PMC:7402624 / 21574-23040
Annnotations
LitCovid-PD-FMA-UBERON
{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T160","span":{"begin":6,"end":10},"obj":"Body_part"},{"id":"T161","span":{"begin":86,"end":90},"obj":"Body_part"},{"id":"T162","span":{"begin":173,"end":177},"obj":"Body_part"},{"id":"T163","span":{"begin":212,"end":216},"obj":"Body_part"},{"id":"T164","span":{"begin":264,"end":269},"obj":"Body_part"},{"id":"T165","span":{"begin":369,"end":374},"obj":"Body_part"},{"id":"T166","span":{"begin":396,"end":401},"obj":"Body_part"},{"id":"T167","span":{"begin":425,"end":430},"obj":"Body_part"},{"id":"T168","span":{"begin":494,"end":497},"obj":"Body_part"},{"id":"T169","span":{"begin":501,"end":512},"obj":"Body_part"},{"id":"T170","span":{"begin":507,"end":512},"obj":"Body_part"},{"id":"T171","span":{"begin":606,"end":609},"obj":"Body_part"},{"id":"T172","span":{"begin":613,"end":624},"obj":"Body_part"},{"id":"T173","span":{"begin":619,"end":624},"obj":"Body_part"},{"id":"T174","span":{"begin":667,"end":672},"obj":"Body_part"},{"id":"T175","span":{"begin":770,"end":775},"obj":"Body_part"},{"id":"T176","span":{"begin":817,"end":822},"obj":"Body_part"},{"id":"T177","span":{"begin":925,"end":932},"obj":"Body_part"},{"id":"T178","span":{"begin":985,"end":998},"obj":"Body_part"},{"id":"T179","span":{"begin":985,"end":989},"obj":"Body_part"},{"id":"T180","span":{"begin":1142,"end":1147},"obj":"Body_part"}],"attributes":[{"id":"A160","pred":"fma_id","subj":"T160","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A161","pred":"fma_id","subj":"T161","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A162","pred":"fma_id","subj":"T162","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A163","pred":"fma_id","subj":"T163","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A164","pred":"fma_id","subj":"T164","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A165","pred":"fma_id","subj":"T165","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A166","pred":"fma_id","subj":"T166","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A167","pred":"fma_id","subj":"T167","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A168","pred":"fma_id","subj":"T168","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A169","pred":"fma_id","subj":"T169","obj":"http://purl.org/sig/ont/fma/fma0326121"},{"id":"A170","pred":"fma_id","subj":"T170","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A171","pred":"fma_id","subj":"T171","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A172","pred":"fma_id","subj":"T172","obj":"http://purl.org/sig/ont/fma/fma0326121"},{"id":"A173","pred":"fma_id","subj":"T173","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A174","pred":"fma_id","subj":"T174","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A175","pred":"fma_id","subj":"T175","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A176","pred":"fma_id","subj":"T176","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A177","pred":"fma_id","subj":"T177","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A178","pred":"fma_id","subj":"T178","obj":"http://purl.org/sig/ont/fma/fma62807"},{"id":"A179","pred":"fma_id","subj":"T179","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A180","pred":"fma_id","subj":"T180","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, 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."}
LitCovid-PD-UBERON
{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T10","span":{"begin":985,"end":998},"obj":"Body_part"}],"attributes":[{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0034922"}],"text":"CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, 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."}
LitCovid-PubTator
