{"id":"W3049615191","doi":"10.1038/s41467-020-17898-8","title":"Single-cell TCR sequencing reveals phenotypically diverse clonally expanded cells harboring inducible HIV proviruses during ART","year":2020,"lang":"en","type":"article","venue":"Nature Communications","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":106,"is_retracted":false,"has_abstract":true,"ca_institutions":"Centre Hospitalier de l’Université de Montréal; McGill University Health Centre; Université de Montréal","funders":"National Institute on Drug Abuse; Canadian Institutes of Health Research; Government of Canada; McGill University; National Institute of Allergy and Infectious Diseases; Division of Intramural Research, National Institute of Allergy and Infectious Diseases; Delaney AIDS Research Enterprise; Styrelsen för Internationellt Utvecklingssamarbete; National Institute of Neurological Disorders and Stroke; National Institute of Mental Health; amfAR, The Foundation for AIDS Research","keywords":"Biology; T-cell receptor; Repertoire; Phenotype; Virology; Gene duplication; T cell; Immunology; Genetics; Immune system; Gene","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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001458565,0.0002121267,0.0002632968,0.00009516276,0.0006490501,0.00005112068,0.001078367,0.0003818015,0.0002695472],"category_scores_gemma":[0.0002421132,0.0001968226,0.0001107363,0.0002914764,0.0002008354,0.0001761915,0.0007052977,0.001585518,0.002858933],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001977171,"about_ca_system_score_gemma":0.0002077645,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001776495,"about_ca_topic_score_gemma":0.00009653707,"domain_scores_codex":[0.9984653,0.0003300976,0.0003094473,0.0003679025,0.00008870121,0.0004385335],"domain_scores_gemma":[0.9981265,0.0003053161,0.0001274615,0.001174838,0.0001560451,0.0001098321],"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":[0.00009823322,0.000310531,0.00612185,0.00003631594,0.000131912,0.00001016954,0.00095754,0.000008865641,0.9850048,0.0003675382,0.006737951,0.0002142638],"study_design_scores_gemma":[0.002351953,0.000192841,0.004532148,0.00009217764,0.00009362153,0.00001407348,0.0006785727,0.000008826199,0.9047475,0.00004272599,0.08688436,0.000361191],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.962858,0.01160439,0.00007666394,0.006353043,0.0002270693,0.0009904114,0.0004616865,0.0003888983,0.01703985],"genre_scores_gemma":[0.9936166,0.0003963309,0.002769382,0.0005429399,0.00004502157,0.00007620228,0.0004797709,0.00002733225,0.002046394],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08025732,"threshold_uncertainty_score":0.9979175,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05320209384530911,"score_gpt":0.2815116670398223,"score_spread":0.2283095731945132,"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."}}