{"id":"W2410809045","doi":"10.1038/srep17607","title":"Differential evolution of a CXCR4-using HIV-1 strain in CCR5wt/wt and CCR5∆32/∆32 hosts revealed by longitudinal deep sequencing and phylogenetic reconstruction","year":2015,"lang":"en","type":"article","venue":"Scientific Reports","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":18,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; AIDS Vancouver; Simon Fraser University","funders":"Canadian Institutes of Health Research; National Institutes of Health; University of British Columbia; National Institute on Drug Abuse; Providence Health Care; Canada Research Chairs; Simon Fraser University; Michael Smith Health Research BC; Canadian Foundation for AIDS Research","keywords":"Biology; Phylogenetic tree; Population; Deep sequencing; Virus; Virology; Phylogenetics; Viral evolution; Viral load; CXCR4; Genetics; Strain (injury); Gene; RNA; Chemokine; Genome; Medicine; Immune system; Anatomy","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002749009,0.000154512,0.0002423317,0.0003435357,0.0004223081,0.0005945446,0.0002222726,0.000260178,0.0005769735],"category_scores_gemma":[0.0004273766,0.0002097707,0.0001668565,0.0002971667,0.0002766575,0.0001988698,0.0004677717,0.0004777969,0.0001143818],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000356254,"about_ca_system_score_gemma":0.0002318196,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006770838,"about_ca_topic_score_gemma":0.01452019,"domain_scores_codex":[0.9998384,0.00002011259,0.000008212934,0.00005316789,0.00002802585,0.00005212308],"domain_scores_gemma":[0.9998302,0.00002571447,0.00005516849,0.00001466219,0.00002279928,0.0000513721],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0006897073,0.00007581236,0.5773054,0.00004673253,0.00008669405,0.0008864129,0.001543689,0.001209786,0.3999466,0.00106506,0.0002471233,0.01689699],"study_design_scores_gemma":[0.00002289116,0.0003666315,0.9622259,0.0000357831,0.00007157066,0.003583725,0.001670849,0.01035184,0.01892713,0.000549814,0.002146888,0.00004706],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9992466,0.00005429633,0.0003729505,0.00001194083,8.403679e-7,0.000004178235,0.0001072772,0.000003810125,0.0001982043],"genre_scores_gemma":[0.9983653,0.00006706555,0.0009155374,0.00003723672,0.000001158686,0.000006772573,0.0003694712,0.00000716181,0.0002302857],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006770838,"threshold_uncertainty_score":0.0134629,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02554630922079431,"score_gpt":0.2569390679722372,"score_spread":0.2313927587514429,"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."}}