PMC:7340597 / 19065-21011 JSONTXT

Annnotations TAB JSON ListView MergeView

    LitCovid_Glycan-Motif-Structure

    {"project":"LitCovid_Glycan-Motif-Structure","denotations":[{"id":"T22","span":{"begin":393,"end":395},"obj":"https://glytoucan.org/Structures/Glycans/G93424OB"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-PD-FMA-UBERON

    {"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T113","span":{"begin":512,"end":517},"obj":"Body_part"},{"id":"T114","span":{"begin":872,"end":876},"obj":"Body_part"},{"id":"T115","span":{"begin":1178,"end":1182},"obj":"Body_part"},{"id":"T116","span":{"begin":1245,"end":1253},"obj":"Body_part"},{"id":"T117","span":{"begin":1269,"end":1281},"obj":"Body_part"},{"id":"T118","span":{"begin":1282,"end":1288},"obj":"Body_part"},{"id":"T119","span":{"begin":1626,"end":1634},"obj":"Body_part"},{"id":"T120","span":{"begin":1671,"end":1684},"obj":"Body_part"},{"id":"T121","span":{"begin":1671,"end":1676},"obj":"Body_part"},{"id":"T122","span":{"begin":1754,"end":1765},"obj":"Body_part"}],"attributes":[{"id":"A113","pred":"fma_id","subj":"T113","obj":"http://purl.org/sig/ont/fma/fma9576"},{"id":"A114","pred":"fma_id","subj":"T114","obj":"http://purl.org/sig/ont/fma/fma7154"},{"id":"A115","pred":"fma_id","subj":"T115","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A116","pred":"fma_id","subj":"T116","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A117","pred":"fma_id","subj":"T117","obj":"http://purl.org/sig/ont/fma/fma63877"},{"id":"A118","pred":"fma_id","subj":"T118","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A119","pred":"fma_id","subj":"T119","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A120","pred":"fma_id","subj":"T120","obj":"http://purl.org/sig/ont/fma/fma63183"},{"id":"A121","pred":"fma_id","subj":"T121","obj":"http://purl.org/sig/ont/fma/fma9670"},{"id":"A122","pred":"fma_id","subj":"T122","obj":"http://purl.org/sig/ont/fma/fma62861"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-PD-UBERON

    {"project":"LitCovid-PD-UBERON","denotations":[{"id":"T67","span":{"begin":512,"end":517},"obj":"Body_part"},{"id":"T68","span":{"begin":872,"end":876},"obj":"Body_part"},{"id":"T69","span":{"begin":1178,"end":1182},"obj":"Body_part"},{"id":"T70","span":{"begin":1282,"end":1288},"obj":"Body_part"},{"id":"T71","span":{"begin":1394,"end":1401},"obj":"Body_part"},{"id":"T72","span":{"begin":1671,"end":1684},"obj":"Body_part"},{"id":"T73","span":{"begin":1671,"end":1676},"obj":"Body_part"},{"id":"T74","span":{"begin":1677,"end":1684},"obj":"Body_part"}],"attributes":[{"id":"A67","pred":"uberon_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A68","pred":"uberon_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/UBERON_0000033"},{"id":"A69","pred":"uberon_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A70","pred":"uberon_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A71","pred":"uberon_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/UBERON_0007780"},{"id":"A72","pred":"uberon_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/UBERON_0001981"},{"id":"A73","pred":"uberon_id","subj":"T73","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"A74","pred":"uberon_id","subj":"T74","obj":"http://purl.obolibrary.org/obo/UBERON_0000055"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-PubTator

