PMC:7402624 / 65898-67084 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T525","span":{"begin":226,"end":231},"obj":"Body_part"},{"id":"T526","span":{"begin":543,"end":549},"obj":"Body_part"},{"id":"T527","span":{"begin":751,"end":759},"obj":"Body_part"},{"id":"T528","span":{"begin":846,"end":853},"obj":"Body_part"},{"id":"T529","span":{"begin":866,"end":869},"obj":"Body_part"},{"id":"T530","span":{"begin":874,"end":877},"obj":"Body_part"},{"id":"T531","span":{"begin":956,"end":960},"obj":"Body_part"},{"id":"T532","span":{"begin":974,"end":978},"obj":"Body_part"}],"attributes":[{"id":"A525","pred":"fma_id","subj":"T525","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A526","pred":"fma_id","subj":"T526","obj":"http://purl.org/sig/ont/fma/fma62970"},{"id":"A527","pred":"fma_id","subj":"T527","obj":"http://purl.org/sig/ont/fma/fma84050"},{"id":"A528","pred":"fma_id","subj":"T528","obj":"http://purl.org/sig/ont/fma/fma241992"},{"id":"A529","pred":"fma_id","subj":"T529","obj":"http://purl.org/sig/ont/fma/fma20935"},{"id":"A530","pred":"fma_id","subj":"T530","obj":"http://purl.org/sig/ont/fma/fma20935"},{"id":"A531","pred":"fma_id","subj":"T531","obj":"http://purl.org/sig/ont/fma/fma86583"},{"id":"A532","pred":"fma_id","subj":"T532","obj":"http://purl.org/sig/ont/fma/fma84051"}],"text":"PBMCs from patients were thawed and rested overnight at 37°C in complete RPMI (cRPMI, table S7). 96-well flat bottom plates were coated with 1 μg/mL of anti-CD3 (UCHT1, #BE0231, BioXell) in PBS at 4°C overnight. The next day, cells were collected and plated at 1 × 105/well in 100 μl in duplicate. 2 μg/mL of anti-human CD28/CD49d was added to the wells containing plate-bound anti-CD3 (Clone L293, 347690, BD). PBMCs were stimulated or left unstimulated for 16 hours, spun down (1200 rpm, 10 min) and 85 μL/well of supernatant was collected. Plasma from matched subjects was thawed on ice, spun (3000 rpm, 1 min) to remove debris, and 85 μl collected in duplicate. Luminex assay was run according to manufacturer’s instructions, using a custom human cytokine 31-plex panel (EMD Millipore Corporation, SPRCUS707). The panel included: EGF, FGF-2, Eotaxin, sIL-2Ra, G-CSF, GM-CSF, IFN-α2, IFN-γ, IL-10, IL-12P40, IL-12P70, IL-13, IL-15, IL-17A, IL-1Ra, HGF, IL-1β, CXCL9/MIG, IL-2, IL-4, IL-5, IL-6, IL-7, CXCL8/IL-8, CXCL10/IP-10, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, RANTES, TNF-α, and VEGF. Assay plates were measured using a Luminex FlexMAP 3D instrument (Thermofisher, Cat#APX1342)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"2033","span":{"begin":320,"end":324},"obj":"Gene"},{"id":"2034","span":{"begin":325,"end":330},"obj":"Gene"},{"id":"2035","span":{"begin":834,"end":837},"obj":"Gene"},{"id":"2036","span":{"begin":839,"end":844},"obj":"Gene"},{"id":"2037","span":{"begin":846,"end":853},"obj":"Gene"},{"id":"2038","span":{"begin":864,"end":869},"obj":"Gene"},{"id":"2039","span":{"begin":871,"end":877},"obj":"Gene"},{"id":"2040","span":{"begin":879,"end":885},"obj":"Gene"},{"id":"2041","span":{"begin":887,"end":892},"obj":"Gene"},{"id":"2042","span":{"begin":894,"end":899},"obj":"Gene"},{"id":"2043","span":{"begin":921,"end":926},"obj":"Gene"},{"id":"2044","span":{"begin":928,"end":933},"obj":"Gene"},{"id":"2045","span":{"begin":935,"end":941},"obj":"Gene"},{"id":"2046","span":{"begin":943,"end":949},"obj":"Gene"},{"id":"2047","span":{"begin":951,"end":954},"obj":"Gene"},{"id":"2048","span":{"begin":956,"end":961},"obj":"Gene"},{"id":"2049","span":{"begin":963,"end":968},"obj":"Gene"},{"id":"2050","span":{"begin":969,"end":972},"obj":"Gene"},{"id":"2051","span":{"begin":974,"end":978},"obj":"Gene"},{"id":"2052","span":{"begin":980,"end":984},"obj":"Gene"},{"id":"2053","span":{"begin":986,"end":990},"obj":"Gene"},{"id":