PMC:7344504 / 6417-7555 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T17","span":{"begin":349,"end":354},"obj":"Body_part"},{"id":"T18","span":{"begin":433,"end":438},"obj":"Body_part"}],"attributes":[{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma63083"}],"text":"Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission. Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was \u003e3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made. Serum galactomannan remained negative (\u003c0.5) in three subsequent samples. Voriconazole i.v. 6 mg/kg q12h was started in addition to caspofungin i.v. 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative. MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin \u003c0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L. Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin. During SDD, bacterial cultures remained negative throughout her stay in the ICU."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T12","span":{"begin":349,"end":354},"obj":"Body_part"},{"id":"T13","span":{"begin":433,"end":438},"obj":"Body_part"}],"attributes":[{"id":"A12","pred":"uberon_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"}],"text":"Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission. Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was \u003e3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made. Serum galactomannan remained negative (\u003c0.5) in three subsequent samples. Voriconazole i.v. 6 mg/kg q12h was started in addition to caspofungin i.v. 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative. MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin \u003c0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L. Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin. During SDD, bacterial cultures remained negative throughout her stay in the ICU."}

{"project":"LitCovid-PubTator","denotations":[{"id":"179","span":{"begin":0,"end":21},"obj":"Species"},{"id":"180","span":{"begin":778,"end":790},"obj":"Species"},{"id":"181","span":{"begin":148,"end":159},"obj":"Species"},{"id":"182","span":{"begin":264,"end":274},"obj":"Chemical"},{"id":"183","span":{"begin":439,"end":452},"obj":"Chemical"},{"id":"184","span":{"begin":507,"end":519},"obj":"Chemical"},{"id":"185","span":{"begin":565,"end":576},"obj":"Chemical"},{"id":"186","span":{"begin":675,"end":680},"obj":"Chemical"},{"id":"187","span":{"begin":816,"end":830},"obj":"Chemical"},{"id":"188","span":{"begin":841,"end":851},"obj":"Chemical"},{"id":"189","span":{"begin":856,"end":869},"obj":"Chemical"},{"id":"190","span":{"begin":883,"end":895},"obj":"Chemical"},{"id":"191","span":{"begin":904,"end":916},"obj":"Chemical"},{"id":"192","span":{"begin":932,"end":944},"obj":"Chemical"},{"id":"193","span":{"begin":957,"end":969},"obj":"Chemical"},{"id":"194","span":{"begin":1045,"end":1056},"obj":"Chemical"},{"id":"195","span":{"begin":112,"end":137},"obj":"Disease"}],"attributes":[{"id":"A179","pred":"tao:has_database_id","subj":"179","obj":"Tax:746128"},{"id":"A180","pred":"tao:has_database_id","subj":"180","obj":"Tax:746128"},{"id":"A181","pred":"tao:has_database_id","subj":"181","obj":"Tax:746128"},{"id":"A183","pred":"tao:has_database_id","subj":"183","obj":"MESH:C012990"},{"id":"A184","pred":"tao:has_database_id","subj":"184","obj":"MESH:D065819"},{"id":"A185","pred":"tao:has_database_id","subj":"185","obj":"MESH:D000077336"},{"id":"A186","pred":"tao:has_database_id","subj":"186","obj":"MESH:D001393"},{"id":"A187","pred":"tao:has_database_id","subj":"187","obj":"MESH:D000666"},{"id":"A188","pred":"tao:has_database_id","subj":"188","obj":"MESH:D000077551"},{"id":"A189","pred":"tao:has_database_id","subj":"189","obj":"MESH:D000077612"},{"id":"A190","pred":"tao:has_database_id","subj":"190","obj":"MESH:D017964"},{"id":"A191","pred":"tao:has_database_id","subj":"191","obj":"MESH:D065819"},{"id":"A192","pred":"tao:has_database_id","subj":"192","obj":"MESH:C101425"},{"id":"A193","pred":"tao:has_database_id","subj":"193","obj":"MESH:D065819"},{"id":"A194","pred":"tao:has_database_id","subj":"194","obj":"MESH:D000077336"},{"id":"A195","pred":"tao:has_database_id","subj":"195","obj":"MESH:D001228"}],"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":"Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission. Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was \u003e3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made. Serum galactomannan remained negative (\u003c0.5) in three subsequent samples. Voriconazole i.v. 6 mg/kg q12h was started in addition to caspofungin i.v. 