{"id":"W2927243788","doi":"10.1172/jci124358","title":"Cross-reactive public TCR sequences undergo positive selection in the human thymic repertoire","year":2019,"lang":"en","type":"article","venue":"Journal of Clinical Investigation","topic":"Lymphatic System and Diseases","field":"Medicine","cited_by":57,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Allergy and Infectious Diseases; National Institute of Diabetes and Digestive and Kidney Diseases; NIH Office of the Director; University of British Columbia; Human Islet Research Network; Massachusetts Institute of Technology; National Cancer Institute; National Institutes of Health; National Center for Research Resources; American Diabetes Association","keywords":"Negative selection; Complementarity determining region; T-cell receptor; Biology; Repertoire; Thymocyte; Genetics; Positive selection; T cell; Immunology; Gene; Peptide sequence; Immune system; Genome","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002461389,0.00009812375,0.0003808455,0.000129215,0.00007705532,0.00008803852,0.0001263122,0.0001363959,0.00007346369],"category_scores_gemma":[0.002620965,0.00005740345,0.0002046758,0.0002958754,0.000200107,0.0005461708,0.00001094793,0.0001678614,0.00002659814],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001349672,"about_ca_system_score_gemma":0.0007644009,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006703432,"about_ca_topic_score_gemma":0.00002527067,"domain_scores_codex":[0.9974555,0.0005598295,0.001187355,0.0001565696,0.000508862,0.0001318227],"domain_scores_gemma":[0.9972954,0.001009444,0.0009499831,0.0001232062,0.0004561477,0.0001657916],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0001245287,0.0001856592,0.9928622,0.00003591164,0.00006664315,0.00002420415,0.0004645993,0.00001602814,0.003908143,0.001222993,0.0003685892,0.0007205008],"study_design_scores_gemma":[0.002062637,0.0008846538,0.9880868,0.000398161,0.00008488396,0.0002794209,0.0008914738,0.0001937646,0.0009173861,0.006002071,0.000130179,0.00006858955],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9915962,0.0001239547,0.00002673224,0.005136715,0.000299689,0.0002826574,0.000001280898,0.000009354911,0.002523457],"genre_scores_gemma":[0.9968849,0.00001667203,0.000118444,0.002088595,0.0005986428,0.000003607312,0.00000864098,0.000007948423,0.0002725889],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005288702,"threshold_uncertainty_score":0.3137729,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1036859488785413,"score_gpt":0.4221158088251755,"score_spread":0.3184298599466342,"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."}}