ventilatory support and developed acute renal failure for which renal replacement therapy was initiated. After six days of mechanical ventilation chest CT-angiography showed pulmonary emboli along with new areas of ground-glass opacity and progression of dens subpleural consolidations with air-bronchograms (Fig. 1-1B). A nosocomial infection was ruled out by bronchial culture. Patient's neurologic status deteriorated and CT head revealed brain ischemia due to infarction of the area supplied by the left and right posterior cerebral artery. The patient died 12 days after admission.\nPostmortem pathologic examination revealed that the overall architecture of the lung tissue remained intact. However, a prominent amount of fibromyxoid or fibroblastic bodies was present in the alveoli with surrounding histiocytes (Fig. 2A . The extent of involved lung tissue was estimated at around 25% (Table 2). No remnants of hyaline membranes or prominent alveolar fibrinous exudate were found. Microthrombi in small blood vessels of the alveolar septa were seen, as well as an organizing thrombus in a larger sized vessel (Fig. 2E). The histologic findings in this case point towards an epithelial, and vascular phenotype of a SARS-CoV2 infection. No fungi were present in de PAS-D stain. This histologic pattern is characteristic for an organizing pneumonia.\nFig. 2 Microscopic lung findings. A, case 1: intra-alveolar fibroblastic bodies, consistent with organizing pneumonia, (H\u0026E, 10×) B, case 2: loss of alveolar architecture with extensive fibrosis (H\u0026E; 10×) C, case 3: inflammatory infiltrate with neutrophils and lymphocytes, note the hyaline membranes (arrows), suggestive for diffuse alveolar damage. (H\u0026E, 20×) D, case 4: prominent fibrinous exudate in alveoli as seen in AFOP (H\u0026E; 10×) E: thrombus in larger vessel (H\u0026E, 5×) F: cytopathogenic changes in pneumocytes due to viral infection seen in all cases: hyperplasia, multinucleated giant cells (asterisks), intranuclear inclusion bodies (H\u0026E, 40×)."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T3","span":{"begin":2345,"end":2360},"obj":"http://purl.obolibrary.org/obo/GO_0016032"}],"text":"3.2 Case 1 – Organizing pneumonia\nA 77-year old male without significant medical history was evaluated in our emergency department (ED) with complaints of general weakness, fever and dyspnoea. Initial chest CT showed extensive bilateral areas of ground-glass opacity with both central and peripheral distribution, patchy subpleural non-dependant consolidations and areas with subpleural sparing (Fig. 1-1A). Soon after admission patient was in need of mechanical ventilatory support and developed acute renal failure for which renal replacement therapy was initiated. After six days of mechanical ventilation chest CT-angiography showed pulmonary emboli along with new areas of ground-glass opacity and progression of dens subpleural consolidations with air-bronchograms (Fig. 1-1B). A nosocomial infection was ruled out by bronchial culture. Patient's neurologic status deteriorated and CT head revealed brain ischemia due to infarction of the area supplied by the left and right posterior cerebral artery. The patient died 12 days after admission.\nPostmortem pathologic examination revealed that the overall architecture of the lung tissue remained intact. However, a prominent amount of fibromyxoid or fibroblastic bodies was present in the alveoli with surrounding histiocytes (Fig. 2A . The extent of involved lung tissue was estimated at around 25% (Table 2). No remnants of hyaline membranes or prominent alveolar fibrinous exudate were found. Microthrombi in small blood vessels of the alveolar septa were seen, as well as an organizing thrombus in a larger sized vessel (Fig. 2E). The histologic findings in this case point towards an epithelial, and vascular phenotype of a SARS-CoV2 infection. No fungi were present in de PAS-D stain. This histologic pattern is characteristic for an organizing pneumonia.