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LitCovid_Glycan-Motif-Structure

{"project":"LitCovid_Glycan-Motif-Structure","denotations":[{"id":"T21","span":{"begin":997,"end":999},"obj":"https://glytoucan.org/Structures/Glycans/G93424OB"}],"text":"3.4 Case 3 – Diffuse alveolar damage\nA 58-year old female was admitted to the ICU and needed mechanical ventilation due to severe hypoxemia. Chest CT-angiography showed dubious unilateral sub-segmental pulmonary emboli and diffuse bilateral ground-glass opacities with anteroposterior gradient along with large dependant consolidations (Fig. 1-3A). On the 8th day of mechanical ventilation, BAL was performed and CT-scan was repeated because of deteriorating pulmonary condition with increasing inflammatory parameters. Chest CT-angiography showed bilateral sub-segmental pulmonary emboli, persistent ground-glass opacities and consolidation. Newly formed coarse cyst-like lesions in the middle and ventral regions (non-dependant regions) were noted, probably due to ventilator induced lung injury (Fig. 1-3B). Considering lack of respiratory improvement and progression of fibrosis on radiological imaging prednisolone was started. After five days prednisolone was stopped because of a positive GM index of 3.4 from repeated BAL fluid. Fungal culture remained negative though. Her respiratory status stabilised but remained critical. After pausing the sedation, the patient remained unresponsive and CT head showed ischemia with small areas of haemorrhage. In light of her pour neurologic and respiratory prognosis, treatment was ended and patient expired after 26 days on ventilator support.\nIn the core needle biopsy specimens the lung tissue largely preserved its preexisting architecture. Histologic findings included an inflammatory infiltrate consisting of neutrophils and lymphocytes, and only a sporadic intra-alveolar fibroblastic plug. The striking, distinctive feature of this case was the presence of thin, delicate hyaline membranes along the alveolar wall (Fig. 2C). Again, micro thrombi were observed in this case. No fungi could be demonstrated in the PAS-D stain. Together with the clinical characteristics, these histologic findings were suggestive of diffuse alveolar damage."}

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T60","span":{"begin":142,"end":147},"obj":"Body_part"},{"id":"T61","span":{"begin":521,"end":526},"obj":"Body_part"},{"id":"T62","span":{"begin":787,"end":791},"obj":"Body_part"},{"id":"T63","span":{"begin":1205,"end":1209},"obj":"Body_part"},{"id":"T64","span":{"begin":1435,"end":1439},"obj":"Body_part"},{"id":"T65","span":{"begin":1440,"end":1446},"obj":"Body_part"},{"id":"T66","span":{"begin":1758,"end":1771},"obj":"Body_part"}],"attributes":[{"id":"A60","pred":"uberon_id","subj":"T60","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A61","pred":"uberon_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A62","pred":"uberon_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A63","pred":"uberon_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/UBERON_0000033"},{"id":"A64","pred":"uberon_id","subj":"T64","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A65","pred":"uberon_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A66","pred":"uberon_id","subj":"T66","obj":"http://purl.obolibrary.org/obo/UBERON_0004894"}],"text":"3.4 Case 3 – Diffuse alveolar damage\nA 58-year old female was admitted to the ICU and needed mechanical ventilation due to severe hypoxemia. Chest CT-angiography showed dubious unilateral sub-segmental pulmonary emboli and diffuse bilateral ground-glass opacities with anteroposterior gradient along with large dependant consolidations (Fig. 1-3A). On the 8th day of mechanical ventilation, BAL was performed and CT-scan was repeated because of deteriorating pulmonary condition with increasing inflammatory parameters. Chest CT-angiography showed bilateral sub-segmental pulmonary emboli, persistent ground-glass opacities and consolidation. Newly formed coarse cyst-like lesions in the middle and ventral regions (non-dependant regions) were noted, probably due to ventilator induced lung injury (Fig. 1-3B). Considering lack of respiratory improvement and progression of fibrosis on radiological imaging prednisolone was started. After five days prednisolone was stopped because of a positive GM index of 3.4 from repeated BAL fluid. Fungal culture remained negative though. Her respiratory status stabilised but remained critical. After pausing the sedation, the patient remained unresponsive and CT head showed ischemia with small areas of haemorrhage. In light of her pour neurologic and respiratory prognosis, treatment was ended and patient expired after 26 days on ventilator support.