PMC:7402624 / 16801-18448 JSON TXT

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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T117","span":{"begin":184,"end":189},"obj":"Body_part"},{"id":"T118","span":{"begin":271,"end":274},"obj":"Body_part"},{"id":"T119","span":{"begin":334,"end":339},"obj":"Body_part"},{"id":"T120","span":{"begin":378,"end":381},"obj":"Body_part"},{"id":"T121","span":{"begin":558,"end":563},"obj":"Body_part"},{"id":"T122","span":{"begin":884,"end":888},"obj":"Body_part"},{"id":"T123","span":{"begin":973,"end":978},"obj":"Body_part"},{"id":"T124","span":{"begin":1207,"end":1210},"obj":"Body_part"},{"id":"T125","span":{"begin":1255,"end":1260},"obj":"Body_part"},{"id":"T126","span":{"begin":1511,"end":1515},"obj":"Body_part"},{"id":"T127","span":{"begin":1615,"end":1620},"obj":"Body_part"}],"attributes":[{"id":"A117","pred":"fma_id","subj":"T117","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A118","pred":"fma_id","subj":"T118","obj":"http://purl.org/sig/ont/fma/fma67847"},{"id":"A119","pred":"fma_id","subj":"T119","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A120","pred":"fma_id","subj":"T120","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A121","pred":"fma_id","subj":"T121","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A122","pred":"fma_id","subj":"T122","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A123","pred":"fma_id","subj":"T123","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A124","pred":"fma_id","subj":"T124","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A125","pred":"fma_id","subj":"T125","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A126","pred":"fma_id","subj":"T126","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A127","pred":"fma_id","subj":"T127","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"To gain more insights, we applied global high-dimensional mapping of the 27-parameter flow cytometry data. A tSNE representation of the data highlighted key regions of non-naïve CD8 T cells found preferentially in COVID-19 patients (Fig. 2G). A major region of this tSNE map present in COVID-19 patients, but not HD or RD, were CD8 T cells that enriched for expression of CD38, HLA-DR, KI67, CD39, and PD1 (Fig. 2G), highlighting the co-expression of these activation markers with other features including CD95 (i.e., FAS). Notably, although non-naïve CD8 T cells from RD were highly similar to those from HD, subtle differences existed, including in the lower region highlighted by T-bet and CX3CR1 (Fig. 2G). To further define and quantify these differences between COVID-19 patients and controls, we performed FlowSOM clustering (Fig. 2H) and compared expression of fourteen CD8 T cell markers to identify each cluster (Fig. 2I). This approach identified an increase in cells in several clusters including Clusters 1, 2, and 5 in COVID-19 patients, reflecting CD45RA+CD27−CCR7− TEMRA-like populations that expressed CX3CR1 and varying levels of T-bet (Fig. 2, I and J). Clusters 12 and 14 contained CD27+HLA-DR+CD38+KI67+PD-1+ activated, proliferating cells and were more prevalent in COVID-19 disease (Fig. 2, I and J, and fig. S2F). In contrast, the central Eomes+CD45RA−CD27+CCR7− EM1-like Cluster 6 and T-bethiCX3CR1+ Cluster 11 were decreased compared to HD (Fig. 2, I and J, and fig. S2F). Thus, CD8 T cell responses in COVID-19 patients were characterized by populations of activated, proliferating CD8 T cells in a subgroup of patients."}

LitCovid-PubTator

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T127","span":{"begin":214,"end":222},"obj":"Disease"},{"id":"T128","span":{"begin":286,"end":294},"obj":"Disease"},{"id":"T129","span":{"begin":313,"end":315},"obj":"Disease"},{"id":"T130","span":{"begin":319,"end":321},"obj":"Disease"},{"id":"T131","span":{"begin":518,"end":521},"obj":"Disease"},{"id":"T132","span":{"begin":569,"end":571},"obj":"Disease"},{"id":"T133","span":{"begin":606,"end":608},"obj":"Disease"},{"id":"T134","span":{"begin":768,"end":776},"obj":"Disease"},{"id":"T135","span":{"begin":1033,"end":1041},"obj":"Disease"},{"id":"T136","span":{"begin":1288,"end":1296},"obj":"Disease"},{"id":"T137","span":{"begin":1463,"end":1465},"obj":"Disease"},{"id":"T138","span":{"begin":1529,"end":1537},"obj":"Disease"}],"attributes":[{"id":"A127","pred":"mondo_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A128","pred":"mondo_id","subj":"T128","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A129","pred":"mondo_id","subj":"T129","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A130","pred":"mondo_id","subj":"T130","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"},{"id":"A131","pred":"mondo_id","subj":"T131","obj":"http://purl.obolibrary.org/obo/MONDO_0016011"},{"id":"A132","pred":"mondo_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"},{"id":"A133","pred":"mondo_id","subj":"T133","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A134","pred":"mondo_id","subj":"T134","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A135","pred":"mondo_id","subj":"T135","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A136","pred":"mondo_id","subj":"T136","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A137","pred":"mondo_id","subj":"T137","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A138","pred":"mondo_id","subj":"T138","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"To