{"id":"W4308884429","doi":"10.1099/ijsem.0.005542","title":"Phylogenomic and comparative genomic studies robustly demarcate two distinct clades of Pseudomonas aeruginosa strains: proposal to transfer the strains from an outlier clade to a novel species Pseudomonas paraeruginosa sp. nov.","year":2022,"lang":"en","type":"article","venue":"INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":47,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"","keywords":"Biology; Clade; Genetics; Phylogenetic tree; 16S ribosomal RNA; Phylogenetics; Evolutionary biology; Strain (injury); Lineage (genetic); Ribosomal RNA; Gene","routes":{"ca_aff":true,"ca_fund":false,"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":[0.0004946397,0.0002771876,0.0007156862,0.0001548854,0.0002324162,0.00002867458,0.0005268673,0.00006068642,0.00001800412],"category_scores_gemma":[0.00006175058,0.0002022734,0.0001471945,0.00007288049,0.0003748196,0.000007244252,0.0004000234,0.0001711164,0.000001954765],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001011221,"about_ca_system_score_gemma":0.0001646181,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005172812,"about_ca_topic_score_gemma":0.0001534717,"domain_scores_codex":[0.99793,0.0003219463,0.0009513643,0.00036886,0.0001863885,0.0002413693],"domain_scores_gemma":[0.9987986,0.000123178,0.0003640663,0.0002035752,0.0004018988,0.0001086985],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0003801264,0.000188326,0.003775771,0.0001795565,0.001656896,0.000009846129,0.004330961,0.003713038,0.9844468,0.0009857982,0.0002922553,0.0000405922],"study_design_scores_gemma":[0.01840147,0.01266278,0.7294785,0.002859687,0.002416904,0.01400744,0.1432853,0.0008916726,0.05605257,0.004514804,0.011976,0.003452852],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9870336,0.007585353,0.001591793,0.001268628,0.0005018405,0.000685762,0.001308072,0.000002302677,0.00002263956],"genre_scores_gemma":[0.9961472,0.0002792026,0.002721068,0.0003267717,0.0003326955,0.00005726086,0.00006664849,0.00001512351,0.0000540207],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9283943,"threshold_uncertainty_score":0.8248471,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04817112384699284,"score_gpt":0.2936024324379341,"score_spread":0.2454313085909413,"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."}}