PMC:7346000 / 11061-14871 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T36","span":{"begin":1572,"end":1576},"obj":"Body_part"},{"id":"T37","span":{"begin":1799,"end":1803},"obj":"Body_part"},{"id":"T38","span":{"begin":1908,"end":1916},"obj":"Body_part"},{"id":"T39","span":{"begin":2028,"end":2032},"obj":"Body_part"},{"id":"T40","span":{"begin":2553,"end":2561},"obj":"Body_part"},{"id":"T41","span":{"begin":2872,"end":2875},"obj":"Body_part"},{"id":"T42","span":{"begin":3192,"end":3205},"obj":"Body_part"},{"id":"T43","span":{"begin":3458,"end":3463},"obj":"Body_part"},{"id":"T44","span":{"begin":3625,"end":3630},"obj":"Body_part"},{"id":"T45","span":{"begin":3716,"end":3720},"obj":"Body_part"}],"attributes":[{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma84050"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma84050"},{"id":"A41","pred":"fma_id","subj":"T41","obj":"http://purl.org/sig/ont/fma/fma7199"},{"id":"A42","pred":"fma_id","subj":"T42","obj":"http://purl.org/sig/ont/fma/fma9825"},{"id":"A43","pred":"fma_id","subj":"T43","obj":"http://purl.org/sig/ont/fma/fma7088"},{"id":"A44","pred":"fma_id","subj":"T44","obj":"http://purl.org/sig/ont/fma/fma7088"},{"id":"A45","pred":"fma_id","subj":"T45","obj":"http://purl.org/sig/ont/fma/fma7195"}],"text":"3. Risk Factors Implicated in CAPA Development\nImportantly, the pathogenesis of IPA differs between neutropenic and non-neutropenic patients, including those with COVID-19, impacting clinical presentation, radiological findings and diagnostic test results in the mycology laboratory [41,42]. Despite these important differences, revised European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) definitions [43] focus primarily on neutropenic patients with underlying hematological malignancies and “typical” presentation of IPA and have been shown to have limited applicability and inferior performance in non-neutropenic patients who frequently do not fulfil radiological and host criteria, including patients with COVID-19 [41,44]. This has resulted in the creation of an alternative clinical algorithm for diagnosing IPA in the ICU setting in 2012 [41], which defines putative IPA and is now the standard of care for defining IPA in the ICU [4,45], where highly reliable definitions of IA are still missing (work on improved definitions is currently in progress [45,46]).\nRapid development of CAPA few days following ICU admission [47] resembles the observation made for influenza-associated pulmonary aspergillosis [4,5]. Risk factors predisposing COVID-19 patients to develop secondary pulmonary aspergillosis are similar to those identified for influenza-IPA superinfections [4,5]. The most important risk factors include severe lung damage during the course of COVID-19 [48], the use of corticosteroids in those with ARDS, the widespread use of broad-spectrum antibiotics in intensive care units [49], and the presence of comorbidities such as structural lung defects [47,50,51,52].\nThere are some reports revealing that pulmonary fibrosis can be triggered by the cytokine storm activated by the viral antigens, toxicity posed by drugs, high airway pressure and hypoxia-induced acute lung injury secondary to mechanical ventilation [53]. While interstitial pulmonary fibrosis per se does not predispose to development of IPA, a small subset of these COVID-19 survivors may require long term corticosteroid treatment, which may predispose them to CAPA years after the acute phase of the viral infection. Overall, 29% of the CAPA cases published to date (10/35) had received systemic corticosteroids (Table 1). In those with ARDS, systemic corticosteroids are used to alleviate the immune responses and prevent cytokine storm [6,54,55,56], but may at the same time increase vulnerability for developing secondary infections [4,5].\nAlthough detailed case series have not reported on antibiotic use among patients, broad-spectrum antibiotics are presumed to be used in 75% of COVID-19 patients admitted to ICU [49]. Since the human gut microbiome is a highly complicated structure of bacteria and fungi, although bacteria are the most diverse constituents, the administration of antibiotics results in perturbation of microbiome steady-state composition, which allows fungi to thrive, and may predispose the host to invasive fungal infections once the immune system becomes impaired [65,66].\nUnderlying medical conditions may also predispose COVID-19 patients to develop CAPA. Among the 35 CAPA cases published to date (Table 1), hypertension (17/35; 49%), diabetes (9/35; 26%), obesity (8/35; 23%), COPD (5/35; 14%), heart diseases (5/35; 14%), hypercholesterinemia (4/35; 11%), and asthma (3/35; 9%) were among the most prevalent comorbidities observed. While hypertension, coronary heart diseases, and diabetes increase the risk of infection overall [67,68,69], structural lung damage caused by COPD or asthma may particularly predispose patients to develop IPA [70]."