PMC:7558333 / 2626-4122 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T4","span":{"begin":284,"end":293},"obj":"Body_part"},{"id":"T5","span":{"begin":1173,"end":1181},"obj":"Body_part"},{"id":"T6","span":{"begin":1277,"end":1282},"obj":"Body_part"},{"id":"T7","span":{"begin":1343,"end":1346},"obj":"Body_part"}],"attributes":[{"id":"A4","pred":"fma_id","subj":"T4","obj":"http://purl.org/sig/ont/fma/fma84050"},{"id":"A5","pred":"fma_id","subj":"T5","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A6","pred":"fma_id","subj":"T6","obj":"http://purl.org/sig/ont/fma/fma9670"},{"id":"A7","pred":"fma_id","subj":"T7","obj":"http://purl.org/sig/ont/fma/fma74412"}],"text":"During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines. Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU. However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity. In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer). However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection. Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools. While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T4","span":{"begin":1277,"end":1282},"obj":"Body_part"}],"attributes":[{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0000178"}],"text":"During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines. Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU. However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity. In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer). However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection. Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools. While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T20","span":{"begin":7,"end":15},"obj":"Disease"},{"id":"T21","span":{"begin":40,"end":75},"obj":"Disease"},{"id":"T22","span":{"begin":46,"end":75},"obj":"Disease"},{"id":"T23","span":{"begin":77,"end":81},"obj":"Disease"},{"id":"T24","span":{"begin":152,"end":154},"obj":"Disease"},{"id":"T25","span":{"begin":418,"end":431},"obj":"Disease"},{"id":"T26","span":{"begin":432,"end":440},"obj":"Disease"},{"id":"T27","span":{"begin":527,"end":529},"obj":"Disease"},{"id":"T28","span":{"begin":695,"end":703},"obj":"Disease"},{"id":"T29","span":{"begin":725,"end":738},"obj":"Disease"},{"id":"T30","span":{"begin":740,"end":744},"obj":"Disease"},{"id":"T31","span":{"begin":973,"end":981},"obj":"Disease"},{"id":"T32","span":{"begin":1061,"end":1076},"obj":"Disease"},{"id":"T33","span":{"begin":1067,"end":1076},"obj":"Disease"}],"attributes":[{"id":"A20","pred":"mondo_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A21","pred":"mondo_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/MONDO_0006502"},{"id":"A22","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0009971"},{"id":"A23","pred":"mondo_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/MONDO_0006502"},{"id":"A24","pred":"mondo_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A25","pred":"mondo_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A26","pred":"mondo_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A27","pred":"mondo_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A29","pred":"mondo_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/MONDO_0005657"},{"id":"A30","pred":"mondo_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/MONDO_0007163"},{"id":"A31","pred":"mondo_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A32","pred":"mondo_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/MONDO_0005108"},{"id":"A33","pred":"mondo_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines. Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU. However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity. In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer). However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection. Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools. While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T21","span":{"begin":398,"end":410},"obj":"http://purl.obolibrary.org/obo/UBERON_0001155"},{"id":"T22","span":{"begin":780,"end":787},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T23","span":{"begin":1277,"end":1282},"obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"T24","span":{"begin":1277,"end":1282},"obj":"http://www.ebi.ac.uk/efo/EFO_0000296"}],"text":"During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines. Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU. However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity. In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer). However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection. Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools. While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T1","span":{"begin":46,"end":66},"obj":"Phenotype"}],"attributes":[{"id":"A1","pred":"hp_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/HP_0002098"}],"text":"During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines. Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU. However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity. In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer). However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection. Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools. While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T1","span":{"begin":1061,"end":1076},"obj":"http://purl.obolibrary.org/obo/GO_0016032"}],"text":"During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines. Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU. However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity. In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer). However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection. Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools. While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T2","span":{"begin":761,"end":774},"obj":"GlycoEpitope"},{"id":"T3","span":{"begin":776,"end":778},"obj":"GlycoEpitope"},{"id":"T4","span":{"begin":1129,"end":1142},"obj":"GlycoEpitope"},{"id":"T5","span":{"begin":1144,"end":1146},"obj":"GlycoEpitope"},{"id":"T6","span":{"begin":1302,"end":1304},"obj":"GlycoEpitope"}],"attributes":[{"id":"A2","pred":"glyco_epitope_db_id","subj":"T2","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A3","pred":"glyco_epitope_db_id","subj":"T3","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A5","pred":"glyco_epitope_db_id","subj":"T5","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A6","pred":"glyco_epitope_db_id","subj":"T6","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines. Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU. However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity. In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer). However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection. Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools. While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU."}