gain more insights, we applied global high-dimensional mapping of the 27-parameter flow cytometry data. A tSNE representation of the data highlighted key regions of non-naïve CD8 T cells found preferentially in COVID-19 patients (Fig. 2G). A major region of this tSNE map present in COVID-19 patients, but not HD or RD, were CD8 T cells that enriched for expression of CD38, HLA-DR, KI67, CD39, and PD1 (Fig. 2G), highlighting the co-expression of these activation markers with other features including CD95 (i.e., FAS). Notably, although non-naïve CD8 T cells from RD were highly similar to those from HD, subtle differences existed, including in the lower region highlighted by T-bet and CX3CR1 (Fig. 2G). To further define and quantify these differences between COVID-19 patients and controls, we performed FlowSOM clustering (Fig. 2H) and compared expression of fourteen CD8 T cell markers to identify each cluster (Fig. 2I). This approach identified an increase in cells in several clusters including Clusters 1, 2, and 5 in COVID-19 patients, reflecting CD45RA+CD27−CCR7− TEMRA-like populations that expressed CX3CR1 and varying levels of T-bet (Fig. 2, I and J). Clusters 12 and 14 contained CD27+HLA-DR+CD38+KI67+PD-1+ activated, proliferating cells and were more prevalent in COVID-19 disease (Fig. 2, I and J, and fig. S2F). In contrast, the central Eomes+CD45RA−CD27+CCR7− EM1-like Cluster 6 and T-bethiCX3CR1+ Cluster 11 were decreased compared to HD (Fig. 2, I and J, and fig. S2F). Thus, CD8 T cell responses in COVID-19 patients were characterized by populations of activated, proliferating CD8 T cells in a subgroup of patients."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T84","span":{"begin":313,"end":315},"obj":"Chemical"},{"id":"T85","span":{"begin":319,"end":321},"obj":"Chemical"},{"id":"T86","span":{"begin":382,"end":384},"obj":"Chemical"},{"id":"T87","span":{"begin":402,"end":405},"obj":"Chemical"},{"id":"T88","span":{"begin":518,"end":521},"obj":"Chemical"},{"id":"T89","span":{"begin":569,"end":571},"obj":"Chemical"},{"id":"T90","span":{"begin":606,"end":608},"obj":"Chemical"},{"id":"T91","span":{"begin":1211,"end":1213},"obj":"Chemical"},{"id":"T92","span":{"begin":1224,"end":1226},"obj":"Chemical"},{"id":"T93","span":{"begin":1463,"end":1465},"obj":"Chemical"}],"attributes":[{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A85","pred":"chebi_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"},{"id":"A86","pred":"chebi_id","subj":"T86","obj":"http://purl.obolibrary.org/obo/CHEBI_73445"},{"id":"A87","pred":"chebi_id","subj":"T87","obj":"http://purl.obolibrary.org/obo/CHEBI_138655"},{"id":"A88","pred":"chebi_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/CHEBI_76181"},{"id":"A89","pred":"chebi_id","subj":"T89","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"},{"id":"A90","pred":"chebi_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A91","pred":"chebi_id","subj":"T91","obj":"http://purl.obolibrary.org/obo/CHEBI_73445"},{"id":"A92","pred":"chebi_id","subj":"T92","obj":"http://purl.obolibrary.org/obo/CHEBI_74756"},{"id":"A93","pred":"chebi_id","subj":"T93","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"}],"text":"To gain more insights, we applied global high-dimensional mapping of the 27-parameter flow cytometry data. A tSNE representation of the data highlighted key regions of non-naïve CD8 T cells found preferentially in COVID-19 patients (Fig. 2G). A major region of this tSNE map present in COVID-19 patients, but not HD or RD, were CD8 T cells that enriched for expression of CD38, HLA-DR, KI67, CD39, and PD1 (Fig. 2G), highlighting the co-expression of these activation markers with other features including CD95 (i.e., FAS). Notably, although non-naïve CD8 T cells from RD were highly similar to those from HD, subtle differences existed, including in the lower region highlighted by T-bet and CX3CR1 (Fig. 2G). To further define and quantify these differences between COVID-19 patients and controls, we performed FlowSOM clustering (Fig. 2H) and compared expression of fourteen CD8 T cell markers to identify each cluster (Fig. 2I). This approach identified an increase in cells in several clusters including Clusters 1, 2, and 5 in COVID-19 patients, reflecting CD45RA+CD27−CCR7− TEMRA-like populations that expressed CX3CR1 and varying levels of T-bet (Fig. 2, I and J). Clusters 12 and 14 contained CD27+HLA-DR+CD38+KI67+PD-1+ activated, proliferating cells and were more prevalent in COVID-19 disease (Fig. 2, I and J, and fig. S2F). In contrast, the central Eomes+CD45RA−CD27+CCR7− EM1-like Cluster 6 and T-bethiCX3CR1+ Cluster 11 were decreased compared to HD (Fig. 2, I and J, and fig. S2F). Thus, CD8 T cell responses in COVID-19 patients were characterized by populations of activated, proliferating CD8 T cells in a subgroup of patients."}