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T6","span":{"begin":1572,"end":1576},"obj":"Body_part"},{"id":"T7","span":{"begin":1799,"end":1803},"obj":"Body_part"},{"id":"T8","span":{"begin":2028,"end":2032},"obj":"Body_part"},{"id":"T9","span":{"begin":3192,"end":3205},"obj":"Body_part"},{"id":"T10","span":{"begin":3458,"end":3463},"obj":"Body_part"},{"id":"T11","span":{"begin":3625,"end":3630},"obj":"Body_part"},{"id":"T12","span":{"begin":3716,"end":3720},"obj":"Body_part"}],"attributes":[{"id":"A6","pred":"uberon_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A9","pred":"uberon_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/UBERON_0002405"},{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0000948"},{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0000948"},{"id":"A12","pred":"uberon_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"}],"text":"3. Risk Factors Implicated in CAPA Development\nImportantly, the pathogenesis of IPA differs between neutropenic and non-neutropenic patients, including those with COVID-19, impacting clinical presentation, radiological findings and diagnostic test results in the mycology laboratory [41,42]. Despite these important differences, revised European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) definitions [43] focus primarily on neutropenic patients with underlying hematological malignancies and “typical” presentation of IPA and have been shown to have limited applicability and inferior performance in non-neutropenic patients who frequently do not fulfil radiological and host criteria, including patients with COVID-19 [41,44]. This has resulted in the creation of an alternative clinical algorithm for diagnosing IPA in the ICU setting in 2012 [41], which defines putative IPA and is now the standard of care for defining IPA in the ICU [4,45], where highly reliable definitions of IA are still missing (work on improved definitions is currently in progress [45,46]).\nRapid development of CAPA few days following ICU admission [47] resembles the observation made for influenza-associated pulmonary aspergillosis [4,5]. Risk factors predisposing COVID-19 patients to develop secondary pulmonary aspergillosis are similar to those identified for influenza-IPA superinfections [4,5]. The most important risk factors include severe lung damage during the course of COVID-19 [48], the use of corticosteroids in those with ARDS, the widespread use of broad-spectrum antibiotics in intensive care units [49], and the presence of comorbidities such as structural lung defects [47,50,51,52].\nThere are some reports revealing that pulmonary fibrosis can be triggered by the cytokine storm activated by the viral antigens, toxicity posed by drugs, high airway pressure and hypoxia-induced acute lung injury secondary to mechanical ventilation [53]. While interstitial pulmonary fibrosis per se does not predispose to development of IPA, a small subset of these COVID-19 survivors may require long term corticosteroid treatment, which may predispose them to CAPA years after the acute phase of the viral infection. Overall, 29% of the CAPA cases published to date (10/35) had received systemic corticosteroids (Table 1). In those with ARDS, systemic corticosteroids are used to alleviate the immune responses and prevent cytokine storm [6,54,55,56], but may at the same time increase vulnerability for developing secondary infections [4,5].\nAlthough detailed case series have not reported on antibiotic use among patients, broad-spectrum antibiotics are presumed to be used in 75% of COVID-19 patients admitted to ICU [49]. Since the human gut microbiome is a highly complicated structure of bacteria and fungi, although bacteria are the most diverse constituents, the administration of antibiotics results in perturbation of microbiome steady-state composition, which allows fungi to thrive, and may predispose the host to invasive fungal infections once the immune system becomes impaired [65,66].\nUnderlying medical conditions may also predispose COVID-19 patients to develop CAPA. Among the 35 CAPA cases published to date (Table 1), hypertension (17/35; 49%), diabetes (9/35; 26%), obesity (8/35; 23%), COPD (5/35; 14%), heart diseases (5/35; 14%), hypercholesterinemia (4/35; 11%), and asthma (3/35; 9%) were among the most prevalent comorbidities observed. While hypertension, coronary heart diseases, and diabetes increase the risk of infection overall [67,68,69], structural lung damage caused by COPD or asthma may particularly predispose patients to develop IPA [70]."}