"2054","span":{"begin":992,"end":996},"obj":"Gene"},{"id":"2055","span":{"begin":998,"end":1002},"obj":"Gene"},{"id":"2056","span":{"begin":1004,"end":1009},"obj":"Gene"},{"id":"2057","span":{"begin":1010,"end":1014},"obj":"Gene"},{"id":"2058","span":{"begin":1016,"end":1022},"obj":"Gene"},{"id":"2059","span":{"begin":1023,"end":1028},"obj":"Gene"},{"id":"2060","span":{"begin":1030,"end":1034},"obj":"Gene"},{"id":"2061","span":{"begin":1035,"end":1040},"obj":"Gene"},{"id":"2062","span":{"begin":1055,"end":1059},"obj":"Gene"},{"id":"2063","span":{"begin":1060,"end":1066},"obj":"Gene"},{"id":"2064","span":{"begin":1068,"end":1074},"obj":"Gene"},{"id":"2065","span":{"begin":1076,"end":1081},"obj":"Gene"},{"id":"2066","span":{"begin":1087,"end":1091},"obj":"Gene"},{"id":"2067","span":{"begin":11,"end":19},"obj":"Species"},{"id":"2068","span":{"begin":745,"end":750},"obj":"Species"},{"id":"2069","span":{"begin":314,"end":319},"obj":"Species"},{"id":"2070","span":{"begin":190,"end":193},"obj":"Chemical"},{"id":"2071","span":{"begin":393,"end":397},"obj":"CellLine"}],"attributes":[{"id":"A2033","pred":"tao:has_database_id","subj":"2033","obj":"Gene:940"},{"id":"A2034","pred":"tao:has_database_id","subj":"2034","obj":"Gene:3676"},{"id":"A2035","pred":"tao:has_database_id","subj":"2035","obj":"Gene:1950"},{"id":"A2036","pred":"tao:has_database_id","subj":"2036","obj":"Gene:2247"},{"id":"A2037","pred":"tao:has_database_id","subj":"2037","obj":"Gene:6356"},{"id":"A2038","pred":"tao:has_database_id","subj":"2038","obj":"Gene:1440"},{"id":"A2039","pred":"tao:has_database_id","subj":"2039","obj":"Gene:1437"},{"id":"A2040","pred":"tao:has_database_id","subj":"2040","obj":"Gene:3440"},{"id":"A2041","pred":"tao:has_database_id","subj":"2041","obj":"Gene:3458"},{"id":"A2042","pred":"tao:has_database_id","subj":"2042","obj":"Gene:3586"},{"id":"A2043","pred":"tao:has_database_id","subj":"2043","obj":"Gene:3596"},{"id":"A2044","pred":"tao:has_database_id","subj":"2044","obj":"Gene:3600"},{"id":"A2045","pred":"tao:has_database_id","subj":"2045","obj":"Gene:3605"},{"id":"A2046","pred":"tao:has_database_id","subj":"2046","obj":"Gene:3557"},{"id":"A2047","pred":"tao:has_database_id","subj":"2047","obj":"Gene:3082"},{"id":"A2048","pred":"tao:has_database_id","subj":"2048","obj":"Gene:3552"},{"id":"A2049","pred":"tao:has_database_id","subj":"2049","obj":"Gene:4283"},{"id":"A2050","pred":"tao:has_database_id","subj":"2050","obj":"Gene:4283"},{"id":"A2051","pred":"tao:has_database_id","subj":"2051","obj":"Gene:3558"},{"id":"A2052","pred":"tao:has_database_id","subj":"2052","obj":"Gene:3565"},{"id":"A2053","pred":"tao:has_database_id","subj":"2053","obj":"Gene:3567"},{"id":"A2054","pred":"tao:has_database_id","subj":"2054","obj":"Gene:3569"},{"id":"A2055","pred":"tao:has_database_id","subj":"2055","obj":"Gene:3574"},{"id":"A2056","pred":"tao:has_database_id","subj":"2056","obj":"Gene:3576"},{"id":"A2057","pred":"tao:has_database_id","subj":"2057","obj":"Gene:3576"},{"id":"A2058","pred":"tao:has_database_id","subj":"2058","obj":"Gene:3627"},{"id":"A2059","pred":"tao:has_database_id","subj":"2059","obj":"Gene:3627"},{"id":"A2060","pred":"tao:has_database_id","subj":"2060","obj":"Gene:6347"},{"id":"A2061","pred":"tao:has_database_id","subj":"2061","obj":"Gene:6347"},{"id":"A2062","pred":"tao:has_database_id","subj":"2062","obj":"Gene:6351"},{"id":"A2063","pred":"tao:has_database_id","subj":"2063","obj":"Gene:6351"},{"id":"A2064","pred":"tao:has_database_id","subj":"2064","obj":"Gene:6352"},{"id":"A2065","pred":"tao:has_database_id","subj":"2065","obj":"Gene:7124"},{"id":"A2066","pred":"tao:has_database_id","subj":"2066","obj":"Gene:7422"},{"id":"A2067","pred":"tao:has_database_id","subj":"2067","obj":"Tax:9606"},{"id":"A2068","pred":"tao:has_database_id","subj":"2068","obj":"Tax:9606"},{"id":"A2069","pred":"tao:has_database_id","subj":"2069","obj":"Tax:9606"},{"id":"A2070","pred":"tao:has_database_id","subj":"2070","obj":"MESH:D007854"},{"id":"A2071","pred":"tao:has_database_id","subj":"2071","obj":"CVCL:M775"}],"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":"PBMCs from patients were thawed and rested overnight at 37°C in complete RPMI (cRPMI, table S7). 