{"id":"W4403262182","doi":"10.1186/s13100-024-00333-w","title":"A T cell receptor specific for an HLA-A*03:01-restricted epitope in the endogenous retrovirus ERV-K-Env exhibits limited recognition of its cognate epitope","year":2024,"lang":"en","type":"article","venue":"Mobile DNA","topic":"T-cell and B-cell Immunology","field":"Immunology and Microbiology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"National Institutes of Health; National Cancer Institute; Children's National Hospital; Cosmos Club Foundation; U.S. Department of Defense","keywords":"Epitope; Biology; Retrovirus; Endogenous retrovirus; Human leukocyte antigen; Receptor; Virology; Genetics; Antibody; Antigen; Gene; Virus","routes":{"ca_aff":true,"ca_fund":false,"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":["metaepi_narrow","insufficient_payload"],"consensus_categories":["insufficient_payload"],"category_scores_codex":[0.0005588323,0.0003641556,0.0005316426,0.000374518,0.0002027031,0.00005198043,0.0005742061,0.0005862429,0.0009447012],"category_scores_gemma":[0.00009194351,0.0002844823,0.0002221812,0.0006868826,0.0002276883,0.0001913365,0.00009051706,0.0006666791,0.001599799],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007523021,"about_ca_system_score_gemma":0.0001069331,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001198286,"about_ca_topic_score_gemma":0.00004855537,"domain_scores_codex":[0.9970719,0.0007179283,0.000746772,0.0007011683,0.0000761103,0.0006860843],"domain_scores_gemma":[0.9982917,0.0007574172,0.0002035914,0.0005534649,0.0001597422,0.00003412606],"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":[0.0005657694,0.0007109835,0.0000448282,0.0001333118,0.00009629359,0.00003061814,0.001471982,0.000004808512,0.9525185,0.00006464867,0.007240112,0.0371181],"study_design_scores_gemma":[0.001813821,0.001969465,0.000117033,0.0001034224,0.00007790534,0.00008879438,0.0007407364,0.00001814672,0.8224254,0.0001702205,0.1721613,0.0003136907],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9547783,0.03897584,0.00002873798,0.0001201061,0.002052692,0.001905943,0.0006415191,0.0001674069,0.001329512],"genre_scores_gemma":[0.9911644,0.004832359,0.00007292304,0.0001334031,0.0001469425,0.0006168681,0.00166366,0.00006083533,0.001308544],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1649212,"threshold_uncertainty_score":0.9999686,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04117880275209982,"score_gpt":0.2416732415615238,"score_spread":0.200494438809424,"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."}}