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2_test

{"project":"2_test","denotations":[{"id":"32505227-18832706-46575337","span":{"begin":1667,"end":1671},"obj":"18832706"},{"id":"T22604","span":{"begin":1667,"end":1671},"obj":"18832706"}],"text":"In addition, several studies reported higher expression of various co-stimulatory and inhibitory molecules such as OX-40 and CD137 (Zhou et al., 2020c), CTLA-4 and TIGIT (Zheng et al., 2020a), and NKG2a (Zheng et al., 2020b). Reduced numbers of CD28+ CD8 T cells (Qin et al., 2020) as well as larger frequencies of PD-1+ TIM3+ CD8 T cells in ICU patients were also reported (Zhou et al., 2020c). Expression of most of these markers was found to be higher in CD8 than in CD4 T cells, and levels tended to increase in severe versus non-severe cases, which may be due to differences in viral load. Cellular functionality was shown to be impaired in CD4 and CD8 T cells of critically ill patients, with reduced frequencies of polyfunctional T cells (producing more than one cytokine) as well as generally lower IFN-γ and TNF-α production following restimulation with phorbol myristate acetate (PMA) and ionomycin (Chen et al., 2020c, Zheng et al., 2020a, Zheng et al., 2020b). Similarly, Zheng et al. reported that CD8 T cells in severe COVID-19 appear less cytotoxic and effector-like with reduced CD107a degranulation and granzyme B (GzmB) production (Zheng et al., 2020b). In contrast, a different study found that both GzmB and perforin were increased in CD8 T cells of severely sick patients (Zheng et al., 2020a). In accordance with the latter observation, when compared to a moderate disease group, convalescent patients with resolved severe SARS-CoV-1 infection had significantly higher frequencies of polyfunctional T cells, with CD4 T cells producing more IFN-γ, TNF-α, and IL-2 and CD8 T cells producing more IFN-γ, TNF-α, and CD107a, respectively (Li et al., 2008). However, given the vigorous dynamics of acute T cell responses and potential differences in sample timing throughout disease course, these observations are not necessarily mutually exclusive. Accordingly, RNA sequencing (RNA-seq) data by Liao et al. showed that CD8 T cells in the BAL fluid of severe COVID-19 patients express cytotoxic genes such as GZMA, GZMB, and GZMK at higher levels, while KLRC1 and XCL1 are enriched in mild cases (Liao et al., 2020)."}

LitCovid-PD-FMA-UBERON

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T268","span":{"begin":890,"end":893},"obj":"Disease"},{"id":"T270","span":{"begin":1033,"end":1041},"obj":"Disease"},{"id":"T271","span":{"begin":1445,"end":1453},"obj":"Disease"},{"id":"T272","span":{"begin":1456,"end":1465},"obj":"Disease"},{"id":"T273","span":{"begin":1975,"end":1983},"obj":"Disease"}],"attributes":[{"id":"A268","pred":"mondo_id","subj":"T268","obj":"http://purl.obolibrary.org/obo/MONDO_0016692"},{"id":"A269","pred":"mondo_id","subj":"T268","obj":"http://purl.obolibrary.org/obo/MONDO_0018687"},{"id":"A270","pred":"mondo_id","subj":"T270","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A271","pred":"mondo_id","subj":"T271","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A272","pred":"mondo_id","subj":"T272","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A273","pred":"mondo_id","subj":"T273","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"In addition, several studies reported higher expression of various co-stimulatory and inhibitory molecules such as OX-40 and CD137 (Zhou et al., 2020c), CTLA-4 and TIGIT (Zheng et al., 2020a), and NKG2a (Zheng et al., 2020b). Reduced numbers of CD28+ CD8 T cells (Qin et al., 2020) as well as larger frequencies of PD-1+ TIM3+ CD8 T cells in ICU patients were also reported (Zhou et al., 2020c). Expression of most of these markers was found to be higher in CD8 than in CD4 T cells, and levels tended to increase in severe versus non-severe cases, which may be due to differences in viral load. Cellular functionality was shown to be impaired in CD4 and CD8 T cells of critically ill patients, with reduced frequencies of polyfunctional T cells (producing more than one cytokine) as well as generally lower IFN-γ and TNF-α production following restimulation with phorbol myristate acetate (PMA) and ionomycin (Chen et al., 2020c, Zheng et al., 2020a, Zheng et al., 2020b). Similarly, Zheng et al. reported that CD8 T cells in severe COVID-19 appear less cytotoxic and effector-like with reduced CD107a degranulation and granzyme B (GzmB) production (Zheng et al., 2020b). In contrast, a different study found that both GzmB and perforin were increased in CD8 T cells of severely sick patients (Zheng et al., 2020a). In accordance with the latter observation, when compared to a moderate disease group, convalescent patients with resolved severe SARS-CoV-1 infection had significantly higher frequencies of polyfunctional T cells, with CD4 T cells producing more IFN-γ, TNF-α, and IL-2 and CD8 T cells producing more IFN-γ, TNF-α, and CD107a, respectively (Li et al., 2008). However, given the vigorous dynamics of acute T cell responses and potential differences in sample timing throughout disease course, these observations are not necessarily mutually exclusive. Accordingly, RNA sequencing (RNA-seq) data by Liao et al. showed that CD8 T cells in the BAL fluid of severe COVID-19 patients express cytotoxic genes such as GZMA, GZMB, and GZMK at higher levels, while KLRC1 and XCL1 are enriched in mild cases (Liao et al., 2020)."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PubTator

