PMC:7340597 / 13626-15049 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T65","span":{"begin":80,"end":84},"obj":"Body_part"},{"id":"T66","span":{"begin":85,"end":91},"obj":"Body_part"},{"id":"T67","span":{"begin":155,"end":167},"obj":"Body_part"},{"id":"T68","span":{"begin":219,"end":230},"obj":"Body_part"},{"id":"T69","span":{"begin":265,"end":269},"obj":"Body_part"},{"id":"T70","span":{"begin":270,"end":276},"obj":"Body_part"},{"id":"T71","span":{"begin":362,"end":370},"obj":"Body_part"},{"id":"T72","span":{"begin":423,"end":436},"obj":"Body_part"},{"id":"T73","span":{"begin":423,"end":428},"obj":"Body_part"},{"id":"T74","span":{"begin":444,"end":452},"obj":"Body_part"},{"id":"T75","span":{"begin":786,"end":790},"obj":"Body_part"},{"id":"T76","span":{"begin":818,"end":826},"obj":"Body_part"},{"id":"T77","span":{"begin":827,"end":839},"obj":"Body_part"},{"id":"T78","span":{"begin":916,"end":924},"obj":"Body_part"},{"id":"T79","span":{"begin":1013,"end":1024},"obj":"Body_part"},{"id":"T80","span":{"begin":1029,"end":1040},"obj":"Body_part"},{"id":"T81","span":{"begin":1102,"end":1110},"obj":"Body_part"},{"id":"T82","span":{"begin":1275,"end":1286},"obj":"Body_part"},{"id":"T83","span":{"begin":1363,"end":1368},"obj":"Body_part"}],"attributes":[{"id":"A65","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A66","pred":"fma_id","subj":"T66","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A67","pred":"fma_id","subj":"T67","obj":"http://purl.org/sig/ont/fma/fma63877"},{"id":"A68","pred":"fma_id","subj":"T68","obj":"http://purl.org/sig/ont/fma/fma83585"},{"id":"A69","pred":"fma_id","subj":"T69","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A70","pred":"fma_id","subj":"T70","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A71","pred":"fma_id","subj":"T71","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A72","pred":"fma_id","subj":"T72","obj":"http://purl.org/sig/ont/fma/fma63183"},{"id":"A73","pred":"fma_id","subj":"T73","obj":"http://purl.org/sig/ont/fma/fma9670"},{"id":"A74","pred":"fma_id","subj":"T74","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A75","pred":"fma_id","subj":"T75","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A76","pred":"fma_id","subj":"T76","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A77","pred":"fma_id","subj":"T77","obj":"http://purl.org/sig/ont/fma/fma63877"},{"id":"A78","pred":"fma_id","subj":"T78","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A79","pred":"fma_id","subj":"T79","obj":"http://purl.org/sig/ont/fma/fma62860"},{"id":"A80","pred":"fma_id","subj":"T80","obj":"http://purl.org/sig/ont/fma/fma62863"},{"id":"A81","pred":"fma_id","subj":"T81","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A82","pred":"fma_id","subj":"T82","obj":"http://purl.org/sig/ont/fma/fma62499"},{"id":"A83","pred":"fma_id","subj":"T83","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Postmortem 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×)."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T33","span":{"begin":80,"end":84},"obj":"Body_part"},{"id":"T34","span":{"begin":85,"end":91},"obj":"Body_part"},{"id":"T35","span":{"begin":265,"end":269},"obj":"Body_part"},{"id":"T36","span":{"begin":270,"end":276},"obj":"Body_part"},{"id":"T37","span":{"begin":381,"end":388},"obj":"Body_part"},{"id":"T38","span":{"begin":423,"end":436},"obj":"Body_part"},{"id":"T39","span":{"begin":423,"end":428},"obj":"Body_part"},{"id":"T40","span":{"begin":429,"end":436},"obj":"Body_part"},{"id":"T41","span":{"begin":522,"end":528},"obj":"Body_part"},{"id":"T42","span":{"begin":786,"end":790},"obj":"Body_part"},{"id":"T43","span":{"begin":1161,"end":1168},"obj":"Body_part"},{"id":"T44","span":{"begin":1229,"end":1235},"obj":"Body_part"}],"attributes":[{"id":"A33","pred":"uberon_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A34","pred":"uberon_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A35","pred":"uberon_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A36