{"id":"W2149011825","doi":"10.1186/1743-422x-4-107","title":"Functional relevance of nonsynonymous mutations in the HIV-1 tat gene within an epidemiologically-linked transmission cohort","year":2007,"lang":"en","type":"article","venue":"Virology Journal","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"National Health and Medical Research Council; Medical Research Council; Australian Centre for HIV and Hepatitis Virology Research","keywords":"Viral quasispecies; Nonsynonymous substitution; Biology; Transactivation; Virology; Gene; Genetics; Transmission (telecommunications); Mutation; Viral evolution; Silent mutation; Phylogenetic tree; Synonymous substitution; Cohort; Exon; Missense mutation; Genome; Gene expression; Medicine","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":[0.003585545,0.0001359386,0.0002849966,0.0001838417,0.0003025412,0.000005966508,0.0002536301,0.0002815838,0.0007190874],"category_scores_gemma":[0.0003004971,0.00007962117,0.00009844193,0.0001597071,0.000483444,0.00008155395,0.0000169779,0.0009129344,0.0002632779],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004636226,"about_ca_system_score_gemma":0.0001103245,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002572109,"about_ca_topic_score_gemma":0.00006948825,"domain_scores_codex":[0.9975321,0.001120088,0.0006094289,0.0002165623,0.00007797193,0.0004438685],"domain_scores_gemma":[0.9984003,0.001064395,0.0002026417,0.0001833352,0.00008733711,0.00006199387],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.003050769,0.00150808,0.2500378,0.000007170934,0.0004038209,0.0006507531,0.002059795,0.001283769,0.7110779,0.0009020271,0.002558918,0.02645917],"study_design_scores_gemma":[0.002637148,0.00127294,0.980979,0.0000114825,0.00005431346,0.003823516,0.000265053,0.0000431368,0.005498005,0.001953805,0.003352865,0.0001087114],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9695597,0.001762851,0.02636449,0.001569161,0.0002016779,0.0002236733,0.00003343505,0.00001319867,0.0002718737],"genre_scores_gemma":[0.9968854,0.0002939649,0.001869774,0.0003672953,0.00005189558,0.00001570883,0.0002332578,0.000007490557,0.0002752811],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7309412,"threshold_uncertainty_score":0.7873503,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03217361244870102,"score_gpt":0.2979450741858908,"score_spread":0.2657714617371898,"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."}}