96-well flat bottom plates were coated with 1 μg/mL of anti-CD3 (UCHT1, #BE0231, BioXell) in PBS at 4°C overnight. The next day, cells were collected and plated at 1 × 105/well in 100 μl in duplicate. 2 μg/mL of anti-human CD28/CD49d was added to the wells containing plate-bound anti-CD3 (Clone L293, 347690, BD). PBMCs were stimulated or left unstimulated for 16 hours, spun down (1200 rpm, 10 min) and 85 μL/well of supernatant was collected. Plasma from matched subjects was thawed on ice, spun (3000 rpm, 1 min) to remove debris, and 85 μl collected in duplicate. Luminex assay was run according to manufacturer’s instructions, using a custom human cytokine 31-plex panel (EMD Millipore Corporation, SPRCUS707). The panel included: EGF, FGF-2, Eotaxin, sIL-2Ra, G-CSF, GM-CSF, IFN-α2, IFN-γ, IL-10, IL-12P40, IL-12P70, IL-13, IL-15, IL-17A, IL-1Ra, HGF, IL-1β, CXCL9/MIG, IL-2, IL-4, IL-5, IL-6, IL-7, CXCL8/IL-8, CXCL10/IP-10, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, RANTES, TNF-α, and VEGF. Assay plates were measured using a Luminex FlexMAP 3D instrument (Thermofisher, Cat#APX1342)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T431","span":{"begin":407,"end":409},"obj":"Disease"}],"attributes":[{"id":"A431","pred":"mondo_id","subj":"T431","obj":"http://purl.obolibrary.org/obo/MONDO_0007191"}],"text":"PBMCs from patients were thawed and rested overnight at 37°C in complete RPMI (cRPMI, table S7). 96-well flat bottom plates were coated with 1 μg/mL of anti-CD3 (UCHT1, #BE0231, BioXell) in PBS at 4°C overnight. The next day, cells were collected and plated at 1 × 105/well in 100 μl in duplicate. 2 μg/mL of anti-human CD28/CD49d was added to the wells containing plate-bound anti-CD3 (Clone L293, 347690, BD). PBMCs were stimulated or left unstimulated for 16 hours, spun down (1200 rpm, 10 min) and 85 μL/well of supernatant was collected. Plasma from matched subjects was thawed on ice, spun (3000 rpm, 1 min) to remove debris, and 85 μl collected in duplicate. Luminex assay was run according to manufacturer’s instructions, using a custom human cytokine 31-plex panel (EMD Millipore Corporation, SPRCUS707). The panel included: EGF, FGF-2, Eotaxin, sIL-2Ra, G-CSF, GM-CSF, IFN-α2, IFN-γ, IL-10, IL-12P40, IL-12P70, IL-13, IL-15, IL-17A, IL-1Ra, HGF, IL-1β, CXCL9/MIG, IL-2, IL-4, IL-5, IL-6, IL-7, CXCL8/IL-8, CXCL10/IP-10, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, RANTES, TNF-α, and VEGF. Assay plates were measured using a Luminex FlexMAP 3D instrument (Thermofisher, Cat#APX1342)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T959","span":{"begin":157,"end":160},"obj":"http://purl.obolibrary.org/obo/CLO_0052882"},{"id":"T960","span":{"begin":157,"end":160},"obj":"http://purl.obolibrary.org/obo/CLO_0053434"},{"id":"T961","span":{"begin":197,"end":200},"obj":"http://purl.obolibrary.org/obo/CLO_0001387"},{"id":"T962","span":{"begin":226,"end":231},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T963","span":{"begin":258,"end":268},"obj":"http://purl.obolibrary.org/obo/CLO_0001040"},{"id":"T964","span":{"begin":314,"end":319},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T965","span":{"begin":382,"end":385},"obj":"http://purl.obolibrary.org/obo/CLO_0052882"},{"id":"T966","span":{"begin":382,"end":385},"obj":"http://purl.obolibrary.org/obo/CLO_0053434"},{"id":"T967","span":{"begin