PMC:7565482 / 19167-20591 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T91","span":{"begin":70,"end":74},"obj":"Body_part"},{"id":"T92","span":{"begin":151,"end":156},"obj":"Body_part"},{"id":"T93","span":{"begin":345,"end":355},"obj":"Body_part"},{"id":"T94","span":{"begin":508,"end":511},"obj":"Body_part"},{"id":"T95","span":{"begin":574,"end":577},"obj":"Body_part"},{"id":"T96","span":{"begin":1148,"end":1153},"obj":"Body_part"},{"id":"T97","span":{"begin":1248,"end":1252},"obj":"Body_part"},{"id":"T98","span":{"begin":1363,"end":1370},"obj":"Body_part"}],"attributes":[{"id":"A91","pred":"fma_id","subj":"T91","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A92","pred":"fma_id","subj":"T92","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A93","pred":"fma_id","subj":"T93","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A94","pred":"fma_id","subj":"T94","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A95","pred":"fma_id","subj":"T95","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A96","pred":"fma_id","subj":"T96","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A97","pred":"fma_id","subj":"T97","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A98","pred":"fma_id","subj":"T98","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Fifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings. However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping. For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity. This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others). Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges. How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required. The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11]. Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T166","span":{"begin":54,"end":57},"obj":"http://purl.obolibrary.org/obo/PR_000001004"},{"id":"T167","span":{"begin":63,"end":66},"obj":"http://purl.obolibrary.org/obo/CLO_0053438"},{"id":"T168","span":{"begin":68,"end":74},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T169","span":{"begin":91,"end":93},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T170","span":{"begin":116,"end":123},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T171","span":{"begin":151,"end":156},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T172","span":{"begin":203,"end":207},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T173","span":{"begin":208,"end":216},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T174","span":{"begin":387,"end":394},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T175","span":{"begin":556,"end":564},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T176","span":{"begin":578,"end":579},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T177","span":{"begin":580,"end":582},"obj":"http://purl.obolibrary.org/obo/CLO_0050509"},{"id":"T178","span":{"begin":585,"end":586},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T179","span":{"begin":730,"end":738},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T180","span":{"begin":993,"end":994},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T181","span":{"begin":1011,"end":1019},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T182","span":{"begin":1071,"end":1079},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T183","span":{"begin":1148,"end":1153},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T184","span":{"begin":1170,"end":1172},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T185","span":{"begin":1231,"end":1236},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T186","span":{"begin":1246,"end":1252},"obj":"http://purl.obolibrary.org/obo/CL_0000084"}],"text":"Fifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings. However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping. For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity. This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others). Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges. How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required. The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11]. Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46]."}

{"project":"LitCovid-PubTator","denotations":[{"id":"239","span":{"begin":54,"end":57},"obj":"Gene"},{"id":"240","span":{"begin":63,"end":66},"obj":"Gene"},{"id":"241","span":{"begin":574,"end":579},"obj":"Gene"},{"id":"242","span":{"begin":1093,"end":1111},"obj":"Chemical"},{"id":"243","span":{"begin":1113,"end":1117},"obj":"Chemical"}],"attributes":[{"id":"A239","pred":"tao:has_database_id","subj":"239","obj":"Gene:920"},{"id":"A240","pred":"tao:has_database_id","subj":"240","obj":"Gene:925"},{"id":"A241","pred":"tao:has_database_id","subj":"241","obj":"Gene:3106"},{"id":"A242","pred":"tao:has_database_id","subj":"242","obj":"MESH:D004121"},{"id":"A243","pred":"tao:has_database_id","subj":"243","obj":"MESH:D004121"}],"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":"Fifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings. However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping. For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity. This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others). Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges. How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required. The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11]. Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46]."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T18","span":{"begin":116,"end":133},"obj":"http://purl.obolibrary.org/obo/GO_0043043"},{"id":"T19","span":{"begin":124,"end":133},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T20","span":{"begin":387,"end":404},"obj":"http://purl.obolibrary.org/obo/GO_0043043"},{"id":"T21","span":{"begin":395,"end":404},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"Fifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings. However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping. For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity. This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others). Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges. How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required. The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11]. Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T137","span":{"begin":0,"end":186},"obj":"Sentence"},{"id":"T138","span":{"begin":187,"end":303},"obj":"Sentence"},{"id":"T139","span":{"begin":304,"end":440},"obj":"Sentence"},{"id":"T140","span":{"begin":441,"end":602},"obj":"Sentence"},{"id":"T141","span":{"begin":603,"end":717},"obj":"Sentence"},{"id":"T142","span":{"begin":718,"end":939},"obj":"Sentence"},{"id":"T143","span":{"begin":940,"end":1174},"obj":"Sentence"},{"id":"T144","span":{"begin":1175,"end":1424},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Fifteen-mer designs allow sensitive screens for both, CD4+ and CD8+ T cell responses while 18 mer allow for cheaper peptide synthesis and require less cells for comprehensive screenings. However, longer test peptides tend to yield fewer responses and imply bigger efforts for subsequent epitope mapping. For the 15 mer design, an alternative 10 amino acid overlap was proposed to reduce peptide synthesis, while maintaining the sensitivity. This approach may be valuable, but may miss epitopes restricted by HLA class I molecules known to presented longer peptides (such as HLA-B*27, -B*57 and others). Regardless of the final OLP design, the use of large OLP data sets for immune screening raises several challenges. How to pool peptides in suitable numbers may depend on the downstream analyses, whether or not subsequent epitope identification are planned, on the experimental setup and whether long incubation periods will be required. The latter may be especially important as pooling of a large number of peptides will possibly require lyophilization of the pooled peptides to eliminate dimethyl sulfoxide (DMSO) as this can be toxic for the cells during culture [11]. Also, as we gain more insights into the distribution of virus-specific T cell responses across the full proteome, more or less reactive regions can be pooled based on expected reactivity, protein expression level, and/or degree of conservation [46]."}