{"id":"W2467570932","doi":"10.1089/aid.2015.0330","title":"Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection","year":2016,"lang":"en","type":"article","venue":"AIDS Research and Human Retroviruses","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"AIDS Vancouver; Simon Fraser University","funders":"Fogarty International Center; National Institute of Allergy and Infectious Diseases; Harvard University; Harvard T.H. Chan School of Public Health; Canadian Institutes of Health Research; Harvard University Center for AIDS Research; National Institutes of Health; Center for AIDS Research, University of Washington; Michael Smith Health Research BC","keywords":"Epitope; Biology; Virology; Immune system; Human leukocyte antigen; Human immunodeficiency virus (HIV); Peptide sequence; Virus; Transmission (telecommunications); Chronic infection; Immunology; Antigen; Genetics; 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":[],"consensus_categories":[],"category_scores_codex":[0.0005241288,0.0003237773,0.0004192289,0.0005626881,0.0007270348,0.000143691,0.000206291,0.0003616193,0.0008030207],"category_scores_gemma":[0.0001094389,0.0002198046,0.00008031337,0.0002323732,0.0009255035,0.000440476,0.0002142781,0.0008993456,0.0001661755],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001821535,"about_ca_system_score_gemma":0.00007211725,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003090684,"about_ca_topic_score_gemma":0.004175232,"domain_scores_codex":[0.9970011,0.000687607,0.0002863548,0.0007053025,0.0002456147,0.00107407],"domain_scores_gemma":[0.9987532,0.0004710896,0.00008281074,0.0003780601,0.0001702599,0.0001445363],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0007396524,0.0002748601,0.8730062,0.0001309577,0.0003459814,0.00007026298,0.0003897446,2.928481e-7,0.1231571,0.0008886051,0.0001060589,0.0008902887],"study_design_scores_gemma":[0.003256597,0.001277143,0.9531294,0.0002870391,0.00002698737,0.00002435229,0.0002827994,5.158229e-8,0.0388517,0.0009432772,0.001671843,0.0002487855],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9926426,0.005713583,0.00006099063,0.0002269794,0.00006849042,0.0006112593,0.0004236979,0.00006854964,0.000183883],"genre_scores_gemma":[0.9941511,0.001699624,0.00000471989,0.00002721355,0.00004962759,0.0001346598,0.0000555786,0.00004119389,0.003836352],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08430538,"threshold_uncertainty_score":0.8963372,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05171563152605195,"score_gpt":0.314921947898629,"score_spread":0.263206316372577,"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."}}