{"id":"W4404029895","doi":"10.1101/2024.11.03.24316634","title":"Gene expression differences in differentially methylated sites associated with HIV status and cocaine use","year":2024,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University; British Columbia Centre on Substance Use; University of British Columbia","funders":"","keywords":"Human immunodeficiency virus (HIV); Gene; Gene expression; Expression (computer science); Genetics; Psychology; Biology; Computer science; Virology","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":true,"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":[0.0001573404,0.0001224573,0.0002204119,0.0006041538,0.0001771768,0.0003118416,0.0001243977,0.0001750602,0.00212701],"category_scores_gemma":[0.0004514834,0.00008621118,0.0001974454,0.0007560022,0.0001528419,0.00008191456,0.00018381,0.0001517422,0.0001381859],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001513857,"about_ca_system_score_gemma":0.0001291798,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003451404,"about_ca_topic_score_gemma":0.00440715,"domain_scores_codex":[0.999849,0.00002453139,0.00000817286,0.00006479168,0.00002206529,0.00003146137],"domain_scores_gemma":[0.9997048,0.0001149688,0.00008961729,0.00001983229,0.00003456884,0.00003618647],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001088852,0.00002046136,0.9115897,0.0000746941,0.0002599613,0.0001347502,0.0001300979,0.00019106,0.07970615,0.00006126143,0.0001442636,0.006598711],"study_design_scores_gemma":[0.000004914476,0.00004591684,0.9966338,0.000003714073,0.0000518964,0.0001536802,0.00008157266,0.0002804527,0.002517235,0.0000499286,0.0001744134,0.00000231563],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9971296,0.000458767,0.0003329815,0.00001895165,0.000002395923,0.00000689133,0.001740852,0.000008725326,0.0003007967],"genre_scores_gemma":[0.9980609,0.0001428096,0.0003461816,0.00002137174,0.000003114355,0.00001424679,0.00100654,0.000003793914,0.0004010479],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.003451404,"threshold_uncertainty_score":0.007115602,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02363230766550503,"score_gpt":0.257604718301272,"score_spread":0.233972410635767,"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."}}