{"id":"W2883188821","doi":"10.1186/s12931-018-0835-7","title":"Decreased microbiome diversity in the HIV small airway epithelium","year":2018,"lang":"en","type":"article","venue":"Respiratory Research","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"St. Paul's Hospital; BC Cancer Agency; University of British Columbia","funders":"Canadian Institutes of Health Research; Michael Smith Health Research BC; British Columbia Lung Association; St. Paul's Foundation; American Thoracic Society","keywords":"Veillonella; Prevotella; Firmicutes; Bacteroidetes; Microbiome; Proteobacteria; Biology; Fusobacterium; Human microbiome; Human immunodeficiency virus (HIV); Immunology; Microbiology; Medicine; Streptococcus; 16S ribosomal RNA; Bacteria; Bioinformatics; Bacteroides; Genetics","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":[0.00267143,0.0001135901,0.000108928,0.0001630524,0.0005589266,0.00003940783,0.0007113112,0.0001743123,0.00008636129],"category_scores_gemma":[0.0001407398,0.00008658359,0.00006013604,0.0003743937,0.0004487314,0.000003085391,0.0006040809,0.0003132821,0.00045097],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004759974,"about_ca_system_score_gemma":0.0003041208,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001683052,"about_ca_topic_score_gemma":0.0008070738,"domain_scores_codex":[0.9978771,0.0007578873,0.0001654049,0.0003907972,0.0002156677,0.000593185],"domain_scores_gemma":[0.9989598,0.00005085764,0.00003040815,0.0006037834,0.0002378797,0.0001172636],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001527594,0.0001113289,0.02091146,0.00002449782,0.000009517177,0.00001315734,0.0003097848,2.899077e-7,0.9494362,0.0000539809,0.02835931,0.0006176541],"study_design_scores_gemma":[0.00112345,0.0009592991,0.08356135,0.00002874369,0.000004768319,0.00001301518,0.0004449387,0.000004739235,0.2100613,0.00005805725,0.7035193,0.0002210908],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9952084,0.0005211759,0.00004378627,0.000593175,0.0000573146,0.00033541,0.00003219119,0.00000727629,0.003201266],"genre_scores_gemma":[0.9968032,0.000048124,0.00007849721,0.001786856,0.0004594613,0.00001452011,0.00003113216,0.00001534008,0.0007629053],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.739375,"threshold_uncertainty_score":0.5796457,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1318009837768454,"score_gpt":0.3760950357304626,"score_spread":0.2442940519536172,"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."}}