{"id":"W2158170462","doi":"10.1128/jb.01234-08","title":"Transcriptome Divergence and the Loss of Plasticity in <i>Bacillus subtilis</i> after 6,000 Generations of Evolution under Relaxed Selection for Sporulation","year":2008,"lang":"en","type":"article","venue":"Journal of Bacteriology","topic":"Bacteriophages and microbial interactions","field":"Environmental Science","cited_by":44,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"University of Arizona; U.S. Department of Agriculture; National Aeronautics and Space Administration; National Science Foundation","keywords":"Biology; Bacillus subtilis; Indel; Spore; Genetics; Transcriptome; Evolutionary biology; Most recent common ancestor; Parallel evolution; Gene; Phylogenetics; Gene expression; Microbiology; Genotype; Bacteria","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":[0.0001669658,0.00006518165,0.0001997051,0.00005834341,0.0000625662,0.000003076119,0.00006024744,0.00006632184,0.0002067937],"category_scores_gemma":[0.00003540379,0.00004713688,0.00007562489,0.0001110415,0.0003344144,0.000231015,0.00001747544,0.0001062939,9.136304e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000853346,"about_ca_system_score_gemma":0.00001838501,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003792697,"about_ca_topic_score_gemma":0.0006427155,"domain_scores_codex":[0.9992398,0.00008283997,0.0004410604,0.0000832743,0.000059427,0.00009360175],"domain_scores_gemma":[0.9994881,0.00009133699,0.0003054837,0.00004393992,0.00004720576,0.00002390166],"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":[0.0009313833,0.00006321083,0.07098041,0.000006398406,0.00001646601,9.40861e-7,0.0005456095,0.002586376,0.9246404,0.000111628,0.00003513502,0.00008203689],"study_design_scores_gemma":[0.001016485,0.0001941992,0.9892362,0.000014338,0.00003033209,0.0002256163,0.00003990405,0.0006710027,0.008060575,0.0002125734,0.0002523709,0.00004643677],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9839063,0.00004095315,0.01550503,0.0001806736,0.0002008616,0.0001278067,0.00002062306,0.000001466837,0.00001626145],"genre_scores_gemma":[0.9990824,0.0001175974,0.0006775341,0.00003428957,0.00003532503,0.000005514941,0.000002013353,0.000003945388,0.00004139493],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9182557,"threshold_uncertainty_score":0.2264246,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01080441245758348,"score_gpt":0.2182105226721591,"score_spread":0.2074061102145756,"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."}}