Digital Commons Network^™

Clinicopathologic And Molecular Characteristics Of High-Grade Appendiceal Mucinous Neoplasms, Ashlee N Seldomridge, Michael G White, Christopher Scally, Richard E Royal, Mark Routbort, Jbryan Iorgulescu, Michael J Overman, Sun Mi Lee, Wai Chin Foo, Melissa W Taggart, Yun Song, Paul F Mansfield, Keith F Fournier, John Paul Shen, Beth A Helmink

Faculty, Staff and Student Publications

Background: Although 2016 consensus guidelines defined high-grade appendiceal mucinous neoplasms (HAMNs) as a distinct histologic entity, their clinical course and optimal management remain poorly characterized. Comparative data with low-grade appendiceal mucinous neoplasms (LAMNs) are limited. This study aims to detail the clinical management and outcomes of patients with HAMN and those with LAMN.

Methods: This retrospective cohort study was conducted at a large academic cancer center. An internal database was queried to identify patients with LAMN or HAMN who underwent appendectomy between 2016 and 2024. Kaplan-Meier survival analyses were used to assess the impact of primary tumor type and peritoneal …

Pharmacogenetics Of Cyp3a5 In Pediatric Patients With Eosinophilic Esophagitis., Janelle R. Noel-Macdonnell Phd, Norah Almahbub, Erin C. Boone, Wendy Y. Wang, Dilyara Cheranova, Lisa Harvey, Valentina Shakhnovich, Rachel Chevalier

Manuscripts, Articles, Book Chapters and Other Papers

Eosinophilic esophagitis (EoE) is an atopic inflammatory disease with limited treatment options. Though swallowed topical steroids are commonly used, they are not effective in all patients. We investigated the presence of CYP3A4/5 and ABCB1 (P-glycoprotein) mRNA in esophageal tissue and its differential expression by genotype in pediatric patients. Esophageal tissue biopsies were obtained from pediatric patients undergoing standard of care endoscopy. Levels of CYP3A4, CYP3A5, and ABCB1 mRNA were measured using droplet digital PCR and compared across patients with and without EoE. Genotypes for common, clinically relevant CYP3A5 variants were evaluated in a cohort of individuals with and without EoE. …

Advancing Trauma-Informed Care For Intimate Partner Violence Survivors., Maya I. Ragavan, Kimberly Randell

Manuscripts, Articles, Book Chapters and Other Papers

No abstract provided.

Use Of A Cystatin C-Based Gfr Equation In A Population Pharmacokinetic Model Of Methotrexate Clearance In Adult Patients With Lymphoma., Zachary L. Taylor, Erin F. Barreto, Kristin C. Cole, Andrew D. Rule, Kianoush B. Kashani, Nelson Leung, Carrie A. Thompson, Thomas E. Witzig, Laura Ramsey, Jason N. Barreto

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: High-dose methotrexate (HDMTX) is a key treatment for lymphoma with central nervous system involvement. Whether incorporating cystatin C into glomerular filtration rate estimation improves methotrexate (MTX) clearance prediction remains unclear.

OBJECTIVES: We aimed to evaluate whether cystatin C-inclusive glomerular filtration rate equations improve MTX clearance prediction and to explore the relationship between MTX exposure and acute kidney injury (AKI) in adult patients with lymphoma receiving HDMTX.

METHODS: This was a prospective single-center study performed on 80 adult patients with lymphoma receiving HDMTX (1.5-8 g/m²) over a 4-h infusion. A population pharmacokinetic model was constructed using data from …

Glomerular Transcriptome Analysis Reveals Endothelial Disturbances In Patients With Idiopathic Nephrotic Syndrome., Sarah K. Nelson-Taylor, Jonathan Troost, Courtney Giannini, Colin Bauer, Tarak Srivastava, Jarcy Zee, Markus Bitzer, Laura Barisoni, Llse Daehn, Julie A. Dougherty, William E. Smoyer, Bryce A. Kerlin, Audrey Fetsko, Imtiazul Islam, Xin Wang, Christine Sethna, Richard J. Johnson, Carmen De Lucas Collantes, Kazunari Kaneko, Gabriel Cara-Fuentes

Manuscripts, Articles, Book Chapters and Other Papers

RATIONALE & OBJECTIVE: Idiopathic nephrotic syndrome (INS) is viewed as a podocyte-specific disease. Recent reports indicate endothelial involvement, but its significance is unclear. Here, we investigated the relationship between the glomerular expression of selected genes relevant to endothelial health and clinical markers of disease severity.