\nIn the core needle biopsy specimens the lung tissue largely preserved its preexisting architecture. Histologic findings included an inflammatory infiltrate consisting of neutrophils and lymphocytes, and only a sporadic intra-alveolar fibroblastic plug. The striking, distinctive feature of this case was the presence of thin, delicate hyaline membranes along the alveolar wall (Fig. 2C). Again, micro thrombi were observed in this case. No fungi could be demonstrated in the PAS-D stain. Together with the clinical characteristics, these histologic findings were suggestive of diffuse alveolar damage."}

LitCovid-PubTator

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T155","span":{"begin":792,"end":798},"obj":"Disease"},{"id":"T156","span":{"begin":1217,"end":1225},"obj":"Disease"},{"id":"T157","span":{"begin":1870,"end":1873},"obj":"Disease"}],"attributes":[{"id":"A155","pred":"mondo_id","subj":"T155","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"},{"id":"A156","pred":"mondo_id","subj":"T156","obj":"http://purl.obolibrary.org/obo/MONDO_0005053"},{"id":"A157","pred":"mondo_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/MONDO_0004277"}],"text":"3.4 Case 3 – Diffuse alveolar damage\nA 58-year old female was admitted to the ICU and needed mechanical ventilation due to severe hypoxemia. Chest CT-angiography showed dubious unilateral sub-segmental pulmonary emboli and diffuse bilateral ground-glass opacities with anteroposterior gradient along with large dependant consolidations (Fig. 1-3A). On the 8th day of mechanical ventilation, BAL was performed and CT-scan was repeated because of deteriorating pulmonary condition with increasing inflammatory parameters. Chest CT-angiography showed bilateral sub-segmental pulmonary emboli, persistent ground-glass opacities and consolidation. Newly formed coarse cyst-like lesions in the middle and ventral regions (non-dependant regions) were noted, probably due to ventilator induced lung injury (Fig. 1-3B). Considering lack of respiratory improvement and progression of fibrosis on radiological imaging prednisolone was started. After five days prednisolone was stopped because of a positive GM index of 3.4 from repeated BAL fluid. Fungal culture remained negative though. Her respiratory status stabilised but remained critical. After pausing the sedation, the patient remained unresponsive and CT head showed ischemia with small areas of haemorrhage. In light of her pour neurologic and respiratory prognosis, treatment was ended and patient expired after 26 days on ventilator support.\nIn the core needle biopsy specimens the lung tissue largely preserved its preexisting architecture. Histologic findings included an inflammatory infiltrate consisting of neutrophils and lymphocytes, and only a sporadic intra-alveolar fibroblastic plug. The striking, distinctive feature of this case was the presence of thin, delicate hyaline membranes along the alveolar wall (Fig. 2C). Again, micro thrombi were observed in this case. No fungi could be demonstrated in the PAS-D stain. Together with the clinical characteristics, these histologic findings were suggestive of diffuse alveolar damage."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T154","span":{"begin":38,"end":39},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T155","span":{"begin":52,"end":58},"obj":"http://purl.obolibrary.org/obo/UBERON_0003100"},{"id":"T156","span":{"begin":142,"end":147},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T157","span":{"begin":521,"end":526},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T158","span":{"begin":787,"end":791},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T159","span":{"begin":787,"end":791},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T160","span":{"begin":986,"end":987},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T161","span":{"begin":1205,"end":1209},"obj":"http://purl.obolibrary.org/obo/UBERON_0000033"},{"id":"T162","span":{"begin":1205,"end":1209},"obj":"http://www.ebi.ac.uk/efo/EFO_0000964"},{"id":"T163","span":{"begin":1435,"end":1439},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T164","span":{"begin":1435,"end":1439},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T165","span":{"begin":1603,"end":1604},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T166","span":{"begin":1629,"end":1641},"obj":"http://purl.obolibrary.org/obo/CL_0000057"},{"id":"T167","span":{"begin":1738,"end":1747},"obj":"http://purl.obolibrary.org/obo/UBERON_0000158"}],"text":"3.4 