PMC:7402624 / 28082-29831 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T232","span":{"begin":45,"end":49},"obj":"Body_part"},{"id":"T233","span":{"begin":77,"end":88},"obj":"Body_part"},{"id":"T234","span":{"begin":113,"end":117},"obj":"Body_part"},{"id":"T235","span":{"begin":174,"end":176},"obj":"Body_part"},{"id":"T236","span":{"begin":179,"end":183},"obj":"Body_part"},{"id":"T237","span":{"begin":252,"end":254},"obj":"Body_part"},{"id":"T238","span":{"begin":357,"end":362},"obj":"Body_part"},{"id":"T239","span":{"begin":449,"end":453},"obj":"Body_part"},{"id":"T240","span":{"begin":497,"end":502},"obj":"Body_part"},{"id":"T241","span":{"begin":546,"end":548},"obj":"Body_part"},{"id":"T242","span":{"begin":602,"end":604},"obj":"Body_part"},{"id":"T243","span":{"begin":624,"end":627},"obj":"Body_part"},{"id":"T244","span":{"begin":706,"end":709},"obj":"Body_part"},{"id":"T245","span":{"begin":718,"end":721},"obj":"Body_part"},{"id":"T246","span":{"begin":762,"end":767},"obj":"Body_part"},{"id":"T247","span":{"begin":800,"end":804},"obj":"Body_part"},{"id":"T248","span":{"begin":899,"end":906},"obj":"Body_part"},{"id":"T249","span":{"begin":1032,"end":1036},"obj":"Body_part"},{"id":"T250","span":{"begin":1164,"end":1169},"obj":"Body_part"},{"id":"T251","span":{"begin":1248,"end":1261},"obj":"Body_part"},{"id":"T252","span":{"begin":1248,"end":1252},"obj":"Body_part"},{"id":"T253","span":{"begin":1361,"end":1366},"obj":"Body_part"}],"attributes":[{"id":"A232","pred":"fma_id","subj":"T232","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A233","pred":"fma_id","subj":"T233","obj":"http://purl.org/sig/ont/fma/fma84371"},{"id":"A234","pred":"fma_id","subj":"T234","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A235","pred":"fma_id","subj":"T235","obj":"http://purl.org/sig/ont/fma/fma84371"},{"id":"A236","pred":"fma_id","subj":"T236","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A237","pred":"fma_id","subj":"T237","obj":"http://purl.org/sig/ont/fma/fma84371"},{"id":"A238","pred":"fma_id","subj":"T238","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A239","pred":"fma_id","subj":"T239","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A240","pred":"fma_id","subj":"T240","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A241","pred":"fma_id","subj":"T241","obj":"http://purl.org/sig/ont/fma/fma84371"},{"id":"A242","pred":"fma_id","subj":"T242","obj":"http://purl.org/sig/ont/fma/fma84371"},{"id":"A243","pred":"fma_id","subj":"T243","obj":"http://purl.org/sig/ont/fma/fma62872"},{"id":"A244","pred":"fma_id","subj":"T244","obj":"http://purl.org/sig/ont/fma/fma62873"},{"id":"A245","pred":"fma_id","subj":"T245","obj":"http://purl.org/sig/ont/fma/fma62872"},{"id":"A246","pred":"fma_id","subj":"T246","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A247","pred":"fma_id","subj":"T247","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A248","pred":"fma_id","subj":"T248","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A249","pred":"fma_id","subj":"T249","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A250","pred":"fma_id","subj":"T250","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A251","pred":"fma_id","subj":"T251","obj":"http://purl.org/sig/ont/fma/fma62807"},{"id":"A252","pred":"fma_id","subj":"T252","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A253","pred":"fma_id","subj":"T253","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Fig. 4 Deep profiling of COVID-19 patient B cell populations reveals robust plasmablast populations and other B cell alterations.\n(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (A to F, P) Dots represent individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 (red) subjects. (A to E, P) 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. (GtoI) Black horizontal line represents positive threshold."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T13","span":{"begin":1248,"end":1261},"obj":"Body_part"}],"attributes":[{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0034922"}],"text":"Fig. 4 Deep profiling of COVID-19 patient B cell populations reveals robust plasmablast populations and other B cell alterations.\n(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (A to F, P) Dots represent individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 (red) subjects. (A to E, P) 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. (GtoI) Black horizontal line represents positive threshold."