{"id":"W3217282564","doi":"10.1099/mgen.0.000681","title":"Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection","year":2021,"lang":"en","type":"article","venue":"Microbial Genomics","topic":"Bacterial biofilms and quorum sensing","field":"Biochemistry, Genetics and Molecular Biology","cited_by":31,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université Laval","funders":"Canadian Institutes of Health Research; Health Research Council of New Zealand; Otago Medical Research Foundation; Cystic Fibrosis Canada","keywords":"Biology; Transcriptome; Pseudomonas aeruginosa; Phenotype; Gene; Genetics; Microbiology; Genome; Experimental evolution; Bacteria; Gene expression","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":[0.00006042188,0.00008861384,0.0001230819,0.00005127138,0.00003491704,0.00001615597,0.00002816082,0.0001205527,0.000004927707],"category_scores_gemma":[0.00001083387,0.0001168923,0.00004784406,0.00007349155,0.0000455582,0.000006645801,0.00003840219,0.00005848001,0.000001553694],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004420739,"about_ca_system_score_gemma":0.00007399562,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001190477,"about_ca_topic_score_gemma":0.000917997,"domain_scores_codex":[0.9993657,0.00004172474,0.0001957096,0.0002271234,0.00002827037,0.0001414281],"domain_scores_gemma":[0.99976,0.000002790579,0.00006016224,0.0001121375,0.00003757748,0.00002729588],"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":[0.0000956223,0.00002682628,0.001284422,0.00002275631,0.00001858534,0.000002562189,0.0002957146,0.0003485524,0.9971356,0.00001711912,0.000001838518,0.0007504438],"study_design_scores_gemma":[0.0006707949,0.0000386708,0.2235133,0.00001218729,0.00001449773,0.00003133404,0.00006749945,0.00003193347,0.7744191,0.00001231668,0.001063574,0.0001247036],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9988233,0.0005289827,0.0003002311,0.00002406795,0.0001751904,0.0000905077,0.00002639761,0.000004949718,0.00002630011],"genre_scores_gemma":[0.9980884,0.0004265762,0.001132302,0.00001768162,0.0001298863,0.000001110312,0.0001418174,0.00001405168,0.00004820321],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2227164,"threshold_uncertainty_score":0.4766732,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006253384314490761,"score_gpt":0.1911467998509393,"score_spread":0.1848934155364486,"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."}}