STUDY DESIGN: A cross-sectional study.

SETTING & PARTICIPANTS: Patients with INS (n = 70 minimal change disease and n = 83 focal segmental glomerulosclerosis) from the Nephrotic Syndrome Study Network cohort study and 53 control participants. Validation studies, including animal and cell culture experiments, were performed.

EXPOSURE: Gene expression analysis from micro-dissected human glomeruli. The …

Epidemiology Of Aspergillosis Diagnoses In Us Adults Using A National Ehr Database, 2013-2023., Brittany L. Morgan Bustamante, Elijah G. Martinez, Aidan Lee, Natalie J. Kane, Simon K. Camponuri, Rose M. Reynolds, Theo T. Snow, Juliana G E Bartels, Mark A. Hoffman, Theodore C. White, Justin V. Remais

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Aspergillosis is a fungal infection associated with rising hospitalizations and substantial morbidity and mortality. In the United States, data remain fragmented due to the absence of centralized surveillance. This study aimed to evaluate demographic, geographic, and temporal trends in aspergillosis diagnoses across the United States and evaluate changes in those patterns following the emergence of COVID-19.

METHODS: We conducted a retrospective cohort study using electronic health record data from 142 US healthcare systems (Oracle Health), including adults aged ≥18 years who received care between 2013 and 2023. The cohort included over 76 million patients and 127 million person-years. Aspergillosis …

Shiny-Magec: A Bayesian R Shiny Application For Meta-Analysis Of Censored Adverse Events, Zihan Zhou, Zizhong Tian, Christine Peterson, Le Bao, Shouhao Zhou

Faculty, Staff and Student Publications

Accurate assessment of adverse event (AE) incidence is critical in clinical research for drug safety. While meta-analysis serves as an essential tool to comprehensively synthesize the evidence across multiple studies, incomplete AE reporting in clinical trials remains a persistent challenge. In particular, AEs occurring below study-specific reporting thresholds are often omitted from publications, leading to left-censored data. Failure to account for these censored AE counts can result in biased AE incidence estimates. We present an R Shiny application that implements a Bayesian meta-analysis model specifically designed to incorporate censored AE data into the estimation process. This interactive tool provides a …

Impact Of Cyp2d6 Metabolizer Status On Ondansetron Efficacy In Early Pregnancy Induced Nausea And Vomiting: A Case Control Study., Michelle Liu, Megan M. Shuey, Sabrina E. Holley, Darlene F. Fountain, James Jaworski, Carol Griffin, Jeewoo Kim, Melissa Stec, Sudeep D. Sunthankar, Henry H. Ong, Srushti Gangireddy, Wei-Qi Wei, Andrea Gaedigk, Digna R. Velez Edwards, Vivian K. Kawai

Manuscripts, Articles, Book Chapters and Other Papers

Real-world data investigating CYP2D6 on the efficacy of ondansetron for nausea and vomiting in pregnancy (NVP) is lacking. Evidence shows CYP2D6 ultrarapid metabolizers are at risk of ondansetron nonresponse due to increased metabolism. We conducted a retrospective cohort study of early pregnant patients on ondansetron for NVP. Genotype data for 11 CYP2D6 variants and copy number variations were translated into activity score (AS) and metabolizer status: poor (PM), intermediate (IM), normal (NM), and ultrarapid (UM) metabolizers. A total of 264 women met inclusion/exclusion criteria (99 cases and 165 controls). Multivariate regression analyses of metabolizer status and AS were adjusted for …

Linkage Disequilibrium Score Regression Identifies Genetic Correlations Between Hepatocellular Carcinoma And Clinically Relevant Traits, Younghun Han, Vikram R Shaw, Jinyoung Byun, Aaron P Thrift, Catherine Zhu, Donghui Li, Rikita I Hatia, Robin Kate Kelley, Sean P Cleary, Anna S Lok, Paige M Bracci, Jennifer B Permuth, Roxana Bucur, Jennifer Knox, Jian-Min Yuan, Amit G Singal, Prasun K Jalal, R Mark Ghobrial, Yuko Kono, Dimpy P Shah, Mindie H Nguyen, Neehar D Parikh, Richard Kim, Hui-Chen Wu, Hashem El-Serag, Ping Chang, Yun Shin Chun, Jian Gu, Chad Huff, Asif Rashid, Lu-Yu Hwang, Alison P Klein, Saira A Khaderi, Ahmed O Kaseb, Kathrine A Mcglynn, Lewis R Roberts, Manal M Hassan, Christopher I Amos