":543,"end":549},"obj":"http://purl.obolibrary.org/obo/UBERON_0001969"},{"id":"T968","span":{"begin":736,"end":737},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T969","span":{"begin":745,"end":750},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T970","span":{"begin":864,"end":869},"obj":"http://purl.obolibrary.org/obo/PR_000005932"},{"id":"T971","span":{"begin":951,"end":954},"obj":"http://purl.obolibrary.org/obo/CLO_0003740"},{"id":"T972","span":{"begin":974,"end":978},"obj":"http://purl.obolibrary.org/obo/PR_000001379"},{"id":"T973","span":{"begin":1010,"end":1014},"obj":"http://purl.obolibrary.org/obo/CLO_0053704"},{"id":"T974","span":{"begin":1126,"end":1127},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T975","span":{"begin":1147,"end":1157},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"}],"text":"PBMCs from patients were thawed and rested overnight at 37°C in complete RPMI (cRPMI, table S7). 96-well flat bottom plates were coated with 1 μg/mL of anti-CD3 (UCHT1, #BE0231, BioXell) in PBS at 4°C overnight. The next day, cells were collected and plated at 1 × 105/well in 100 μl in duplicate. 2 μg/mL of anti-human CD28/CD49d was added to the wells containing plate-bound anti-CD3 (Clone L293, 347690, BD). PBMCs were stimulated or left unstimulated for 16 hours, spun down (1200 rpm, 10 min) and 85 μL/well of supernatant was collected. Plasma from matched subjects was thawed on ice, spun (3000 rpm, 1 min) to remove debris, and 85 μl collected in duplicate. Luminex assay was run according to manufacturer’s instructions, using a custom human cytokine 31-plex panel (EMD Millipore Corporation, SPRCUS707). The panel included: EGF, FGF-2, Eotaxin, sIL-2Ra, G-CSF, GM-CSF, IFN-α2, IFN-γ, IL-10, IL-12P40, IL-12P70, IL-13, IL-15, IL-17A, IL-1Ra, HGF, IL-1β, CXCL9/MIG, IL-2, IL-4, IL-5, IL-6, IL-7, CXCL8/IL-8, CXCL10/IP-10, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, RANTES, TNF-α, and VEGF. Assay plates were measured using a Luminex FlexMAP 3D instrument (Thermofisher, Cat#APX1342)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T94021","span":{"begin":834,"end":837},"obj":"Chemical"},{"id":"T65282","span":{"begin":871,"end":873},"obj":"Chemical"},{"id":"T7701","span":{"begin":894,"end":896},"obj":"Chemical"},{"id":"T70736","span":{"begin":901,"end":903},"obj":"Chemical"},{"id":"T87965","span":{"begin":911,"end":913},"obj":"Chemical"},{"id":"T48479","span":{"begin":921,"end":923},"obj":"Chemical"},{"id":"T16150","span":{"begin":928,"end":930},"obj":"Chemical"},{"id":"T29560","span":{"begin":935,"end":937},"obj":"Chemical"},{"id":"T21327","span":{"begin":943,"end":945},"obj":"Chemical"},{"id":"T47948","span":{"begin":956,"end":958},"obj":"Chemical"},{"id":"T94087","span":{"begin":963,"end":968},"obj":"Chemical"},{"id":"T89357","span":{"begin":974,"end":976},"obj":"Chemical"},{"id":"T78875","span":{"begin":980,"end":982},"obj":"Chemical"},{"id":"T30910","span":{"begin":986,"end":988},"obj":"Chemical"},{"id":"T92516","span":{"begin":992,"end":994},"obj":"Chemical"},{"id":"T24109","span":{"begin":998,"end":1000},"obj":"Chemical"},{"id":"T31035","span":{"begin":1010,"end":1012},"obj":"Chemical"},{"id":"T89429","span":{"begin":1016,"end":1022},"obj":"Chemical"},{"id":"T61718","span":{"begin":1023,"end":1028},"obj":"Chemical"},{"id":"T96412","span":{"begin":1023,"end":1025},"obj":"Chemical"},{"id":"T85413","span":{"begin":1035,"end":1038},"obj":"Chemical"}],"attributes":[{"id":"A39477","pred":"chebi_id","subj":"T94021","obj":"http://purl.obolibrary.org/obo/CHEBI_140739"},{"id":"A5713","pred":"chebi_id","subj":"T65282","obj":"http://purl.obolibrary.org/obo/CHEBI_74120"},{"id":"A84385","pred":"chebi_id","subj":"T7701","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A64199","pred":"chebi_id