{"project":"LitCovid-PubTator","denotations":[{"id":"744","span":{"begin":0,"end":3},"obj":"Gene"},{"id":"745","span":{"begin":80,"end":83},"obj":"Gene"},{"id":"746","span":{"begin":46,"end":54},"obj":"Species"},{"id":"747","span":{"begin":37,"end":45},"obj":"Disease"},{"id":"773","span":{"begin":167,"end":170},"obj":"Gene"},{"id":"774","span":{"begin":206,"end":209},"obj":"Gene"},{"id":"775","span":{"begin":390,"end":393},"obj":"Gene"},{"id":"776","span":{"begin":419,"end":422},"obj":"Gene"},{"id":"777","span":{"begin":501,"end":505},"obj":"Gene"},{"id":"778","span":{"begin":613,"end":617},"obj":"Gene"},{"id":"779","span":{"begin":640,"end":643},"obj":"Gene"},{"id":"780","span":{"begin":661,"end":664},"obj":"Gene"},{"id":"781","span":{"begin":764,"end":767},"obj":"Gene"},{"id":"782","span":{"begin":811,"end":814},"obj":"Gene"},{"id":"783","span":{"begin":979,"end":982},"obj":"Gene"},{"id":"784","span":{"begin":1136,"end":1139},"obj":"Gene"},{"id":"785","span":{"begin":465,"end":473},"obj":"Species"},{"id":"786","span":{"begin":707,"end":715},"obj":"Species"},{"id":"787","span":{"begin":849,"end":857},"obj":"Species"},{"id":"788","span":{"begin":1325,"end":1332},"obj":"Species"},{"id":"789","span":{"begin":1181,"end":1188},"obj":"Species"},{"id":"790","span":{"begin":317,"end":319},"obj":"Disease"},{"id":"791","span":{"begin":456,"end":464},"obj":"Disease"},{"id":"792","span":{"begin":560,"end":562},"obj":"Disease"},{"id":"793","span":{"begin":698,"end":706},"obj":"Disease"},{"id":"794","span":{"begin":828,"end":830},"obj":"Disease"},{"id":"795","span":{"begin":840,"end":848},"obj":"Disease"},{"id":"796","span":{"begin":1273,"end":1275},"obj":"Disease"},{"id":"797","span":{"begin":1316,"end":1324},"obj":"Disease"}],"attributes":[{"id":"A744","pred":"tao:has_database_id","subj":"744","obj":"Gene:920"},{"id":"A745","pred":"tao:has_database_id","subj":"745","obj":"Gene:920"},{"id":"A746","pred":"tao:has_database_id","subj":"746","obj":"Tax:9606"},{"id":"A747","pred":"tao:has_database_id","subj":"747","obj":"MESH:C000657245"},{"id":"A773","pred":"tao:has_database_id","subj":"773","obj":"Gene:920"},{"id":"A774","pred":"tao:has_database_id","subj":"774","obj":"Gene:920"},{"id":"A775","pred":"tao:has_database_id","subj":"775","obj":"Gene:920"},{"id":"A776","pred":"tao:has_database_id","subj":"776","obj":"Gene:925"},{"id":"A777","pred":"tao:has_database_id","subj":"777","obj":"Gene:952"},{"id":"A778","pred":"tao:has_database_id","subj":"778","obj":"Gene:952"},{"id":"A779","pred":"tao:has_database_id","subj":"779","obj":"Gene:920"},{"id":"A780","pred":"tao:has_database_id","subj":"780","obj":"Gene:925"},{"id":"A781","pred":"tao:has_database_id","subj":"781","obj":"Gene:920"},{"id":"A782","pred":"tao:has_database_id","subj":"782","obj":"Gene:920"},{"id":"A783","pred":"tao:has_database_id","subj":"783","obj":"Gene:920"},{"id":"A784","pred":"tao:has_database_id","subj":"784","obj":"Gene:920"},{"id":"A785","pred":"tao:has_database_id","subj":"785","obj":"Tax:9606"},{"id":"A786","pred":"tao:has_database_id","subj":"786","obj":"Tax:9606"},{"id":"A787","pred":"tao:has_database_id","subj":"787","obj":"Tax:9606"},{"id":"A788","pred":"tao:has_database_id","subj":"788","obj":"Tax:9606"},{"id":"A789","pred":"tao:has_database_id","subj":"789","obj":"Tax:100569"},{"id":"A790","pred":"tao:has_database_id","subj":"790","obj":"MESH:D006816"},{"id":"A791","pred":"tao:has_database_id","subj":"791","obj":"MESH:C000657245"},{"id":"A792","pred":"tao:has_database_id","subj":"792","obj":"MESH:D006816"},{"id":"A793","pred":"tao:has_database_id","subj":"793","obj":"MESH:C000657245"},{"id":"A794","pred":"tao:has_database_id","subj":"794","obj":"MESH:D006816"},{"id":"A795","pred":"tao:has_database_id","subj":"795","obj":"MESH:C000657245"},{"id":"A796","pred":"tao:has_database_id","subj":"796","obj":"MESH:D006816"},{"id":"A797","pred":"tao:has_database_id","subj":"797","obj":"MESH:C000657245"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, 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."}
LitCovid-PD-MONDO
{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T154","span":{"begin":37,"end":45},"obj":"Disease"},{"id":"T155","span":{"begin":317,"end":319},"obj":"Disease"},{"id":"T156","span":{"begin":456,"end":464},"obj":"Disease"},{"id":"T157","span":{"begin":560,"end":562},"obj":"Disease"},{"id":"T158","span":{"begin":698,"end":706},"obj":"Disease"},{"id":"T159","span":{"begin":828,"end":830},"obj":"Disease"},{"id":"T160","span":{"begin":832,"end":834},"obj":"Disease"},{"id":"T161","span":{"begin":840,"end":848},"obj":"Disease"},{"id":"T162","span":{"begin":1273,"end":1275},"obj":"Disease"},{"id":"T163","span":{"begin":1302,"end":1304},"obj":"Disease