LitCovid-PubTator

LitCovid-PD-MONDO

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T27","span":{"begin":64,"end":76},"obj":"http://purl.obolibrary.org/obo/GO_0009405"},{"id":"T28","span":{"begin":2330,"end":2345},"obj":"http://purl.obolibrary.org/obo/GO_0016032"},{"id":"T29","span":{"begin":2524,"end":2540},"obj":"http://purl.obolibrary.org/obo/GO_0006955"}],"text":"3. Risk Factors Implicated in CAPA Development\nImportantly, the pathogenesis of IPA differs between neutropenic and non-neutropenic patients, including those with COVID-19, impacting clinical presentation, radiological findings and diagnostic test results in the mycology laboratory [41,42]. Despite these important differences, revised European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) definitions [43] focus primarily on neutropenic patients with underlying hematological malignancies and “typical” presentation of IPA and have been shown to have limited applicability and inferior performance in non-neutropenic patients who frequently do not fulfil radiological and host criteria, including patients with COVID-19 [41,44]. This has resulted in the creation of an alternative clinical algorithm for diagnosing IPA in the ICU setting in 2012 [41], which defines putative IPA and is now the standard of care for defining IPA in the ICU [4,45], where highly reliable definitions of IA are still missing (work on improved definitions is currently in progress [45,46]).\nRapid development of CAPA few days following ICU admission [47] resembles the observation made for influenza-associated pulmonary aspergillosis [4,5]. Risk factors predisposing COVID-19 patients to develop secondary pulmonary aspergillosis are similar to those identified for influenza-IPA superinfections [4,5]. The most important risk factors include severe lung damage during the course of COVID-19 [48], the use of corticosteroids in those with ARDS, the widespread use of broad-spectrum antibiotics in intensive care units [49], and the presence of comorbidities such as structural lung defects [47,50,51,52].\nThere are some reports revealing that pulmonary fibrosis can be triggered by the cytokine storm activated by the viral antigens, toxicity posed by drugs, high airway pressure and hypoxia-induced acute lung injury secondary to mechanical ventilation [53]. While interstitial pulmonary fibrosis per se does not predispose to development of IPA, a small subset of these COVID-19 survivors may require long term corticosteroid treatment, which may predispose them to CAPA years after the acute phase of the viral infection. Overall, 29% of the CAPA cases published to date (10/35) had received systemic corticosteroids (Table 1). In those with ARDS, systemic corticosteroids are used to alleviate the immune responses and prevent cytokine storm [6,54,55,56], but may at the same time increase vulnerability for developing secondary infections [4,5].\nAlthough detailed case series have not reported on antibiotic use among patients, broad-spectrum antibiotics are presumed to be used in 75% of COVID-19 patients admitted to ICU [49]. Since the human gut microbiome is a highly complicated structure of bacteria and fungi, although bacteria are the most diverse constituents, the administration of antibiotics results in perturbation of microbiome steady-state composition, which allows fungi to thrive, and may predispose the host to invasive fungal infections once the immune system becomes impaired [65,66].\nUnderlying medical conditions may also predispose COVID-19 patients to develop CAPA. Among the 35 CAPA cases published to date (Table 1), hypertension (17/35; 49%), diabetes (9/35; 26%), obesity (8/35; 23%), COPD (5/35; 14%), heart diseases (5/35; 14%), hypercholesterinemia (4/35; 11%), and asthma (3/35; 9%) were among the most prevalent comorbidities observed. While hypertension, coronary heart diseases, and diabetes increase the risk of infection overall [67,68,69], structural lung damage caused by COPD or asthma may particularly predispose patients to develop IPA [70]."}