    {"project":"LitCovid-PubTator","denotations":[{"id":"437","span":{"begin":45,"end":54},"obj":"Disease"},{"id":"450","span":{"begin":199,"end":206},"obj":"Species"},{"id":"451","span":{"begin":409,"end":430},"obj":"Species"},{"id":"452","span":{"begin":799,"end":806},"obj":"Species"},{"id":"453","span":{"begin":1087,"end":1094},"obj":"Species"},{"id":"454","span":{"begin":435,"end":447},"obj":"Species"},{"id":"455","span":{"begin":393,"end":395},"obj":"Chemical"},{"id":"456","span":{"begin":101,"end":124},"obj":"Disease"},{"id":"457","span":{"begin":179,"end":184},"obj":"Disease"},{"id":"458","span":{"begin":189,"end":197},"obj":"Disease"},{"id":"459","span":{"begin":340,"end":349},"obj":"Disease"},{"id":"460","span":{"begin":550,"end":566},"obj":"Disease"},{"id":"461","span":{"begin":894,"end":923},"obj":"Disease"},{"id":"466","span":{"begin":1178,"end":1189},"obj":"Disease"},{"id":"467","span":{"begin":1328,"end":1337},"obj":"Disease"},{"id":"468","span":{"begin":1496,"end":1505},"obj":"Disease"},{"id":"469","span":{"begin":1920,"end":1929},"obj":"Disease"}],"attributes":[{"id":"A437","pred":"tao:has_database_id","subj":"437","obj":"MESH:D011014"},{"id":"A450","pred":"tao:has_database_id","subj":"450","obj":"Tax:9606"},{"id":"A451","pred":"tao:has_database_id","subj":"451","obj":"Tax:746128"},{"id":"A452","pred":"tao:has_database_id","subj":"452","obj":"Tax:9606"},{"id":"A453","pred":"tao:has_database_id","subj":"453","obj":"Tax:9606"},{"id":"A454","pred":"tao:has_database_id","subj":"454","obj":"Tax:1351"},{"id":"A455","pred":"tao:has_database_id","subj":"455","obj":"MESH:C012990"},{"id":"A456","pred":"tao:has_database_id","subj":"456","obj":"MESH:D006323"},{"id":"A457","pred":"tao:has_database_id","subj":"457","obj":"MESH:D005334"},{"id":"A458","pred":"tao:has_database_id","subj":"458","obj":"MESH:D004417"},{"id":"A459","pred":"tao:has_database_id","subj":"459","obj":"MESH:D007239"},{"id":"A460","pred":"tao:has_database_id","subj":"460","obj":"MESH:D011655"},{"id":"A461","pred":"tao:has_database_id","subj":"461","obj":"MESH:D007511"},{"id":"A466","pred":"tao:has_database_id","subj":"466","obj":"MESH:D055370"},{"id":"A467","pred":"tao:has_database_id","subj":"467","obj":"MESH:D011014"},{"id":"A468","pred":"tao:has_database_id","subj":"468","obj":"MESH:D011014"},{"id":"A469","pred":"tao:has_database_id","subj":"469","obj":"MESH:D011014"}],"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":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-PD-MONDO