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T7","span":{"begin":1387,"end":1390},"obj":"GlycoEpitope"}],"attributes":[{"id":"A7","pred":"glyco_epitope_db_id","subj":"T7","obj":"http://www.glycoepitope.jp/epitopes/AN0701"}],"text":"To gain more insights, we applied global high-dimensional mapping of the 27-parameter flow cytometry data. A tSNE representation of the data highlighted key regions of non-naïve CD8 T cells found preferentially in COVID-19 patients (Fig. 2G). A major region of this tSNE map present in COVID-19 patients, but not HD or RD, were CD8 T cells that enriched for expression of CD38, HLA-DR, KI67, CD39, and PD1 (Fig. 2G), highlighting the co-expression of these activation markers with other features including CD95 (i.e., FAS). Notably, although non-naïve CD8 T cells from RD were highly similar to those from HD, subtle differences existed, including in the lower region highlighted by T-bet and CX3CR1 (Fig. 2G). To further define and quantify these differences between COVID-19 patients and controls, we performed FlowSOM clustering (Fig. 2H) and compared expression of fourteen CD8 T cell markers to identify each cluster (Fig. 2I). This approach identified an increase in cells in several clusters including Clusters 1, 2, and 5 in COVID-19 patients, reflecting CD45RA+CD27−CCR7− TEMRA-like populations that expressed CX3CR1 and varying levels of T-bet (Fig. 2, I and J). Clusters 12 and 14 contained CD27+HLA-DR+CD38+KI67+PD-1+ activated, proliferating cells and were more prevalent in COVID-19 disease (Fig. 2, I and J, and fig. S2F). In contrast, the central Eomes+CD45RA−CD27+CCR7− EM1-like Cluster 6 and T-bethiCX3CR1+ Cluster 11 were decreased compared to HD (Fig. 2, I and J, and fig. S2F). Thus, CD8 T cell responses in COVID-19 patients were characterized by populations of activated, proliferating CD8 T cells in a subgroup of patients."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T107","span":{"begin":0,"end":106},"obj":"Sentence"},{"id":"T108","span":{"begin":107,"end":242},"obj":"Sentence"},{"id":"T109","span":{"begin":243,"end":523},"obj":"Sentence"},{"id":"T110","span":{"begin":524,"end":710},"obj":"Sentence"},{"id":"T111","span":{"begin":711,"end":932},"obj":"Sentence"},{"id":"T112","span":{"begin":933,"end":1172},"obj":"Sentence"},{"id":"T113","span":{"begin":1173,"end":1337},"obj":"Sentence"},{"id":"T114","span":{"begin":1338,"end":1498},"obj":"Sentence"},{"id":"T115","span":{"begin":1499,"end":1647},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To gain more insights, we applied global high-dimensional mapping of the 27-parameter flow cytometry data. A tSNE representation of the data highlighted key regions of non-naïve CD8 T cells found preferentially in COVID-19 patients (Fig. 2G). A major region of this tSNE map present in COVID-19 patients, but not HD or RD, were CD8 T cells that enriched for expression of CD38, HLA-DR, KI67, CD39, and PD1 (Fig. 2G), highlighting the co-expression of these activation markers with other features including CD95 (i.e., FAS). Notably, although non-naïve CD8 T cells from RD were highly similar to those from HD, subtle differences existed, including in the lower region highlighted by T-bet and CX3CR1 (Fig. 2G). To further define and quantify these differences between COVID-19 patients and controls, we performed FlowSOM clustering (Fig. 2H) and compared expression of fourteen CD8 T cell markers to identify each cluster (Fig. 2I). This approach identified an increase in cells in several clusters including Clusters 1, 2, and 5 in COVID-19 patients, reflecting CD45RA+CD27−CCR7− TEMRA-like populations that expressed CX3CR1 and varying levels of T-bet (Fig. 2, I and J). Clusters 12 and 14 contained CD27+HLA-DR+CD38+KI67+PD-1+ activated, proliferating cells and were more prevalent in COVID-19 disease (Fig. 2, I and J, and fig. S2F). In contrast, the central Eomes+CD45RA−CD27+CCR7− EM1-like Cluster 6 and T-bethiCX3CR1+ Cluster 11 were decreased compared to HD (Fig. 2, I and J, and fig. S2F). Thus, CD8 T cell responses in COVID-19 patients were characterized by populations of activated, proliferating CD8 T cells in a subgroup of patients."}