LitCovid-PD-HP

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T59","span":{"begin":0,"end":2},"obj":"Sentence"},{"id":"T60","span":{"begin":3,"end":46},"obj":"Sentence"},{"id":"T61","span":{"begin":47,"end":291},"obj":"Sentence"},{"id":"T62","span":{"begin":292,"end":870},"obj":"Sentence"},{"id":"T63","span":{"begin":871,"end":1211},"obj":"Sentence"},{"id":"T64","span":{"begin":1212,"end":1362},"obj":"Sentence"},{"id":"T65","span":{"begin":1363,"end":1524},"obj":"Sentence"},{"id":"T66","span":{"begin":1525,"end":1826},"obj":"Sentence"},{"id":"T67","span":{"begin":1827,"end":2081},"obj":"Sentence"},{"id":"T68","span":{"begin":2082,"end":2346},"obj":"Sentence"},{"id":"T69","span":{"begin":2347,"end":2452},"obj":"Sentence"},{"id":"T70","span":{"begin":2453,"end":2672},"obj":"Sentence"},{"id":"T71","span":{"begin":2673,"end":2855},"obj":"Sentence"},{"id":"T72","span":{"begin":2856,"end":3231},"obj":"Sentence"},{"id":"T73","span":{"begin":3232,"end":3316},"obj":"Sentence"},{"id":"T74","span":{"begin":3317,"end":3595},"obj":"Sentence"},{"id":"T75","span":{"begin":3596,"end":3810},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3. Risk Factors Implicated in CAPA Development\nImportantly, the pathogenesis of IPA differs between neutropenic and non-neutropenic patients, including those with COVID-19, impacting clinical presentation, radiological findings and diagnostic test results in the mycology laboratory [41,42]. Despite these important differences, revised European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) definitions [43] focus primarily on neutropenic patients with underlying hematological malignancies and “typical” presentation of IPA and have been shown to have limited applicability and inferior performance in non-neutropenic patients who frequently do not fulfil radiological and host criteria, including patients with COVID-19 [41,44]. This has resulted in the creation of an alternative clinical algorithm for diagnosing IPA in the ICU setting in 2012 [41], which defines putative IPA and is now the standard of care for defining IPA in the ICU [4,45], where highly reliable definitions of IA are still missing (work on improved definitions is currently in progress [45,46]).\nRapid development of CAPA few days following ICU admission [47] resembles the observation made for influenza-associated pulmonary aspergillosis [4,5]. Risk factors predisposing COVID-19 patients to develop secondary pulmonary aspergillosis are similar to those identified for influenza-IPA superinfections [4,5]. The most important risk factors include severe lung damage during the course of COVID-19 [48], the use of corticosteroids in those with ARDS, the widespread use of broad-spectrum antibiotics in intensive care units [49], and the presence of comorbidities such as structural lung defects [47,50,51,52].\nThere are some reports revealing that pulmonary fibrosis can be triggered by the cytokine storm activated by the viral antigens, toxicity posed by drugs, high airway pressure and hypoxia-induced acute lung injury secondary to mechanical ventilation [53]. While interstitial pulmonary fibrosis per se does not predispose to development of IPA, a small subset of these COVID-19 survivors may require long term corticosteroid treatment, which may predispose them to CAPA years after the acute phase of the viral infection. Overall, 29% of the CAPA cases published to date (10/35) had received systemic corticosteroids (Table 1). In those with ARDS, systemic corticosteroids are used to alleviate the immune responses and prevent cytokine storm [6,54,55,56], but may at the same time increase vulnerability for developing secondary infections [4,5].\nAlthough detailed case series have not reported on antibiotic use among patients, broad-spectrum antibiotics are presumed to be used in 75% of COVID-19 patients admitted to ICU [49]. Since the human gut microbiome is a highly complicated structure of bacteria and fungi, although bacteria are the most diverse constituents, the administration of antibiotics results in perturbation of microbiome steady-state composition, which allows fungi to thrive, and may predispose the host to invasive fungal infections once the immune system becomes impaired [65,66].\nUnderlying medical conditions may also predispose COVID-19 patients to develop CAPA. Among the 35 CAPA cases published to date (Table 1), hypertension (17/35; 49%), diabetes (9/35; 26%), obesity (8/35; 23%), COPD (5/35; 14%), heart diseases (5/35; 14%), hypercholesterinemia (4/35; 11%), and asthma (3/35; 9%) were among the most prevalent comorbidities observed. While hypertension, coronary heart diseases, and diabetes increase the risk of infection overall [67,68,69], structural lung damage caused by COPD or asthma may particularly predispose patients to develop IPA [70]."}

2_test

PMC:7346000 / 11061-14871 JSONTXT

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PMC:7346000 / 11061-14871 JSON TXT