{"id":"W3084374422","doi":"10.1093/molbev/msaa226","title":"Evolutionary Genomics of Niche-Specific Adaptation to the Cystic Fibrosis Lung in <i>Pseudomonas aeruginosa</i>","year":2020,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Bacterial biofilms and quorum sensing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":29,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa; Agriculture and Agri-Food Canada","funders":"Natural Sciences and Engineering Research Council of Canada; Cystic Fibrosis Canada","keywords":"Biology; Pseudomonas aeruginosa; Cystic fibrosis; Adaptation (eye); Niche; Genomics; Evolutionary biology; Computational biology; Genome; Genetics; Ecology; Bacteria; Gene; Neuroscience","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":[0.0001332184,0.0001266246,0.0001428269,0.00003300001,0.00007128825,0.000007601551,0.0001043483,0.0001774225,0.000003127839],"category_scores_gemma":[0.00007112965,0.000109701,0.00005446017,0.0001611314,0.000097498,0.000004189951,0.0001108289,0.00008575839,0.000004661631],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002473809,"about_ca_system_score_gemma":0.00004579044,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005257475,"about_ca_topic_score_gemma":0.00002575019,"domain_scores_codex":[0.9990653,0.0001368739,0.0002307381,0.0003235585,0.00004903638,0.0001945208],"domain_scores_gemma":[0.9996332,0.00001401621,0.00007167431,0.0001659866,0.00004990355,0.0000652132],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0002633377,0.00001734564,0.002297822,0.00001160724,0.00001645478,0.000001364889,0.000130443,0.0009837513,0.9941308,0.0008570613,0.0004333244,0.0008567143],"study_design_scores_gemma":[0.002400953,0.002282396,0.1051978,0.00008429305,0.0001024832,0.00007134592,0.0007921274,0.01395612,0.8235548,0.0007096477,0.04984175,0.001006287],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9581885,0.003959188,0.03578649,0.001613591,0.0001246358,0.0002342444,0.00003625843,0.000007525733,0.00004953836],"genre_scores_gemma":[0.9947251,0.0001885042,0.004269378,0.0005023342,0.0001301199,0.000009580967,0.0001583704,0.00001119755,0.000005403837],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.170576,"threshold_uncertainty_score":0.4473479,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.008157260596635007,"score_gpt":0.2195735401867738,"score_spread":0.2114162795901388,"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."}}