{"id":"W2134273787","doi":"10.1196/annals.1355.006","title":"New Perspectives on Rickettsial Evolution from New Genome Sequences of <i>Rickettsia</i>, particularly <i>R. canadensis</i>, and <i>Orientia tsutsugamushi</i>","year":2005,"lang":"en","type":"review","venue":"Annals of the New York Academy of Sciences","topic":"Vector-borne infectious diseases","field":"Immunology and Microbiology","cited_by":40,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"National Institute of Allergy and Infectious Diseases","keywords":"Biology; Synteny; Orientia tsutsugamushi; Anaplasmataceae; Genome; Genetics; Rickettsia; Phylogenetics; Comparative genomics; Phylogenetic tree; Rickettsiales; Ehrlichia chaffeensis; Gene; Evolutionary biology; Genomics; Scrub typhus; Polymerase chain reaction; Virus","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0006210098,0.0005736578,0.001753553,0.0003529148,0.000289449,0.00003901717,0.001551564,0.0006636019,0.0002542188],"category_scores_gemma":[0.0003192271,0.0003928445,0.0007671051,0.001136133,0.002111551,0.0002727768,0.0002676251,0.0006616795,0.00003718136],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00006664734,"about_ca_system_score_gemma":0.002213372,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01231759,"about_ca_topic_score_gemma":0.0002164239,"domain_scores_codex":[0.9963698,0.0005874944,0.001139382,0.0009197607,0.0003644699,0.00061907],"domain_scores_gemma":[0.9969808,0.0005935422,0.001815767,0.0003352803,0.00009082915,0.0001838203],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003498514,0.0007326778,0.001051846,0.002026445,0.004542074,0.000003148544,0.009421271,0.0002634364,0.02031674,0.009124042,0.4187594,0.5334091],"study_design_scores_gemma":[0.0006568667,0.0005841747,0.002890624,0.004860464,0.001982175,0.00005643386,0.001104702,6.926288e-7,0.008744635,0.003888461,0.97444,0.0007907793],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.01177712,0.9850471,0.00001991977,0.001711656,0.0003855632,0.0005684697,0.0002469622,0.00003356744,0.0002096661],"genre_scores_gemma":[0.05271819,0.9453244,0.0001851587,0.0003426132,0.0004567616,0.000008689931,0.00001340179,0.00002981257,0.0009210155],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.5556806,"threshold_uncertainty_score":0.9998524,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06654151084789281,"score_gpt":0.3250766144265862,"score_spread":0.2585351035786934,"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."}}