{"id":"W2128498548","doi":"10.1093/molbev/msr023","title":"Pentatricopeptide Repeat Proteins Constrain Genome Evolution in Chloroplasts","year":2011,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Photosynthetic Processes and Mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":27,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Egg Farmers of Canada","keywords":"Pentatricopeptide repeat; Biology; Indel; Genetics; Gene; RNA editing; Genome; Pseudogene; RNA; Phylogenetic tree; Gene conversion; Codon usage bias; Intron; Conserved sequence; Computational biology; Peptide sequence; Single-nucleotide polymorphism","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002337609,0.0001678709,0.0001488977,0.0001009271,0.00007337446,0.000006162507,0.0001176047,0.0002595204,0.0000229726],"category_scores_gemma":[0.00007230165,0.0001643328,0.0000525397,0.0001165839,0.0001600526,0.000006792678,0.0001031073,0.0001075431,0.00001098817],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004053473,"about_ca_system_score_gemma":0.00008401187,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001796154,"about_ca_topic_score_gemma":0.0001099387,"domain_scores_codex":[0.998877,0.00009240138,0.0002111342,0.000449166,0.00005288885,0.0003173947],"domain_scores_gemma":[0.9995793,0.00000330735,0.00007625172,0.0002168689,0.00004526117,0.00007907324],"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":[0.0001277626,0.00006641888,0.004209271,0.00001470885,0.00001833543,0.00001205039,0.00004893596,0.000003719447,0.9870009,0.008249279,0.000002354644,0.0002462579],"study_design_scores_gemma":[0.001249576,0.001004381,0.04893402,0.00002930378,0.0000328547,0.0002261901,0.0001937718,0.00007236585,0.9282765,0.01890453,0.0006252113,0.0004512582],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8785679,0.001056321,0.1184766,0.00002838185,0.00008761012,0.0003093261,0.00001671892,0.00001680629,0.001440358],"genre_scores_gemma":[0.9980817,0.0001173112,0.001431082,0.00008980562,0.00003998771,0.00006815086,0.00008418542,0.00001466782,0.00007308403],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1195138,"threshold_uncertainty_score":0.6701298,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007575639070756311,"score_gpt":0.2295236617059419,"score_spread":0.2219480226351855,"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."}}