{"project":"LitCovid-sentences","denotations":[{"id":"T24","span":{"begin":0,"end":294},"obj":"Sentence"},{"id":"T25","span":{"begin":295,"end":484},"obj":"Sentence"},{"id":"T26","span":{"begin":485,"end":642},"obj":"Sentence"},{"id":"T27","span":{"begin":643,"end":885},"obj":"Sentence"},{"id":"T28","span":{"begin":886,"end":1077},"obj":"Sentence"},{"id":"T29","span":{"begin":1078,"end":1254},"obj":"Sentence"},{"id":"T30","span":{"begin":1255,"end":1496},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines. Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU. However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity. In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer). However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection. Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools. While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU."}

{"project":"LitCovid-PubTator","denotations":[{"id":"82","span":{"begin":17,"end":25},"obj":"Species"},{"id":"83","span":{"begin":452,"end":460},"obj":"Species"},{"id":"84","span":{"begin":1391,"end":1399},"obj":"Species"},{"id":"85","span":{"begin":563,"end":574},"obj":"Species"},{"id":"86","span":{"begin":1331,"end":1342},"obj":"Species"},{"id":"87","span":{"begin":761,"end":774},"obj":"Chemical"},{"id":"88","span":{"begin":776,"end":778},"obj":"Chemical"},{"id":"89","span":{"begin":1129,"end":1142},"obj":"Chemical"},{"id":"90","span":{"begin":1144,"end":1146},"obj":"Chemical"},{"id":"91","span":{"begin":1302,"end":1304},"obj":"Chemical"},{"id":"92","span":{"begin":1311,"end":1321},"obj":"Chemical"},{"id":"93","span":{"begin":1323,"end":1326},"obj":"Chemical"},{"id":"94","span":{"begin":7,"end":15},"obj":"Disease"},{"id":"95","span":{"begin":40,"end":75},"obj":"Disease"},{"id":"96","span":{"begin":77,"end":81},"obj":"Disease"},{"id":"97","span":{"begin":415,"end":428},"obj":"Disease"},{"id":"98","span":{"begin":432,"end":451},"obj":"Disease"},{"id":"99","span":{"begin":695,"end":703},"obj":"Disease"},{"id":"100","span":{"begin":715,"end":738},"obj":"Disease"},{"id":"101","span":{"begin":973,"end":992},"obj":"Disease"},{"id":"102","span":{"begin":1061,"end":1076},"obj":"Disease"},{"id":"103","span":{"begin":1379,"end":1390},"obj":"Disease"}],"attributes":[{"id":"A82","pred":"tao:has_database_id","subj":"82","obj":"Tax:9606"},{"id":"A83","pred":"tao:has_database_id","subj":"83","obj":"Tax:9606"},{"id":"A84","pred":"tao:has_database_id","subj":"84","obj":"Tax:9606"},{"id":"A85","pred":"tao:has_database_id","subj":"85","obj":"Tax:746128"},{"id":"A86","pred":"tao:has_database_id","subj":"86","obj":"Tax:746128"},{"id":"A87","pred":"tao:has_database_id","subj":"87","obj":"MESH:C012990"},{"id":"A88","pred":"tao:has_database_id","subj":"88","obj":"MESH:C012990"},{"id":"A89","pred":"tao:has_database_id","subj":"89","obj":"MESH:C012990"},{"id":"A90","pred":"tao:has_database_id","subj":"90","obj":"MESH:C012990"},{"id":"A91","pred":"tao:has_database_id","subj":"91","obj":"MESH:C012990"},{"id":"A93","pred":"tao:has_database_id","subj":"93","obj":"MESH:C480180"},{"id":"A94","pred":"tao:has_database_id","subj":"94","obj":"MESH:C000657245"},{"id":"A95","pred":"tao:has_database_id","subj":"95","obj":"MESH:D012128"},{"id":"A96","pred":"tao:has_database_id","subj":"96","obj":"MESH:D012128"},{"id":"A97","pred":"tao:has_database_id","subj":"97","obj":"MESH:D060085"},{"id":"A98","pred":"tao:has_database_id","subj":"98","obj":"MESH:C000657245"},{"id":"A99","pred":"tao:has_database_id","subj":"99","obj":"MESH:C000657245"},{"id":"A100","pred":"tao:has_database_id","subj":"100","obj":"MESH:D055732"},{"id":"A101","pred":"tao:has_database_id","subj":"101","obj":"MESH:C000657245"},{"id":"A102","pred":"tao:has_database_id","subj":"102","obj":"MESH:D001102"},{"id":"A103","pred":"tao:has_database_id","subj":"103","obj":"MESH:D009503"}],"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":"During COVID-19, patients presenting an acute respiratory distress syndrome (ARDS) shared risk factors and underlying diseases classically reported for IA, such as intubation and mechanical ventilation, corticosteroid therapy, immunological storm with high production of inflammatory cytokines. Warnings following preliminary cohort studies from various countries prompted the monitoring of fungal colonization and co-infections in SARS-CoV-2-infected patients hospitalized in an ICU. However, the entry criterion for putative IA, according to Blot et al., is an Aspergillus-positive culture endotracheal aspirate, which may lack specificity. In the recent review by Arastehfar et al. [6], many COVID-19-associated pulmonary aspergillosis (CAPA) benefited from galactomannan (GM) testing of bronchoalveolar fluid (BALF) or even of tracheal aspirates (not approved by the manufacturer). However, some laboratories, such as ours, have stopped various manipulations of highly SARS-CoV-2-infected samples in order to limit the exposure of laboratory technicians to viral infection. Then, direct examination of respiratory samples or galactomannan (GM) determination in broncho-alveolar lavage have thus been replaced by the systematic use of molecular tools. While performances of blood biomarkers such as GM, (1-3)β-d-glucan (BDG) or Aspergillus DNA detection are well evaluated in neutropenic patients, their clinical value is far less known in other conditions and still need evaluation in an ICU."}