Digital Commons Network^™

Vacmap: An Accurate Long-Read Aligner For Unraveling Complex Genomic Rearrangements, Hongyu Ding, Fritz J Sedlazeck, Christos Proukakis, Caoimhe Morley, Marco Toffoli, Anthony Hv Schapira, Zhirui Liao, Lianrong Pu, Shanfeng Zhu

Faculty, Staff and Students Publications

Sequence alignment is essential for genomic research and clinical diagnostics, yet detecting complex rearrangements such as inversions, duplications, and gene conversions remains challenging due to allele complexity and limitations of current methods. We introduce VACmap, a non-linear mapping approach to enhance the detection and representation of all genetic variations. VACmap improves duplication detection from 20% to 90% in the Challenging Medically-Relevant Genes (CMRG) benchmark and improves characterization of complex inversions in repetitive regions and gene conversion events. It improves resolving clinically significant loci, including the LPA gene (with repetitive KIV-2 units linked to coronary heart disease), GBA1 and STRC genes …

Anti-Csf-1r Therapy With Combined Immuno-Chemotherapy Coordinate An Adaptive Immune Response To Eliminate Macrophage Enriched Triple Negative Breast Cancers, Diego A Pedroza, Xueying Yuan, Fengshuo Liu, Hilda L Chan, Christina Zhang, William Bowie, Alex J Smith, Sebastian J Calderon, Nadia Lieu, Weiguo Wu, Paul Porter, Poonam Sarkar, Na Zhao, Constanze V Oehler, Ondrej Peller, M Waleed Gaber, Qian Zhu, Charles M Perou, Xiang H-F Zhang, Jeffrey M Rosen

Faculty, Staff and Students Publications

Women diagnosed with metastatic triple negative breast cancer (mTNBC) have limited treatment options, are more prone to develop resistance and are associated with high mortality. A cold tumor immune microenvironment (TIME) characterized by low T cells and high tumor associated macrophages (TAMs) in mTNBC is associated with the failure of standard-of-care chemotherapy and immune checkpoint blockade (ICB) treatment. We demonstrate that the combination of immunomodulatory low-dose Cyclophosphamide (CTX) coupled with anti-CSF-1R antibody targeted therapy (SNDX-ms6352) and anti-PD-1 (ICB), was highly effective against aggressive metastatic Trp53 null TNBC transplantable syngeneic models that present with high macrophage infiltration. Mechanistically, CSF-1R inhibition along …

Celltra: Aligning Cell Names With Gene Expression Via A Pathway-Informed Transformer, Zhao Li, Zaiyi Zheng, Rongbin Li, Wenbo Chen, Yuntao Yang, Meer A Ali, Jundong Li, W Jim Zheng

Faculty, Staff and Student Publications

Motivation: Single-cell RNA sequencing (scRNA-Seq) technology enables detailed exploration of gene expression at the individual cell level, crucial for annotating cell types and understanding cellular diversity. Traditional methods for cell type annotation often rely on marker genes and manual labeling, posing challenges due to low data quality and incomplete reference datasets.

Results: We developed CeLLTra, a novel contrastive learning framework that leverages a Transformer-based model integrating biological pathway information to group genes into super tokens, effectively capturing comprehensive gene expression from scRNA-Seq data. By combining this pathway-informed Transformer with a pretrained domain-specific language model, CeLLTra accurately aligns cell-type annotations with …

Machine Learning Models Predict Long Covid Outcomes Based On Baseline Clinical And Immunologic Factors, Naresh Doni Jayavelu, Hady Samaha, Sonia Tandon Wimalasena, Annmarie Hoch, Jeremy P Gygi, Gisela Gabernet, Al Ozonoff, Shanshan Liu, Carly E Milliren, Ofer Levy, Lindsey R Baden, Esther Melamed, Lauren I R Ehrlich, Grace A Mccomsey, Rafick P Sekaly, Charles B Cairns, Elias K Haddad, Joanna Schaenman, Albert C Shaw, David A Hafler, Ruth R Montgomery, David B Corry, Farrah Kheradmand, Mark A Atkinson, Scott C Brakenridge, Nelson I Agudelo Higuit, Jordan P Metcalf, Catherine L Hough, William B Messer, Bali Pulendran, Kari C Nadeau, Mark M Davis, Linda N Gen, Ana Fernandez Sesma, Viviana Simon, Florian Krammer, Monica Kraft, Chris Bime, Carolyn S Calfee, David J Erle, Charles R Langelier, Leying Guan, Holden T Maecker, Bjoern Peters, Steven H Kleinstein, Elaine F Reed, Alison D Augustine, Joann Diray-Arce, Patrice M Becker, Nadine Rouphael, Matthew C Altman

Faculty, Staff and Students Publications

Background: The post-acute sequelae of SARS-CoV-2 (PASC), also known as long COVID, remain a significant health issue that is incompletely understood. Predicting which acutely infected individuals will develop long COVID is challenging due to the absence of established biomarkers, clear disease mechanisms, or well-defined sub-phenotypes. Machine learning (ML) models may address this gap by leveraging clinical data to enhance diagnostic precision.

