{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:20:00Z","timestamp":1792790400417,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,24]]},"group-title":"Physiology","reference-count":29,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T00:00:00Z","timestamp":1790208000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"name":"National Institute of Diabetes and Digestive and Kidney Diseases","award":["K23DK117061-01A1"],"award-info":[{"award-number":["K23DK117061-01A1"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institute of Diabetes and Digestive and Kidney Diseases","award":["R01DK131491"],"award-info":[{"award-number":["R01DK131491"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>Pediatric endoscopy is performed only when clinically indicated, limiting access to healthy duodenal tissue. Biopsies with duodenal no pathologic abnormality (NPA) are often used as controls despite the presence of symptoms or inflammatory disease found elsewhere in the gastrointestinal (GI) tract. We characterized pediatric duodenal NPA tissue across clinical, histologic, cellular, and transcriptomic domains.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>Archival duodenal NPA biopsies were obtained with clinical metadata and hematoxylin-and-eosin whole-slide images (WSIs). Duodenal mRNA-seq data were analyzed from a subset of patients with duodenal NPA. Clinical metadata and WSIs underwent machine-learning analysis, cell populations were quantified from WSIs, and RNA-seq data underwent differential expression and pathway-enrichment analyses.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The primary cohort included 195 patients with duodenal NPA. Comparisons between patients with non-duodenal GI disease and those with no GI disease showed differences in inflammatory biomarkers and follow-up utilization. Unsupervised clinical clustering identified three clusters with partial enrichment for IBD with colonic inflammation and Eosinophilic Esophagitis (EoE) with esophageal inflammation. Supervised clinical classification showed modest discrimination. WSI clustering showed limited disease-status discrimination, and cell quantification showed no significant group differences. In the separate RNA-seq cohort of 43 patients, differential-expression and pathway-enrichment analyses identified transcriptional and pathway-level differences between disease-status groups.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>This multi-level characterization indicates that pediatric duodenal NPA tissue should not be treated as a uniform control category. Clinical metadata and transcriptomics revealed clinical and molecular heterogeneity, while histologic and cell analyses showed limited disease-status separation, supporting a refined definition of control tissue.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Study Highlights<\/jats:title>\n                  <jats:sec>\n                    <jats:title>What is Known<\/jats:title>\n                    <jats:list list-type=\"simple\">\n                      <jats:list-item>\n                        <jats:p>\u2370 Pediatric duodenal control tissue is difficult to define because asymptomatic children rarely undergo endoscopy.<\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\u2370 Biopsies with duodenal no pathologic abnormality are often used as controls, even when patients have gastrointestinal symptoms or inflammatory disease outside the duodenum.<\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\u2370 Literature suggests there may be variations in control pediatric duodenal tissue.<\/jats:p>\n                      <\/jats:list-item>\n                    <\/jats:list>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>What is New<\/jats:title>\n                    <jats:list list-type=\"simple\">\n                      <jats:list-item>\n                        <jats:p>\u2370 There are variations in inflammatory markers, GI follow-up visits, repeat endoscopies, and gene expression profiles between patients who have no GI disease versus those with non-duodenal GI disease.<\/jats:p>\n                      <\/jats:list-item>\n                      <jats:list-item>\n                        <jats:p>\u2370 Digital histology, pathologist review, and cell quantification showed limited disease-status separation rather than robust disease-specific histologic differences.