{"id":"W4416701937","doi":"10.1016/j.immuni.2025.10.025","title":"Deep profiling of human T cells defines compartmentalized clones and phenotypic trajectories across blood and tonsils","year":2025,"lang":"en","type":"article","venue":"Immunity","topic":"T-cell and B-cell Immunology","field":"Immunology and Microbiology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"National Center for Research Resources; National Institute of Allergy and Infectious Diseases; National Institute of Arthritis and Musculoskeletal and Skin Diseases; National Institute on Aging; University of California, Irvine; National Cancer Institute; National Institutes of Health; St. Louis Children's Hospital; Children's Discovery Institute; Wellcome Trust; Wellcome; Genome Technology Access Center","keywords":"Phenotype; Repertoire; T-cell receptor; Immune system; T cell; Concordance; Peripheral blood","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001359768,0.0001262761,0.0001938431,0.000319918,0.0001765971,0.0004618387,0.0001080394,0.0002037648,0.0007564087],"category_scores_gemma":[0.0002825726,0.0001210044,0.0001285479,0.0002705362,0.0001514905,0.0001380855,0.0002795324,0.0002730648,0.000263776],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001046878,"about_ca_system_score_gemma":0.00007853429,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007227427,"about_ca_topic_score_gemma":0.00132671,"domain_scores_codex":[0.999903,0.00001331558,0.000004661508,0.00003391347,0.00001946172,0.00002575473],"domain_scores_gemma":[0.999917,0.00002901793,0.00001295724,0.00001140304,0.00001334282,0.0000162209],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0002237091,0.0000144857,0.02194192,0.00003795595,0.00001776564,0.00006289937,0.0001990177,0.0007990202,0.9607177,0.0001245788,0.0001485538,0.01571238],"study_design_scores_gemma":[0.00002789153,0.0005806604,0.5367244,0.00004087952,0.0001229214,0.001883549,0.0008982421,0.02140319,0.4307581,0.001088932,0.006428559,0.00004275794],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9924138,0.0002859458,0.005894898,0.00001838807,0.000002166959,0.00001291833,0.0006589402,0.00005234487,0.0006606671],"genre_scores_gemma":[0.9942839,0.0002018093,0.003798796,0.00004958177,0.000003243156,0.00003238296,0.001011689,0.00003575017,0.0005828838],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0007564087,"threshold_uncertainty_score":0.002530456,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01553054210891863,"score_gpt":0.2723023152088707,"score_spread":0.256771773099952,"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."}}