    {"project":"LitCovid-PD-MONDO","denotations":[{"id":"T158","span":{"begin":34,"end":54},"obj":"Disease"},{"id":"T160","span":{"begin":45,"end":54},"obj":"Disease"},{"id":"T161","span":{"begin":101,"end":124},"obj":"Disease"},{"id":"T162","span":{"begin":340,"end":349},"obj":"Disease"},{"id":"T163","span":{"begin":767,"end":781},"obj":"Disease"},{"id":"T164","span":{"begin":915,"end":923},"obj":"Disease"},{"id":"T165","span":{"begin":1183,"end":1189},"obj":"Disease"},{"id":"T166","span":{"begin":1317,"end":1337},"obj":"Disease"},{"id":"T168","span":{"begin":1328,"end":1337},"obj":"Disease"},{"id":"T169","span":{"begin":1485,"end":1505},"obj":"Disease"},{"id":"T171","span":{"begin":1496,"end":1505},"obj":"Disease"},{"id":"T172","span":{"begin":1791,"end":1794},"obj":"Disease"},{"id":"T173","span":{"begin":1909,"end":1929},"obj":"Disease"},{"id":"T175","span":{"begin":1920,"end":1929},"obj":"Disease"}],"attributes":[{"id":"A158","pred":"mondo_id","subj":"T158","obj":"http://purl.obolibrary.org/obo/MONDO_0015265"},{"id":"A159","pred":"mondo_id","subj":"T158","obj":"http://purl.obolibrary.org/obo/MONDO_0056821"},{"id":"A160","pred":"mondo_id","subj":"T160","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A161","pred":"mondo_id","subj":"T161","obj":"http://purl.obolibrary.org/obo/MONDO_0004596"},{"id":"A162","pred":"mondo_id","subj":"T162","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A163","pred":"mondo_id","subj":"T163","obj":"http://purl.obolibrary.org/obo/MONDO_0004822"},{"id":"A164","pred":"mondo_id","subj":"T164","obj":"http://purl.obolibrary.org/obo/MONDO_0005053"},{"id":"A165","pred":"mondo_id","subj":"T165","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"},{"id":"A166","pred":"mondo_id","subj":"T166","obj":"http://purl.obolibrary.org/obo/MONDO_0015265"},{"id":"A167","pred":"mondo_id","subj":"T166","obj":"http://purl.obolibrary.org/obo/MONDO_0056821"},{"id":"A168","pred":"mondo_id","subj":"T168","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A169","pred":"mondo_id","subj":"T169","obj":"http://purl.obolibrary.org/obo/MONDO_0015265"},{"id":"A170","pred":"mondo_id","subj":"T169","obj":"http://purl.obolibrary.org/obo/MONDO_0056821"},{"id":"A171","pred":"mondo_id","subj":"T171","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"},{"id":"A172","pred":"mondo_id","subj":"T172","obj":"http://purl.obolibrary.org/obo/MONDO_0004277"},{"id":"A173","pred":"mondo_id","subj":"T173","obj":"http://purl.obolibrary.org/obo/MONDO_0015265"},{"id":"A174","pred":"mondo_id","subj":"T173","obj":"http://purl.obolibrary.org/obo/MONDO_0056821"},{"id":"A175","pred":"mondo_id","subj":"T175","obj":"http://purl.obolibrary.org/obo/MONDO_0005249"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-PD-CLO

    {"project":"LitCovid-PD-CLO","denotations":[{"id":"T168","span":{"begin":34,"end":44},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T169","span":{"begin":55,"end":56},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T170","span":{"begin":69,"end":73},"obj":"http://purl.obolibrary.org/obo/UBERON_0003101"},{"id":"T171","span":{"begin":69,"end":73},"obj":"http://www.ebi.ac.uk/efo/EFO_0000970"},{"id":"T172","span":{"begin":153,"end":154},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T173","span":{"begin":382,"end":383},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T174","span":{"begin":512,"end":517},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T175","span":{"begin":872,"end":876},"obj":"http://purl.obolibrary.org/obo/UBERON_0000033"},{"id":"T176","span":{"begin":872,"end":876},"obj":"http://www.ebi.ac.uk/efo/EFO_0000964"},{"id":"T177","span":{"begin":1165,"end":1166},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T178","span":{"begin":1178,"end":1182},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T179","span":{"begin":1178,"end":1182},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T180","span":{"begin":1269,"end":1281},"obj":"http://purl.obolibrary.org/obo/CL_0000057"},{"id":"T181","span":{"begin":1317,"end":1327},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T182","span":{"begin":1348,"end":1349},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T183","span":{"begin":1485,"end":1495},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"},{"id":"T184","span":{"begin":1538,"end":1539},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T185","span":{"begin":1671,"end":1684},"obj":"http://purl.obolibrary.org/obo/UBERON_0001981"},{"id":"T186","span":{"begin":1671,"end":1684},"obj":"http://www.ebi.ac.uk/efo/EFO_0000817"},{"id":"T187","span":{"begin":1730,"end":1739},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"},{"id":"T188","span":{"begin":1909,"end":1919},"obj":"http://purl.obolibrary.org/obo/OBI_0000245"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-PD-CHEBI