Faculty, Staff and Students Publications

Hepatocellular carcinoma (HCC) mortality is increasing globally, partly due to the growing prevalence of nonviral liver diseases. Genome-wide association studies (GWAS) have identified genetic variants associated with HCC development. Leveraging GWAS summary statistics and linkage disequilibrium score regression (LDSR), we investigated disease co-development with hepatitis C virus-negative (HCV-negative) HCC to provide unique insights into HCC etiology and prioritize relationships for further causal inquiry. We utilized the LDSR statistical framework to estimate the genetic correlation and heritability between HCV-negative HCC with 901 epidemiologic, behavioral, and clinical traits from the United Kingdom Biobank (UKBB). First, we set the threshold for observed scale …

The Role Of Top-Down Appetite Self-Regulation In The Development Of Healthy Eating Behaviors Among Children: A Narrative Review And Socialization Framework, David J Bridgett, Sheryl O Hughes, Matthew Broussard, Daniela Mccourt, Christina M Croce, Jennifer O Fisher

Faculty, Staff and Students Publications

Appetite self-regulation (ASR) among children is thought to have a fundamental role in shaping the development of healthy eating behaviors, dietary intake, and growth during childhood. Parallel to developmental frameworks for understanding "general" self-regulation among children, ASR has been described as involving children's use of "top-down" cognitive processes to moderate "bottom-up" biological drives around food approach and avoidance in the interest of achieving desired eating behaviors or outcomes. Whereas bottom-up ASR processes during early childhood are well characterized, particularly in the context of dysregulation and obesity risk, the role of top-down ASR processes in the development of healthy eating behaviors …

The Influence Of Community Engagement On Educator Job Satisfaction And School Culture In K–5 Schools: A Multicase Study, Hailee Jo Fojtasek

Electronic Theses and Dissertations

This qualitative multicase study examined how school leaders and educators perceived the

influence of community engagement, particularly volunteerism, on campus culture and teacher

job satisfaction in K–5 schools in the North Texas region. Continuous teacher attrition and

weakening campus morale have resulted in increased attention to leadership strategies that

support retention. However, the role community engagement has in supporting educators has

been underexplored. The purpose of this study was to investigate how educators and

administrators experienced and interpreted community engagement efforts on their campus and

how those efforts shaped school culture and teacher job satisfaction. Guided by social capital

theory, …

Exploring The Personal Management Interview Program As A Burnout Prevention Strategy In Policing: A Qualitative Case Study, Lance C. Arnold

Electronic Theses and Dissertations

Police officers in the United States experience severe burnout at rates exceeding other service professions, with approximately 75% experiencing burnout symptoms. Current interventions predominantly focus on individual coping mechanisms rather than addressing organizational and leadership factors contributing to burnout. This qualitative single-case study explored the perceptions and experiences of police leaders and officers concerning the utility of a personal management interview program to foster positive leadership behaviors as a resource-oriented preventive strategy against burnout in a midsize municipal police department in Texas. The study employed semistructured virtual interviews with eight participants: four police leaders and four police officers who had …

Texas Secondary Spanish Teachers’ Perceptions Of Factors Influencing Instructional Self- Efficacy, Satisfaction, And Effectiveness, Tana Verlane Palafox

Electronic Theses and Dissertations

Ongoing shortages of certified world language teachers and declining enrollment in secondary language programs have intensified concerns about teacher burnout, professional isolation, and instructional quality. Research has indicated that collaboration, targeted professional development, and supportive leadership influence teachers’ instructional self-efficacy, job satisfaction, and instructional effectiveness. However, limited research has examined how secondary Spanish teachers in Texas experience these issues. This qualitative collective case study explored how Texas secondary school Spanish teachers perceive the impact of their professional experiences on instructional self-efficacy, job satisfaction, and instructional effectiveness. Grounded in Bandura’s social cognitive theory and Vygotsky’s social constructivism, the study examined how …

New Teacher Attrition Rate In Relation To Lack Of Administrative Support, Amy Avina

