PMC:7388103 / 2632-4583 JSONTXT

{"project":"LitCovid_Glycan-Motif-Structure","denotations":[{"id":"T15","span":{"begin":687,"end":694},"obj":"https://glytoucan.org/Structures/Glycans/G00021MO"},{"id":"T16","span":{"begin":687,"end":694},"obj":"https://glytoucan.org/Structures/Glycans/G54161DR"},{"id":"T17","span":{"begin":1129,"end":1136},"obj":"https://glytoucan.org/Structures/Glycans/G00021MO"},{"id":"T18","span":{"begin":1129,"end":1136},"obj":"https://glytoucan.org/Structures/Glycans/G54161DR"},{"id":"T19","span":{"begin":1478,"end":1485},"obj":"https://glytoucan.org/Structures/Glycans/G00021MO"},{"id":"T20","span":{"begin":1478,"end":1485},"obj":"https://glytoucan.org/Structures/Glycans/G54161DR"},{"id":"T21","span":{"begin":1613,"end":1620},"obj":"https://glytoucan.org/Structures/Glycans/G00021MO"},{"id":"T22","span":{"begin":1613,"end":1620},"obj":"https://glytoucan.org/Structures/Glycans/G54161DR"}],"text":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T15","span":{"begin":213,"end":218},"obj":"Body_part"},{"id":"T16","span":{"begin":323,"end":330},"obj":"Body_part"},{"id":"T17","span":{"begin":357,"end":370},"obj":"Body_part"},{"id":"T18","span":{"begin":501,"end":509},"obj":"Body_part"},{"id":"T19","span":{"begin":520,"end":525},"obj":"Body_part"},{"id":"T20","span":{"begin":687,"end":694},"obj":"Body_part"},{"id":"T21","span":{"begin":868,"end":889},"obj":"Body_part"},{"id":"T22","span":{"begin":983,"end":1002},"obj":"Body_part"},{"id":"T23","span":{"begin":1059,"end":1063},"obj":"Body_part"},{"id":"T24","span":{"begin":1129,"end":1136},"obj":"Body_part"},{"id":"T25","span":{"begin":1327,"end":1335},"obj":"Body_part"},{"id":"T26","span":{"begin":1373,"end":1378},"obj":"Body_part"},{"id":"T27","span":{"begin":1451,"end":1459},"obj":"Body_part"},{"id":"T28","span":{"begin":1478,"end":1485},"obj":"Body_part"},{"id":"T29","span":{"begin":1486,"end":1494},"obj":"Body_part"},{"id":"T30","span":{"begin":1613,"end":1620},"obj":"Body_part"},{"id":"T31","span":{"begin":1739,"end":1748},"obj":"Body_part"},{"id":"T32","span":{"begin":1808,"end":1817},"obj":"Body_part"}],"attributes":[{"id":"A15","pred":"fma_id","subj":"T15","obj":"http://purl.org/sig/ont/fma/fma9576"},{"id":"A16","pred":"fma_id","subj":"T16","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma264829"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma62851"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma7197"},{"id":"A20","pred":"fma_id","subj":"T20","obj":"http://purl.org/sig/ont/fma/fma82839"},{"id":"A21","pred":"fma_id","subj":"T21","obj":"http://purl.org/sig/ont/fma/fma7187"},{"id":"A22","pred":"fma_id","subj":"T22","obj":"http://purl.org/sig/ont/fma/fma0323829"},{"id":"A23","pred":"fma_id","subj":"T23","obj":"http://purl.org/sig/ont/fma/fma50723"},{"id":"A24","pred":"fma_id","subj":"T24","obj":"http://purl.org/sig/ont/fma/fma82839"},{"id":"A25","pred":"fma_id","subj":"T25","obj":"http://purl.org/sig/ont/fma/fma62851"},{"id":"A26","pred":"fma_id","subj":"T26","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A27","pred":"fma_id","subj":"T27","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A28","pred":"fma_id","subj":"T28","obj":"http://purl.org/sig/ont/fma/fma82839"},{"id":"A29","pred":"fma_id","subj":"T29","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A30","pred":"fma_id","subj":"T30","obj":"http://purl.org/sig/ont/fma/fma82839"},{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma67245"},{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma67245"}],"text":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T2","span":{"begin":213,"end":218},"obj":"Body_part"},{"id":"T3","span":{"begin":520,"end":525},"obj":"Body_part"},{"id":"T4","span":{"begin":990,"end":1002},"obj":"Body_part"},{"id":"T5","span":{"begin":998,"end":1002},"obj":"Body_part"},{"id":"T6","span":{"begin":1054,"end":1063},"obj":"Body_part"},{"id":"T7","span":{"begin":1059,"end":1063},"obj":"Body_part"}],"attributes":[{"id":"A2","pred":"uberon_