"},{"id":"T164","span":{"begin":1316,"end":1324},"obj":"Disease"},{"id":"T165","span":{"begin":1395,"end":1397},"obj":"Disease"}],"attributes":[{"id":"A154","pred":"mondo_id","subj":"T154","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A155","pred":"mondo_id","subj":"T155","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A156","pred":"mondo_id","subj":"T156","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A157","pred":"mondo_id","subj":"T157","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A158","pred":"mondo_id","subj":"T158","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A159","pred":"mondo_id","subj":"T159","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A160","pred":"mondo_id","subj":"T160","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"},{"id":"A161","pred":"mondo_id","subj":"T161","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A162","pred":"mondo_id","subj":"T162","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A163","pred":"mondo_id","subj":"T163","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"},{"id":"A164","pred":"mondo_id","subj":"T164","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A165","pred":"mondo_id","subj":"T165","obj":"http://purl.obolibrary.org/obo/MONDO_0010873"}],"text":"CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, 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."}
LitCovid-PD-CLO
{"project":"LitCovid-PD-CLO","denotations":[{"id":"T385","span":{"begin":0,"end":3},"obj":"http://purl.obolibrary.org/obo/PR_000001004"},{"id":"T386","span":{"begin":4,"end":10},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T387","span":{"begin":11,"end":21},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T388","span":{"begin":25,"end":26},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T389","span":{"begin":80,"end":83},"obj":"http://purl.obolibrary.org/obo/PR_000001004"},{"id":"T390","span":{"begin":84,"end":90},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T391","span":{"begin":101,"end":102},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T392","span":{"begin":167,"end":170},"obj":"http://purl.obolibrary.org/obo/PR_000001004"},{"id":"T393","span":{"begin":171,"end":177},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T394","span":{"begin":188,"end":189},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T395","span":{"begin":206,"end":209},"obj":"http://purl.obolibrary.org/obo/PR_000001004"},{"id":"T396","span":{"begin":210,"end":216},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T397","span":{"begin":264,"end":269},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T398","span":{"begin":369,"end":374},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T399","span":{"begin":384,"end":401},"obj":"http://purl.obolibrary.org/obo/CL_0000895"},{"id":"T400","span":{"begin":419,"end":422},"obj":"http://purl.obolibrary.org/obo/CLO_0053438"},{"id":"T401","span":{"begin":423,"end":430},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T402","span":{"begin":501,"end":505},"obj":"http://purl.obolibrary.org/obo/PR_000001408"},{"id":"T403","span":{"begin":507,"end":512},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T404","span":{"begin":613,"end":617},"obj":"http://purl.obolibrary.org/obo/PR_000001408"},{"id":"T405","span":{"begin":619,"end":624},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T406","span":{"begin":640,"end":643},"obj":"http://purl.obolibrary.org/obo/PR_000001004"},{"id":"T407","span":{"begin":661,"end":664},"obj":"http://purl.obolibrary.org/obo/CLO_0053438"},{"id":"T408","span":{"begin":665,"end":672},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T409","span":{"begin":758,"end":775},"obj":"http://purl.obolibrary.org/obo/CL_0000895"},{"id":"T410","span":{"begin":805,"end":822},"obj":"http://purl.obolibrary.org/obo/CL_0000895"},{"id":"T411","span":{"begin":832,"end":834},"obj":"http://purl.obolibrary.org/obo/CLO_0008770"},{"id":"T412","span":{"begin":973,"end":989},"obj":"http://purl.obolibrary.org/obo/CL_0000895"},{"id":"T413","span":{"begin":1130,"end":1147},"obj":"http://purl.obolibrary.org/obo/CL_0000895"},{"id":"T414","span":{"begin":1212,"end":1213},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T415","span":{"begin":1302,"end":1304},"obj":"http://purl.obolibrary.org/obo/CLO_0008770"},{"id":"T416","span":{"begin":1385,"end":1389},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"text":"CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, 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."}