Electronic Theses and Dissertations

The purpose of this qualitative study was to examine new teacher attrition in relation to perceived administrative support. Teacher attrition remains a persistent challenge in U.S. public education, particularly among novice teachers within their first 5 years of service. High turnover rates negatively affect school stability, instructional continuity, and student achievement, underscoring the need to better understand factors influencing teachers’ decisions to remain in or leave the profession. The problem addressed in this study was the limited understanding of how novice teachers perceive administrative support and how these perceptions influence their willingness to stay in the teaching profession. The researcher …

A Narrative Study On The Resilience Of Women In Technology Careers, Gina J. Baldridge

Electronic Theses and Dissertations

In spite of the promotion of science, technology, engineering, and mathematics (STEM) education and careers, there is a lack of women entering the STEM workforce and majoring in STEM subjects. Women can experience gender bias and workplace marginalization in STEM careers, but have learned coping strategies that have contributed to their technology career resilience. The purpose of this narrative qualitative study was to explore how women working as individual performers and leaders in technology companies told their career stories of resilience through the perspective of change acceptance, confidence, and communication, three factors in Kumar’s CR8 model of resilience. The model …

Interaction Of Peep And Neurally-Adjusted Ventilatory Assist In Infants With Acute Viral Bronchiolitis, Julia Harris, Benjamin Crulli, Jos M. Latour, Andrew Nyman, Xabier Freire-Gomez, Federico Minen, Shane M. Tibby

School of Nursing and Midwifery

BACKGROUND: Neurally Adjusted Ventilatory Assist (NAVA) is a ventilator mode providing improved patient-ventilator synchrony compared to flow- or pressure-triggering. We examined the effect of various NAVA, pressure support (PSV), and PEEP combinations in infants with acute viral bronchiolitis. METHODS: This was a mechanistic study, nested within a randomized controlled feasibility trial. A set of 16 ventilatory combinations (each of 10-15 min), including PEEP of 1, 5, and 10 cm H2O; PSV of 20 cm H2O; and NAVA support ranging from 0.5 to 2.0 cm H2O/μV, were administered on each of 2 consecutive days to 13 invasively ventilated infants: mean (range) …

Trust Transference And Cognitive Affective Trust Dichotomy In Tiktok Short-Form Videos: The Moderating Role Of Source Homophily, Rajat Subhra Chatterjee, Mosharrof Hosen, Irfan Hameed, Hafiz Mudassir Rehman

Plymouth Business School

This study explores the under-researched area of cognitive-affective trust transference within the context of short-form videos (SFV) on the TikTok platform. It also provides new insights into the impact of source homophily that arises from viewing SFV. The study incorporates trust transfer theory into the Stimulus-Organism-Response (SOR) model perspective to examine trust transference. Data were gathered from 411 online users in Malaysia using a purposive sampling technique. Partial least squares structural equation modeling has been used to analyze the data via SmartPLS. The findings suggest that video characteristics, platform trust, and source credibility of SFVs on TikTok affect affective trust …

A Manifesto For Plant Science Education, Elizabeth Alvey, Andrea Paterlini, Mary E. Williams, Mia E. Cerfonteyn, Samantha Dobbie, Steven Dodsworth, Sonja D. Dunbar, Lauren R. Headland, Anastasia Kolesnikova, Pankaj Kumar, Silvia Manrique, Catherine Mansfield, Sebastian Stroud, Shannon Woodhouse, Hailey Ashton, Yoselin Benitez-Alfonso, Emily Breeze, Kelsey J.R.P. Byers, Chana P. Chetariya, Beth C. Dyson, Alec Forsyth, Beatriz Gonçalves, Camila Gonzalez, Daniel M. Jenkins, Joanna Kacprzyk, Kirsten Knox, George R. Littlejohn, Sara Lopez-Gomollon, Enrique López-Juez, Claudia Martinho

School of Biological and Marine Sciences

Societal Impact Statement: Plants provide oxygen, food, shelter, medicines and environmental services, without which human society could not exist. Tackling pressing and global challenges requires well-trained plant scientists and plant-aware individuals. This manifesto provides a practical evidence-based vision to strengthen plant science education, focused on five strategic priorities. It is relevant to all stakeholders within plant science and beyond: from frontline educators to institutional leaders; from commercial or charitable professionals to entrepreneurs and donors; from individual community members to their legislative representatives. Strengthening plant science education demands concrete actions from all stakeholders, ultimately to the benefit of us all. Summary: …

