PMC:7346000 / 25760-27751 JSON TXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T60","span":{"begin":1655,"end":1662},"obj":"Body_part"},{"id":"T61","span":{"begin":1787,"end":1791},"obj":"Body_part"}],"attributes":[{"id":"A60","pred":"fma_id","subj":"T60","obj":"http://purl.org/sig/ont/fma/fma7394"},{"id":"A61","pred":"fma_id","subj":"T61","obj":"http://purl.org/sig/ont/fma/fma24728"}],"text":"Bacterial, fungal and viral secondary infections or co-infections affect mortality. Acinetobacter baumanii, Klebsiella pneumonia and Aspergillus species are important nosocomial pathogens [93] complicating the disease course. Studies from France [51], Germany [50], Belgium [52], and the Netherlands [47], underline the role of CAPA. Diagnosing co-infections is complex and rapid diagnosis plays a crucial role in this setting [49]. Close monitoring for infection development is needed, as well as longitudinal sampling throughout the disease course using culture dependent and independent techniques. Aspergillus antigen and PCR testing of respiratory fluids should be a routine procedure for critically ill patients [94], specifically for those suffering from ARDS [50]. Co-infection with human metapneumovirus has been reported in two of five cases in the German CAPA series [50]. It is unknown whether hospitals caring for COVID-19 test comprehensive respiratory pathogen panels, and to date no analysis of mixed viral infection in COVID-19 patients has been reported. In the context of COVID-19, mixed viral infection may be misinterpreted as presence of innocent bystanders and thus remain underreported. With bronchoalveolar lavage and autopsy regarded as high-risk procedures, key diagnostic instruments are lacking. Autopsy studies are key to understanding pathophysiology of COVID-19 [95] and are critically enlighten interaction between SARS-CoV-2 and different pathogens. With availability of lower respiratory samples, normally obtained by BALF, the quality of microbiological and virological work up would be greatly improved. Inspection of trachea and bronchi is achieved by bronchoscopy, which is critical to find possible Aspergillus tracheobronchitis. Thus, physicians face the dilemma of taking the hazard of aerosolization of SARS-CoV-2, risking transmission versus the endeavor of facilitating the optimal diagnosis and treatment to the patients entrusted to their care."}

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T29","span":{"begin":1655,"end":1662},"obj":"Body_part"},{"id":"T30","span":{"begin":1667,"end":1674},"obj":"Body_part"},{"id":"T31","span":{"begin":1787,"end":1791},"obj":"Body_part"}],"attributes":[{"id":"A29","pred":"uberon_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/UBERON_0003126"},{"id":"A30","pred":"uberon_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/UBERON_0002185"},{"id":"A31","pred":"uberon_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/UBERON_0001456"}],"text":"Bacterial, fungal and viral secondary infections or co-infections affect mortality. Acinetobacter baumanii, Klebsiella pneumonia and Aspergillus species are important nosocomial pathogens [93] complicating the disease course. Studies from France [51], Germany [50], Belgium [52], and the Netherlands [47], underline the role of CAPA. Diagnosing co-infections is complex and rapid diagnosis plays a crucial role in this setting [49]. Close monitoring for infection development is needed, as well as longitudinal sampling throughout the disease course using culture dependent and independent techniques. Aspergillus antigen and PCR testing of respiratory fluids should be a routine procedure for critically ill patients [94], specifically for those suffering from ARDS [50]. Co-infection with human metapneumovirus has been reported in two of five cases in the German CAPA series [50]. It is unknown whether hospitals caring for COVID-19 test comprehensive respiratory pathogen panels, and to date no analysis of mixed viral infection in COVID-19 patients has been reported. In the context of COVID-19, mixed viral infection may be misinterpreted as presence of innocent bystanders and thus remain underreported. With bronchoalveolar lavage and autopsy regarded as high-risk procedures, key diagnostic instruments are lacking. Autopsy studies are key to understanding pathophysiology of COVID-19 [95] and are critically enlighten interaction between SARS-CoV-2 and different pathogens. With availability of lower respiratory samples, normally obtained by BALF, the quality of microbiological and virological work up would be greatly improved. Inspection of trachea and bronchi is achieved by bronchoscopy, which is critical to find possible Aspergillus tracheobronchitis. Thus, physicians face the dilemma of taking the hazard of aerosolization of SARS-CoV-2, risking transmission versus the endeavor of facilitating the optimal diagnosis and treatment to the patients entrusted to their care."}

