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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T30","span":{"begin":503,"end":508},"obj":"Body_part"},{"id":"T31","span":{"begin":751,"end":756},"obj":"Body_part"},{"id":"T32","span":{"begin":935,"end":952},"obj":"Body_part"},{"id":"T33","span":{"begin":1081,"end":1089},"obj":"Body_part"},{"id":"T34","span":{"begin":1296,"end":1301},"obj":"Body_part"},{"id":"T35","span":{"begin":1507,"end":1515},"obj":"Body_part"}],"attributes":[{"id":"A30","pred":"fma_id","subj":"T30","obj":"http://purl.org/sig/ont/fma/fma9576"},{"id":"A31","pred":"fma_id","subj":"T31","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A32","pred":"fma_id","subj":"T32","obj":"http://purl.org/sig/ont/fma/fma265130"},{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma62871"},{"id":"A34","pred":"fma_id","subj":"T34","obj":"http://purl.org/sig/ont/fma/fma63083"},{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma264783"}],"text":"3.4. Relevance of Various Tests and Categorization of Patients and Outcome\nTable 6 presents the classification of the 45 patients using original or modified AspICU algorithms. It appears that using an AspICU algorithm, nine patients were considered as having a putative IA (22% of the cohort). When including PCR, the number of patients with putative IA would increase from 9 to 15 (33%) patients, while most patients might be only colonized because all presented compatible clinical signs and abnormal chest CT scan (Table 5). Regarding Aspergillus detection, eight patients had a single detection of fungi using culture and/or PCR in respiratory samples and thus were classified as colonized. One of these patients had a concomitant GM detection in serum (index = 0.551), was not treated and is still alive, thus was considered as a false positive result. Finally, seven (16%) patients presented a heavy burden of Aspergillus in the respiratory tract with repeated positive cultures and/or PCR. In order to rule out a chronic colonization before the episode, an anti-Aspergillus antibody testing was performed and showed negative results. These patients were classified as putative IA, and three of them could even be considered as probable IA because of a positive biomarker of angioinvasion (serum PCR and/or GM) in agreement with EORTC/MSG classification.\nInterestingly, following these classification criteria, CT scan abnormalities showed a gradation according to patient group. Diffuse reticular or alveolar opacities were observed in patients classified as probable IA (Figure 2), nodules in half of putative IA, and in colonized patients, only non-specific and hard to interpret signs in the context of COVID-19 infection could be described.\nIn addition, putative/probable aspergillosis patients appeared more severely ill than patients without aspergillosis, since SOFA score at day seven was significantly higher in this group (p = 0.01) with a continuum between no infection, colonization and IA (Table 5). Similarly, the mean ICU length of stay increased significantly from 12 days in patients without aspergillosis to 23 days in colonized patients, and 27 days in putative/probable invasive aspergillosis (p = 0.02). All patients with a putative/probable IA were treated either with voriconazole or isavuconazole. Only one colonized patient was treated with voriconazole. Six patients died; there was a trend towards higher mortality in the group of putative/probable IA compared to uninfected patients, although not significant (2/7; 28.6%) versus 4/30 (13.3%), respectively (Table 7)."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T20","span":{"begin":503,"end":508},"obj":"Body_part"},{"id":"T21","span":{"begin":751,"end":756},"obj":"Body_part"},{"id":"T22","span":{"begin":935,"end":952},"obj":"Body_part"},{"id":"T23","span":{"begin":1296,"end":1301},"obj":"Body_part"}],"attributes":[{"id":"A20","pred":"uberon_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/UBERON_0001443"},{"id":"A21","pred":"uberon_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"},{"id":"A22","pred":"uberon_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/UBERON_0000065"},{"id":"A23","pred":"uberon_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/UBERON_0001977"}],"text":"3.4. Relevance of Various Tests and Categorization of Patients and Outcome\nTable 6 presents the classification of the 45 patients using original or modified AspICU algorithms. It appears that using an AspICU algorithm, nine patients were considered as having a putative IA (22% of the cohort). When including PCR, the number of patients with putative IA would increase from 9 to 15 (33%) patients, while most patients might be only colonized because all presented compatible clinical signs and abnormal chest CT scan (Table 5). Regarding Aspergillus detection, eight patients had a single detection of fungi using culture and/or PCR in respiratory samples and thus were classified as colonized. One of these patients had a concomitant GM detection in serum (index = 0.551), was not treated and is still alive, thus was considered as a false positive result. Finally, seven (16%) patients presented a heavy burden of Aspergillus in the respiratory tract with repeated positive cultures and/or PCR. In order to rule out a chronic colonization before the episode, an anti-Aspergillus antibody testing was performed and showed negative results. These patients were classified as putative IA, and three of them could even be considered as probable IA because of a positive biomarker of angioinvasion (serum PCR and/or GM) in agreement with EORTC/MSG classification.