Systematic, Bibliographic And Statistical Aspects On Multi Generation Recycled Concrete Materials Research: A Review, Henrique Comba Gomes, Maozhou Meng, Katie Jones, William Vevers, Aissa Bouaissi, Boksun Kim

School of Engineering, Computing and Mathematics

This article aimed to review the current literature related to the topic of multiple generation recycled concrete materials considering systematic, bibliographic and statistical aspects. The review was conducted from an adaptation from the systematic review for engineering and experiments (SREE) method. Papers wrote in English with scientific relevance, title and abstract full aligned with the topic were selected from Scopus and Web of Science databases. Bibliographic aspects highlighted the research novelty, the quality of research and prominence for future works. The systematic review aimed to provide insights in the literature concerning multiple recycling concrete materials. Some of the main aspects …

Evaluating Icd-11 Against Established Terminology Standards: A Dual-Framework Analysis, Kathy L. Giannangelo, Susan H. Fenton, Mary H. Stanfill

Faculty, Staff and Student Publications

Background

The healthcare world is evaluating and adopting the World Health Organization’s (WHO’s) International Statistical Classification of Diseases and Related Health Problems Eleventh Revision (ICD-11) for Mortality and Morbidity Statistics (MMS). The objective of this study is to evaluate the degree to which the ICD-11 Foundation and the ICD-11 MMS linearization adhere to accepted terminology practices.

Methods

This study consisted of an evaluation of the ICD-11 Foundation and ICD-11 MMS, using two established evaluation frameworks. Initial assessments were independently evaluated using publicly available documentation and designated one of five endpoints: meets criterion, partially meets criterion, does not meet criterion, criterion …

Classification Of Major Depressive Disorder Using Vertex-Wise Brain Sulcal Depth, Curvature, And Thickness With A Deep And A Shallow Learning Model, Roberto Goya-Maldonado, Tracy Erwin-Grabner, Ling-Li Zeng, Christopher R K Ching, Andre Aleman, Alyssa R Amod, Zeynep Basgoze, Francesco Benedetti, Bianca Besteher, Katharina Brosch, Robin Bülow, Romain Colle, Colm G Connolly, Emmanuelle Corruble, Baptiste Couvy-Duchesne, Kathryn Cullen, Udo Dannlowski, Christopher G Davey, Annemiek Dols, Jan Ernsting, Jennifer W Evans, Lukas Fisch, Paola Fuentes-Claramonte, Ali Saffet Gonul, Ian H Gotlib, Hans J Grabe, Nynke A Groenewold, Dominik Grotegerd, Tim Hahn, J Paul Hamilton, Laura K M Han, Ben J Harrison, Tiffany C Ho, Neda Jahanshad, Alec J Jamieson, Andriana Karuk, Tilo Kircher, Bonnie Klimes-Dougan, Sheri-Michelle Koopowitz, Thomas Lancaster, Ramona Leenings, Meng Li, David E J Linden, Frank P Macmaster, David M A Mehler, Susanne Meinert, Elisa Melloni, Bryon A Mueller, Benson Mwangi, Igor Nenadić, Amar Ojha, Yasumasa Okamoto, Mardien L Oudega, Brenda W J H Penninx, Sara Poletti, Edith Pomarol-Clotet, Maria J Portella, Joaquim Radua, Elena Rodríguez-Cano, Matthew D Sacchet, Raymond Salvador, Anouk Schrantee, Kang Sim, Jair C Soares, Aleix Solanes, Dan J Stein, Frederike Stein, Aleks Stolicyn, Sophia I Thomopoulos, Yara J Toenders, Aslihan Uyar-Demir, Eduard Vieta, Yolanda Vives-Gilabert, Henry Völzke, Martin Walter, Heather C Whalley, Sarah Whittle, Nils Winter, Katharina Wittfeld, Margaret J Wright, Mon-Ju Wu, Tony T Yang, Carlos Zarate, Dick J Veltman, Lianne Schmaal, Paul M Thompson, Enigma Major Depressive Disorder Working Group

Faculty, Staff and Student Publications

Major depressive disorder (MDD) is a complex psychiatric disorder that affects the lives of hundreds of millions of individuals around the globe. Even today, researchers debate if morphological alterations in the brain are linked to MDD, likely due to the heterogeneity of this disorder. The application of deep learning tools to neuroimaging data, capable of capturing complex non-linear patterns, has the potential to provide diagnostic and predictive biomarkers for MDD. However, previous attempts to demarcate MDD patients and healthy controls (HC) based on segmented cortical features via linear machine learning approaches have reported low accuracies. In this study, we used …

