{"id":"W4408314698","doi":"10.1101/2025.03.05.641653","title":"Immune signaling mediates stromal changes to support epithelial reprogramming in Celiac duodenum","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Digestive system and related health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Trinity College","funders":"","keywords":"Duodenum; Immune system; Reprogramming; Stromal cell; Cell biology; Biology; Immunology; Cancer research; Medicine; Internal medicine; Cell; Genetics","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.001226682,0.0006089067,0.0007373726,0.0004003652,0.0001353315,0.0001168991,0.0006542137,0.001082588,0.0000177987],"category_scores_gemma":[0.0003077544,0.0006471127,0.0001846277,0.0004448631,0.00008103557,0.00000686605,0.0008846288,0.0006985252,0.00003919357],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001629835,"about_ca_system_score_gemma":0.001052729,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002289152,"about_ca_topic_score_gemma":0.00004791799,"domain_scores_codex":[0.996378,0.0002227642,0.0007732662,0.001419904,0.0003212077,0.0008848322],"domain_scores_gemma":[0.9977297,0.00003257543,0.0003771636,0.001163776,0.0003689709,0.0003278414],"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":[0.00009375253,0.0001213518,0.006594955,0.000582652,0.000148482,0.00006788912,0.00003406538,0.0002160005,0.9918765,0.00006773293,0.0001777592,0.00001880553],"study_design_scores_gemma":[0.0007540453,0.000421653,0.01800046,0.001211361,0.00008229583,5.12173e-8,0.00002603003,0.00002467602,0.9612415,0.000001028382,0.01732807,0.0009088409],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9918247,0.003100644,0.0004482942,0.0005123052,0.002145068,0.001327232,0.0004670444,0.0001296785,0.00004503762],"genre_scores_gemma":[0.9953862,0.0006182445,0.00230165,0.0003007243,0.0008925194,0.00032162,0.000007305164,0.00009616148,0.00007557855],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03063507,"threshold_uncertainty_score":0.999598,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01135885654256312,"score_gpt":0.2476185371452112,"score_spread":0.2362596806026481,"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."}}