","subj":"T7701","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A3957","pred":"chebi_id","subj":"T70736","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A36642","pred":"chebi_id","subj":"T70736","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A94956","pred":"chebi_id","subj":"T87965","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A41276","pred":"chebi_id","subj":"T87965","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A24936","pred":"chebi_id","subj":"T48479","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A40350","pred":"chebi_id","subj":"T48479","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A18977","pred":"chebi_id","subj":"T16150","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A32147","pred":"chebi_id","subj":"T16150","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A57588","pred":"chebi_id","subj":"T29560","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A33066","pred":"chebi_id","subj":"T29560","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A78307","pred":"chebi_id","subj":"T21327","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A42431","pred":"chebi_id","subj":"T21327","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A30905","pred":"chebi_id","subj":"T47948","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A6040","pred":"chebi_id","subj":"T47948","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A44037","pred":"chebi_id","subj":"T94087","obj":"http://purl.obolibrary.org/obo/CHEBI_138154"},{"id":"A6601","pred":"chebi_id","subj":"T89357","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A48903","pred":"chebi_id","subj":"T89357","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A29044","pred":"chebi_id","subj":"T78875","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A46576","pred":"chebi_id","subj":"T78875","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A3476","pred":"chebi_id","subj":"T30910","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A46122","pred":"chebi_id","subj":"T30910","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A58626","pred":"chebi_id","subj":"T92516","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A30503","pred":"chebi_id","subj":"T92516","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A24037","pred":"chebi_id","subj":"T24109","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A9735","pred":"chebi_id","subj":"T24109","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A93434","pred":"chebi_id","subj":"T31035","obj":"http://purl.obolibrary.org/obo/CHEBI_63895"},{"id":"A92365","pred":"chebi_id","subj":"T31035","obj":"http://purl.obolibrary.org/obo/CHEBI_74072"},{"id":"A33208","pred":"chebi_id","subj":"T89429","obj":"http://purl.obolibrary.org/obo/CHEBI_138157"},{"id":"A73809","pred":"chebi_id","subj":"T61718","obj":"http://purl.obolibrary.org/obo/CHEBI_138157"},{"id":"A29008","pred":"chebi_id","subj":"T96412","obj":"http://purl.obolibrary.org/obo/CHEBI_74076"},{"id":"A44521","pred":"chebi_id","subj":"T85413","obj":"http://purl.obolibrary.org/obo/CHEBI_132592"},{"id":"A60395","pred":"chebi_id","subj":"T85413","obj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from patients were thawed and rested overnight at 37°C in complete RPMI (cRPMI, table S7). 96-well flat bottom plates were coated with 1 μg/mL of anti-CD3 (UCHT1, #BE0231, BioXell) in PBS at 4°C overnight. The next day, cells were collected and plated at 1 × 105/well in 100 μl in duplicate. 