LitCovid-PD-CHEBI
{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T116","span":{"begin":317,"end":319},"obj":"Chemical"},{"id":"T117","span":{"begin":498,"end":500},"obj":"Chemical"},{"id":"T118","span":{"begin":560,"end":562},"obj":"Chemical"},{"id":"T119","span":{"begin":610,"end":612},"obj":"Chemical"},{"id":"T120","span":{"begin":828,"end":830},"obj":"Chemical"},{"id":"T121","span":{"begin":832,"end":834},"obj":"Chemical"},{"id":"T122","span":{"begin":925,"end":932},"obj":"Chemical"},{"id":"T123","span":{"begin":1266,"end":1271},"obj":"Chemical"},{"id":"T124","span":{"begin":1273,"end":1275},"obj":"Chemical"},{"id":"T125","span":{"begin":1295,"end":1300},"obj":"Chemical"},{"id":"T126","span":{"begin":1302,"end":1304},"obj":"Chemical"}],"attributes":[{"id":"A116","pred":"chebi_id","subj":"T116","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A117","pred":"chebi_id","subj":"T117","obj":"http://purl.obolibrary.org/obo/CHEBI_73445"},{"id":"A118","pred":"chebi_id","subj":"T118","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A119","pred":"chebi_id","subj":"T119","obj":"http://purl.obolibrary.org/obo/CHEBI_73445"},{"id":"A120","pred":"chebi_id","subj":"T120","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A121","pred":"chebi_id","subj":"T121","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"},{"id":"A122","pred":"chebi_id","subj":"T122","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A123","pred":"chebi_id","subj":"T123","obj":"http://purl.obolibrary.org/obo/CHEBI_17891"},{"id":"A124","pred":"chebi_id","subj":"T124","obj":"http://purl.obolibrary.org/obo/CHEBI_73925"},{"id":"A125","pred":"chebi_id","subj":"T125","obj":"http://purl.obolibrary.org/obo/CHEBI_17891"},{"id":"A126","pred":"chebi_id","subj":"T126","obj":"http://purl.obolibrary.org/obo/CHEBI_73812"}],"text":"CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, 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."}
LitCovid-PD-GO-BP
{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T54","span":{"begin":4,"end":21},"obj":"http://purl.obolibrary.org/obo/GO_0042110"},{"id":"T55","span":{"begin":6,"end":21},"obj":"http://purl.obolibrary.org/obo/GO_0001775"}],"text":"CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, 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."}
LitCovid-sentences
{"project":"LitCovid-sentences","denotations":[{"id":"T135","span":{"begin":100,"end":321},"obj":"Sentence"},{"id":"T136","span":{"begin":322,"end":564},"obj":"Sentence"},{"id":"T137","span":{"begin":565,"end":1189},"obj":"Sentence"},{"id":"T138","span":{"begin":1190,"end":1339},"obj":"Sentence"},{"id":"T139","span":{"begin":1340,"end":1466},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"CD4 T cell activation in a subset of COVID-19 patients associates with distinct CD4 T cell subsets.\n(A) Representative flow cytometry plots of the gating strategy for CD4 T cell subsets. (B) Frequencies of CD4 T cell subsets as indicated. (C) Frequencies of KI67+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (D) KI67+ cells from non-naïve CD4 T cells versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (E) Frequencies of HLA-DR+CD38+ cells; green line at upper decile of healthy donors (HD). Representative flow cytometry plots. (F) HLA-DR+CD38+ cells from non-naïve CD4 versus non-naïve CD8 T cells, Spearman correlation of COVID-19 patients. (G) (Top) Global viSNE projection of non-naïve CD4 T cells for all subjects pooled, non-naïve CD4 T cells from HD, RD, and COVID-19 patients concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (H) viSNE projection of non-naïve CD4 T cell clusters identified by FlowSOM clustering. (I) Mean fluorescence intensity (MFI) as indicated, column-scaled z-score. (J) Percentage of non-naïve CD4 T cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (B, C, E, 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."}