{"id":"W4406851961","doi":"10.1093/gbe/evaf015","title":"Massive Gene Loss in the Fungus <i>Sporothrix epigloea</i> Accompanied a Shift to Life in a Glucuronoxylomannan-based Gel Matrix","year":2025,"lang":"en","type":"article","venue":"Genome Biology and Evolution","topic":"Fungal Biology and Applications","field":"Medicine","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Athabasca University; University of Alberta","funders":"Natural Sciences and Engineering Research Council of Canada; Alliance de recherche numérique du Canada; Canada's Michael Smith Genome Sciences Centre; Athabasca University; Génome Québec; Ministerio de Ciencia, Tecnología e Innovación","keywords":"Biology; Sporothrix; Sporothrix schenckii; Fungus; Polysaccharide; Microbiology; Axenic; Biochemistry; Botany; Genetics; Bacteria","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":[0.0003710383,0.0001397852,0.0002684731,0.0001926464,0.0001104225,0.000005275112,0.0001390281,0.000252684,0.00001899052],"category_scores_gemma":[0.00009348931,0.0001033862,0.00004255119,0.0005007049,0.000159064,0.00002118524,0.00004404853,0.000246562,0.00005652401],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009366783,"about_ca_system_score_gemma":0.0001648336,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001814522,"about_ca_topic_score_gemma":0.0002508762,"domain_scores_codex":[0.9989033,0.0001370971,0.0002822665,0.0003440937,0.00003708281,0.0002961689],"domain_scores_gemma":[0.9994588,0.0001380734,0.00005243024,0.0002582858,0.00002813887,0.00006424823],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0009496724,0.0003061822,0.934759,0.00005261508,0.0000364769,0.000017249,0.0004241399,0.0001517799,0.04314493,0.01949113,0.0003270018,0.0003397842],"study_design_scores_gemma":[0.001331871,0.0001807955,0.9907652,0.00002739738,0.00002862264,0.000006758386,0.0001180392,0.0001286089,0.0002312709,0.002682798,0.004396045,0.0001026538],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9769708,0.004232545,0.00167424,0.01579754,0.00008184844,0.0008020586,0.00004261487,0.00002657734,0.0003717556],"genre_scores_gemma":[0.9953839,0.00006410691,0.0002992951,0.003700444,0.00007758627,0.0002646255,0.0001332504,0.000004860519,0.00007198115],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0560061,"threshold_uncertainty_score":0.4215967,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009847187826232078,"score_gpt":0.2907075951251358,"score_spread":0.2808604072989037,"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."}}