\nInterestingly, following these classification criteria, CT scan abnormalities showed a gradation according to patient group. Diffuse reticular or alveolar opacities were observed in patients classified as probable IA (Figure 2), nodules in half of putative IA, and in colonized patients, only non-specific and hard to interpret signs in the context of COVID-19 infection could be described.\nIn addition, putative/probable aspergillosis patients appeared more severely ill than patients without aspergillosis, since SOFA score at day seven was significantly higher in this group (p = 0.01) with a continuum between no infection, colonization and IA (Table 5). Similarly, the mean ICU length of stay increased significantly from 12 days in patients without aspergillosis to 23 days in colonized patients, and 27 days in putative/probable invasive aspergillosis (p = 0.02). All patients with a putative/probable IA were treated either with voriconazole or isavuconazole. Only one colonized patient was treated with voriconazole. Six patients died; there was a trend towards higher mortality in the group of putative/probable IA compared to uninfected patients, although not significant (2/7; 28.6%) versus 4/30 (13.3%), respectively (Table 7)."}

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T5","span":{"begin":589,"end":607},"obj":"http://purl.obolibrary.org/obo/GO_0016046"}],"text":"3.4. Relevance of Various Tests and Categorization of Patients and Outcome\nTable 6 presents the classification of the 45 patients using original or modified AspICU algorithms. It appears that using an AspICU algorithm, nine patients were considered as having a putative IA (22% of the cohort). When including PCR, the number of patients with putative IA would increase from 9 to 15 (33%) patients, while most patients might be only colonized because all presented compatible clinical signs and abnormal chest CT scan (Table 5). Regarding Aspergillus detection, eight patients had a single detection of fungi using culture and/or PCR in respiratory samples and thus were classified as colonized. One of these patients had a concomitant GM detection in serum (index = 0.551), was not treated and is still alive, thus was considered as a false positive result. Finally, seven (16%) patients presented a heavy burden of Aspergillus in the respiratory tract with repeated positive cultures and/or PCR. In order to rule out a chronic colonization before the episode, an anti-Aspergillus antibody testing was performed and showed negative results. These patients were classified as putative IA, and three of them could even be considered as probable IA because of a positive biomarker of angioinvasion (serum PCR and/or GM) in agreement with EORTC/MSG classification.\nInterestingly, following these classification criteria, CT scan abnormalities showed a gradation according to patient group. Diffuse reticular or alveolar opacities were observed in patients classified as probable IA (Figure 2), nodules in half of putative IA, and in colonized patients, only non-specific and hard to interpret signs in the context of COVID-19 infection could be described.\nIn addition, putative/probable aspergillosis patients appeared more severely ill than patients without aspergillosis, since SOFA score at day seven was significantly higher in this group (p = 0.01) with a continuum between no infection, colonization and IA (Table 5). Similarly, the mean ICU length of stay increased significantly from 12 days in patients without aspergillosis to 23 days in colonized patients, and 27 days in putative/probable invasive aspergillosis (p = 0.02). All patients with a putative/probable IA were treated either with voriconazole or isavuconazole. Only one colonized patient was treated with voriconazole. Six patients died; there was a trend towards higher mortality in the group of putative/probable IA compared to uninfected patients, although not significant (2/7; 28.6%) versus 4/30 (13.3%), respectively (Table 7)."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T13","span":{"begin":735,"end":737},"obj":"GlycoEpitope"},{"id":"T14","span":{"begin":1313,"end":1315},"obj":"GlycoEpitope"}],"attributes":[{"id":"A13","pred":"glyco_epitope_db_id","subj":"T13","obj":"http://www.glycoepitope.jp/epitopes/EP0510"},{"id":"A14","pred":"glyco_epitope_db_id","subj":"T14","obj":"http://www.glycoepitope.jp/epitopes/EP0510"}],"text":"3.4. Relevance of Various Tests and Categorization of Patients and Outcome\nTable 6 presents the classification of the 45 patients using original or modified AspICU algorithms. It appears that using an AspICU algorithm, nine patients were considered as having a putative IA (22% of the cohort). When including PCR, the number of patients with putative IA would increase from 9 to 15 (33%) patients, while most patients might be only colonized because all presented compatible clinical signs and abnormal chest CT scan (Table 5). Regarding Aspergillus detection, eight patients had a single detection of fungi using culture and/or PCR in respiratory samples and thus were classified as colonized. One of these patients had a concomitant GM detection in serum (index = 0.551), was not treated and is still alive, thus was considered as a false positive result. Finally, seven (16%) patients presented a heavy burden of Aspergillus in the respiratory tract with repeated positive cultures and/or PCR. In order to rule out a chronic colonization before the episode, an anti-Aspergillus antibody testing was performed and showed negative results. These patients were classified as putative IA, and three of them could even be considered as probable IA because of a positive biomarker of angioinvasion (serum PCR and/or GM) in agreement with EORTC/MSG classification.