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A3","pred":"uberon_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/UBERON_0002107"},{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0001361"},{"id":"A5","pred":"uberon_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/UBERON_0001638"},{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_0035552"},{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0001638"}],"text":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T40","span":{"begin":108,"end":116},"obj":"Disease"},{"id":"T41","span":{"begin":134,"end":136},"obj":"Disease"},{"id":"T42","span":{"begin":590,"end":598},"obj":"Disease"},{"id":"T43","span":{"begin":754,"end":756},"obj":"Disease"},{"id":"T44","span":{"begin":957,"end":965},"obj":"Disease"},{"id":"T45","span":{"begin":1064,"end":1074},"obj":"Disease"},{"id":"T46","span":{"begin":1217,"end":1236},"obj":"Disease"},{"id":"T47","span":{"begin":1238,"end":1240},"obj":"Disease"},{"id":"T48","span":{"begin":1421,"end":1424},"obj":"Disease"},{"id":"T49","span":{"begin":1447,"end":1450},"obj":"Disease"},{"id":"T50","span":{"begin":1593,"end":1595},"obj":"Disease"},{"id":"T51","span":{"begin":1690,"end":1692},"obj":"Disease"},{"id":"T52","span":{"begin":1723,"end":1737},"obj":"Disease"},{"id":"T53","span":{"begin":1947,"end":1950},"obj":"Disease"}],"attributes":[{"id":"A40","pred":"mondo_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/MONDO_0001673"},{"id":"A41","pred":"mondo_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/MONDO_0017319"},{"id":"A42","pred":"mondo_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0017319"},{"id":"A44","pred":"mondo_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/MONDO_0000831"},{"id":"A45","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0000831"},{"id":"A46","pred":"mondo_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/MONDO_0021113"},{"id":"A47","pred":"mondo_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/MONDO_0017319"},{"id":"A48","pred":"mondo_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/MONDO_0018048"},{"id":"A49","pred":"mondo_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/MONDO_0018048"},{"id":"A50","pred":"mondo_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/MONDO_0017178"},{"id":"A51","pred":"mondo_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/MONDO_0017319"},{"id":"A52","pred":"mondo_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/MONDO_0000745"},{"id":"A53","pred":"mondo_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/MONDO_0018048"}],"text":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T29","span":{"begin":17,"end":18},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T30","span":{"begin":31,"end":35},"obj":"http://purl.obolibrary.org/obo/UBERON_0003101"},{"id":"T31","span":{"begin":31,"end":35},"obj":"http://www.ebi.ac.uk/efo/EFO_0000970"},{"id":"T32","span":{"begin":213,"end":218},"obj":"http://www.ebi.ac.uk/efo/EFO_0000965"},{"id":"T33","span":{"begin":285,"end":290},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T34","span":{"begin":350,"end":351},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T35","span":{"begin":357,"end":370},"obj":"http://purl.obolibrary.org/obo/PR_000001393"},{"id":"T36","span":{"begin":383,"end":385},"obj":"http://purl.obolibrary.org/obo/CLO_0008426"},{"id":"T37","span":{"begin":520,"end":525},"obj":"http://purl.obolibrary.org/obo/UBERON_0002107"},{"id":"T38","span":{"begin":520,"end":525},"obj":"http://www.ebi.ac.uk/efo/EFO_0000887"},{"id":"T39","span":{"begin":535,"end":540},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T40","span":{"begin":880,"end":889},"obj":"http://www.ebi.ac.uk/efo/EFO_0000876"},{"id":"T41","span":{"begin":942,"end":943},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T42","span":{"begin":998,"end":1002},"obj":"http://purl.obolibrary.org/obo/UBERON_0001638"},{"id":"T43","span":{"begin":998,"end":1002},"obj":"http://www.ebi.ac.uk/efo/EFO_0000816"},{"