    {"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T103","span":{"begin":69,"end":73},"obj":"Chemical"},{"id":"T104","span":{"begin":147,"end":149},"obj":"Chemical"},{"id":"T105","span":{"begin":351,"end":354},"obj":"Chemical"},{"id":"T106","span":{"begin":393,"end":395},"obj":"Chemical"},{"id":"T108","span":{"begin":848,"end":856},"obj":"Chemical"},{"id":"T109","span":{"begin":1791,"end":1794},"obj":"Chemical"}],"attributes":[{"id":"A103","pred":"chebi_id","subj":"T103","obj":"http://purl.obolibrary.org/obo/CHEBI_30780"},{"id":"A104","pred":"chebi_id","subj":"T104","obj":"http://purl.obolibrary.org/obo/CHEBI_73503"},{"id":"A105","pred":"chebi_id","subj":"T105","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A106","pred":"chebi_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A107","pred":"chebi_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A108","pred":"chebi_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/CHEBI_35717"},{"id":"A109","pred":"chebi_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/CHEBI_27565"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-PD-HP

    {"project":"LitCovid-PD-HP","denotations":[{"id":"T48","span":{"begin":45,"end":54},"obj":"Phenotype"},{"id":"T49","span":{"begin":179,"end":184},"obj":"Phenotype"},{"id":"T50","span":{"begin":189,"end":197},"obj":"Phenotype"},{"id":"T51","span":{"begin":767,"end":781},"obj":"Phenotype"},{"id":"T52","span":{"begin":1328,"end":1337},"obj":"Phenotype"},{"id":"T53","span":{"begin":1496,"end":1505},"obj":"Phenotype"},{"id":"T54","span":{"begin":1920,"end":1929},"obj":"Phenotype"}],"attributes":[{"id":"A48","pred":"hp_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A49","pred":"hp_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/HP_0001945"},{"id":"A50","pred":"hp_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/HP_0002094"},{"id":"A51","pred":"hp_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/HP_0002110"},{"id":"A52","pred":"hp_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A53","pred":"hp_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A54","pred":"hp_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-PD-GlycoEpitope

    {"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T20","span":{"begin":393,"end":395},"obj":"GlycoEpitope"}],"attributes":[{"id":"A20","pred":"glyco_epitope_db_id","subj":"T20","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-sentences

    {"project":"LitCovid-sentences","denotations":[{"id":"T161","span":{"begin":0,"end":54},"obj":"Sentence"},{"id":"T162","span":{"begin":55,"end":198},"obj":"Sentence"},{"id":"T163","span":{"begin":199,"end":318},"obj":"Sentence"},{"id":"T164","span":{"begin":319,"end":456},"obj":"Sentence"},{"id":"T165","span":{"begin":457,"end":511},"obj":"Sentence"},{"id":"T166","span":{"begin":512,"end":706},"obj":"Sentence"},{"id":"T167","span":{"begin":707,"end":794},"obj":"Sentence"},{"id":"T168","span":{"begin":795,"end":868},"obj":"Sentence"},{"id":"T169","span":{"begin":869,"end":959},"obj":"Sentence"},{"id":"T170","span":{"begin":960,"end":1082},"obj":"Sentence"},{"id":"T171","span":{"begin":1083,"end":1140},"obj":"Sentence"},{"id":"T172","span":{"begin":1141,"end":1238},"obj":"Sentence"},{"id":"T173","span":{"begin":1239,"end":1338},"obj":"Sentence"},{"id":"T174","span":{"begin":1339,"end":1506},"obj":"Sentence"},{"id":"T175","span":{"begin":1507,"end":1641},"obj":"Sentence"},{"id":"T176","span":{"begin":1642,"end":1704},"obj":"Sentence"},{"id":"T177","span":{"begin":1705,"end":1779},"obj":"Sentence"},{"id":"T178","span":{"begin":1780,"end":1826},"obj":"Sentence"},{"id":"T179","span":{"begin":1827,"end":1946},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}