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1038","span":{"begin":35,"end":42},"obj":"Species"},{"id":"1039","span":{"begin":26,"end":34},"obj":"Disease"},{"id":"1054","span":{"begin":404,"end":409},"obj":"Gene"},{"id":"1055","span":{"begin":433,"end":438},"obj":"Gene"},{"id":"1056","span":{"begin":467,"end":472},"obj":"Gene"},{"id":"1057","span":{"begin":491,"end":494},"obj":"Gene"},{"id":"1058","span":{"begin":956,"end":961},"obj":"Gene"},{"id":"1059","span":{"begin":1400,"end":1407},"obj":"Species"},{"id":"1060","span":{"begin":614,"end":623},"obj":"Species"},{"id":"1061","span":{"begin":692,"end":701},"obj":"Species"},{"id":"1062","span":{"begin":507,"end":511},"obj":"Chemical"},{"id":"1063","span":{"begin":546,"end":548},"obj":"Chemical"},{"id":"1064","span":{"begin":563,"end":567},"obj":"Chemical"},{"id":"1065","span":{"begin":286,"end":288},"obj":"Disease"},{"id":"1066","span":{"begin":1483,"end":1485},"obj":"Disease"},{"id":"1067","span":{"begin":1526,"end":1534},"obj":"Disease"}],"attributes":[{"id":"A1038","pred":"tao:has_database_id","subj":"1038","obj":"Tax:9606"},{"id":"A1039","pred":"tao:has_database_id","subj":"1039","obj":"MESH:C000657245"},{"id":"A1054","pred":"tao:has_database_id","subj":"1054","obj":"Gene:643"},{"id":"A1055","pred":"tao:has_database_id","subj":"1055","obj":"Gene:643"},{"id":"A1056","pred":"tao:has_database_id","subj":"1056","obj":"Gene:643"},{"id":"A1057","pred":"tao:has_database_id","subj":"1057","obj":"Gene:920"},{"id":"A1058","pred":"tao:has_database_id","subj":"1058","obj":"Gene:127262"},{"id":"A1059","pred":"tao:has_database_id","subj":"1059","obj":"Tax:100569"},{"id":"A1060","pred":"tao:has_database_id","subj":"1060","obj":"Tax:2697049"},{"id":"A1061","pred":"tao:has_database_id","subj":"1061","obj":"Tax:2697049"},{"id":"A1065","pred":"tao:has_database_id","subj":"1065","obj":"MESH:D006816"},{"id":"A1066","pred":"tao:has_database_id","subj":"1066","obj":"MESH:D006816"},{"id":"A1067","pred":"tao:has_database_id","subj":"1067","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":"Fig. 4 Deep profiling of COVID-19 patient B cell populations reveals robust plasmablast populations and other B cell alterations.\n(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (A to F, P) Dots represent individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 (red) subjects. (A to E, P) 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. (GtoI) Black horizontal line represents positive threshold."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T219","span":{"begin":26,"end":34},"obj":"Disease"},{"id":"T220","span":{"begin":174,"end":176},"obj":"Disease"},{"id":"T221","span":{"begin":252,"end":254},"obj":"Disease"},{"id":"T222","span":{"begin":286,"end":288},"obj":"Disease"},{"id":"T223","span":{"begin":546,"end":548},"obj":"Disease"},{"id":"T224","span":{"begin":602,"end":604},"obj":"Disease"},{"id":"T225","span":{"begin":614,"end":618},"obj":"Disease"},{"id":"T226","span":{"begin":692,"end":696},"obj":"Disease"},{"id":"T227","span":{"begin":1483,"end":1485},"obj":"Disease"},{"id":"T228","span":{"begin":1512,"end":1514},"obj":"Disease"},{"id":"T229","span":{"begin":1526,"end":1534},"obj":"Disease"},{"id":"T230","span":{"begin":1618,"end":1620},"obj":"Disease"}],"attributes":[{"id":"A219","pred":"mondo_id","subj":"T219","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A220","pred":"mondo_id","subj":"T220","obj":"http://purl.obolibrary.org/obo/MONDO_0019035"},{"id":"A221","pred":"mondo_id","subj":"T221","obj":"http://purl.obolibrary.org/obo/MONDO_0019035"},{"id":"A222","pred":"mondo_id","subj":"T222","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A223","pred":"mondo_id","subj":"T223","obj":"http://purl.obolibrary.org/obo/MONDO_0019035"},{"id":"A224","pred":"mondo_id","subj":"T224","obj":"http://purl.obolibrary.org/obo/MONDO_0019035"},{"id":"A225","pred":"mondo_id","subj":"T225","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A226","pred":"mondo_id","subj":"T226","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A227","pred":"mondo_id","subj":"T227","obj":"http://purl.obolibrary.org/obo/MONDO_0007739"},{"id":"A228","pred":"mondo_id","subj":"T228","obj":"http://purl.obolibrary.org/obo/MONDO_0009973"},{"id":"A229","pred":"mondo_id","subj":"T229","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A230","pred":"mondo_id","subj":"T230","obj":"http://purl.obolibrary.org/obo/MONDO_0010873"}],"text":"Fig. 4 Deep profiling of COVID-19 patient B cell populations reveals robust plasmablast populations and other B cell alterations.