id":"T44","span":{"begin":1059,"end":1063},"obj":"http://purl.obolibrary.org/obo/UBERON_0001638"},{"id":"T45","span":{"begin":1059,"end":1063},"obj":"http://www.ebi.ac.uk/efo/EFO_0000816"},{"id":"T46","span":{"begin":1297,"end":1299},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T47","span":{"begin":1373,"end":1378},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T48","span":{"begin":1390,"end":1391},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T49","span":{"begin":1430,"end":1431},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T50","span":{"begin":1460,"end":1467},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T51","span":{"begin":1698,"end":1699},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T52","span":{"begin":1721,"end":1722},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T53","span":{"begin":1739,"end":1748},"obj":"http://purl.obolibrary.org/obo/CHEBI_28790"},{"id":"T54","span":{"begin":1808,"end":1817},"obj":"http://purl.obolibrary.org/obo/CHEBI_28790"},{"id":"T55","span":{"begin":1859,"end":1860},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T12","span":{"begin":31,"end":35},"obj":"Chemical"},{"id":"T13","span":{"begin":323,"end":330},"obj":"Chemical"},{"id":"T14","span":{"begin":687,"end":694},"obj":"Chemical"},{"id":"T15","span":{"begin":1129,"end":1136},"obj":"Chemical"},{"id":"T16","span":{"begin":1478,"end":1485},"obj":"Chemical"},{"id":"T17","span":{"begin":1613,"end":1620},"obj":"Chemical"},{"id":"T18","span":{"begin":1663,"end":1673},"obj":"Chemical"},{"id":"T19","span":{"begin":1739,"end":1748},"obj":"Chemical"},{"id":"T20","span":{"begin":1808,"end":1817},"obj":"Chemical"}],"attributes":[{"id":"A12","pred":"chebi_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/CHEBI_30780"},{"id":"A13","pred":"chebi_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A14","pred":"chebi_id","subj":"T14","obj":"http://purl.obolibrary.org/obo/CHEBI_28304"},{"id":"A15","pred":"chebi_id","subj":"T15","obj":"http://purl.obolibrary.org/obo/CHEBI_28304"},{"id":"A16","pred":"chebi_id","subj":"T16","obj":"http://purl.obolibrary.org/obo/CHEBI_28304"},{"id":"A17","pred":"chebi_id","subj":"T17","obj":"http://purl.obolibrary.org/obo/CHEBI_28304"},{"id":"A18","pred":"chebi_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/CHEBI_48720"},{"id":"A19","pred":"chebi_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/CHEBI_28790"},{"id":"A20","pred":"chebi_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/CHEBI_28790"},{"id":"A21","pred":"chebi_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/CHEBI_350546"}],"text":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T5","span":{"begin":625,"end":638},"obj":"http://purl.obolibrary.org/obo/GO_0003968"},{"id":"T6","span":{"begin":625,"end":638},"obj":"http://purl.obolibrary.org/obo/GO_0003899"},{"id":"T7","span":{"begin":1739,"end":1756},"obj":"http://purl.obolibrary.org/obo/GO_0001820"},{"id":"T8","span":{"begin":1808,"end":1825},"obj":"http://purl.obolibrary.org/obo/GO_0001820"}],"text":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}

{"project":"LitCovid-sentences","denotations":[{"id":"T23","span":{"begin":0,"end":16},"obj":"Sentence"},{"id":"T24","span":{"begin":17,"end":117},"obj":"Sentence"},{"id":"T25","span":{"begin":118,"end":212},"obj":"Sentence"},{"id":"T26","span":{"begin":213,"end":265},"obj":"Sentence"},{"id":"T27","span":{"begin":266,"end":389},"obj":"Sentence"},{"id":"T28","span":{"begin":390,"end":496},"obj":"Sentence"},{"id":"T29","span":{"begin":497,"end":567},"obj":"Sentence"},{"id":"T30","span":{"begin":568,"end":665},"obj":"Sentence"},{"id":"T31","span":{"begin":666,"end":730},"obj":"Sentence"},{"id":"T32","span":{"begin":731,"end":853},"obj":"Sentence"},{"id":"T33","span":{"begin":854,"end":914},"obj":"Sentence"},{"id":"T34","span":{"begin":915,"end":1003},"obj":"Sentence"},{"id":"T35","span":{"begin":1004,"end":1182},"obj":"Sentence"},{"id":"T36","span":{"begin":1183,"end":1283},"obj":"Sentence"},