Methods: Clinical data, including antibody titers and viral load measurements collected at the time of hospital admission, are used to predict the likelihood of acute COVID-19 progressing to long COVID. Machine learning models are trained and evaluated for predictive …

Circadian-Shaped Immune Variability Predicts Infection Outcome, Jonathan Lalsiamthara, Mariko Locke, Alejandro Aballay

Faculty, Staff and Student Publications

Disease risk and severity are influenced by genetics, epigenetics, and environmental factors. However, immune responses vary even among genetically similar or related individuals, shaped by inherited and noninherited factors. Using Caenorhabditis elegans, we found that pathogen susceptibility can be predicted by preinfection biomarkers. Individuals with high-basal expression of irg-5, an infection response gene regulated by the p38 mitogen-activated protein kinase-1 (PMK-1) pathway, were more susceptible to Pseudomonas aeruginosa infection. A genome-wide screen identified the myeloid ecotropic viral integration site-1 (MEIS) homeobox protein UNC-62 as a regulator of irg-5 expression, acting through PMK-1 and GATA binding erythroid-like transcription factor …

Cost-Effectiveness Of Home-Based Self-Sampling Vs Clinician Sampling For Anal Precancer Screening, Haluk Damgacioglu, Timothy L Mcauliffe, Timothy J Ridolfi, Elizabeth Chiao, Maria E Fernandez, Vanessa Schick, Jennifer S Smith, Bridgett Brzezinski, Jenna Nitkowski, Ashish A Deshmukh, Alan G Nyitray

Faculty, Staff and Student Publications

Importance: Anal cancer screening is recommended for high-risk populations, particularly sexual and gender minority (SGM) individuals. However, the cost-effectiveness of home-based self-sampling in increasing anal cancer screening uptake has not yet been evaluated in the US.

Objective: To evaluate the cost-effectiveness of home-based anal self-sampling compared with clinic-based screening among SGM individuals.

Design, setting, and participants: This economic evaluation used data from a 2-group randomized clinical trial conducted in Milwaukee, Wisconsin, from January 2020 to August 2022, enrolling SGM individuals aged 25 years or older. Participants were randomized to home-based self-sampling or clinic-based screening. Costs for home-based screening were obtained …

Type Iv Secretion Systems: Reconciling Diversity Through A Unified Nomenclature, Peter J Christie, Gabriel Waksman, Ronnie Per-Arne Berntsson, Nicolas Soler, Nathalie Leblond-Bourget, Badreddine Douzi

Faculty, Staff and Student Publications

Type IV secretion systems (T4SS) are versatile nanomachines responsible for the transfer of DNA and proteins across cell envelopes. From their ancestral role in conjugation, these systems have diversified into a superfamily with functions ranging from horizontal gene transfer to the delivery of toxins to eukaryotic and prokaryotic hosts. Recent structural and functional studies have uncovered unexpected architectural variations not only among Gram-negative systems but also between Gram-negative and Gram-positive systems. Despite this diversity, a conserved set of core proteins is maintained across the superfamily. To facilitate cross-system comparisons, we propose in this review a unified nomenclature for conserved T4SS …

Cholesterol Efflux Protein, Abca1, Supports Anticancer Functions Of Myeloid Immune Cells, Shruti V Bendre, Yu Wang, Basel Hajyousif, Rajendra K C, Shounak G Bhogale, Dhanya Pradeep, Natalia Krawczynska, Claire P Schane, Erin Weisser, Avni Singh, Simon Han, Hannah Kim, Lara Kockaya, Anasuya Das Gupta, Adam T Nelczyk, Hashni Epa Vidana Gamage, Yifan Fei, Desirée Rodríguez-Casiano, Xingyu Guo, Haoyun Li, Ryan J Deaton, Fei Mo, Maria Sverdlov, Peter H Gann, Saurabh Sinha, Sahil Sahni, Kun Wang, Kevin Van Bortle, Emad Tajkorshid, Wendy A Woodward, Wonhwa Cho, Erik R Nelson

