{"id":"W2074171589","doi":"10.1371/journal.pone.0027754","title":"Gene Decay in Shigella as an Incipient Stage of Host-Adaptation","year":2011,"lang":"en","type":"article","venue":"PLoS ONE","topic":"Escherichia coli research studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":53,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"Specialized Research Fund for the Doctoral Program of Higher Education of China; National Natural Science Foundation of China; Harbin Medical University","keywords":"Biology; Pseudogene; Gene; Shigella; Operon; Genetics; Genome; Shigella flexneri; Mutant; Escherichia coli","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":[0.0001590296,0.0000750885,0.0001158231,0.00004300486,0.00002183071,0.000003830113,0.0001284901,0.00006069873,0.0000412501],"category_scores_gemma":[0.00008681187,0.00007427481,0.00002129867,0.000083841,0.00005827098,0.0000038359,0.0001120688,0.00005888234,0.000007379343],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001285635,"about_ca_system_score_gemma":0.00006585752,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002623469,"about_ca_topic_score_gemma":0.0005782482,"domain_scores_codex":[0.9992543,0.00006600086,0.0001408579,0.0001889543,0.0001870069,0.000162887],"domain_scores_gemma":[0.999535,0.000007212865,0.00004873024,0.0002320095,0.000120567,0.00005649417],"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":[0.0001345418,0.001028319,0.01967148,0.00003916585,0.00007603139,0.000003692841,0.0006549712,0.000003208632,0.978066,0.000140745,0.000003468261,0.0001784259],"study_design_scores_gemma":[0.0002884093,0.0006273183,0.03265801,0.00001622809,0.000009051183,1.901139e-7,0.0002629011,0.00009664211,0.9658486,0.00002580423,0.00008373972,0.00008309774],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9955348,0.0003112264,0.00004525747,0.000017224,0.000009186653,0.0001896325,0.0000114822,0.00000533123,0.003875804],"genre_scores_gemma":[0.9954529,0.0004129853,0.003299835,0.00003694381,0.00003110767,0.00003677198,0.00002178866,0.00001192812,0.0006957641],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01298653,"threshold_uncertainty_score":0.3028839,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.08406761635251496,"score_gpt":0.282014227765201,"score_spread":0.197946611412686,"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."}}