LitCovid-PubTator

LitCovid-PD-MONDO

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T209","span":{"begin":275,"end":277},"obj":"http://purl.obolibrary.org/obo/CLO_0001407"},{"id":"T210","span":{"begin":396,"end":397},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T211","span":{"begin":630,"end":637},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T212","span":{"begin":670,"end":671},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T213","span":{"begin":719,"end":721},"obj":"http://purl.obolibrary.org/obo/CLO_0001527"},{"id":"T214","span":{"begin":791,"end":796},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T215","span":{"begin":813,"end":816},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T216","span":{"begin":936,"end":940},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T217","span":{"begin":1054,"end":1057},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T218","span":{"begin":1300,"end":1311},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"},{"id":"T219","span":{"begin":1787,"end":1791},"obj":"http://purl.obolibrary.org/obo/UBERON_0001456"}],"text":"Bacterial, fungal and viral secondary infections or co-infections affect mortality. Acinetobacter baumanii, Klebsiella pneumonia and Aspergillus species are important nosocomial pathogens [93] complicating the disease course. Studies from France [51], Germany [50], Belgium [52], and the Netherlands [47], underline the role of CAPA. Diagnosing co-infections is complex and rapid diagnosis plays a crucial role in this setting [49]. Close monitoring for infection development is needed, as well as longitudinal sampling throughout the disease course using culture dependent and independent techniques. Aspergillus antigen and PCR testing of respiratory fluids should be a routine procedure for critically ill patients [94], specifically for those suffering from ARDS [50]. Co-infection with human metapneumovirus has been reported in two of five cases in the German CAPA series [50]. It is unknown whether hospitals caring for COVID-19 test comprehensive respiratory pathogen panels, and to date no analysis of mixed viral infection in COVID-19 patients has been reported. In the context of COVID-19, mixed viral infection may be misinterpreted as presence of innocent bystanders and thus remain underreported. With bronchoalveolar lavage and autopsy regarded as high-risk procedures, key diagnostic instruments are lacking. Autopsy studies are key to understanding pathophysiology of COVID-19 [95] and are critically enlighten interaction between SARS-CoV-2 and different pathogens. With availability of lower respiratory samples, normally obtained by BALF, the quality of microbiological and virological work up would be greatly improved. Inspection of trachea and bronchi is achieved by bronchoscopy, which is critical to find possible Aspergillus tracheobronchitis. Thus, physicians face the dilemma of taking the hazard of aerosolization of SARS-CoV-2, risking transmission versus the endeavor of facilitating the optimal diagnosis and treatment to the patients entrusted to their care."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T187","span":{"begin":614,"end":621},"obj":"Chemical"},{"id":"T188","span":{"begin":773,"end":775},"obj":"Chemical"}],"attributes":[{"id":"A187","pred":"chebi_id","subj":"T187","obj":"http://purl.obolibrary.org/obo/CHEBI_59132"},{"id":"A188","pred":"chebi_id","subj":"T188","obj":"http://purl.obolibrary.org/obo/CHEBI_27638"}],"text":"Bacterial, fungal and viral secondary infections or co-infections affect mortality. Acinetobacter baumanii, Klebsiella pneumonia and Aspergillus species are important nosocomial pathogens [93] complicating the disease course. Studies from France [51], Germany [50], Belgium [52], and the Netherlands [47], underline the role of CAPA. Diagnosing co-infections is complex and rapid diagnosis plays a crucial role in this setting [49]. Close monitoring for infection development is needed, as well as longitudinal sampling throughout the disease course using culture dependent and independent techniques. Aspergillus antigen and PCR testing of respiratory fluids should be a routine procedure for critically ill patients [94], specifically for those suffering from ARDS [50]. Co-infection with human metapneumovirus has been reported in two of five cases in the German CAPA series [50]. It is unknown whether hospitals caring for COVID-19 test comprehensive respiratory pathogen panels, and to date no analysis of mixed viral infection in COVID-19 patients has been reported. In the context of COVID-19, mixed viral infection may be misinterpreted as presence of innocent bystanders and thus remain underreported. With bronchoalveolar lavage and autopsy regarded as high-risk procedures, key diagnostic instruments are lacking. Autopsy studies are key to understanding pathophysiology of COVID-19 [95] and are critically enlighten interaction between SARS-CoV-2 and different pathogens. With availability of lower respiratory samples, normally obtained by BALF, the quality of microbiological and virological work up would be greatly improved. Inspection of trachea and bronchi is achieved by bronchoscopy, which is critical to find possible Aspergillus tracheobronchitis. Thus, physicians face the dilemma of taking the hazard of aerosolization of SARS-CoV-2, risking transmission versus the endeavor of facilitating the optimal diagnosis and treatment to the patients entrusted to their care."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T36","span":{"begin":1017,"end":1032},"obj":"http://purl.obolibrary.org/obo/GO_0016032"},{"id":"T37","span":{"begin":1107,"end":1122},"obj":"http://purl.obolibrary.org/obo/GO_0016032"}],"text":"Bacterial, fungal and viral secondary infections or co-infections affect mortality. Acinetobacter baumanii, Klebsiella pneumonia and Aspergillus species are important nosocomial pathogens [93] complicating the disease course. Studies from France [51], Germany [50], Belgium [52], and the Netherlands [47], underline the role of CAPA. Diagnosing co-infections is complex and rapid diagnosis plays a crucial role in this setting [49]. Close monitoring for infection development is needed, as well as longitudinal sampling throughout the disease course using culture dependent and independent techniques. Aspergillus antigen and PCR testing of respiratory fluids should be a routine procedure for critically ill patients [94], specifically for those suffering from ARDS [50]. Co-infection with human metapneumovirus has been reported in two of five cases in the German CAPA series [50]. It is unknown whether hospitals caring for COVID-19 test comprehensive respiratory pathogen panels, and to date no analysis of mixed viral infection in COVID-19 patients has been reported. In the context of COVID-19, mixed viral infection may be misinterpreted as presence of innocent bystanders and thus remain underreported. With bronchoalveolar lavage and autopsy regarded as high-risk procedures, key diagnostic instruments are lacking. Autopsy studies are key to understanding pathophysiology of COVID-19 [95] and are critically enlighten interaction between SARS-CoV-2 and different pathogens. With availability of lower respiratory samples, normally obtained by BALF, the quality of microbiological and virological work up would be greatly improved. Inspection of trachea and bronchi is achieved by bronchoscopy, which is critical to find possible Aspergillus tracheobronchitis. Thus, physicians face the dilemma of taking the hazard of aerosolization of SARS-CoV-2, risking transmission versus the endeavor of facilitating the optimal diagnosis and treatment to the patients entrusted to their care."}