{"id":"T37","span":{"begin":1284,"end":1382},"obj":"Sentence"},{"id":"T38","span":{"begin":1383,"end":1446},"obj":"Sentence"},{"id":"T39","span":{"begin":1447,"end":1612},"obj":"Sentence"},{"id":"T40","span":{"begin":1613,"end":1674},"obj":"Sentence"},{"id":"T41","span":{"begin":1675,"end":1738},"obj":"Sentence"},{"id":"T42","span":{"begin":1739,"end":1914},"obj":"Sentence"},{"id":"T43","span":{"begin":1915,"end":1951},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T23","span":{"begin":83,"end":92},"obj":"Phenotype"},{"id":"T24","span":{"begin":94,"end":102},"obj":"Phenotype"},{"id":"T25","span":{"begin":108,"end":116},"obj":"Phenotype"},{"id":"T26","span":{"begin":792,"end":799},"obj":"Phenotype"},{"id":"T27","span":{"begin":1054,"end":1074},"obj":"Phenotype"},{"id":"T28","span":{"begin":1217,"end":1236},"obj":"Phenotype"},{"id":"T29","span":{"begin":1421,"end":1424},"obj":"Phenotype"},{"id":"T30","span":{"begin":1447,"end":1450},"obj":"Phenotype"},{"id":"T31","span":{"begin":1723,"end":1737},"obj":"Phenotype"},{"id":"T32","span":{"begin":1947,"end":1950},"obj":"Phenotype"}],"attributes":[{"id":"A23","pred":"hp_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/HP_0031246"},{"id":"A24","pred":"hp_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/HP_0003326"},{"id":"A25","pred":"hp_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/HP_0002014"},{"id":"A26","pred":"hp_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/HP_0002094"},{"id":"A27","pred":"hp_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/HP_0002625"},{"id":"A28","pred":"hp_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/HP_0002878"},{"id":"A29","pred":"hp_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/HP_0011874"},{"id":"A30","pred":"hp_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/HP_0011874"},{"id":"A31","pred":"hp_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/HP_0001695"},{"id":"A32","pred":"hp_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/HP_0011874"}],"text":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}

{"project":"LitCovid-PubTator","denotations":[{"id":"118","span":{"begin":312,"end":330},"obj":"Gene"},{"id":"119","span":{"begin":357,"end":370},"obj":"Gene"},{"id":"120","span":{"begin":390,"end":400},"obj":"Gene"},{"id":"121","span":{"begin":454,"end":464},"obj":"Gene"},{"id":"122","span":{"begin":687,"end":694},"obj":"Chemical"},{"id":"123","span":{"begin":83,"end":92},"obj":"Disease"},{"id":"124","span":{"begin":94,"end":102},"obj":"Disease"},{"id":"125","span":{"begin":108,"end":116},"obj":"Disease"},{"id":"126","span":{"begin":590,"end":598},"obj":"Disease"},{"id":"127","span":{"begin":792,"end":799},"obj":"Disease"},{"id":"134","span":{"begin":1080,"end":1090},"obj":"Chemical"},{"id":"135","span":{"begin":1129,"end":1136},"obj":"Chemical"},{"id":"136","span":{"begin":1138,"end":1141},"obj":"Chemical"},{"id":"137","span":{"begin":944,"end":965},"obj":"Disease"},{"id":"138","span":{"begin":1054,"end":1074},"obj":"Disease"},{"id":"139","span":{"begin":1217,"end":1236},"obj":"Disease"},{"id":"152","span":{"begin":1474,"end":1477},"obj":"Gene"},{"id":"153","span":{"begin":1478,"end":1485},"obj":"Chemical"},{"id":"154","span":{"begin":1613,"end":1620},"obj":"Chemical"},{"id":"155","span":{"begin":1663,"end":1673},"obj":"Chemical"},{"id":"156","span":{"begin":1739,"end":1748},"obj":"Chemical"},{"id":"157","span":{"begin":1808,"end":1817},"obj":"Chemical"},{"id":"158","span":{"begin":1833,"end":1836},"obj":"Chemical"},{"id":"159","span":{"begin":1893,"end":1896},"obj":"Chemical"},{"id":"160","span":{"begin":1421,"end":1424},"obj":"Disease"},{"id":"161","span":{"begin":1447,"end":1450},"obj":"Disease"},{"id":"162","span":{"begin":1723,"end":1737},"obj":"Disease"},{"id":"163","span":{"begin":1947,"end":1950},"obj":"Disease"}],"attributes":[{"id":"A118","pred":"tao:has_database_id","subj":"118","obj":"Gene:1401"},{"id":"A119","pred":"tao:has_database_id","subj":"119","obj":"Gene:3569"},{"id":"A