<\/jats:p>\n                      <\/jats:list-item>\n                    <\/jats:list>\n                  <\/jats:sec>\n                <\/jats:sec>","DOI":"10.64898\/2026.09.16.752095","type":"posted-content","created":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T15:45:11Z","timestamp":1790264711000},"source":"Crossref","is-referenced-by-count":0,"title":["WHAT IS NORMAL? MULTIMODAL CHARACTERIZATION OF NON-DISEASED PEDIATRIC DUODENAL BIOPSIES USING MACHINE LEARNING IMAGE ANALYSIS AND TRANSCRIPTOMICS"],"prefix":"10.64898","author":[{"given":"Anum","family":"Chotani","sequence":"first","affiliation":[{"name":"Duke University Medical Center, Durham, NC;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiebei","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Data Science, University of Virginia, Charlottesville, VA, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nazanin","family":"Moradinasab","sequence":"additional","affiliation":[{"name":"School of Data Science, University of Virginia, Charlottesville, VA, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shahzaib","family":"Khan","sequence":"additional","affiliation":[{"name":"SUNY Downstate Health Sciences University, Brooklyn, NY;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia","family":"Sessions","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S. Fisher","family":"Rhoads","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Srivastava M.","family":"Sanjana","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatima","family":"Zulqarnain","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Varun","family":"Jain","sequence":"additional","affiliation":[{"name":"University of Pittsburgh Medical Center"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shyam","family":"Raghavan","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Moskaluk","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Virginia, Charlottesville, VA, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Greene","sequence":"additional","affiliation":[{"name":"Duke University Medical Center, Durham, NC;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chelsea","family":"Marie","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Virginia, Charlottesville, VA, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Donald","family":"Brown","sequence":"additional","affiliation":[{"name":"School of Data Science, University of Virginia, Charlottesville, VA, United States;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sana","family":"Syed","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Virginia, Charlottesville, VA, United States;"},{"name":"School of Data Science, University of Virginia, Charlottesville, VA, United States;"},{"name":"Duke University Medical Center, Durham, NC;"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026092808500925000_2026.09.16.752095v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.dld.2022.08.020"},{"key":"2026092808500925000_2026.09.16.752095v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-40055-1"},{"key":"2026092808500925000_2026.09.16.752095v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbi.2022.01.019"},{"key":"2026092808500925000_2026.09.16.752095v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2016.07.030"},{"key":"2026092808500925000_2026.09.16.752095v1.5","doi-asserted-by":"publisher","DOI":"10.1007\/s10620-006-9176-3"},{"key":"2026092808500925000_2026.09.16.752095v1.6","doi-asserted-by":"publisher","DOI":"10.1002\/hep.22411"},{"key":"2026092808500925000_2026.09.16.752095v1.7","doi-asserted-by":"publisher","DOI":"10.1038\/nature14539"},{"key":"2026092808500925000_2026.09.16.752095v1.8","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics13182862"},{"key":"2026092808500925000_2026.09.16.752095v1.9","doi-asserted-by":"publisher","DOI":"10.4103\/jpi.jpi_87_18"},{"key":"2026092808500925000_2026.09.16.752095v1.10","doi-asserted-by":"publisher","DOI":"10.1001\/jamanetworkopen.2019.5822"},{"key":"2026092808500925000_2026.09.16.752095v1.11","unstructured":"Hollmann, Noah , et al. \u201cTabpfn: A transformer that solves small tabular classification problems in a second.\u201d arXiv preprint arXiv:2207.01848 (2022)."},{"issue":"4","key":"2026092808500925000_2026.09.16.752095v1.12","doi-asserted-by":"crossref","first-page":"141","DOI":"10.3390\/jpm10040141","article-title":"Deep Learning for Whole-Slide Tissue Histopathology Classification: A Comparative Study in the Identification of Dysplastic and Non-Dysplastic Barrett\u2019s Esophagus","volume":"10","year":"2020","journal-title":"Journal of Personalized Medicine"},{"key":"2026092808500925000_2026.09.16.752095v1.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.media.2019.101563"},{"key":"2026092808500925000_2026.09.16.752095v1.14","unstructured":"Graham, Simon , et al. \u201cLizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification.\u201d Proceedings of the IEEE\/CVF International Conference on Computer Vision"},{"key":"2026092808500925000_2026.09.16.752095v1.15","doi-asserted-by":"publisher","DOI":"10.1136\/bmjopen-2017-017768"},{"key":"2026092808500925000_2026.09.16.752095v1.16","unstructured":"Human Cell Atlas. https:\/\/www.humancellatlas.org\/learn-more\/#event-launch-of-the-human-cell-atlas"},{"key":"2026092808500925000_2026.09.16.752095v1.17","unstructured":"C ZI. 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