\nInterestingly, following these classification criteria, CT scan abnormalities showed a gradation according to patient group. Diffuse reticular or alveolar opacities were observed in patients classified as probable IA (Figure 2), nodules in half of putative IA, and in colonized patients, only non-specific and hard to interpret signs in the context of COVID-19 infection could be described.\nIn addition, putative/probable aspergillosis patients appeared more severely ill than patients without aspergillosis, since SOFA score at day seven was significantly higher in this group (p = 0.01) with a continuum between no infection, colonization and IA (Table 5). Similarly, the mean ICU length of stay increased significantly from 12 days in patients without aspergillosis to 23 days in colonized patients, and 27 days in putative/probable invasive aspergillosis (p = 0.02). All patients with a putative/probable IA were treated either with voriconazole or isavuconazole. Only one colonized patient was treated with voriconazole. Six patients died; there was a trend towards higher mortality in the group of putative/probable IA compared to uninfected patients, although not significant (2/7; 28.6%) versus 4/30 (13.3%), respectively (Table 7)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T96","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T97","span":{"begin":5,"end":74},"obj":"Sentence"},{"id":"T98","span":{"begin":75,"end":175},"obj":"Sentence"},{"id":"T99","span":{"begin":176,"end":293},"obj":"Sentence"},{"id":"T100","span":{"begin":294,"end":527},"obj":"Sentence"},{"id":"T101","span":{"begin":528,"end":694},"obj":"Sentence"},{"id":"T102","span":{"begin":695,"end":857},"obj":"Sentence"},{"id":"T103","span":{"begin":858,"end":996},"obj":"Sentence"},{"id":"T104","span":{"begin":997,"end":1140},"obj":"Sentence"},{"id":"T105","span":{"begin":1141,"end":1360},"obj":"Sentence"},{"id":"T106","span":{"begin":1361,"end":1485},"obj":"Sentence"},{"id":"T107","span":{"begin":1486,"end":1751},"obj":"Sentence"},{"id":"T108","span":{"begin":1752,"end":2019},"obj":"Sentence"},{"id":"T109","span":{"begin":2020,"end":2231},"obj":"Sentence"},{"id":"T110","span":{"begin":2232,"end":2328},"obj":"Sentence"},{"id":"T111","span":{"begin":2329,"end":2386},"obj":"Sentence"},{"id":"T112","span":{"begin":2387,"end":2601},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.4. Relevance of Various Tests and Categorization of Patients and Outcome\nTable 6 presents the classification of the 45 patients using original or modified AspICU algorithms. It appears that using an AspICU algorithm, nine patients were considered as having a putative IA (22% of the cohort). When including PCR, the number of patients with putative IA would increase from 9 to 15 (33%) patients, while most patients might be only colonized because all presented compatible clinical signs and abnormal chest CT scan (Table 5). Regarding Aspergillus detection, eight patients had a single detection of fungi using culture and/or PCR in respiratory samples and thus were classified as colonized. One of these patients had a concomitant GM detection in serum (index = 0.551), was not treated and is still alive, thus was considered as a false positive result. Finally, seven (16%) patients presented a heavy burden of Aspergillus in the respiratory tract with repeated positive cultures and/or PCR. In order to rule out a chronic colonization before the episode, an anti-Aspergillus antibody testing was performed and showed negative results. These patients were classified as putative IA, and three of them could even be considered as probable IA because of a positive biomarker of angioinvasion (serum PCR and/or GM) in agreement with EORTC/MSG classification.\nInterestingly, following these classification criteria, CT scan abnormalities showed a gradation according to patient group. Diffuse reticular or alveolar opacities were observed in patients classified as probable IA (Figure 2), nodules in half of putative IA, and in colonized patients, only non-specific and hard to interpret signs in the context of COVID-19 infection could be described.\nIn addition, putative/probable aspergillosis patients appeared more severely ill than patients without aspergillosis, since SOFA score at day seven was significantly higher in this group (p = 0.01) with a continuum between no infection, colonization and IA (Table 5). Similarly, the mean ICU length of stay increased significantly from 12 days in patients without aspergillosis to 23 days in colonized patients, and 27 days in putative/probable invasive aspergillosis (p = 0.02). All patients with a putative/probable IA were treated either with voriconazole or isavuconazole. Only one colonized patient was treated with voriconazole. Six patients died; there was a trend towards higher mortality in the group of putative/probable IA compared to uninfected patients, although not significant (2/7; 28.6%) versus 4/30 (13.3%), respectively (Table 7)."}

LitCovid-PubTator

PMC:7558333 / 12076-14677 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7558333 / 12076-14677 JSON TXT