Case 3 – Diffuse alveolar damage\nA 58-year old female was admitted to the ICU and needed mechanical ventilation due to severe hypoxemia. Chest CT-angiography showed dubious unilateral sub-segmental pulmonary emboli and diffuse bilateral ground-glass opacities with anteroposterior gradient along with large dependant consolidations (Fig. 1-3A). On the 8th day of mechanical ventilation, BAL was performed and CT-scan was repeated because of deteriorating pulmonary condition with increasing inflammatory parameters. Chest CT-angiography showed bilateral sub-segmental pulmonary emboli, persistent ground-glass opacities and consolidation. Newly formed coarse cyst-like lesions in the middle and ventral regions (non-dependant regions) were noted, probably due to ventilator induced lung injury (Fig. 1-3B). Considering lack of respiratory improvement and progression of fibrosis on radiological imaging prednisolone was started. After five days prednisolone was stopped because of a positive GM index of 3.4 from repeated BAL fluid. Fungal culture remained negative though. Her respiratory status stabilised but remained critical. After pausing the sedation, the patient remained unresponsive and CT head showed ischemia with small areas of haemorrhage. In light of her pour neurologic and respiratory prognosis, treatment was ended and patient expired after 26 days on ventilator support.\nIn the core needle biopsy specimens the lung tissue largely preserved its preexisting architecture. Histologic findings included an inflammatory infiltrate consisting of neutrophils and lymphocytes, and only a sporadic intra-alveolar fibroblastic plug. The striking, distinctive feature of this case was the presence of thin, delicate hyaline membranes along the alveolar wall (Fig. 2C). Again, micro thrombi were observed in this case. No fungi could be demonstrated in the PAS-D stain. Together with the clinical characteristics, these histologic findings were suggestive of diffuse alveolar damage."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T96","span":{"begin":392,"end":395},"obj":"Chemical"},{"id":"T97","span":{"begin":908,"end":920},"obj":"Chemical"},{"id":"T98","span":{"begin":950,"end":962},"obj":"Chemical"},{"id":"T99","span":{"begin":997,"end":999},"obj":"Chemical"},{"id":"T101","span":{"begin":1027,"end":1030},"obj":"Chemical"},{"id":"T102","span":{"begin":1870,"end":1873},"obj":"Chemical"}],"attributes":[{"id":"A96","pred":"chebi_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A97","pred":"chebi_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/CHEBI_8378"},{"id":"A98","pred":"chebi_id","subj":"T98","obj":"http://purl.obolibrary.org/obo/CHEBI_8378"},{"id":"A99","pred":"chebi_id","subj":"T99","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A100","pred":"chebi_id","subj":"T99","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A101","pred":"chebi_id","subj":"T101","obj":"http://purl.obolibrary.org/obo/CHEBI_64198"},{"id":"A102","pred":"chebi_id","subj":"T102","obj":"http://purl.obolibrary.org/obo/CHEBI_27565"}],"text":"3.4 Case 3 – Diffuse alveolar damage\nA 58-year old female was admitted to the ICU and needed mechanical ventilation due to severe hypoxemia. Chest CT-angiography showed dubious unilateral sub-segmental pulmonary emboli and diffuse bilateral ground-glass opacities with anteroposterior gradient along with large dependant consolidations (Fig. 1-3A). On the 8th day of mechanical ventilation, BAL was performed and CT-scan was repeated because of deteriorating pulmonary condition with increasing inflammatory parameters. Chest CT-angiography showed bilateral sub-segmental pulmonary emboli, persistent ground-glass opacities and consolidation. Newly formed coarse cyst-like lesions in the middle and ventral regions (non-dependant regions) were noted, probably due to ventilator induced lung injury (Fig. 1-3B). Considering lack of respiratory improvement and progression of fibrosis on radiological imaging prednisolone was started. After five days prednisolone was stopped because of a positive GM index of 3.4 from repeated BAL fluid. Fungal culture remained negative though. Her respiratory status stabilised but remained critical. After pausing the sedation, the patient remained unresponsive and CT head showed ischemia with small areas of haemorrhage. In light of her pour neurologic and respiratory prognosis, treatment was ended and patient expired after 26 days on ventilator support.