Faculty, Staff and Student Publications

Breast and other solid tumors respond poorly to immune therapy. Myeloid cells (MCs) such as macrophages contribute to resistance. Established clinical evidence links cholesterol to cancer outcomes, with MC function being regulated by cholesterol metabolism. We screened MC-expressed regulators of cholesterol homeostasis linked to survival and identified the cholesterol efflux protein ABCA1. ABCA1 activity increases anticancer functions of macrophages: enhancing tumor infiltration, decreasing angiogenic potential, reducing efferocytosis, and improving support of CD8+ T cell activity. Mechanistically, different AKT isoforms are involved, through both PI3K-dependent and PI3K-independent mechanisms. Highlighting the clinical relevance of our findings are correlations between ABCA1 in macrophages …

Nf2 Loss Malignantly Transforms Human Pancreatic Acinar Cells And Enhances Cell Fitness Under Environmental Stress, Yi Xu, Michael H Nipper, Angel A Dominguez, Chenhui He, Francis E Sharkey, Sajid Khan, Han Xu, Daohong Zhou, Lei Zheng, Yu Luan, Jun Liu, Pei Wang

Faculty, Staff and Student Publications

Pancreatic ductal adenocarcinoma (PDAC) occurs as a complex, multifaceted event driven by the interplay of tumor-permissive genetic mutations, the nature of the cellular origin, and microenvironmental stress. In this study, using primary human pancreatic acinar 3D organoids, we performed a CRISPR-KO screen targeting 199 potential tumor suppressors curated from clinical PDAC samples. Our data revealed significant enrichment of a list of candidate genes, with neurofibromatosis type 2 associated gene (NF2) emerging as the top target. Functional validation confirmed that loss of NF2 promoted the transition of PDAC to an invasive state, potentially through extracellular matrix modulation. NF2 inactivation …

Racial, Ethnic, And Socioeconomic Survival Disparities In Early-Onset Metastatic Colorectal Cancer, Jennifer S Wang, Benny Johnson, Caitlin C Murphy

Faculty, Staff and Student Publications

Importance: Rates of metastatic colorectal cancer (mCRC) are rising among young adults. Disparities by race and ethnicity and neighborhood-level socioeconomic status (SES) among this population are understudied.

Objective: To examine the association of race and ethnicity and neighborhood-level SES with mortality among a community-based sample of young adults with mCRC.

Design, setting, and participants: This cohort study used a large electronic health record-derived database of young adults with cancer treated at 280 community-based US clinics between 2013 and 2021. Eligible patients were young adults aged 18 to 49 years diagnosed with de novo or recurrent mCRC. Patients were followed up …

Public Support For Alcohol-Control Policies And Political Ideology In The Us, Joël Fokom Domgue, Robert Yu, Ernest Hawk, Sanjay Shete

Faculty, Staff and Student Publications

This cross-sectional study examines the role of US adults’ political affiliation, perception about alcohol use and cancer, and sociodemographic and behavioral factors in banning outdoor alcohol advertising and adding cancer warnings on alcohol containers.

Peroxisomal Integrity In Demyelination-Associated Microglia Enables Cellular Debris Clearance And Myelin Renewal In Mice, Joseph A Barnes-Vélez, Xiaohong Zhang, Yaren L Peña Señeriz, Kiersten A Scott, Yinglu Guan, Jian Hu

Faculty, Staff and Student Publications

Demyelination associated microglia (DMAM) orchestrate the regenerative response to demyelination by clearing myelin debris and promoting oligodendrocyte maturation. Peroxisomal metabolism has emerged as a candidate regulator of DMAMs, though the cell-intrinsic contribution in microglia remains undefined. Here we elucidate the role of peroxisome integrity in DMAMs, using cuprizone-mediated demyelination coupled with conditional KO of peroxisome biogenesis factor 5 (PEX5) in microglia. Absent demyelination, PEX5 conditional KO (PEX5cKO) had minimal impact on homeostatic microglia. However, during cuprizone-induced demyelination, the emergence of DMAMs unmasked a critical requirement for peroxisome integrity. At peak demyelination, PEX5cKO DMAMs exhibited increased lipid droplet burden and reduced …

Reported Safety Practices Of Publicly Advertised Psychedelic Retreats, Amy L Mcguire, Logan Neitzke-Spruill, Jill O Robinson, Caroline S Beit, Nikita Singh, David S Mathai, Lynnette A Averill

Center for Medical Ethics and Health Policy Staff Publications

Importance: The availability of psychedelic retreats has grown to meet the demand for access to these substances. Despite centuries of use among Indigenous communities, psychedelics can pose serious risks for some users.