","pred":"uberon_id","subj":"T36","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A37","pred":"uberon_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/UBERON_0007780"},{"id":"A38","pred":"uberon_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/UBERON_0001981"},{"id":"A39","pred":"uberon_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"A40","pred":"uberon_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/UBERON_0000055"},{"id":"A41","pred":"uberon_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/UBERON_0000055"},{"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_0007780"},{"id":"A44","pred":"uberon_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/UBERON_0000055"}],"text":"Postmortem 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×)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"369","span":{"begin":875,"end":884},"obj":"Disease"},{"id":"370","span":{"begin":953,"end":961},"obj":"Disease"},{"id":"371","span":{"begin":1102,"end":1117},"obj":"Disease"},{"id":"372","span":{"begin":1294,"end":1309},"obj":"Disease"},{"id":"373","span":{"begin":1329,"end":1340},"obj":"Disease"},{"id":"375","span":{"begin":634,"end":643},"obj":"Species"}],"attributes":[{"id":"A369","pred":"tao:has_database_id","subj":"369","obj":"MESH:D011014"},{"id":"A370","pred":"tao:has_database_id","subj":"370","obj":"MESH:D005355"},{"id":"A371","pred":"tao:has_database_id","subj":"371","obj":"MESH:D055370"},{"id":"A372","pred":"tao:has_database_id","subj":"372","obj":"MESH:D001102"},{"id":"A373","pred":"tao:has_database_id","subj":"373","obj":"MESH:D006965"},{"id":"A375","pred":"tao:has_database_id","subj":"375","obj":"Tax:2697049"}],"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":"Postmortem 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×)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T133","span":{"begin":495,"end":503},"obj":"Disease"},{"id":"T134","span":{"begin":634,"end":638},"obj":"Disease"},{"id":"T135","span":{"begin":644,"end":653},"obj":"Disease"},{"id":"T136","span":{"begin":683,"end":686},"obj":"Disease"},{"id":"T137","span":{"begin":745,"end":765},"obj":"Disease"},{"id":"T139","span":{"begin":756,"end":765},"obj":"Disease"},{"id":"T140","span":{"begin":864,"end":884},"obj":"Disease"},{"id":"T142","span":{"begin":875,"end":884},"obj":"Disease"},{"id":"T143","span":{"begin":1210,"end":1218},"obj":"Disease"},{"id":"T144","span":{"begin":1294,"end":1309},"obj":"Disease"},{"id":"T145","span":{"begin":1300,"end":1309},"obj":"Disease"},{"id":"T146","span":{"begin":1329,"end":1340},"obj":"Disease"}],"attributes":[{"id":"A133","pred":"mondo_id","subj":"T133","obj":"http://purl.obolibrary.org/obo/MONDO_0000831"},{"id":"A134","pred":"mondo_id","subj":"T134","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A135","pred":"mondo_id","subj":"T135","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A136","pred":"mondo_id","subj":"T136","obj":"http://purl.obolibrary.org/obo/MONDO_0004277"},{"id":"A137","pred":"mondo_id","subj":"T137","obj":"http://purl.obolibrary.org/obo/MONDO_0015265"},{"id":"A138","pred":"mondo_id","subj":"T137","obj":"http://purl.obolibrary.org/obo/MONDO_0056821"},{"id":"A139","pred":"mondo_id","subj":"T139","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A140","pred":"mondo_id","subj":"T140","obj":"http://purl.obolibrary.org/obo/MONDO_0015265"},{"id":"A141","pred":"mondo_id","subj":"T140","obj":"http://purl.obolibrary.org/obo/MONDO_0056821"},{"id":"A142","pred":"mondo_id","subj":"T142","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A143","pred":"mondo_id","subj":"T143","obj":"http://purl.obolibrary.org/obo/MONDO_0000831"},{"id":"A144","pred":"mondo_id","subj":"T144","obj":"http://purl.obolibrary.org/obo/MONDO_0005108"},{"id":"A145","pred":"mondo_id","subj":"T145","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A146","pred":"mondo_id","subj":"T146","obj":"http://purl.obolibrary.org/obo/MONDO_0005043"}],"text":"Postmortem 