{"id":"W1142774649","doi":"10.1016/j.jim.2015.08.010","title":"A robust and scalable TCR-based reporter cell assay to measure HIV-1 Nef-mediated T cell immune evasion","year":2015,"lang":"en","type":"article","venue":"Journal of Immunological Methods","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":24,"is_retracted":false,"has_abstract":false,"ca_institutions":"St. Paul's Hospital; University of Toronto; Simon Fraser University","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research; Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada; Ministry of Education, Culture, Sports, Science and Technology","keywords":"Biology; Cytotoxic T cell; T-cell receptor; Streptamer; T cell; Antigen; Human leukocyte antigen; Cell biology; Context (archaeology); Heterologous; Immune system; Cell; Molecular biology; Immunology; Gene; In vitro; Genetics","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.006293183,0.0003085629,0.0008127817,0.0003096204,0.0001679836,0.00005251517,0.0003822763,0.0004922065,0.0004563016],"category_scores_gemma":[0.003038012,0.000194457,0.0002387479,0.0003501137,0.0002366181,0.000135172,0.0001949181,0.0009316287,0.0004587616],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001906366,"about_ca_system_score_gemma":0.0003352691,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002723961,"about_ca_topic_score_gemma":0.00000123353,"domain_scores_codex":[0.9948735,0.003018812,0.0009353877,0.0003480003,0.0001928076,0.0006314716],"domain_scores_gemma":[0.9970443,0.001101135,0.0005367804,0.0004020597,0.0006623361,0.0002533914],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.002398264,0.001013336,0.002551164,0.00002070548,0.0002365485,0.000331845,0.0002109309,0.00008288528,0.9660023,0.000006778251,0.004671045,0.02247413],"study_design_scores_gemma":[0.017199,0.01185934,0.0249998,0.0002325861,0.0002732867,0.001245425,0.001301195,0.00005123339,0.8322127,0.0003544074,0.1095448,0.0007262522],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8485137,0.0580997,0.08028039,0.003839424,0.001549296,0.0009144857,0.00005838146,0.0001008971,0.00664378],"genre_scores_gemma":[0.7377961,0.000322975,0.2582971,0.0002887126,0.00006527645,0.00003335161,0.00006307736,0.00003831233,0.003095064],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1780167,"threshold_uncertainty_score":0.7929726,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.08959673312395308,"score_gpt":0.3325881058794364,"score_spread":0.2429913727554834,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}