{"id":"W4414372028","doi":"10.1002/ctm2.70466","title":"Gene expression differences in differentially methylated sites associated with HIV status and cocaine use","year":2025,"lang":"en","type":"article","venue":"Clinical and Translational Medicine","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":false,"ca_institutions":"Simon Fraser University; British Columbia Centre on Substance Use; University of British Columbia","funders":"National Institute on Drug Abuse","keywords":"Human immunodeficiency virus (HIV); Gene expression; Cocaine use; Gene; Cocaine dependence; Drug","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":[0.0002764724,0.0001169696,0.0002386929,0.00006019173,0.00005028008,0.00001229358,0.00003682958,0.0001477685,0.00001157268],"category_scores_gemma":[0.0004084791,0.00007850512,0.00002128819,0.0001035288,0.0002699841,0.000005562571,0.00002056227,0.0001109914,1.207509e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000001650241,"about_ca_system_score_gemma":0.00003694283,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001476286,"about_ca_topic_score_gemma":0.0001243718,"domain_scores_codex":[0.9989774,0.0001343366,0.0003545714,0.0002913454,0.0001149908,0.0001273877],"domain_scores_gemma":[0.9993085,0.0003863249,0.00006344094,0.00008543592,0.00007436401,0.00008198721],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0002172761,0.00007723081,0.9077112,0.00001041997,0.00005043995,0.000001303981,0.00003700216,0.000007695399,0.08944611,0.00009893351,0.00001275208,0.00232964],"study_design_scores_gemma":[0.002841868,0.0003164989,0.9854432,0.0001308836,0.00004602564,2.302481e-7,0.00001268624,0.0003418057,0.008932172,0.001668438,0.0001723845,0.00009381428],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9918751,0.00349086,0.003501554,0.0008423238,0.00005092717,0.0001322536,0.00001944257,0.000006239834,0.00008127071],"genre_scores_gemma":[0.9965358,0.002006941,0.0006257572,0.0001205153,0.00005786999,0.000006132617,0.0004352893,0.00000605619,0.0002056344],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08051394,"threshold_uncertainty_score":0.3201346,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04163469064744831,"score_gpt":0.3268513576041104,"score_spread":0.2852166669566621,"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."}}