Objective: To determine safety precautions that retreat organizations that offer psychedelic substances currently use.

Design, setting, and participants: This qualitative study included structured interviews conducted by phone or email with representatives from 49 organizations publicly advertising psychedelic retreat offerings from July to October 2023. Organizations were eligible if they marketed their services in English, offered at least 1 psychedelic substance, and made contact information available online. Organizations were …

Strengthening Rural Health Care: A Scoping Review Of Nurse Recruitment And Retention Strategies, Kelley Arredondo, Laura Witte, Alexander Paterson-Roberts, Alexandra Caloudas, Matthew Vincenti, Bradley V Watts, Bronwyn Sutherland, Hilary Touchett

Library Staff Publications

Background: Despite nursing being the largest US health profession, only 16% of registered nurses (RNs) practice in rural areas, where health care access is limited. This significantly impacts rural residents, including over 2.7 million rural veterans receiving care at the Veterans Health Administration, leading to compromised health outcomes. Nurses are vital in primary care, improving coordination and management of chronic conditions.

Objectives: Identify recruitment and retention programs for rural nurses (licensed vocational nurses/licensed practical nurses and RNs), including strategy characteristics and location.

Research design: We conducted a scoping review of published and gray literature. Eligible studies targeted US rural nurse …

Implementation Of A Turn Team To Reduce Hospital-Acquired Pressure Injuries In A Medical Intensive Care Unit, Heather A, Adair

Doctor of Nursing Practice Final Project Abstract

Implementation of a Turn Team to Reduce Hospital-Acquired Pressure Injuries in a Medical Intensive Care Unit

PURPOSE

The project aimed to reduce hospital-acquired pressure injury (HAPI) rates in a Medical Intensive Care Unit (MICU) by improving nurses' knowledge of the Braden Scale and implementing a structured two-nurse turn team workflow to reposition high-risk patients every two hours.

RESULTS

Repositioning compliance improved substantially and consistently exceeded the project goal of 90% after implementing a pod-based workflow. The HAPI prevalence rate decreased from a baseline of 8% to below the project goal of ≤5% during implementation but was not sustained in the …

Corticotropin-Releasing Factor Neurons In The Bed Nucleus Of The Stria Terminalis Modulate Avoidance Behaviors And Feeding, Juan Manuel Romero, Shae-Marie Stafford-Trujillo, Mitzy Mendoza, Pey-Shyuan Chin, Snigdha Srivastava, Mikhail Kochukov, Qingchun Tong, Benjamin Russell Arenkiel

The Brown Foundation: Institute of Molecular Medicine

Introduction: Animals rely on defensive avoidance of exposed or potentially threatening environments as a fundamental survival strategy, often expressing this behavior as thigmotaxis, or a preference for the periphery of an open space. However, researchers still do not understand how neural circuits coordinate avoidance behavior with competing physiological drives such as feeding. In this study, we investigate how corticotropin-releasing factor (CRF)-expressing neurons in the bed nucleus of the stria terminalis (BNST) integrate environmental avoidance and feeding behavior.

Methods: We used adult male and female mice and applied fiber photometry to monitor BNST CRF neuronal activity in vivo. We performed both …

Cone Beam Computed Tomography For Endodontics: Incidental Findings And Respective Significance, Erin J Key, Nina K Anderson, Dan Colosi, Mina Mahdian

Faculty, Staff and Student Publications

Background: The aim of this study is to determine the prevalence, distribution, and follow-up recommendations of incidental findings in cone beam computed tomography (CBCT) scans acquired for endodontic treatment.

Methods: This was a retrospective review of limited field-of-view (FOV) CBCT images for endodontic evaluation obtained at the Stony Brook University School of Dental Medicine between 2018 and 2022. All scans were reviewed by 1 oral and maxillofacial radiology (OMR) resident and all incidental findings were corroborated with the radiology report approved by 1 of 2 board-certified OMRs. Data extracted for each case included age, gender, and reason for scan; and …

Evaluating The Impact Of Proactive Rounding On Early Recognition And Rapid Response, Alicia Mcintosh

Doctor of Nursing Practice Final Project Abstract

Purpose: This quality improvement project evaluated the impact of a Rapid Response Team (RRT)-led proactive rounding model on the early recognition of clinical deterioration and selected patient outcomes.

