{"id":"W2999496229","doi":"10.1186/s12977-019-0510-1","title":"Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study","year":2020,"lang":"en","type":"article","venue":"Retrovirology","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":13,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; AIDS Vancouver; Simon Fraser University","funders":"National Institute of Allergy and Infectious Diseases; National Institute on Drug Abuse; National Institute of Neurological Disorders and Stroke; National Institute of Mental Health; National Institute for Health and Care Research; Canadian Institutes of Health Research; Canada Excellence Research Chairs, Government of Canada; National Institutes of Health; Michael Smith Health Research BC","keywords":"Downregulation and upregulation; Biology; Nonsynonymous substitution; Infectivity; Human leukocyte antigen; Virology; Viral replication; Genome; Immune system; Antigen; Genetics; Cell biology; Immunology; Gene; Virus","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007318914,0.0003298435,0.0004641989,0.0006465923,0.001033089,0.0007245661,0.0004696597,0.0008202677,0.0007449129],"category_scores_gemma":[0.00216541,0.0002036812,0.000443108,0.0004749724,0.0005587994,0.0003819748,0.0005576315,0.0007653768,0.0002079678],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007827391,"about_ca_system_score_gemma":0.0002365484,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005096292,"about_ca_topic_score_gemma":0.005069793,"domain_scores_codex":[0.999443,0.0001432127,0.00003454423,0.0001701316,0.00009331836,0.0001157837],"domain_scores_gemma":[0.9985822,0.00047652,0.0002983522,0.0002314981,0.0002124236,0.0001991201],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001127439,0.002002134,0.8332207,0.0001138655,0.0002103972,0.06600685,0.006656388,0.001557299,0.04061143,0.000978834,0.0007833816,0.04673124],"study_design_scores_gemma":[0.00004383398,0.003501643,0.7930199,0.00005763177,0.0002869985,0.167105,0.003698729,0.007916744,0.01788396,0.0006611773,0.005719287,0.0001050809],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9984825,0.0002548139,0.0005315122,0.00003921458,0.000003227763,0.00001586447,0.00004513037,0.000006950029,0.0006207145],"genre_scores_gemma":[0.9984677,0.0003087975,0.0006445094,0.0000281986,0.00001183188,0.000009068416,0.00008981431,0.000006053728,0.0004340915],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005096292,"threshold_uncertainty_score":0.01013327,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02095547540321554,"score_gpt":0.2617833548058694,"score_spread":0.2408278794026538,"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."}}