\nIn the core needle biopsy specimens the lung tissue largely preserved its preexisting architecture. Histologic findings included an inflammatory infiltrate consisting of neutrophils and lymphocytes, and only a sporadic intra-alveolar fibroblastic plug. The striking, distinctive feature of this case was the presence of thin, delicate hyaline membranes along the alveolar wall (Fig. 2C). Again, micro thrombi were observed in this case. No fungi could be demonstrated in the PAS-D stain. Together with the clinical characteristics, these histologic findings were suggestive of diffuse alveolar damage."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T45","span":{"begin":14,"end":37},"obj":"Phenotype"},{"id":"T46","span":{"begin":131,"end":140},"obj":"Phenotype"},{"id":"T47","span":{"begin":1972,"end":1995},"obj":"Phenotype"}],"attributes":[{"id":"A45","pred":"hp_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/HP_0033006"},{"id":"A46","pred":"hp_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/HP_0012418"},{"id":"A47","pred":"hp_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/HP_0033006"}],"text":"3.4 Case 3 – Diffuse alveolar damage\nA 58-year old female was admitted to the ICU and needed mechanical ventilation due to severe hypoxemia. Chest CT-angiography showed dubious unilateral sub-segmental pulmonary emboli and diffuse bilateral ground-glass opacities with anteroposterior gradient along with large dependant consolidations (Fig. 1-3A). On the 8th day of mechanical ventilation, BAL was performed and CT-scan was repeated because of deteriorating pulmonary condition with increasing inflammatory parameters. Chest CT-angiography showed bilateral sub-segmental pulmonary emboli, persistent ground-glass opacities and consolidation. Newly formed coarse cyst-like lesions in the middle and ventral regions (non-dependant regions) were noted, probably due to ventilator induced lung injury (Fig. 1-3B). Considering lack of respiratory improvement and progression of fibrosis on radiological imaging prednisolone was started. After five days prednisolone was stopped because of a positive GM index of 3.4 from repeated BAL fluid. Fungal culture remained negative though. Her respiratory status stabilised but remained critical. After pausing the sedation, the patient remained unresponsive and CT head showed ischemia with small areas of haemorrhage. In light of her pour neurologic and respiratory prognosis, treatment was ended and patient expired after 26 days on ventilator support.\nIn the core needle biopsy specimens the lung tissue largely preserved its preexisting architecture. Histologic findings included an inflammatory infiltrate consisting of neutrophils and lymphocytes, and only a sporadic intra-alveolar fibroblastic plug. The striking, distinctive feature of this case was the presence of thin, delicate hyaline membranes along the alveolar wall (Fig. 2C). Again, micro thrombi were observed in this case. No fungi could be demonstrated in the PAS-D stain. Together with the clinical characteristics, these histologic findings were suggestive of diffuse alveolar damage."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T19","span":{"begin":997,"end":999},"obj":"GlycoEpitope"}],"attributes":[{"id":"A19","pred":"glyco_epitope_db_id","subj":"T19","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"3.4 Case 3 – Diffuse alveolar damage\nA 58-year old female was admitted to the ICU and needed mechanical ventilation due to severe hypoxemia. Chest CT-angiography showed dubious unilateral sub-segmental pulmonary emboli and diffuse bilateral ground-glass opacities with anteroposterior gradient along with large dependant consolidations (Fig. 1-3A). On the 8th day of mechanical ventilation, BAL was performed and CT-scan was repeated because of deteriorating pulmonary condition with increasing inflammatory parameters. Chest CT-angiography showed bilateral sub-segmental pulmonary emboli, persistent ground-glass opacities and consolidation. Newly formed coarse cyst-like lesions in the middle and ventral regions (non-dependant regions) were noted, probably due to ventilator induced lung injury (Fig. 1-3B). Considering lack of respiratory improvement and progression of fibrosis on radiological imaging prednisolone was started. After five days prednisolone was stopped because of a positive GM index of 3.4 from repeated BAL fluid. Fungal culture remained negative though. Her respiratory status stabilised but remained critical. After pausing the sedation, the patient remained unresponsive and CT head showed ischemia with small areas of haemorrhage. In light of her pour neurologic and respiratory prognosis, treatment was ended and patient expired after 26 days on ventilator support.