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×)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T106","span":{"begin":80,"end":84},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T107","span":{"begin":80,"end":84},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T108","span":{"begin":118,"end":119},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T109","span":{"begin":155,"end":167},"obj":"http://purl.obolibrary.org/obo/CL_0000057"},{"id":"T110","span":{"begin":219,"end":230},"obj":"http://purl.obolibrary.org/obo/CL_0000235"},{"id":"T111","span":{"begin":237,"end":239},"obj":"http://purl.obolibrary.org/obo/CLO_0001236"},{"id":"T112","span":{"begin":265,"end":269},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T113","span":{"begin":265,"end":269},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T114","span":{"begin":339,"end":348},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T115","span":{"begin":423,"end":436},"obj":"http://purl.obolibrary.org/obo/UBERON_0001981"},{"id":"T116","span":{"begin":423,"end":436},"obj":"http://www.ebi.ac.uk/efo/EFO_0000817"},{"id":"T117","span":{"begin":484,"end":494},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T118","span":{"begin":507,"end":508},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T119","span":{"begin":522,"end":528},"obj":"http://purl.obolibrary.org/obo/UBERON_0000055"},{"id":"T120","span":{"begin":594,"end":604},"obj":"http://purl.obolibrary.org/obo/CL_0000066"},{"id":"T121","span":{"begin":632,"end":633},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T122","span":{"begin":745,"end":755},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T123","span":{"begin":786,"end":790},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T124","span":{"begin":786,"end":790},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T125","span":{"begin":801,"end":802},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T126","span":{"begin":827,"end":839},"obj":"http://purl.obolibrary.org/obo/CL_0000057"},{"id":"T127","span":{"begin":864,"end":874},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T128","span":{"begin":897,"end":898},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T129","span":{"begin":1059,"end":1068},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T130","span":{"begin":1122,"end":1127},"obj":"http://purl.obolibrary.org/obo/CLO_0002850"},{"id":"T131","span":{"begin":1229,"end":1235},"obj":"http://purl.obolibrary.org/obo/UBERON_0000055"},{"id":"T132","span":{"begin":1363,"end":1368},"obj":"http://purl.obolibrary.org/obo/GO_0005623"}],"text":"Postmortem 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×)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T84","span":{"begin":683,"end":686},"obj":"Chemical"}],"attributes":[{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_27565"}],"text":"Postmortem 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×)."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T36","span":{"begin":756,"end":765},"obj":"Phenotype"},{"id":"T37","span":{"begin":875,"end":884},"obj":"Phenotype"},{"id":"T38","span":{"begin":1094,"end":1117},"obj":"Phenotype"}],"attributes":[{"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":"Postmortem 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×)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T3","span":{"begin":1294,"end":1309},"obj":"http://purl.obolibrary.org/obo/GO_0016032"}],"text":"Postmortem 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×)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T110","span":{"begin":0,"end":108},"obj":"Sentence"},{"id":"T111","span":{"begin":109,"end":241},"obj":"Sentence"},{"id":"T112","span":{"begin":242,"end":315},"obj":"Sentence"},{"id":"T113","span":{"begin":316,"end":400},"obj":"Sentence"},{"id":"T114","span":{"begin":401,"end":539},"obj":"Sentence"},{"id":"T115","span":{"begin":540,"end":654},"obj":"Sentence"},{"id":"T116","span":{"begin":655,"end":695},"obj":"Sentence"},{"id":"T117","span":{"begin":696,"end":766},"obj":"Sentence"},{"id":"T118","span":{"begin":767,"end":800},"obj":"Sentence"},{"id":"T119","span":{"begin":801,"end":1423},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Postmortem 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×)."