PMC:7394275 / 9787-11136 JSONTXT

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T163","span":{"begin":270,"end":281},"obj":"NCBITaxon:5052"},{"id":"T164","span":{"begin":313,"end":319},"obj":"NCBITaxon:4751"},{"id":"T165","span":{"begin":397,"end":408},"obj":"NCBITaxon:5052"},{"id":"T166","span":{"begin":670,"end":679},"obj":"GO:0005840"},{"id":"T167","span":{"begin":735,"end":746},"obj":"NCBITaxon:5052"},{"id":"T168","span":{"begin":750,"end":757},"obj":"UBERON:0000479"},{"id":"T169","span":{"begin":761,"end":765},"obj":"BV_4"},{"id":"T170","span":{"begin":817,"end":828},"obj":"NCBITaxon:5052"},{"id":"T171","span":{"begin":829,"end":832},"obj":"NCBITaxon:species"},{"id":"T172","span":{"begin":838,"end":844},"obj":"PR:000006147"},{"id":"T173","span":{"begin":869,"end":870},"obj":"NCBITaxon:8296"},{"id":"T174","span":{"begin":870,"end":881},"obj":"NCBITaxon:31032"},{"id":"T175","span":{"begin":990,"end":998},"obj":"CHEBI:33893;CHEBI:33893"},{"id":"T176","span":{"begin":1028,"end":1033},"obj":"UBERON:0001977"},{"id":"T177","span":{"begin":1038,"end":1042},"obj":"BV_4"},{"id":"T178","span":{"begin":1274,"end":1279},"obj":"UBERON:0000178"},{"id":"T179","span":{"begin":1324,"end":1335},"obj":"UBERON:0001004"},{"id":"T71196","span":{"begin":270,"end":281},"obj":"NCBITaxon:5052"},{"id":"T95830","span":{"begin":313,"end":319},"obj":"NCBITaxon:4751"},{"id":"T31042","span":{"begin":397,"end":408},"obj":"NCBITaxon:5052"},{"id":"T44167","span":{"begin":670,"end":679},"obj":"GO:0005840"},{"id":"T80438","span":{"begin":735,"end":746},"obj":"NCBITaxon:5052"},{"id":"T62724","span":{"begin":750,"end":757},"obj":"UBERON:0000479"},{"id":"T23730","span":{"begin":761,"end":765},"obj":"BV_4"},{"id":"T49081","span":{"begin":817,"end":828},"obj":"NCBITaxon:5052"},{"id":"T81108","span":{"begin":829,"end":832},"obj":"NCBITaxon:species"},{"id":"T34970","span":{"begin":838,"end":844},"obj":"PR:000006147"},{"id":"T26672","span":{"begin":869,"end":870},"obj":"NCBITaxon:8296"},{"id":"T47994","span":{"begin":870,"end":881},"obj":"NCBITaxon:31032"},{"id":"T85259","span":{"begin":990,"end":998},"obj":"CHEBI:33893;CHEBI:33893"},{"id":"T55352","span":{"begin":1028,"end":1033},"obj":"UBERON:0001977"},{"id":"T62010","span":{"begin":1038,"end":1042},"obj":"BV_4"},{"id":"T90815","span":{"begin":1274,"end":1279},"obj":"UBERON:0000178"},{"id":"T48524","span":{"begin":1324,"end":1335},"obj":"UBERON:0001004"}],"text":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T17","span":{"begin":455,"end":458},"obj":"Body_part"},{"id":"T18","span":{"begin":670,"end":679},"obj":"Body_part"},{"id":"T19","span":{"begin":680,"end":683},"obj":"Body_part"},{"id":"T20","span":{"begin":750,"end":757},"obj":"Body_part"},{"id":"T21","span":{"begin":1028,"end":1033},"obj":"Body_part"},{"id":"T22","span":{"begin":1274,"end":1279},"obj":"Body_part"}],"attributes":[{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma66867"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A20","pred":"fma_id","subj":"T20","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A21","pred":"fma_id","subj":"T21","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A22","pred":"fma_id","subj":"T22","obj":"http://purl.org/sig/ont/fma/fma9670"}],"text":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T11","span":{"begin":371,"end":393},"obj":"Body_part"},{"id":"T12","span":{"begin":1028,"end":1033},"obj":"Body_part"},{"id":"T13","span":{"begin":1274,"end":1279},"obj":"Body_part"}],"attributes":[{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0034768"},{"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_0000178"}],"text":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}

