{"id":"W2903248410","doi":"10.1093/gbe/evy251","title":"<i>Nephromyces</i>Encodes a Urate Metabolism Pathway and Predicted Peroxisomes, Demonstrating That These Are Not Ancient Losses of Apicomplexans","year":2018,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Parasitic Infections and Diagnostics","field":"Immunology and Microbiology","cited_by":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"National Institute of Allergy and Infectious Diseases; Natural Sciences and Engineering Research Council of Canada; National Institutes of Health; National Science Foundation","keywords":"Biology; Peroxisome; In silico; Transcriptome; Apicomplexa; Lineage (genetic); Genetics; Purine metabolism; Phylogenetics; Purine; Evolutionary biology; Gene; Computational biology; Biochemistry; Enzyme; Gene expression; Plasmodium falciparum","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":[0.0002440731,0.0001585874,0.0002845183,0.00009554756,0.0003446737,0.000009777097,0.00007201148,0.0002692756,0.00007207743],"category_scores_gemma":[0.0001346327,0.000127663,0.00003785602,0.0001117345,0.001179434,0.00008178781,0.0000695717,0.0001364731,0.00001342682],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001958592,"about_ca_system_score_gemma":0.00005451851,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001291623,"about_ca_topic_score_gemma":0.00007516531,"domain_scores_codex":[0.9989657,0.000186381,0.0002392179,0.0002837515,0.0000198397,0.0003050771],"domain_scores_gemma":[0.9993462,0.0001742206,0.000177104,0.0001512618,0.0001197289,0.00003151619],"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":[0.00008120744,0.0000926916,0.2385197,0.00002390702,0.0001195168,9.293444e-7,0.0005493696,0.000002154234,0.7521284,0.007769547,0.0000670233,0.0006455607],"study_design_scores_gemma":[0.0007131695,0.0003483796,0.9615793,0.00002855363,0.00007536879,0.0001427539,0.0005145327,0.00003605793,0.0284331,0.0009738641,0.006986808,0.000168119],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9889753,0.007444258,0.002203851,0.00007313339,0.0003803146,0.0001670663,0.0003651695,0.00004336079,0.0003474799],"genre_scores_gemma":[0.9989485,0.0003477312,0.00030641,0.0001095256,0.00008598763,0.00001690492,0.0001183336,0.000005202472,0.00006143729],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7236953,"threshold_uncertainty_score":0.5205947,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01867533129012403,"score_gpt":0.2418082496440338,"score_spread":0.2231329183539097,"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."}}