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LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T49","span":{"begin":40,"end":44},"obj":"Body_part"},{"id":"T50","span":{"begin":554,"end":571},"obj":"Body_part"},{"id":"T51","span":{"begin":565,"end":571},"obj":"Body_part"},{"id":"T52","span":{"begin":595,"end":599},"obj":"Body_part"},{"id":"T53","span":{"begin":1048,"end":1057},"obj":"Body_part"},{"id":"T54","span":{"begin":1058,"end":1065},"obj":"Body_part"},{"id":"T55","span":{"begin":1532,"end":1536},"obj":"Body_part"},{"id":"T56","span":{"begin":2524,"end":2535},"obj":"Body_part"}],"attributes":[{"id":"A49","pred":"uberon_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A50","pred":"uberon_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/UBERON_0002384"},{"id":"A51","pred":"uberon_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A52","pred":"uberon_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/UBERON_0000058"},{"id":"A53","pred":"uberon_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/UBERON_0001982"},{"id":"A54","pred":"uberon_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/UBERON_0000055"},{"id":"A55","pred":"uberon_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A56","pred":"uberon_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/UBERON_0002371"}],"text":"Microscopic Findings.\nA range of common lung findings were seen on light microscopy. Parenchymal multifocal damage with intraalveolar exudative and proliferative inflammation (Figure 1A2), with fibrin, hyaline membranes (Figure 1A3) consistent with a diagnosis of diffuse alveolar damage (Table 3). Organizing pneumonia with fibrosis and type II pneumocyte hyperplasia, amphophilic cytoplasm, large nuclei, and prominent nucleoli, were indicative of cytopathic virus-induced changes (Figure 1A3 and 1A4). Fibroblastic foci consisting of loose organizing connective tissue reflective of alveolar duct fibrosis were seen (fibrotic phase) (Figure 1B1). Other findings included: pleural fibrosis (Figure 1B4), vascular injury with thrombi (Figure 1B2), and vasculitis (Figure 1B3). A main feature was the presence of numerous inflammatory cells consisting of granulocytes (CD15+) (Supplementary Figure 1A1 and 1A2), macrophages (CD68+) (Supplementary Figure 1A3 and 1A4), and T lymphocytes (CD3+) infiltrating into alveolar septa and clustering around capillary vessels (Supplementary 1B1). Immunohistochemistry showed the presence of both CD4+ and CD8+ T lymphocytes (Supplementary Figure 1B2 and 1B3). Of note, lymphocytes were CD20− indicating an absence of infiltrating B lymphocytes. Thrombi were present and immunohistochemistry showed the presence of platelet aggregates and megakaryocytes within thrombi (Supplementary Figure 1B4).\nTable 3. Histopathology Findings\nFindings Group 1, No. (%) (n = 18) Group 2, No. (%) (n = 4)\nLung\n Hyaline membranes 8 (44.4) 2 (50.0)\n Hyperplasia of type II pneumocyte 11 (61.2) 4 (100)\n Alveolar plug 8 (44.4) 4 (100)\n Alveolar fibrin deposit 9 (50.0) 3 (75.0)\n Hemorrhage 10 (55.6) 2 (50.0)\n Inflammatory cells 13 (72.3) 4 (100)\n Diffuse alveolar damage, fibrotic phase 12 (66.7) 1 (25.0)\n Microthrombi 14 (77.8) 2 (50.0)\n Vasculitis 8 (44.4) 4 (100)\n Multinucleated giant cells 4 (22.3) 2 (50.0)\nCardiac\n Myocarditis 9 (50.0) 3 (75.0)\n Vasculitis 5 (27.8) 3 (75.0)\n Inflammatory infiltrate 13 (72.3) 3 (75.0)\n Focal necrosis 6 (33.4) 2 (50.0)\n Pericarditis 9 (50.0) 4 (100)\n Vascular fibrosis 4 (22.3) 2 (50.0)\nHepatic\n Inflammatory infiltrate 8 (44.4) 3 (75.0)\n Congestion 8 (44.4) 2 (50.0)\n Steatosis 9 (50.0) 3 (75.0)\nRenal\n Inflammatory infiltrate 9 (50.0) 3 (75.0)\n Glomerulosclerosis 9 (50.0) 3 (75.0)\n Interstitial fibrosis 9 (50.0) 4 (100)\nSplenic\n Congested red pulp 15 (83.4) 4 (100)\n Lymphoid hypoplasia 11 (61.2) 4 (100)\nBone marrow\n Megakaryocytes hyperplasia 0 2 (50.0)\n Adipocytes 7 (38.9) 1 (25.0)"}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PubTator