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T53","span":{"begin":119,"end":128},"obj":"Phenotype"}],"attributes":[{"id":"A53","pred":"hp_id","subj":"T53","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"Bacterial, fungal and viral secondary infections or co-infections affect mortality. Acinetobacter baumanii, Klebsiella pneumonia and Aspergillus species are important nosocomial pathogens [93] complicating the disease course. Studies from France [51], Germany [50], Belgium [52], and the Netherlands [47], underline the role of CAPA. Diagnosing co-infections is complex and rapid diagnosis plays a crucial role in this setting [49]. Close monitoring for infection development is needed, as well as longitudinal sampling throughout the disease course using culture dependent and independent techniques. Aspergillus antigen and PCR testing of respiratory fluids should be a routine procedure for critically ill patients [94], specifically for those suffering from ARDS [50]. Co-infection with human metapneumovirus has been reported in two of five cases in the German CAPA series [50]. It is unknown whether hospitals caring for COVID-19 test comprehensive respiratory pathogen panels, and to date no analysis of mixed viral infection in COVID-19 patients has been reported. In the context of COVID-19, mixed viral infection may be misinterpreted as presence of innocent bystanders and thus remain underreported. With bronchoalveolar lavage and autopsy regarded as high-risk procedures, key diagnostic instruments are lacking. Autopsy studies are key to understanding pathophysiology of COVID-19 [95] and are critically enlighten interaction between SARS-CoV-2 and different pathogens. With availability of lower respiratory samples, normally obtained by BALF, the quality of microbiological and virological work up would be greatly improved. Inspection of trachea and bronchi is achieved by bronchoscopy, which is critical to find possible Aspergillus tracheobronchitis. Thus, physicians face the dilemma of taking the hazard of aerosolization of SARS-CoV-2, risking transmission versus the endeavor of facilitating the optimal diagnosis and treatment to the patients entrusted to their care."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T136","span":{"begin":0,"end":83},"obj":"Sentence"},{"id":"T137","span":{"begin":84,"end":225},"obj":"Sentence"},{"id":"T138","span":{"begin":226,"end":333},"obj":"Sentence"},{"id":"T139","span":{"begin":334,"end":432},"obj":"Sentence"},{"id":"T140","span":{"begin":433,"end":601},"obj":"Sentence"},{"id":"T141","span":{"begin":602,"end":772},"obj":"Sentence"},{"id":"T142","span":{"begin":773,"end":883},"obj":"Sentence"},{"id":"T143","span":{"begin":884,"end":1072},"obj":"Sentence"},{"id":"T144","span":{"begin":1073,"end":1210},"obj":"Sentence"},{"id":"T145","span":{"begin":1211,"end":1324},"obj":"Sentence"},{"id":"T146","span":{"begin":1325,"end":1483},"obj":"Sentence"},{"id":"T147","span":{"begin":1484,"end":1640},"obj":"Sentence"},{"id":"T148","span":{"begin":1641,"end":1769},"obj":"Sentence"},{"id":"T149","span":{"begin":1770,"end":1991},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Bacterial, fungal and viral secondary infections or co-infections affect mortality. Acinetobacter baumanii, Klebsiella pneumonia and Aspergillus species are important nosocomial pathogens [93] complicating the disease course. Studies from France [51], Germany [50], Belgium [52], and the Netherlands [47], underline the role of CAPA. Diagnosing co-infections is complex and rapid diagnosis plays a crucial role in this setting [49]. Close monitoring for infection development is needed, as well as longitudinal sampling throughout the disease course using culture dependent and independent techniques. Aspergillus antigen and PCR testing of respiratory fluids should be a routine procedure for critically ill patients [94], specifically for those suffering from ARDS [50]. Co-infection with human metapneumovirus has been reported in two of five cases in the German CAPA series [50]. It is unknown whether hospitals caring for COVID-19 test comprehensive respiratory pathogen panels, and to date no analysis of mixed viral infection in COVID-19 patients has been reported. In the context of COVID-19, mixed viral infection may be misinterpreted as presence of innocent bystanders and thus remain underreported. With bronchoalveolar lavage and autopsy regarded as high-risk procedures, key diagnostic instruments are lacking. Autopsy studies are key to understanding pathophysiology of COVID-19 [95] and are critically enlighten interaction between SARS-CoV-2 and different pathogens. With availability of lower respiratory samples, normally obtained by BALF, the quality of microbiological and virological work up would be greatly improved. Inspection of trachea and bronchi is achieved by bronchoscopy, which is critical to find possible Aspergillus tracheobronchitis. Thus, physicians face the dilemma of taking the hazard of aerosolization of SARS-CoV-2, risking transmission versus the endeavor of facilitating the optimal diagnosis and treatment to the patients entrusted to their care."}

