{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002239317,0.0002157911,0.0004934479,0.00007787599,0.0005904571,0.00002128921,0.0001871758,0.000231687,0.00005885425],"category_scores_gemma":[0.00003224006,0.000193106,0.00005897213,0.0001376233,0.0009923638,0.00007212253,0.0002672875,0.0003029156,0.000008471043],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001045103,"about_ca_system_score_gemma":0.00002859985,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008719309,"about_ca_topic_score_gemma":0.0002715742,"domain_scores_codex":[0.9987636,0.0002682478,0.0003762196,0.000239176,0.00002095224,0.0003318466],"domain_scores_gemma":[0.9992456,0.0002174535,0.0001309515,0.0003208441,0.00007039105,0.00001475159],"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":[0.000164895,0.0003121323,0.02447252,0.0001125903,0.0003367469,0.000001535355,0.001243794,6.157941e-7,0.9695671,0.002710613,0.00003079509,0.001046713],"study_design_scores_gemma":[0.002888031,0.0002127779,0.01841657,0.00004516042,0.0001397707,0.00002469417,0.001964655,0.00000120212,0.9747416,0.0008806603,0.0005123387,0.0001725344],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9790081,0.01957907,0.000024856,0.00004034215,0.0004287652,0.0002579636,0.0000337077,0.00006039236,0.0005667927],"genre_scores_gemma":[0.9986296,0.0002917458,0.0001987521,0.00004479581,0.000007284668,0.00001879192,0.00007939702,0.000009817691,0.0007198341],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01962147,"threshold_uncertainty_score":0.7874636,"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."}}