2 μg/mL of anti-human CD28/CD49d was added to the wells containing plate-bound anti-CD3 (Clone L293, 347690, BD). PBMCs were stimulated or left unstimulated for 16 hours, spun down (1200 rpm, 10 min) and 85 μL/well of supernatant was collected. Plasma from matched subjects was thawed on ice, spun (3000 rpm, 1 min) to remove debris, and 85 μl collected in duplicate. Luminex assay was run according to manufacturer’s instructions, using a custom human cytokine 31-plex panel (EMD Millipore Corporation, SPRCUS707). The panel included: EGF, FGF-2, Eotaxin, sIL-2Ra, G-CSF, GM-CSF, IFN-α2, IFN-γ, IL-10, IL-12P40, IL-12P70, IL-13, IL-15, IL-17A, IL-1Ra, HGF, IL-1β, CXCL9/MIG, IL-2, IL-4, IL-5, IL-6, IL-7, CXCL8/IL-8, CXCL10/IP-10, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, RANTES, TNF-α, and VEGF. Assay plates were measured using a Luminex FlexMAP 3D instrument (Thermofisher, Cat#APX1342)."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T135","span":{"begin":943,"end":949},"obj":"http://purl.obolibrary.org/obo/GO_0005152"}],"text":"PBMCs from patients were thawed and rested overnight at 37°C in complete RPMI (cRPMI, table S7). 96-well flat bottom plates were coated with 1 μg/mL of anti-CD3 (UCHT1, #BE0231, BioXell) in PBS at 4°C overnight. The next day, cells were collected and plated at 1 × 105/well in 100 μl in duplicate. 2 μg/mL of anti-human CD28/CD49d was added to the wells containing plate-bound anti-CD3 (Clone L293, 347690, BD). PBMCs were stimulated or left unstimulated for 16 hours, spun down (1200 rpm, 10 min) and 85 μL/well of supernatant was collected. Plasma from matched subjects was thawed on ice, spun (3000 rpm, 1 min) to remove debris, and 85 μl collected in duplicate. Luminex assay was run according to manufacturer’s instructions, using a custom human cytokine 31-plex panel (EMD Millipore Corporation, SPRCUS707). The panel included: EGF, FGF-2, Eotaxin, sIL-2Ra, G-CSF, GM-CSF, IFN-α2, IFN-γ, IL-10, IL-12P40, IL-12P70, IL-13, IL-15, IL-17A, IL-1Ra, HGF, IL-1β, CXCL9/MIG, IL-2, IL-4, IL-5, IL-6, IL-7, CXCL8/IL-8, CXCL10/IP-10, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, RANTES, TNF-α, and VEGF. Assay plates were measured using a Luminex FlexMAP 3D instrument (Thermofisher, Cat#APX1342)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T400","span":{"begin":0,"end":96},"obj":"Sentence"},{"id":"T401","span":{"begin":97,"end":211},"obj":"Sentence"},{"id":"T402","span":{"begin":212,"end":297},"obj":"Sentence"},{"id":"T403","span":{"begin":298,"end":411},"obj":"Sentence"},{"id":"T404","span":{"begin":412,"end":542},"obj":"Sentence"},{"id":"T405","span":{"begin":543,"end":665},"obj":"Sentence"},{"id":"T406","span":{"begin":666,"end":813},"obj":"Sentence"},{"id":"T407","span":{"begin":814,"end":1092},"obj":"Sentence"},{"id":"T408","span":{"begin":1093,"end":1186},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"PBMCs from patients were thawed and rested overnight at 37°C in complete RPMI (cRPMI, table S7). 96-well flat bottom plates were coated with 1 μg/mL of anti-CD3 (UCHT1, #BE0231, BioXell) in PBS at 4°C overnight. The next day, cells were collected and plated at 1 × 105/well in 100 μl in duplicate. 2 μg/mL of anti-human CD28/CD49d was added to the wells containing plate-bound anti-CD3 (Clone L293, 347690, BD). PBMCs were stimulated or left unstimulated for 16 hours, spun down (1200 rpm, 10 min) and 85 μL/well of supernatant was collected. Plasma from matched subjects was thawed on ice, spun (3000 rpm, 1 min) to remove debris, and 85 μl collected in duplicate. Luminex assay was run according to manufacturer’s instructions, using a custom human cytokine 31-plex panel (EMD Millipore Corporation, SPRCUS707). The panel included: EGF, FGF-2, Eotaxin, sIL-2Ra, G-CSF, GM-CSF, IFN-α2, IFN-γ, IL-10, IL-12P40, IL-12P70, IL-13, IL-15, IL-17A, IL-1Ra, HGF, IL-1β, CXCL9/MIG, IL-2, IL-4, IL-5, IL-6, IL-7, CXCL8/IL-8, CXCL10/IP-10, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, RANTES, TNF-α, and VEGF. Assay plates were measured using a Luminex FlexMAP 3D instrument (Thermofisher, Cat#APX1342)."}