{"project":"LitCovid-PubTator","denotations":[{"id":"348","span":{"begin":869,"end":881},"obj":"Species"},{"id":"349","span":{"begin":1183,"end":1191},"obj":"Species"},{"id":"353","span":{"begin":270,"end":281},"obj":"Species"},{"id":"354","span":{"begin":397,"end":408},"obj":"Species"},{"id":"355","span":{"begin":735,"end":746},"obj":"Species"},{"id":"356","span":{"begin":817,"end":828},"obj":"Species"},{"id":"361","span":{"begin":1043,"end":1045},"obj":"Chemical"},{"id":"373","span":{"begin":1171,"end":1182},"obj":"Disease"}],"attributes":[{"id":"A348","pred":"tao:has_database_id","subj":"348","obj":"Tax:746128"},{"id":"A349","pred":"tao:has_database_id","subj":"349","obj":"Tax:9606"},{"id":"A353","pred":"tao:has_database_id","subj":"353","obj":"Tax:746128"},{"id":"A354","pred":"tao:has_database_id","subj":"354","obj":"Tax:746128"},{"id":"A355","pred":"tao:has_database_id","subj":"355","obj":"Tax:746128"},{"id":"A356","pred":"tao:has_database_id","subj":"356","obj":"Tax:746128"},{"id":"A361","pred":"tao:has_database_id","subj":"361","obj":"MESH:C012990"},{"id":"A373","pred":"tao:has_database_id","subj":"373","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":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T131","span":{"begin":633,"end":635},"obj":"Disease"},{"id":"T132","span":{"begin":1217,"end":1223},"obj":"Disease"}],"attributes":[{"id":"A131","pred":"mondo_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/MONDO_0000240"},{"id":"A132","pred":"mondo_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/MONDO_0021178"}],"text":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T51","span":{"begin":35,"end":36},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T52","span":{"begin":581,"end":582},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T53","span":{"begin":869,"end":870},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T54","span":{"begin":1046,"end":1053},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T55","span":{"begin":1266,"end":1270},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T56","span":{"begin":1274,"end":1279},"obj":"http://purl.obolibrary.org/obo/UBERON_0000178"},{"id":"T57","span":{"begin":1274,"end":1279},"obj":"http://www.ebi.ac.uk/efo/EFO_0000296"}],"text":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T46","span":{"begin":455,"end":458},"obj":"Chemical"},{"id":"T47","span":{"begin":633,"end":635},"obj":"Chemical"},{"id":"T48","span":{"begin":638,"end":641},"obj":"Chemical"},{"id":"T49","span":{"begin":680,"end":683},"obj":"Chemical"},{"id":"T50","span":{"begin":990,"end":998},"obj":"Chemical"},{"id":"T51","span":{"begin":1043,"end":1045},"obj":"Chemical"}],"attributes":[{"id":"A46","pred":"chebi_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A47","pred":"chebi_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/CHEBI_74062"},{"id":"A48","pred":"chebi_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/CHEBI_74062"},{"id":"A49","pred":"chebi_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A50","pred":"chebi_id","subj":"T50","obj":"http://purl.obolibrary.org/obo/CHEBI_33893"},{"id":"A51","pred":"chebi_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A52","pred":"chebi_id","subj":"T51","obj":"http://purl.obolibrary.org/obo/CHEBI_27680"}],"text":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T4","span":{"begin":1043,"end":1045},"obj":"GlycoEpitope"}],"attributes":[{"id":"A4","pred":"glyco_epitope_db_id","subj":"T4","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T56","span":{"begin":0,"end":1349},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}

{"project":"2_test","denotations":[{"id":"32737747-27365388-73473616","span":{"begin":1018,"end":1020},"obj":"27365388"}],"text":"Therefore, it is necessary to have a definitive confirmation by culture or nonculture technique, including (i) direct microscopic examination with the optical brightener methods, Calcofluor or Blankophor, which may increase the sensitivity and specificity for detecting Aspergillus-like features; (ii) culture on fungal-specific media at 37 °C for 2–5 days, if positive, morphological features of Aspergillus can be identified under the microscope or the DNA sequencing may be used in reference laboratories to identify the species accurately, but usually culture yield is low and a negative result does not exclude the diagnosis of IA; (iii) molecular assays targeting ribosomal DNA (rDNA) sequences can also be used for detection of Aspergillus in tissues or BALF, especially PCR-based assays can be used to detect Aspergillus spp. and CYP51A resistance mutations in A. fumigatus, although these methods have not been standardized or limited by laboratory conditions or proven commercial reagents in some countries [30]; (iv) serum and BALF GM testing are also recommended as an early and accurate marker using less invasive techniques for the diagnosis, especially in neutropenic patients, with advantages of less injury and time-efficient, though sometimes this test in blood samples are less sensitive than cultures of respiratory samples [25]."}