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative. MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin \u003c0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L. Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin. During SDD, bacterial cultures remained negative throughout her stay in the ICU."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T33","span":{"begin":418,"end":422},"obj":"Disease"},{"id":"T34","span":{"begin":627,"end":629},"obj":"Disease"}],"attributes":[{"id":"A33","pred":"mondo_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/MONDO_0007163"},{"id":"A34","pred":"mondo_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/MONDO_0005316"}],"text":"Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission. Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was \u003e3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made. Serum galactomannan remained negative (\u003c0.5) in three subsequent samples. Voriconazole i.v. 6 mg/kg q12h was started in addition to caspofungin i.v. 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative. MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin \u003c0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L. Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin. During SDD, bacterial cultures remained negative throughout her stay in the ICU."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T44","span":{"begin":240,"end":241},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T45","span":{"begin":359,"end":363},"obj":"http://purl.obolibrary.org/obo/CLO_0053133"},{"id":"T46","span":{"begin":364,"end":366},"obj":"http://purl.obolibrary.org/obo/CLO_0008426"},{"id":"T47","span":{"begin":394,"end":395},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T48","span":{"begin":778,"end":779},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T49","span":{"begin":829,"end":830},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"}],"text":"Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission. Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was \u003e3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made. Serum galactomannan remained negative (\u003c0.5) in three subsequent samples. Voriconazole i.v. 6 mg/kg q12h was started in addition to caspofungin i.v. 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative. MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin \u003c0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L. Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin. During SDD, bacterial cultures remained negative throughout her stay in the ICU."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T42","span":{"begin":124,"end":137},"obj":"Chemical"},{"id":"T43","span":{"begin":177,"end":179},"obj":"Chemical"},{"id":"T44","span":{"begin":268,"end":274},"obj":"Chemical"},{"id":"T45","span":{"begin":337,"end":339},"obj":"Chemical"},{"id":"T48","span":{"begin":439,"end":452},"obj":"Chemical"},{"id":"T49","span":{"begin":565,"end":576},"obj":"Chemical"},{"id":"T50","span":{"begin":675,"end":680},"obj":"Chemical"},{"id":"T51","span":{"begin":816,"end":830},"obj":"Chemical"},{"id":"T52","span":{"begin":841,"end":851},"obj":"Chemical"},{"id":"T53","span":{"begin":856,"end":869},"obj":"Chemical"},{"id":"T54","span":{"begin":883,"end":895},"obj":"Chemical"},{"id":"T55","span":{"begin":904,"end":916},"obj":"Chemical"},{"id":"T56","span":{"begin":932,"end":944},"obj":"Chemical"},{"id":"T57","span":{"begin":1045,"end":1056},"obj":"Chemical"}],"attributes":[{"id":"A42","pred":"chebi_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A43","pred":"chebi_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/CHEBI_33336"},{"id":"A44","pred":"chebi_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/CHEBI_37163"},{"id":"A45","pred":"chebi_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/CHEBI_474859"},{"id":"A46","pred":"chebi_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/CHEBI_73610"},{"id":"A47","pred":"chebi_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/CHEBI_90325"},{"id":"A48","pred":"chebi_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"},{"id":"A49","pred":"chebi_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/CHEBI_474180"},{"id":"A50","pred":"chebi_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/CHEBI_68452"},{"id":"A51","pred":"chebi_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/CHEBI_2682"},{"id":"A52","pred":"chebi_id","subj":"T52","obj":"http://purl.obolibrary.org/obo/CHEBI_600520"},{"id":"A53","pred":"chebi_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/CHEBI_55346"},{"id":"A54","pred":"chebi_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/CHEBI_6076"},{"id":"A55","pred":"chebi_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/CHEBI_10023"},{"id":"A56","pred":"chebi_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/CHEBI_64355"},{"id":"A57","pred":"chebi_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/CHEBI_474180"}],"text":"Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission. Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was \u003e3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made. Serum galactomannan remained negative (\u003c0.5) in three subsequent samples. Voriconazole i.v. 6 mg/kg q12h was started in addition to caspofungin i.v. 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative. MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin \u003c0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L. Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin. During SDD, bacterial cultures remained negative throughout her stay in the ICU."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T1","span":{"begin":124,"end":137},"obj":"GlycoEpitope"},{"id":"T2","span":{"begin":439,"end":452},"obj":"GlycoEpitope"}],"attributes":[{"id":"A1","pred":"glyco_epitope_db_id","subj":"T1","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A2","pred":"glyco_epitope_db_id","subj":"T2","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission. Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was \u003e3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made. Serum galactomannan remained negative (\u003c0.5) in three subsequent samples. Voriconazole i.v. 6 mg/kg q12h was started in addition to caspofungin i.v. 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative. MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin \u003c0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L. Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin. During SDD, bacterial cultures remained negative throughout her stay in the ICU."}

{"project":"LitCovid-sentences","denotations":[{"id":"T58","span":{"begin":0,"end":111},"obj":"Sentence"},{"id":"T59","span":{"begin":112,"end":432},"obj":"Sentence"},{"id":"T60","span":{"begin":433,"end":506},"obj":"Sentence"},{"id":"T61","span":{"begin":507,"end":524},"obj":"Sentence"},{"id":"T62","span":{"begin":525,"end":581},"obj":"Sentence"},{"id":"T63","span":{"begin":582,"end":706},"obj":"Sentence"},{"id":"T64","span":{"begin":707,"end":956},"obj":"Sentence"},{"id":"T65","span":{"begin":957,"end":1057},"obj":"Sentence"},{"id":"T66","span":{"begin":1058,"end":1138},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission. Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was \u003e3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made. Serum galactomannan remained negative (\u003c0.5) in three subsequent samples. Voriconazole i.v. 6 mg/kg q12h was started in addition to caspofungin i.v. 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative. MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin \u003c0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L. Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin. During SDD, bacterial cultures remained negative throughout her stay in the ICU."}

{"project":"2_test","denotations":[{"id":"32517166-31811917-60114385","span":{"begin":81,"end":83},"obj":"31811917"}],"text":"Aspergillus fumigatus was recovered from high-volume tracheal aspirate cultures [14] obtained at ICU admission. Aspergillus galactomannan (Platelia Aspergillus; Bio-Rad, Marnes-La-Coquette, France) ratio at this time was \u003e3.0 (positive) in a tracheal aspirate and β-d-glucan (Fungitell assay; Associates of Cape Cod Inc., East Falmouth, MA, USA) in serum was 1590 pg/mL (positive), after which a putative diagnosis of CAPA was made. Serum galactomannan remained negative (\u003c0.5) in three subsequent samples. Voriconazole i.v. 6 mg/kg q12h was started in addition to caspofungin i.v. 70 mg q24h until the VIPcheck (Mediaproducts BV, Groningen, The Netherlands), used to detect azole resistance, was negative. MICs determined with broth microdilution using CLSI methodology of the A. fumigatus isolate were as follows: amphotericin B 0.5 mg/L, micafungin and anidulafungin \u003c0.016 mg/L, itraconazole 1 mg/L, voriconazole 0.25 mg/L, and posaconazole 0.063 mg/L. Voriconazole was switched to oral administration of 200 mg q12h with discontinuation of caspofungin. During SDD, bacterial cultures remained negative throughout her stay in the ICU."}