\nIn the core needle biopsy specimens the lung tissue largely preserved its preexisting architecture. Histologic findings included an inflammatory infiltrate consisting of neutrophils and lymphocytes, and only a sporadic intra-alveolar fibroblastic plug. The striking, distinctive feature of this case was the presence of thin, delicate hyaline membranes along the alveolar wall (Fig. 2C). Again, micro thrombi were observed in this case. No fungi could be demonstrated in the PAS-D stain. Together with the clinical characteristics, these histologic findings were suggestive of diffuse alveolar damage."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T143","span":{"begin":0,"end":37},"obj":"Sentence"},{"id":"T144","span":{"begin":38,"end":141},"obj":"Sentence"},{"id":"T145","span":{"begin":142,"end":349},"obj":"Sentence"},{"id":"T146","span":{"begin":350,"end":520},"obj":"Sentence"},{"id":"T147","span":{"begin":521,"end":643},"obj":"Sentence"},{"id":"T148","span":{"begin":644,"end":811},"obj":"Sentence"},{"id":"T149","span":{"begin":812,"end":933},"obj":"Sentence"},{"id":"T150","span":{"begin":934,"end":1037},"obj":"Sentence"},{"id":"T151","span":{"begin":1038,"end":1078},"obj":"Sentence"},{"id":"T152","span":{"begin":1079,"end":1135},"obj":"Sentence"},{"id":"T153","span":{"begin":1136,"end":1258},"obj":"Sentence"},{"id":"T154","span":{"begin":1259,"end":1394},"obj":"Sentence"},{"id":"T155","span":{"begin":1395,"end":1494},"obj":"Sentence"},{"id":"T156","span":{"begin":1495,"end":1647},"obj":"Sentence"},{"id":"T157","span":{"begin":1648,"end":1782},"obj":"Sentence"},{"id":"T158","span":{"begin":1783,"end":1831},"obj":"Sentence"},{"id":"T159","span":{"begin":1832,"end":1882},"obj":"Sentence"},{"id":"T160","span":{"begin":1883,"end":1996},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.4 Case 3 – Diffuse alveolar damage\nA 58-year old female was admitted to the ICU and needed mechanical ventilation due to severe hypoxemia. Chest CT-angiography showed dubious unilateral sub-segmental pulmonary emboli and diffuse bilateral ground-glass opacities with anteroposterior gradient along with large dependant consolidations (Fig. 1-3A). On the 8th day of mechanical ventilation, BAL was performed and CT-scan was repeated because of deteriorating pulmonary condition with increasing inflammatory parameters. Chest CT-angiography showed bilateral sub-segmental pulmonary emboli, persistent ground-glass opacities and consolidation. Newly formed coarse cyst-like lesions in the middle and ventral regions (non-dependant regions) were noted, probably due to ventilator induced lung injury (Fig. 1-3B). Considering lack of respiratory improvement and progression of fibrosis on radiological imaging prednisolone was started. After five days prednisolone was stopped because of a positive GM index of 3.4 from repeated BAL fluid. Fungal culture remained negative though. Her respiratory status stabilised but remained critical. After pausing the sedation, the patient remained unresponsive and CT head showed ischemia with small areas of haemorrhage. In light of her pour neurologic and respiratory prognosis, treatment was ended and patient expired after 26 days on ventilator support.\nIn the core needle biopsy specimens the lung tissue largely preserved its preexisting architecture. Histologic findings included an inflammatory infiltrate consisting of neutrophils and lymphocytes, and only a sporadic intra-alveolar fibroblastic plug. The striking, distinctive feature of this case was the presence of thin, delicate hyaline membranes along the alveolar wall (Fig. 2C). Again, micro thrombi were observed in this case. No fungi could be demonstrated in the PAS-D stain. Together with the clinical characteristics, these histologic findings were suggestive of diffuse alveolar damage."}

LitCovid-PMC-OGER-BB

PMC:7340597 / 17067-19063 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7340597 / 17067-19063 JSON TXT