    LitCovid-PMC-OGER-BB

    {"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T31499","span":{"begin":222,"end":234},"obj":"UBERON:0001852"},{"id":"T16403","span":{"begin":306,"end":317},"obj":"GO:0015671"},{"id":"T14517","span":{"begin":409,"end":430},"obj":"NCBITaxon:746128"},{"id":"T4434","span":{"begin":435,"end":455},"obj":"NCBITaxon:1352"},{"id":"T32949","span":{"begin":550,"end":559},"obj":"UBERON:0002048"},{"id":"T23048","span":{"begin":872,"end":876},"obj":"UBERON:0000033"},{"id":"T39092","span":{"begin":904,"end":914},"obj":"UBERON:0002037"},{"id":"T74431","span":{"begin":1008,"end":1019},"obj":"UBERON:0001004"},{"id":"T28835","span":{"begin":1178,"end":1182},"obj":"UBERON:0002048"},{"id":"T46508","span":{"begin":1245,"end":1253},"obj":"UBERON:0003215"},{"id":"T32950","span":{"begin":1269,"end":1281},"obj":"CL:0000057"},{"id":"T85905","span":{"begin":1282,"end":1288},"obj":"UBERON:0000479"},{"id":"T72453","span":{"begin":1409,"end":1416},"obj":"UBERON:0003215"},{"id":"T83892","span":{"begin":1582,"end":1594},"obj":"UBERON:0005169"},{"id":"T50871","span":{"begin":1626,"end":1634},"obj":"UBERON:0003215"},{"id":"T65185","span":{"begin":1635,"end":1640},"obj":"UBERON:0003037"},{"id":"T3448","span":{"begin":1664,"end":1670},"obj":"UBERON:0003037"},{"id":"T58151","span":{"begin":1671,"end":1684},"obj":"UBERON:0001981"},{"id":"T66331","span":{"begin":1730,"end":1739},"obj":"GO:0016020"},{"id":"T96825","span":{"begin":1754,"end":1765},"obj":"CL:0000771"},{"id":"T62230","span":{"begin":1820,"end":1825},"obj":"NCBITaxon:4751"}],"text":"3.5 Case 4 – Acute fibrinous and organizing pneumonia\nA 68-year old male without medical history of cardiopulmonary disease, was presented at the ED in a critical condition with fever and dyspnoea. Patient was in need of endotracheal intubation and mechanical ventilation in prone position to improve his oxygenation. To exclude secondary infection, BAL was performed and revealed a positive GM and cultured Aspergillus fumigatus and Enterococcus faecium. Antifungal therapy was added to his treatment regimen. Chest CT-angiography showed segmental pulmonary emboli along with extensive bilateral areas of ground-glass opacity with reticulation and multiple patchy non-dependant peripheral consolidations. In contrast to normal areas, the abnormal areas showed mild bronchiectasis (Fig. 1-4A). The patient remained unresponsive after cessation of sedative medication. CT head showed extensive bilateral cerebellar ischemia with small haemorrhagic components. After three weeks of mechanical ventilation his respiratory status worsened and treatment was ended due to poor prognosis. The patient passed away 21 days after hospital admission.\nBiopsy specimens showed a pattern of lung injury, that was partially identical to that of case 1. Intra-alveolar depositions of fibroblastic tissue were found, consistent with organizing pneumonia. However, a predominant, diffuse component of fibrinous exudate in the alveoli was present, which was not the case in the aforementioned case with organizing pneumonia. Other histologic findings were a chronic inflammatory infiltrate, and mild interstitial changes, including widening of alveolar septa. Microthrombi in small septal blood vessels were also observed. Neither remnants hyaline membranes nor prominent eosinophils were present. Additional PAS-D stain did not show any fungi. The overall histologic pattern of this case was classified as acute fibrinous and organizing pneumonia (AFOP), Fig. 2D."}