{"id":"W4404710929","doi":"10.1152/ajpgi.00182.2024","title":"In silico integrative scRNA analysis of human colonic epithelium indicates four tuft cell subtypes","year":2024,"lang":"en","type":"article","venue":"American Journal of Physiology-Gastrointestinal and Liver Physiology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Alberta Children's Hospital; Alberta Bone and Joint Health Institute; University of Calgary","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Biology; In silico; Gene; Gene expression; Cell; Tuft; Gene expression profiling; Cell biology; Population; Downregulation and upregulation; Cell type; Genetics; Immunology; Computational biology; Medicine","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":[0.0002186677,0.0002690347,0.0008132131,0.0004430866,0.00005140694,0.00001220018,0.0002938764,0.00007156158,0.00004443014],"category_scores_gemma":[0.00005090956,0.0002056683,0.0003387617,0.000542176,0.001025317,0.00001787034,0.00008758921,0.0003960236,0.0000026389],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002274385,"about_ca_system_score_gemma":0.0001272188,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003648137,"about_ca_topic_score_gemma":0.0001094478,"domain_scores_codex":[0.998338,0.0002779431,0.0005648916,0.0004010884,0.00009759537,0.0003204868],"domain_scores_gemma":[0.9989492,0.0001610963,0.0004437163,0.0001676822,0.0001734935,0.0001047757],"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":[0.0004809611,0.0002302238,0.007673263,0.0000526531,0.0004369346,0.00002336322,0.0003280736,0.0002503403,0.9898139,0.00012662,0.0001041495,0.0004795556],"study_design_scores_gemma":[0.001218011,0.02058931,0.6550249,0.0003315913,0.001087897,0.0004521665,0.001409504,0.0018489,0.3157989,0.001359384,0.0002934315,0.0005859701],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9984032,0.001066712,0.0001851263,0.00009417987,0.0000937032,0.00007300694,0.000031244,0.000006078817,0.00004675775],"genre_scores_gemma":[0.9983048,0.0003530718,0.0008969775,0.0001364805,0.0002001862,0.000003907745,0.00003518823,0.00001960696,0.00004975909],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.674015,"threshold_uncertainty_score":0.838691,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007553691142698703,"score_gpt":0.2371873242361691,"score_spread":0.2296336330934703,"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."}}