{"id":"W2106665579","doi":"10.1073/pnas.0901260106","title":"On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales","year":2009,"lang":"en","type":"article","venue":"Proceedings of the National Academy of Sciences","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":218,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta; Dalhousie University","funders":"Lawrence Berkeley National Laboratory; Lawrence Livermore National Laboratory; Los Alamos National Laboratory; Biological and Environmental Research; National Aeronautics and Space Administration; Office of Science; Norges Forskningsråd; Canadian Institutes of Health Research; University of Connecticut; U.S. Department of Energy","keywords":"Biology; Genome; Phylogenetic tree; Genetics; Horizontal gene transfer; Thermophile; Gene; Firmicutes; Phylogenetics; Thermotoga maritima; Evolutionary biology; Archaea; Bacteria; Escherichia coli; 16S ribosomal RNA","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":[0.0004302447,0.00008286566,0.00008748432,0.00002470753,0.0001665885,0.000007287422,0.0005830431,0.00006336858,0.000002313098],"category_scores_gemma":[0.0001518751,0.00003694043,0.000060648,0.0001894079,0.0006486489,0.000001462594,0.0001231734,0.00009007991,1.009635e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004248596,"about_ca_system_score_gemma":0.00001948384,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001074536,"about_ca_topic_score_gemma":5.900183e-8,"domain_scores_codex":[0.9992052,0.000009121553,0.0001545063,0.0001644803,0.0003742551,0.00009238461],"domain_scores_gemma":[0.9995983,0.00004188902,0.0002329911,0.00001878657,0.00009645153,0.0000116268],"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":[0.00001475283,0.00002570368,0.002974669,0.000007119429,0.00002187456,4.461605e-10,0.00006038688,0.00006484777,0.973573,0.02272241,0.0002162148,0.0003189847],"study_design_scores_gemma":[0.00009582073,0.0001479715,0.3325312,0.00002160213,0.00001063157,0.000001972482,0.00007605977,0.00003831155,0.6392352,0.02750216,0.0002902266,0.00004879896],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9921983,0.001370183,1.113018e-7,0.002784149,0.00001628834,0.0001814146,0.000009250316,5.64977e-7,0.003439707],"genre_scores_gemma":[0.9987885,0.0002489938,0.0000643682,0.000787704,0.00004586417,0.000005029632,4.830001e-8,0.000002324033,0.00005716373],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3343378,"threshold_uncertainty_score":0.2389974,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02137951927549708,"score_gpt":0.2765950600771165,"score_spread":0.2552155408016194,"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."}}