{"id":"W2096861682","doi":"10.1093/gbe/evt195","title":"Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past","year":2013,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":28,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"Canadian Institutes of Health Research; Genome Atlantic; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Biology; Aquifex aeolicus; Archaea; Phylogenetic tree; Lineage (genetic); Phylogenetics; Evolutionary biology; Hyperthermophile; Genome; Operational taxonomic unit; Proteobacteria; Genetics; Phylogenetic diversity; Gene","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":[0.00009740573,0.0001485583,0.0001419815,0.00003125248,0.0001850367,0.00001190554,0.00009398081,0.0001832772,0.00001952104],"category_scores_gemma":[0.00002001239,0.0001321536,0.00004923794,0.00004999869,0.0001411708,0.000001407897,0.0001342931,0.00005952349,0.00003635121],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001609597,"about_ca_system_score_gemma":0.00001898213,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000863237,"about_ca_topic_score_gemma":0.00001747789,"domain_scores_codex":[0.9991602,0.00004390863,0.0001612369,0.0003252404,0.00002876943,0.0002806345],"domain_scores_gemma":[0.9996326,0.00000788711,0.0000524883,0.0001780193,0.00006282603,0.00006619758],"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":[0.00001661234,0.00001376828,0.09588042,0.000007111057,0.00006133301,2.766708e-7,0.0001073142,0.00001088923,0.9019341,0.0004918586,0.00008592867,0.00139036],"study_design_scores_gemma":[0.0005186465,0.0003276751,0.976156,0.000005654304,0.00002590833,0.00003096125,0.0002194961,0.00007899279,0.003276817,0.005516277,0.01352476,0.0003188267],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9922734,0.005575624,0.0005060869,0.0002424204,0.0001525981,0.0001837645,0.00001201367,0.000007591619,0.001046442],"genre_scores_gemma":[0.9979138,0.0005765411,0.0004468703,0.0002070182,0.0005496099,0.00004835779,0.00006165708,0.000013468,0.0001826285],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8986573,"threshold_uncertainty_score":0.5389068,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006669287724599684,"score_gpt":0.2072455229131228,"score_spread":0.2005762351885231,"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."}}