{"id":"W2158238436","doi":"10.1371/journal.pone.0006687","title":"HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins","year":2009,"lang":"en","type":"article","venue":"PLoS ONE","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":167,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; AIDS Vancouver; Simon Fraser University","funders":"National Center for Research Resources; National Institute of Allergy and Infectious Diseases; University of California, San Francisco; University of California, San Diego; University of North Carolina at Chapel Hill; Center for AIDS Research, University of Washington; ACT Government; University of California, Davis; Deutsches Krebsforschungszentrum; University of Minnesota; Case Western Reserve University; University of Miami; York University; Northwestern University; University of Rochester; University of Cincinnati; University of Pittsburgh; Los Alamos National Laboratory; Johns Hopkins University; University of Washington; Washington University in St. Louis; Canadian Institutes of Health Research; University of California, Los Angeles; University of Texas Southwestern Medical Center; University of Pennsylvania; Vanderbilt University; National Institutes of Health; Ohio State University; University of Southern California; Bill and Melinda Gates Foundation","keywords":"Human leukocyte antigen; Immune system; Biology; Genetics; Immune escape; Population; HLA-B Antigens; HIV vaccine; Immunology; Virology; Antigen; Antibody; Medicine; Vaccine trial","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001584488,0.0001464029,0.0002117321,0.00004720042,0.00005571749,0.00003389733,0.000131091,0.0001484357,0.00001535228],"category_scores_gemma":[0.0001062052,0.0001388182,0.00004088657,0.0001051047,0.00001808493,0.00000863784,0.00006838672,0.0001228891,0.00001348053],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001185564,"about_ca_system_score_gemma":0.00003540224,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001927997,"about_ca_topic_score_gemma":0.00001222567,"domain_scores_codex":[0.9991558,0.00002758074,0.0002682962,0.0001786356,0.0001118188,0.0002579273],"domain_scores_gemma":[0.9995385,0.00000451735,0.00009751333,0.0002604263,0.00004961024,0.00004947545],"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":[0.00007171166,0.0009088911,0.003504257,0.00004104222,0.0001077979,0.000001422967,0.0001920924,0.000005315623,0.9939182,0.000132973,0.00009303632,0.001023234],"study_design_scores_gemma":[0.003281152,0.001666976,0.1828402,0.0002298632,0.0001168704,0.000008508006,0.0003159822,0.003851142,0.8058904,0.0004111347,0.000708858,0.0006789956],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9957546,0.001723063,0.00001939449,0.000383394,0.00001000844,0.0003574258,0.00001746463,0.00001713308,0.001717493],"genre_scores_gemma":[0.9977203,0.000385702,0.0009455067,0.0001767428,0.00004462594,0.00002055757,0.0001831527,0.0000142849,0.000509151],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1880279,"threshold_uncertainty_score":0.5660843,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02187523204499001,"score_gpt":0.1954259889403283,"score_spread":0.1735507568953383,"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."}}