LitCovid-PD-HP

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T5","span":{"begin":162,"end":174},"obj":"http://purl.obolibrary.org/obo/GO_0006954"},{"id":"T6","span":{"begin":1354,"end":1373},"obj":"http://purl.obolibrary.org/obo/GO_0070527"},{"id":"T7","span":{"begin":2085,"end":2093},"obj":"http://purl.obolibrary.org/obo/GO_0070265"},{"id":"T8","span":{"begin":2085,"end":2093},"obj":"http://purl.obolibrary.org/obo/GO_0019835"},{"id":"T9","span":{"begin":2085,"end":2093},"obj":"http://purl.obolibrary.org/obo/GO_0008219"},{"id":"T10","span":{"begin":2085,"end":2093},"obj":"http://purl.obolibrary.org/obo/GO_0001906"}],"text":"Microscopic Findings.\nA range of common lung findings were seen on light microscopy. Parenchymal multifocal damage with intraalveolar exudative and proliferative inflammation (Figure 1A2), with fibrin, hyaline membranes (Figure 1A3) consistent with a diagnosis of diffuse alveolar damage (Table 3). Organizing pneumonia with fibrosis and type II pneumocyte hyperplasia, amphophilic cytoplasm, large nuclei, and prominent nucleoli, were indicative of cytopathic virus-induced changes (Figure 1A3 and 1A4). Fibroblastic foci consisting of loose organizing connective tissue reflective of alveolar duct fibrosis were seen (fibrotic phase) (Figure 1B1). Other findings included: pleural fibrosis (Figure 1B4), vascular injury with thrombi (Figure 1B2), and vasculitis (Figure 1B3). A main feature was the presence of numerous inflammatory cells consisting of granulocytes (CD15+) (Supplementary Figure 1A1 and 1A2), macrophages (CD68+) (Supplementary Figure 1A3 and 1A4), and T lymphocytes (CD3+) infiltrating into alveolar septa and clustering around capillary vessels (Supplementary 1B1). Immunohistochemistry showed the presence of both CD4+ and CD8+ T lymphocytes (Supplementary Figure 1B2 and 1B3). Of note, lymphocytes were CD20− indicating an absence of infiltrating B lymphocytes. Thrombi were present and immunohistochemistry showed the presence of platelet aggregates and megakaryocytes within thrombi (Supplementary Figure 1B4).\nTable 3. Histopathology Findings\nFindings Group 1, No. (%) (n = 18) Group 2, No. (%) (n = 4)\nLung\n Hyaline membranes 8 (44.4) 2 (50.0)\n Hyperplasia of type II pneumocyte 11 (61.2) 4 (100)\n Alveolar plug 8 (44.4) 4 (100)\n Alveolar fibrin deposit 9 (50.0) 3 (75.0)\n Hemorrhage 10 (55.6) 2 (50.0)\n Inflammatory cells 13 (72.3) 4 (100)\n Diffuse alveolar damage, fibrotic phase 12 (66.7) 1 (25.0)\n Microthrombi 14 (77.8) 2 (50.0)\n Vasculitis 8 (44.4) 4 (100)\n Multinucleated giant cells 4 (22.3) 2 (50.0)\nCardiac\n Myocarditis 9 (50.0) 3 (75.0)\n Vasculitis 5 (27.8) 3 (75.0)\n Inflammatory infiltrate 13 (72.3) 3 (75.0)\n Focal necrosis 6 (33.4) 2 (50.0)\n Pericarditis 9 (50.0) 4 (100)\n Vascular fibrosis 4 (22.3) 2 (50.0)\nHepatic\n Inflammatory infiltrate 8 (44.4) 3 (75.0)\n Congestion 8 (44.4) 2 (50.0)\n Steatosis 9 (50.0) 3 (75.0)\nRenal\n Inflammatory infiltrate 9 (50.0) 3 (75.0)\n Glomerulosclerosis 9 (50.0) 3 (75.0)\n Interstitial fibrosis 9 (50.0) 4 (100)\nSplenic\n Congested red pulp 15 (83.4) 4 (100)\n Lymphoid hypoplasia 11 (61.2) 4 (100)\nBone marrow\n Megakaryocytes hyperplasia 0 2 (50.0)\n Adipocytes 7 (38.9) 1 (25.0)"}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":644,"end":647},"obj":"GlycoEpitope"},{"id":"T2","span":{"begin":743,"end":746},"obj":"GlycoEpitope"},{"id":"T3","span":{"begin":1081,"end":1084},"obj":"GlycoEpitope"},{"id":"T4","span":{"begin":1186,"end":1189},"obj":"GlycoEpitope"}],"attributes":[{"id":"A1","pred":"glyco_epitope_db_id","subj":"T1","obj":"http://www.glycoepitope.jp/epitopes/AN0633"},{"id":"A2","pred":"glyco_epitope_db_id","subj":"T2","obj":"http://www.glycoepitope.jp/epitopes/AN0389"},{"id":"A3","pred":"glyco_epitope_db_id","subj":"T3","obj":"http://www.glycoepitope.jp/epitopes/AN0633"},{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/AN0389"}],"text":"Microscopic Findings.\nA range of common lung findings were seen on light microscopy. Parenchymal multifocal damage with intraalveolar exudative and proliferative inflammation (Figure 1A2), with fibrin, hyaline membranes (Figure 1A3) consistent with a diagnosis of diffuse alveolar damage (Table 3). Organizing pneumonia with fibrosis and type II pneumocyte hyperplasia, amphophilic cytoplasm, large nuclei, and prominent nucleoli, were indicative of cytopathic virus-induced changes (Figure 1A3 and 1A4). Fibroblastic foci consisting of loose organizing connective tissue reflective of alveolar duct fibrosis were seen (fibrotic phase) (Figure 1B1). Other findings included: pleural fibrosis (Figure 1B4), vascular injury with thrombi (Figure 1B2), and vasculitis (Figure 1B3). A main feature was the presence of numerous inflammatory cells consisting of granulocytes (CD15+) (Supplementary Figure 1A1 and 1A2), macrophages (CD68+) (Supplementary Figure 1A3 and 1A4), and T lymphocytes (CD3+) infiltrating into alveolar septa and clustering around capillary vessels (Supplementary 1B1). Immunohistochemistry showed the presence of both CD4+ and CD8+ T lymphocytes (Supplementary Figure 1B2 and 1B3). Of note, lymphocytes were CD20− indicating an absence of infiltrating B lymphocytes. Thrombi were present and immunohistochemistry showed the presence of platelet aggregates and megakaryocytes within thrombi (Supplementary Figure 1B4).\nTable 3. Histopathology Findings\nFindings Group 1, No. (%) (n = 18) Group 2, No. (%) (n = 4)\nLung\n Hyaline membranes 8 (44.4) 2 (50.0)\n Hyperplasia of type II pneumocyte 11 (61.2) 4 (100)\n Alveolar plug 8 (44.4) 4 (100)\n Alveolar fibrin deposit 9 (50.0) 3 (75.0)\n Hemorrhage 10 (55.6) 2 (50.0)\n Inflammatory cells 13 (72.3) 4 (100)\n Diffuse alveolar damage, fibrotic phase 12 (66.7) 1 (25.0)\n Microthrombi 14 (77.8) 2 (50.0)\n Vasculitis 8 (44.4) 4 (100)\n Multinucleated giant cells 4 (22.3) 2 (50.0)\nCardiac\n Myocarditis 9 (50.0) 3 (75.0)\n Vasculitis 5 (27.8) 3 (75.0)\n Inflammatory infiltrate 13 (72.3) 3 (75.0)\n Focal necrosis 6 (33.4) 2 (50.0)\n Pericarditis 9 (50.0) 4 (100)\n Vascular fibrosis 4 (22.3) 2 (50.0)\nHepatic\n Inflammatory infiltrate 8 (44.4) 3 (75.0)\n Congestion 8 (44.4) 2 (50.0)\n Steatosis 9 (50.0) 3 (75.0)\nRenal\n Inflammatory infiltrate 9 (50.0) 3 (75.0)\n Glomerulosclerosis 9 (50.0) 3 (75.0)\n Interstitial fibrosis 9 (50.0) 4 (100)\nSplenic\n Congested red pulp 15 (83.4) 4 (100)\n Lymphoid hypoplasia 11 (61.2) 4 (100)\nBone marrow\n Megakaryocytes hyperplasia 0 2 (50.0)\n Adipocytes 7 (38.9) 1 (25.0)"}

LitCovid-sentences

PMC:7543426 / 11080-13688 JSONTXT

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PMC:7543426 / 11080-13688 JSON TXT