Impact Of Intra- And Interfractional Motion On The Dose Distribution And Urinary Adverse Events For Magnetic Resonance-Guided Prostate Cancer Radiotherapy, Shu Xing, Sarah Burleson, Xiao Tan, Qijie Huang, Nima Hassan-Razein, Chengcheng Gui, Ergys Subashi, Himanshu Nagar, Victoria Brennan, Neelam Tyagi

Faculty, Staff and Student Publications

Purpose: To evaluate the impact of intra- and interfractional motion on dose distribution and clinical outcome in prostate magnetic resonance (MR)-guided adaptive radiotherapy.

Methods: Seventy-six patients were treated with five-fraction stereotactic radiotherapy on a 1.5 T MR linear accelerator. Cine MR images were acquired during treatment and exported to a motion monitoring research package, to generate motion traces in the anterior-posterior (AP), superior-inferior (SI) and left-right (LR) directions. Planned dose distributions were shifted according to motion trace to reconstruct intrafraction motion-blurred dose. Intrafraction motion-blurred doses were deformably registered to fraction one motion-blurred dose to obtain interfraction accumulated dose. The impact …

Frontotemporal Network Interactions Causally Support Rapid Concreteness Judgments During Reading, Elliot Murphy, Oscar Woolnough, Cale W Morse, Xavier Scherschligt, Nitin Tandon

Faculty, Staff and Student Publications

Neurobiological models of conceptual processing have been limited in spatiotemporal resolution, and uncertainty remains about the causal role of specific regions in concept representation. We utilized intracranial recordings in human neurosurgical patients with epilepsy (n = 19) during a concreteness judgement paradigm of single word reading. Concrete concepts showed greater high-frequency activation across a frontal and ventrotemporal network, while greater activation for abstract words was found in lateral posterior middle temporal cortex. Intercortical communications, measured by high-frequency partial direct coherence, revealed bidirectional frontal and ventral plus lateral temporal interactions. Words occupying the middle range of the concreteness scale (e.g., "profit") …

Trends And Challenges: A 15-Year Review Of Imaging And Radiation Oncology Core Anthropomorphic Phantom Audits For Proton Therapy, Lian Duan, Hunter S Mehrens, Stephen F Kry, Jessica R L Lowenstein, Nadia Hernandez, Lucas B Acuna Scafati, Paige A Taylor

Faculty, Staff and Student Publications

Purpose: This study aims to analyze the trends in institutional performance on Imaging and Radiation Oncology Core (IROC) proton phantoms and to investigate the impact of treatment parameters on proton therapy delivery accuracy.

Materials and methods: We analyzed 402 IROC anthropomorphic phantom audits performed by 57 institutions worldwide between 2009 and 2024, including brain, head and neck (H&N), spine, prostate, lung, and liver phantoms. Dosimetric assessments included thermoluminescent dosimeters (TLDs) for dose comparison and gamma analysis of radiochromic film. The lung and liver phantoms were irradiated with simulated motion. Univariate analysis was performed to evaluate the relationships between treatment parameters …

Selective Deletion Of Fgfr1 In Agrp Neurons Impairs Energy Homeostasis Under High-Fat Diet In Mice, Daniel Shookster, Shea O'Connell, Patel Darshan, Taylor Landry, Wyatt Bunner, Zhiying Jiang, Qingchun Tong, Hu Huang

Faculty, Staff and Student Publications

Background: The global obesity crisis and the limited success of current treatments underscore the need to identify novel regulatory pathways. While central administration of α-Klotho exerts anti-obesity effects in rodents through AgRP neurons, the intracellular signaling mechanisms that mediate this process remain undefined.

Methods: To define the role of FGFR1 within the α-Klotho signaling pathway in AgRP neurons, we performed a targeted deletion of the receptor in adult mice using an AAV-mediated CRISPR/Cas9 system alongside transgenic models.