\n(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (A to F, P) Dots represent individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 (red) subjects. (A to E, P) 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. (GtoI) Black horizontal line represents positive threshold."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T487","span":{"begin":43,"end":49},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T488","span":{"begin":111,"end":117},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T489","span":{"begin":132,"end":133},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T490","span":{"begin":177,"end":183},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T491","span":{"begin":194,"end":195},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T492","span":{"begin":286,"end":293},"obj":"http://purl.obolibrary.org/obo/CLO_0050940"},{"id":"T493","span":{"begin":355,"end":362},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T494","span":{"begin":447,"end":453},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T495","span":{"begin":485,"end":502},"obj":"http://purl.obolibrary.org/obo/CL_0000895"},{"id":"T496","span":{"begin":553,"end":562},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T497","span":{"begin":668,"end":677},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T498","span":{"begin":760,"end":767},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T499","span":{"begin":798,"end":804},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T500","span":{"begin":1030,"end":1036},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T501","span":{"begin":1162,"end":1169},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T502","span":{"begin":1246,"end":1252},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T503","span":{"begin":1359,"end":1366},"obj":"http://purl.obolibrary.org/obo/CL_0000236"},{"id":"T504","span":{"begin":1431,"end":1432},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T505","span":{"begin":1512,"end":1514},"obj":"http://purl.obolibrary.org/obo/CLO_0008770"},{"id":"T506","span":{"begin":1552,"end":1553},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T507","span":{"begin":1608,"end":1612},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"}],"text":"Fig. 4 Deep profiling of COVID-19 patient B cell populations reveals robust plasmablast populations and other B cell alterations.\n(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (A to F, P) Dots represent individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 (red) subjects. (A to E, P) 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. (GtoI) Black horizontal line represents positive threshold."}

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{"project":"LitCovid-sentences","denotations":[{"id":"T171","span":{"begin":0,"end":130},"obj":"Sentence"},{"id":"T172","span":{"begin":131,"end":1408},"obj":"Sentence"},{"id":"T173","span":{"begin":1409,"end":1749},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Fig. 4 Deep profiling of COVID-19 patient B cell populations reveals robust plasmablast populations and other B cell alterations.\n(A) Gating strategy and frequencies of non-PB B cell subsets. (B) Representative flow cytometry plots and frequencies of PB; green line at upper decile of HD. (C) Representative flow cytometry plots and frequencies of KI67+ B cells. (D) (Left) Representative histograms of CXCR5 expression and (right) CXCR5 GMFI of B cell subsets. (E) CXCR5 GMFI of non-naïve CD4 T cells and cTfh. (F) Spearman correlation between PB and activated cTfh. (G) Spearman correlation between PB and anti-SARS-CoV2 IgG. (H and I) Spearman correlation between activated cTfh and anti-SARS-CoV2 (H) IgM and (I) IgG. (J) (Top) Global viSNE projection of B cells for all subjects pooled, with B cell populations of each cohort concatenated and overlaid. (Bottom) viSNE projections of indicated protein expression. (K) Hierarchical clustering of Earth Mover’s Distance (EMD) using Pearson correlation, calculated pairwise for B cell populations for all subjects; row-scaled z-score. (L) Percentage of cohort in each EMD group. (M) Global viSNE projection of B cells for all subjects pooled, with EMD groups 1-3 concatenated and overlaid. (N) B cell clusters identified by FlowSOM clustering. (O) MFI as indicated; column-scaled z-score. (P) Percentage of B cells from each cohort in each FlowSOM cluster. Boxes represent IQR. (A to F, P) Dots represent individual healthy donor (HD; green), recovered donor (RD; blue), or COVID-19 (red) subjects. (A to E, P) 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. (GtoI) Black horizontal line represents positive threshold."}