PMC:7402624 / 13598-14884 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T77","span":{"begin":6,"end":10},"obj":"Body_part"},{"id":"T78","span":{"begin":96,"end":100},"obj":"Body_part"},{"id":"T79","span":{"begin":108,"end":117},"obj":"Body_part"},{"id":"T80","span":{"begin":266,"end":270},"obj":"Body_part"},{"id":"T81","span":{"begin":305,"end":309},"obj":"Body_part"},{"id":"T82","span":{"begin":366,"end":371},"obj":"Body_part"},{"id":"T83","span":{"begin":406,"end":409},"obj":"Body_part"},{"id":"T84","span":{"begin":413,"end":424},"obj":"Body_part"},{"id":"T85","span":{"begin":419,"end":424},"obj":"Body_part"},{"id":"T86","span":{"begin":553,"end":558},"obj":"Body_part"},{"id":"T87","span":{"begin":600,"end":605},"obj":"Body_part"},{"id":"T88","span":{"begin":742,"end":749},"obj":"Body_part"},{"id":"T89","span":{"begin":802,"end":815},"obj":"Body_part"},{"id":"T90","span":{"begin":802,"end":806},"obj":"Body_part"},{"id":"T91","span":{"begin":959,"end":964},"obj":"Body_part"}],"attributes":[{"id":"A77","pred":"fma_id","subj":"T77","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A78","pred":"fma_id","subj":"T78","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A79","pred":"fma_id","subj":"T79","obj":"http://purl.org/sig/ont/fma/fma84050"},{"id":"A80","pred":"fma_id","subj":"T80","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A81","pred":"fma_id","subj":"T81","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A82","pred":"fma_id","subj":"T82","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A83","pred":"fma_id","subj":"T83","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A84","pred":"fma_id","subj":"T84","obj":"http://purl.org/sig/ont/fma/fma0326121"},{"id":"A85","pred":"fma_id","subj":"T85","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A86","pred":"fma_id","subj":"T86","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A87","pred":"fma_id","subj":"T87","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A88","pred":"fma_id","subj":"T88","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A89","pred":"fma_id","subj":"T89","obj":"http://purl.org/sig/ont/fma/fma62807"},{"id":"A90","pred":"fma_id","subj":"T90","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A91","pred":"fma_id","subj":"T91","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"CD8 T cell subset skewing and activation patterns in COVID-19 patients and potential links to T cell driven cytokines.\n(A) Principle Component Analysis (PCA) of aggregated flow cytometry data. (B) Representative flow cytometry plots of the gating strategy for CD8 T cell subsets. (C) Frequencies of CD8 T cell subsets as indicated. (D) Frequencies of PD1+ and CD39+ cells. Frequencies of (E) KI67+ and (F) HLA-DR+CD38+ cells and representative flow cytometry plots; green line at upper decile of HD. (G) (Top) Global viSNE projection of non-naïve CD8 T cells for all subjects pooled, non-naïve CD8 T cells from healthy donor (HD), recovered donor (RD), and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD8 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naive CD8 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (C, D, E, F, J) Each dot represents an individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 patient (red). Significance determined by unpaired Wilcoxon test with BH correction: *p \u003c 0.05, **p \u003c 0.01, ***p \u003c 0.001, and ****p \u003c 0.0001."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T7","span":{"begin":802,"end":815},"obj":"Body_part"}],"attributes":[{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0034922"}],"text":"CD8 T cell subset skewing and activation patterns in COVID-19 patients and potential links to T cell driven cytokines.\n(A) Principle Component Analysis (PCA) of aggregated flow cytometry data. (B) Representative flow cytometry plots of the gating strategy for CD8 T cell subsets. (C) Frequencies of CD8 T cell subsets as indicated. (D) Frequencies of PD1+ and CD39+ cells. Frequencies of (E) KI67+ and (F) HLA-DR+CD38+ cells and representative flow cytometry plots; green line at upper decile of HD. (G) (Top) Global viSNE projection of non-naïve CD8 T cells for all subjects pooled, non-naïve CD8 T cells from healthy donor (HD), recovered donor (RD), and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD8 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naive CD8 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (C, D, E, F, J) Each dot represents an individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 patient (red). Significance determined by unpaired Wilcoxon test with BH correction: *p \u003c 0.05, **p \u003c 0.01, ***p \u003c 0.001, and ****p \u003c 0.0001."}

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{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T54","span":{"begin":153,"end":156},"obj":"Chemical"},{"id":"T56","span":{"begin":351,"end":354},"obj":"Chemical"},{"id":"T57","span":{"begin":410,"end":412},"obj":"Chemical"},{"id":"T58","span":{"begin":496,"end":498},"obj":"Chemical"},{"id":"T59","span":{"begin":619,"end":624},"obj":"Chemical"},{"id":"T60","span":{"begin":626,"end":628},"obj":"Chemical"},{"id":"T61","span":{"begin":641,"end":646},"obj":"Chemical"},{"id":"T62","span":{"begin":648,"end":650},"obj":"Chemical"},{"id":"T63","span":{"begin":742,"end":749},"obj":"Chemical"},{"id":"T64","span":{"begin":1086,"end":1091},"obj":"Chemical"},{"id":"T65","span":{"begin":1093,"end":1095},"obj":"Chemical"},{"id":"T66","span":{"begin":1115,"end":1120},"obj":"Chemical"},{"id":"T67","span":{"begin":1122,"end":1124},"obj":"Chemical"}],"attributes":[{"id":"A54","pred":"chebi_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/CHEBI_36751"},{"id":"A55","pred":"chebi_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/CHEBI_62248"},{"id":"A56","pred":"chebi_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/CHEBI_138655"},{"id":"A57","pred":"chebi_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/CHEBI_73445"},{"id":"A58","pred":"chebi_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A59","pred":"chebi_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/CHEBI_17891"},{"id":"A60","pred":"chebi_id","subj":"T60","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A61","pred":"chebi_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/CHEBI_17891"},{"id":"A62","pred":"chebi_id","subj":"T62","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"},{"id":"A63","pred":"chebi_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A64","pred":"chebi_id","subj":"T64","obj":"http://purl.obolibrary.org/obo/CHEBI_17891"},{"id":"A65","pred":"chebi_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A66","pred":"chebi_id","subj":"T66","obj":"http://purl.obolibrary.org/obo/CHEBI_17891"},{"id":"A67","pred":"chebi_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"}],"text":"CD8 T cell subset skewing and activation patterns in COVID-19 patients and potential links to T cell driven cytokines.\n(A) Principle Component Analysis (PCA) of aggregated flow cytometry data. (B) Representative flow cytometry plots of the gating strategy for CD8 T cell subsets. (C) Frequencies of CD8 T cell subsets as indicated. (D) Frequencies of PD1+ and CD39+ cells. Frequencies of (E) KI67+ and (F) HLA-DR+CD38+ cells and representative flow cytometry plots; green line at upper decile of HD. (G) (Top) Global viSNE projection of non-naïve CD8 T cells for all subjects pooled, non-naïve CD8 T cells from healthy donor (HD), recovered donor (RD), and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD8 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naive CD8 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (C, D, E, F, J) Each dot represents an individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 patient (red). Significance determined by unpaired Wilcoxon test with BH correction: *p \u003c 0.05, **p \u003c 0.01, ***p \u003c 0.001, and ****p \u003c 0.0001."}

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