}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T334","span":{"begin":260,"end":269},"obj":"UBERON:0002048"},{"id":"T335","span":{"begin":602,"end":618},"obj":"UBERON:0003215"},{"id":"T336","span":{"begin":658,"end":695},"obj":"CL:0000057"},{"id":"T337","span":{"begin":696,"end":711},"obj":"UBERON:0000479"},{"id":"T338","span":{"begin":1172,"end":1179},"obj":"UBERON:0003215"},{"id":"T231","span":{"begin":2,"end":7},"obj":"NCBITaxon:4751"},{"id":"T232","span":{"begin":129,"end":133},"obj":"UBERON:0002048"},{"id":"T233","span":{"begin":161,"end":169},"obj":"UBERON:0003215"},{"id":"T234","span":{"begin":170,"end":182},"obj":"CL:0000057"},{"id":"T235","span":{"begin":230,"end":231},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T236","span":{"begin":259,"end":267},"obj":"UBERON:0003215"},{"id":"T237","span":{"begin":304,"end":305},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T74625","span":{"begin":354,"end":363},"obj":"CL:0000775"},{"id":"T239","span":{"begin":368,"end":379},"obj":"CL:0000542"},{"id":"T79223","span":{"begin":441,"end":449},"obj":"UBERON:0003215"},{"id":"T241","span":{"begin":459,"end":460},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T242","span":{"begin":511,"end":518},"obj":"UBERON:0003215"},{"id":"T243","span":{"begin":536,"end":537},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T244","span":{"begin":549,"end":557},"obj":"UBERON:0010210"},{"id":"T245","span":{"begin":568,"end":574},"obj":"UBERON:0000055"},{"id":"T246","span":{"begin":576,"end":577},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T247","span":{"begin":615,"end":626},"obj":"CL:0000322"},{"id":"T55890","span":{"begin":634,"end":639},"obj":"NCBITaxon:10239"},{"id":"T46051","span":{"begin":682,"end":694},"obj":"GO:0005634;CL:0000647"},{"id":"T11789","span":{"begin":695,"end":706},"obj":"CL:0000647"},{"id":"T23332","span":{"begin":720,"end":731},"obj":"GO:0005634"},{"id":"T84342","span":{"begin":732,"end":748},"obj":"GO:0016234"},{"id":"T253","span":{"begin":750,"end":751},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T81672","span":{"begin":786,"end":790},"obj":"UBERON:0002048"},{"id":"T27688","span":{"begin":818,"end":826},"obj":"UBERON:0003215"},{"id":"T256","span":{"begin":827,"end":839},"obj":"CL:0000057"},{"id":"T1033","span":{"begin":887,"end":888},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T258","span":{"begin":916,"end":924},"obj":"UBERON:0003215"},{"id":"T259","span":{"begin":963,"end":964},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T42968","span":{"begin":1013,"end":1024},"obj":"CL:0000775"},{"id":"T261","span":{"begin":1029,"end":1040},"obj":"CL:0000542"},{"id":"T262","span":{"begin":1102,"end":1110},"obj":"UBERON:0003215"},{"id":"T263","span":{"begin":1120,"end":1121},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T70845","span":{"begin":1172,"end":1179},"obj":"UBERON:0003215"},{"id":"T265","span":{"begin":1197,"end":1198},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T266","span":{"begin":1210,"end":1218},"obj":"UBERON:0010210"},{"id":"T267","span":{"begin":1229,"end":1235},"obj":"UBERON:0000055"},{"id":"T268","span":{"begin":1237,"end":1238},"obj":"CHEBI:51686;CHEBI:51686"},{"id":"T269","span":{"begin":1275,"end":1286},"obj":"CL:0000322"},{"id":"T29843","span":{"begin":1294,"end":1299},"obj":"NCBITaxon:10239"},{"id":"T271","span":{"begin":1342,"end":1356},"obj":"GO:0005634;CL:0000647"},{"id":"T25696","span":{"begin":1357,"end":1368},"obj":"CL:0000647"},{"id":"T273","span":{"begin":1382,"end":1394},"obj":"GO:0005634"},{"id":"T99425","span":{"begin":1395,"end":1411},"obj":"GO:0016234"},{"id":"T275","span":{"begin":1413,"end":1414},"obj":"CHEBI:51686;CHEBI:51686"}],"text":"Postmortem 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×)."}