120","pred":"tao:has_database_id","subj":"120","obj":"Gene:2244"},{"id":"A121","pred":"tao:has_database_id","subj":"121","obj":"Gene:2244"},{"id":"A122","pred":"tao:has_database_id","subj":"122","obj":"MESH:D006493"},{"id":"A123","pred":"tao:has_database_id","subj":"123","obj":"MESH:D003371"},{"id":"A124","pred":"tao:has_database_id","subj":"124","obj":"MESH:D063806"},{"id":"A125","pred":"tao:has_database_id","subj":"125","obj":"MESH:D003967"},{"id":"A126","pred":"tao:has_database_id","subj":"126","obj":"MESH:C000657245"},{"id":"A127","pred":"tao:has_database_id","subj":"127","obj":"MESH:D004417"},{"id":"A134","pred":"tao:has_database_id","subj":"134","obj":"MESH:D017984"},{"id":"A135","pred":"tao:has_database_id","subj":"135","obj":"MESH:D006493"},{"id":"A136","pred":"tao:has_database_id","subj":"136","obj":"MESH:D006493"},{"id":"A137","pred":"tao:has_database_id","subj":"137","obj":"MESH:D013927"},{"id":"A138","pred":"tao:has_database_id","subj":"138","obj":"MESH:D020246"},{"id":"A139","pred":"tao:has_database_id","subj":"139","obj":"MESH:D012131"},{"id":"A152","pred":"tao:has_database_id","subj":"152","obj":"Gene:5196"},{"id":"A153","pred":"tao:has_database_id","subj":"153","obj":"MESH:D006493"},{"id":"A154","pred":"tao:has_database_id","subj":"154","obj":"MESH:D006493"},{"id":"A155","pred":"tao:has_database_id","subj":"155","obj":"MESH:C031942"},{"id":"A156","pred":"tao:has_database_id","subj":"156","obj":"MESH:D012701"},{"id":"A157","pred":"tao:has_database_id","subj":"157","obj":"MESH:D012701"},{"id":"A158","pred":"tao:has_database_id","subj":"158","obj":"MESH:D006493"},{"id":"A159","pred":"tao:has_database_id","subj":"159","obj":"MESH:D006493"},{"id":"A160","pred":"tao:has_database_id","subj":"160","obj":"MESH:D013921"},{"id":"A161","pred":"tao:has_database_id","subj":"161","obj":"MESH:D013921"},{"id":"A162","pred":"tao:has_database_id","subj":"162","obj":"MESH:D006323"},{"id":"A163","pred":"tao:has_database_id","subj":"163","obj":"MESH:D013921"}],"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":"Case Description\nA 63-year-old male without comorbidities presented with 1 week of dry cough, myalgias, and diarrhea. On examination, he was afebrile but appeared to be in distress, saturating at 89% on room air. Chest X-ray showed bilateral interstitial opacities. Initial laboratory tests revealed an elevated C-reactive protein of 24.49 mg/dL and a high interleukin-6 level of 58 pg/mL. Fibrinogen and D-dimer were also elevated to 708 mg/dL and 1.44 fibrinogen equivalent units, respectively. The platelet count and liver function tests were within normal limits. He was diagnosed with COVID-19 by nasopharyngeal reverse-transcriptase–polymerase chain reaction. Low-molecular-weight heparin was started for thromboprophylaxis. On day 2 of admission, he developed progressive worsening of dyspnea and was transferred to the intensive care unit (ICU).\nOn day 7, his right lower extremity was noted to be swollen. Ultrasound duplex revealed a nonocclusive thrombus within the right common femoral vein. He was started on therapeutic anticoagulation for deep vein thrombosis with enoxaparin, which was switched to unfractionated heparin (UFH) later, due to worsening renal function. On the same day, due to worsening respiratory failure, he was intubated and mechanically ventilated.\nBetween days 11 and 12 of hospitalization, platelet count dropped from 304 000 to 96 000 cells/µL. He had a high pretest probability for HIT with a 4T score of 6. HIT antibody testing (anti-PF4/heparin antibody, by enzyme-linked immunosorbent assay) was sent, which returned positive with an optical density (OD) of 1.243 units. Heparin drip was discontinued and was switched to argatroban. Unfortunately, he died a day later, following a cardiac arrest. Serotonin release assay (SRA) eventually returned positive, with 49% serotonin release at low UFH dose (0.1 IU/mL) with a reduction to 0% release at high UFH dose (100 IU/mL). This confirmed the diagnosis of HIT."}