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T222","span":{"begin":0,"end":225},"obj":"Sentence"},{"id":"T223","span":{"begin":226,"end":395},"obj":"Sentence"},{"id":"T224","span":{"begin":396,"end":594},"obj":"Sentence"},{"id":"T225","span":{"begin":595,"end":972},"obj":"Sentence"},{"id":"T226","span":{"begin":973,"end":1171},"obj":"Sentence"},{"id":"T227","span":{"begin":1172,"end":1315},"obj":"Sentence"},{"id":"T228","span":{"begin":1316,"end":1673},"obj":"Sentence"},{"id":"T229","span":{"begin":1674,"end":1865},"obj":"Sentence"},{"id":"T230","span":{"begin":1866,"end":2132},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In addition, several studies reported higher expression of various co-stimulatory and inhibitory molecules such as OX-40 and CD137 (Zhou et al., 2020c), CTLA-4 and TIGIT (Zheng et al., 2020a), and NKG2a (Zheng et al., 2020b). Reduced numbers of CD28+ CD8 T cells (Qin et al., 2020) as well as larger frequencies of PD-1+ TIM3+ CD8 T cells in ICU patients were also reported (Zhou et al., 2020c). Expression of most of these markers was found to be higher in CD8 than in CD4 T cells, and levels tended to increase in severe versus non-severe cases, which may be due to differences in viral load. Cellular functionality was shown to be impaired in CD4 and CD8 T cells of critically ill patients, with reduced frequencies of polyfunctional T cells (producing more than one cytokine) as well as generally lower IFN-γ and TNF-α production following restimulation with phorbol myristate acetate (PMA) and ionomycin (Chen et al., 2020c, Zheng et al., 2020a, Zheng et al., 2020b). Similarly, Zheng et al. reported that CD8 T cells in severe COVID-19 appear less cytotoxic and effector-like with reduced CD107a degranulation and granzyme B (GzmB) production (Zheng et al., 2020b). In contrast, a different study found that both GzmB and perforin were increased in CD8 T cells of severely sick patients (Zheng et al., 2020a). In accordance with the latter observation, when compared to a moderate disease group, convalescent patients with resolved severe SARS-CoV-1 infection had significantly higher frequencies of polyfunctional T cells, with CD4 T cells producing more IFN-γ, TNF-α, and IL-2 and CD8 T cells producing more IFN-γ, TNF-α, and CD107a, respectively (Li et al., 2008). However, given the vigorous dynamics of acute T cell responses and potential differences in sample timing throughout disease course, these observations are not necessarily mutually exclusive. Accordingly, RNA sequencing (RNA-seq) data by Liao et al. showed that CD8 T cells in the BAL fluid of severe COVID-19 patients express cytotoxic genes such as GZMA, GZMB, and GZMK at higher levels, while KLRC1 and XCL1 are enriched in mild cases (Liao et al., 2020)."}