2_test

{"project":"2_test","denotations":[{"id":"32599813-32339350-60095161","span":{"begin":261,"end":263},"obj":"32339350"},{"id":"32599813-32488446-60095162","span":{"begin":275,"end":277},"obj":"32488446"},{"id":"32599813-31905234-60095163","span":{"begin":719,"end":721},"obj":"31905234"},{"id":"32599813-32339350-60095164","span":{"begin":768,"end":770},"obj":"32339350"},{"id":"32599813-32339350-60095165","span":{"begin":879,"end":881},"obj":"32339350"},{"id":"32599813-32437596-60095166","span":{"begin":1395,"end":1397},"obj":"32437596"}],"text":"Bacterial, fungal and viral secondary infections or co-infections affect mortality. Acinetobacter baumanii, Klebsiella pneumonia and Aspergillus species are important nosocomial pathogens [93] complicating the disease course. Studies from France [51], Germany [50], Belgium [52], and the Netherlands [47], underline the role of CAPA. Diagnosing co-infections is complex and rapid diagnosis plays a crucial role in this setting [49]. Close monitoring for infection development is needed, as well as longitudinal sampling throughout the disease course using culture dependent and independent techniques. Aspergillus antigen and PCR testing of respiratory fluids should be a routine procedure for critically ill patients [94], specifically for those suffering from ARDS [50]. Co-infection with human metapneumovirus has been reported in two of five cases in the German CAPA series [50]. It is unknown whether hospitals caring for COVID-19 test comprehensive respiratory pathogen panels, and to date no analysis of mixed viral infection in COVID-19 patients has been reported. In the context of COVID-19, mixed viral infection may be misinterpreted as presence of innocent bystanders and thus remain underreported. With bronchoalveolar lavage and autopsy regarded as high-risk procedures, key diagnostic instruments are lacking. Autopsy studies are key to understanding pathophysiology of COVID-19 [95] and are critically enlighten interaction between SARS-CoV-2 and different pathogens. With availability of lower respiratory samples, normally obtained by BALF, the quality of microbiological and virological work up would be greatly improved. Inspection of trachea and bronchi is achieved by bronchoscopy, which is critical to find possible Aspergillus tracheobronchitis. Thus, physicians face the dilemma of taking the hazard of aerosolization of SARS-CoV-2, risking transmission versus the endeavor of facilitating the optimal diagnosis and treatment to the patients entrusted to their care."}

PMC:7346000 / 25760-27751 JSONTXT

Annnotations TAB JSON ListView MergeView

PMC:7346000 / 25760-27751 JSON TXT