{"id":"W2386785318","doi":"10.1371/journal.ppat.1005619","title":"Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus","year":2016,"lang":"en","type":"article","venue":"PLoS Pathogens","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":103,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"National Institute of Allergy and Infectious Diseases; amfAR, The Foundation for AIDS Research; National Institute of General Medical Sciences; Harvard University Center for AIDS Research; Michael Smith Health Research BC; Howard Hughes Medical Institute","keywords":"Founder effect; Bottleneck; Selection (genetic algorithm); Biology; Human immunodeficiency virus (HIV); Transmission (telecommunications); Population bottleneck; Sexual transmission; Genetics; Virus; Virology; Composition (language); Evolutionary biology; Telecommunications; Computer science; Gene; Genotype; Allele; Haplotype; Microsatellite","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":[0.0001366017,0.00008638362,0.0001374052,0.00003465036,0.0001385444,0.000004330425,0.0002447049,0.00007632692,0.000047671],"category_scores_gemma":[0.00001997125,0.00003087272,0.00004103433,0.0001206666,0.000260081,0.00003185872,0.00002679576,0.0001076033,0.00003793872],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002179242,"about_ca_system_score_gemma":0.0000388743,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009452671,"about_ca_topic_score_gemma":0.00004539597,"domain_scores_codex":[0.9988904,0.0005370721,0.0001869877,0.0001302011,0.00008162289,0.0001737054],"domain_scores_gemma":[0.9993308,0.0003491071,0.00007305558,0.0001932155,0.00004455135,0.000009252923],"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":[0.00004104331,0.0001268167,0.2042494,0.00001144301,0.00006360728,4.089963e-7,0.0006235286,0.000006421364,0.7907733,0.00002455984,0.00001659427,0.004062972],"study_design_scores_gemma":[0.0004272332,0.0002220472,0.6990311,0.00004800739,0.0000575195,0.000004984969,0.000117801,0.000009054446,0.2998744,0.0001174033,0.00005095128,0.00003949391],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9981759,0.0003406316,0.00043209,0.0004622734,0.00001242788,0.0003068914,0.0002137048,0.000006251252,0.00004989383],"genre_scores_gemma":[0.9997466,0.00008266568,0.00003182208,0.0000165742,0.00000954437,0.00003402288,0.00001383433,0.000004456432,0.00006052863],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4947817,"threshold_uncertainty_score":0.1258953,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02913769553655113,"score_gpt":0.2507433815881079,"score_spread":0.2216056860515568,"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."}}