\nFig. 2 Microscopic lung findings. A, case 1: intra-alveolar fibroblastic bodies, consistent with organizing pneumonia, (H\u0026E, 10×) B, case 2: loss of alveolar architecture with extensive fibrosis (H\u0026E; 10×) C, case 3: inflammatory infiltrate with neutrophils and lymphocytes, note the hyaline membranes (arrows), suggestive for diffuse alveolar damage. (H\u0026E, 20×) D, case 4: prominent fibrinous exudate in alveoli as seen in AFOP (H\u0026E; 10×) E: thrombus in larger vessel (H\u0026E, 5×) F: cytopathogenic changes in pneumocytes due to viral infection seen in all cases: hyperplasia, multinucleated giant cells (asterisks), intranuclear inclusion bodies (H\u0026E, 40×)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T102","span":{"begin":0,"end":34},"obj":"Sentence"},{"id":"T103","span":{"begin":35,"end":193},"obj":"Sentence"},{"id":"T104","span":{"begin":194,"end":408},"obj":"Sentence"},{"id":"T105","span":{"begin":409,"end":568},"obj":"Sentence"},{"id":"T106","span":{"begin":569,"end":784},"obj":"Sentence"},{"id":"T107","span":{"begin":785,"end":843},"obj":"Sentence"},{"id":"T108","span":{"begin":844,"end":1008},"obj":"Sentence"},{"id":"T109","span":{"begin":1009,"end":1050},"obj":"Sentence"},{"id":"T110","span":{"begin":1051,"end":1159},"obj":"Sentence"},{"id":"T111","span":{"begin":1160,"end":1292},"obj":"Sentence"},{"id":"T112","span":{"begin":1293,"end":1366},"obj":"Sentence"},{"id":"T113","span":{"begin":1367,"end":1451},"obj":"Sentence"},{"id":"T114","span":{"begin":1452,"end":1590},"obj":"Sentence"},{"id":"T115","span":{"begin":1591,"end":1705},"obj":"Sentence"},{"id":"T116","span":{"begin":1706,"end":1746},"obj":"Sentence"},{"id":"T117","span":{"begin":1747,"end":1817},"obj":"Sentence"},{"id":"T118","span":{"begin":1818,"end":1851},"obj":"Sentence"},{"id":"T119","span":{"begin":1852,"end":2474},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.2 Case 1 – Organizing pneumonia\nA 77-year old male without significant medical history was evaluated in our emergency department (ED) with complaints of general weakness, fever and dyspnoea. Initial chest CT showed extensive bilateral areas of ground-glass opacity with both central and peripheral distribution, patchy subpleural non-dependant consolidations and areas with subpleural sparing (Fig. 1-1A). Soon after admission patient was in need of mechanical ventilatory support and developed acute renal failure for which renal replacement therapy was initiated. After six days of mechanical ventilation chest CT-angiography showed pulmonary emboli along with new areas of ground-glass opacity and progression of dens subpleural consolidations with air-bronchograms (Fig. 1-1B). A nosocomial infection was ruled out by bronchial culture. Patient's neurologic status deteriorated and CT head revealed brain ischemia due to infarction of the area supplied by the left and right posterior cerebral artery. The patient died 12 days after admission.\nPostmortem pathologic examination revealed that the overall architecture of the lung tissue remained intact. However, a prominent amount of fibromyxoid or fibroblastic bodies was present in the alveoli with surrounding histiocytes (Fig. 2A . The extent of involved lung tissue was estimated at around 25% (Table 2). No remnants of hyaline membranes or prominent alveolar fibrinous exudate were found. Microthrombi in small blood vessels of the alveolar septa were seen, as well as an organizing thrombus in a larger sized vessel (Fig. 2E). The histologic findings in this case point towards an epithelial, and vascular phenotype of a SARS-CoV2 infection. No fungi were present in de PAS-D stain. This histologic pattern is characteristic for an organizing pneumonia.\nFig. 2 Microscopic lung findings. A, case 1: intra-alveolar fibroblastic bodies, consistent with organizing pneumonia, (H\u0026E, 10×) B, case 2: loss of alveolar architecture with extensive fibrosis (H\u0026E; 10×) C, case 3: inflammatory infiltrate with neutrophils and lymphocytes, note the hyaline membranes (arrows), suggestive for diffuse alveolar damage. (H\u0026E, 20×) D, case 4: prominent fibrinous exudate in alveoli as seen in AFOP (H\u0026E; 10×) E: thrombus in larger vessel (H\u0026E, 5×) F: cytopathogenic changes in pneumocytes due to viral infection seen in all cases: hyperplasia, multinucleated giant cells (asterisks), intranuclear inclusion bodies (H\u0026E, 40×)."}

LitCovid-PMC-OGER-BB

PMC:7340597 / 12575-15049 JSONTXT

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PMC:7340597 / 12575-15049 JSON TXT