Results: Deletion of FGFR1 in AgRP neurons disrupted energy homeostasis, promoting weight gain induced by a high-fat diet. Electrophysiological recordings revealed that FGFR1 …

Quantifying Rate-Limiting Genetic Variation In Breast And Ovarian Tumourigenesis, Kathleen E Houlahan, Mahad Bihie, Yves Greatti, Julián Grandvallet Contreras, Daniel J Fulop, Gonzalo Lopez, Marc Williams, Hsin-Hsiung Huang, Peter Van Loo, Paul C Boutros, Kuan-Lin Huang

Faculty, Staff and Student Publications

Background: The number and type of genetic alterations required to initiate breast and ovarian cancer remain unclear. While germline BRCA1/2 carriers show markedly elevated cancer risk, it is uncertain whether point mutations or copy number alterations constitute the rate-limiting events of tumourigenesis.

Methods: We developed a statistical framework extending prior incidence-mutation models to estimate the minimal number and type of driver events required for cancer initiation. Somatic mutation and copy-number data from >3000 breast and ovarian cancers in TCGA and METABRIC were compared between germline BRCA1/2 carriers and non-carriers matched on subtypes. Results were validated through analyses of evolutionary timing …

Cd44v9 As A Therapeutic Target For Antibody-Drug Conjugate In Advanced Breast Cancer, Dileep R Reddy, Mckenna E Flynn, Yasuaki Anami, Zhaoxuan Yang, Jayden Aleman, Minji Seo, Kyoji Tsuchikama, Jennifer A Maynard, Naoto T Ueno, Jangsoon Lee

Faculty, Staff and Student Publications

Antibody-drug conjugates (ADCs) have revolutionized breast cancer therapy. HER2 is the only validated biomarker guiding ADC therapy in breast cancer. However, their clinical benefit remains confined to HER2- and TROP2-targeted therapies. Tumor heterogeneity and acquired resistance often limit durable responses, underscoring the need for novel, tumor-specific ADC targets. CD44 variant isoform 9 (CD44v9), a splice variant of the CD44 family, is largely absent in normal tissues but enriched in aggressive breast cancers, where it contributes to stemness, redox regulation, and therapy resistance. In this study, we developed a chimeric monoclonal antibody against CD44v9 (clone SUM24.1, IgG1) and conjugated it to …

Fare-Free Public Transportation: A Systematic Review Of Outcomes, Joseph S. Lightner, Nancy Ziegler, Tyler Prochnow, Sammi Ford, Jordan A. Carlson, Mallory Moon, Jannette Berkley-Patton, Steven Chesnut, Amanda Grimes

Manuscripts, Articles, Book Chapters and Other Papers

Introduction

Methods

Large Language Models For Bioinformatics, Wei Ruan, Yanjun Lyu, Jing Zhang, Jiazhang Cai, Peng Shu, Yang Ge, Yao Lu, Shang Gao, Yue Wang, Peilong Wang, Lin Zhao, Tao Wang, Yufang Liu, Luyang Fang, Ziyu Liu, Zhengliang Liu, Yiwei Li, Zihao Wu, Junhao Chen, Hanqi Jiang, Yi Pan, Zhenyuan Yang, Jingyuan Chen, Shizhe Liang, Wei Zhang, Terry Ma, Yuan Dou, Jianli Zhang, Xinyu Gong, Qi Gan, Yusong Zou, Zebang Chen, Yuanxin Qian, Shuo Yu, Jin Lu, Kenan Song, Xianqiao Wang, Andrea Sikora, Gang Li, Xiang Li, Quanzheng Li, Yingfeng Wang, Lu Zhang, Yohannes Abate, Lifang He, Wenxuan Zhong, Rongjie Liu, Chao Huang, Wei Liu, Ye Shen, Ping Ma, Hongtu Zhu, Yajun Yan, Dajiang Zhu, Tianming Liu

Faculty, Staff and Student Publications

With the rapid advancements in large language model technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and …

Tuscan: Tumor Segmentation And Classification Analysis In Spatial Transcriptomics, Chenxuan Zang, Charles C Guo, Yaohong Wang, Peng Wei, Ziyi Li

Faculty, Staff and Student Publications

The identification of tumor cells is pivotal for understanding tumor heterogeneity and the tumor microenvironment. Recent advances in spatially resolved transcriptomics (SRT) have revolutionized the way that transcriptomic profiles are characterized and have enabled the simultaneous quantification of transcript locations in intact tissue samples. SRT is a promising alternative method to study gene expression patterns in spatial domains. Nevertheless, the precise detection of tumor regions within intact tissue remains a great challenge. A common strategy for identifying tumor cells is via tumor-specific marker gene expression signatures, which are highly dependent on marker accuracy. Another effective approach is through aneuploid copy …