{"id":"W2034589608","doi":"10.1371/journal.pone.0064129","title":"Phylogenetic Reconstruction of the Legionella pneumophila Philadelphia-1 Laboratory Strains through Comparative Genomics","year":2013,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Legionella and Acanthamoeba research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":71,"is_retracted":false,"has_abstract":true,"ca_institutions":"Public Health Ontario; University of Toronto","funders":"National Institutes of Health; University of Toronto","keywords":"Legionella pneumophila; Biology; Phylogenetic tree; Phylogenetics; Most recent common ancestor; Lineage (genetic); Evolutionary biology; Legionella; Comparative genomics; Genomics; Genetics; Genome; Gene; Bacteria","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":[0.00007362661,0.0001383276,0.0001947113,0.0000251958,0.0001107011,0.00002075596,0.0002885752,0.0001292744,0.00003611582],"category_scores_gemma":[0.00002618284,0.0001082599,0.00007499658,0.0001572383,0.0003432102,0.00000847908,0.0001261095,0.0001517802,0.00003293907],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002131497,"about_ca_system_score_gemma":0.0001393749,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004014309,"about_ca_topic_score_gemma":0.00001656885,"domain_scores_codex":[0.9989588,0.00009291693,0.0002288085,0.000270168,0.0002216818,0.0002276385],"domain_scores_gemma":[0.999097,0.000011884,0.0001253223,0.000427701,0.0002807649,0.00005726799],"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":[0.00001261925,0.0002675101,0.002384954,0.00003399277,0.0001561381,2.582776e-7,0.0001757151,0.00002789064,0.9961874,0.00005757549,0.0006196827,0.00007629185],"study_design_scores_gemma":[0.0003215581,0.0001410118,0.008768326,0.00003869784,0.00003503493,0.000004919651,0.0003117674,0.0001186796,0.9892704,0.0003409724,0.0005008561,0.0001477855],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9963098,0.0004486765,0.00002357809,0.001014096,0.00006932335,0.0004518175,0.00004170135,0.000007541714,0.001633473],"genre_scores_gemma":[0.9981356,0.0004343322,0.0006590847,0.0001700225,0.00026327,0.00003972221,0.00002018496,0.00001776415,0.0002599761],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00691698,"threshold_uncertainty_score":0.441471,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05360074682937372,"score_gpt":0.2561840828222058,"score_spread":0.2025833359928321,"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."}}