{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006322544,0.0001570996,0.0003086022,0.0005259178,0.000239098,0.0007092117,0.00020222,0.0002589244,0.001190441],"category_scores_gemma":[0.001856791,0.0001684141,0.0002278896,0.000302513,0.0002804194,0.0003746452,0.000405406,0.0003072307,0.0002085301],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001426278,"about_ca_system_score_gemma":0.0001660535,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007428462,"about_ca_topic_score_gemma":0.001338374,"domain_scores_codex":[0.9996,0.0001247904,0.00002930358,0.0001182203,0.00007214054,0.00005564715],"domain_scores_gemma":[0.9993234,0.0003031286,0.0001818505,0.00007179385,0.0000542249,0.00006557579],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0004959566,0.00007648675,0.7683975,0.00009937069,0.0003095215,0.0001796589,0.0007458003,0.0007289774,0.1970999,0.0006237938,0.0001511108,0.03109196],"study_design_scores_gemma":[0.000008956916,0.0001978957,0.9835116,0.00002307327,0.00008660299,0.0006053367,0.0005497694,0.003557298,0.01009155,0.0006424183,0.0007104863,0.00001514477],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9982022,0.0003436669,0.000949961,0.00002069418,0.000002804392,0.000005144989,0.0001007548,0.000007255971,0.000367427],"genre_scores_gemma":[0.9989074,0.0001575226,0.0006081901,0.00002433954,0.000003690239,0.00000528109,0.0001348868,0.000006306776,0.0001522571],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001190441,"threshold_uncertainty_score":0.003982484,"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."}}