Background: Delays in recognizing clinical deterioration contribute to preventable adverse events, highlighting the need for proactive strategies to support early identification and timely intervention. To address this need, the project was implemented on a 36-bed intermediate care unit at a community medical center in Southeast United States.

Methodology: Guided by the Plan-Do-Study-Act framework, the project used a six-week pre-post intervention in which an Advanced Practice Provider (APP) conducted proactive rounds on patients …

Assessing The Impact Of The 2021 Vwd Guidelines On The Diagnosis/Management Of Low Vwf Patients, Michael Dong, Joanna Larson, Sepideh Saroukhani, Miguel Escobar, Lakshmi Srivaths

Faculty, Staff and Student Publications

Introduction: The 2021 ASH/ISTH/NHF/WFH VWD diagnosis guidelines recommend Type 1 VWD diagnoses for patients with (a) VWF < 0.30 IU/mL or (b) 'Low VWF' 0.30-0.50 IU/mL with the presence of abnormal bleeding. This recommendation recategorizes 'Low VWF' patients with abnormal bleeding into Type 1 VWD.

Aim: To assess the impact of the 2021 VWD guidelines on the diagnosis and management of 'Low VWF' patients.

Methods: A single centre retrospective study was conducted to review all patients presenting for VWD evaluation between January 2000 to September 2024, analyzing for clinical features, ISTH-BAT scores, VWF/FVIII levels, and management of bleeding. 149 patients, totalling 305 clinical encounters, were included in the study.

Results: Seventy five percent of patient encounters had a change in diagnosis from 'Low VWF' to Type 1 VWD …

Safety And Effectiveness Of Stereotactic Radiosurgery For Larger Hemangioblastomas (>2cc): A Multi-Center Retrospective Study, Pavel S Pichardo-Rojas, Salem M Tos, Georgios Mantziaris, Ahmed Shaaban, Ahmed M Nabeel, Wael A Reda, Sameh R Tawadros, Khaled Abdelkarim, Amr M N El-Shehaby, Reem M Emad, Zhishuo Wei, Lindsay M Mckendrick, Ajay Niranjan, L Dade Lunsford, Selcuk Peker, Yavuz Samanci, Roman Liscak, Jaromir May, David Mathieu, Cheng-Chia Lee, Huai-Che Yang, Antonio Dono, Angel I Blanco, Yoshua Esquenazi, Nuria Martinez Moreno, Roberto Martinez Álvarez, Piero Picozzi, Andrea Franzini, Manjul Tripathi, Takuma Sumi, Takeo Uzuka, Hideyuki Kano, David Bailey, Brad E Zacharia, Christopher P Cifarelli, Daniel T Cifarelli, Joshua D Hack, Herwin Speckter, Erwin Lazo, Ronald E Warnick, Jonathan E Schoenhals, Joshua D Palmer, Zhiyuan Xu, Jason P Sheehan

Faculty, Staff and Student Publications

INTRODUCTION: Hemangioblastomas (HGB) are the most common primary intra-axial tumors in the posterior fossa in adults, with an overall occurrence of 7-10%. They occur sporadically or as part of von Hippel-Lindau (VHL) disease. The role of stereotactic radiosurgery (SRS) as a minimally invasive treatment in larger HGB (>2cc) has not been thoroughly investigated.

METHODS: This multi-center study retrospectively analyzed data from 91 patients with large HGB (>2cc) treated between 1993 and 2023. Patients were stratified into VHL-associated and sporadic groups, with assessments including radiosurgical parameters, tumor response, overall survival (OS), and progression-free survival (PFS).

RESULTS: Patients with VHL-associated …

Evaluation Of Interventions For Cognitive Symptoms In Long Covid: A Randomized Clinical Trial, David S Knopman, Deborah Koltai, Daniel T Laskowitz, Jacqueline Becker, Leigh Charvet, Juan Wisnivesky, Alex Federman, Adam Silverstein, Yuliya Lokhnygina, Giuseppina Pilloni, Michelle Haddad, Henry Mahncke, Tom Van Vleet, Rong Huang, Wendy Cox, Diana Terry, Jeannie Karwowski, Netia Mccray, Jenny J Lin, Grace A Mccomsey, Upinder Singh, Linda N Geng, Helen Y Chu, Rebecca Reece, James Moy, Zoe Arvanitakis, Sairam Parthasarathy, Thomas F Patterson, Aditi Gupta, Luis Ostrosky-Zeichner, Jeffrey Parsonnet, Elaine T Kiriakopoulos, Tamara G Fong, Janet Mullington, Sarah Jolley, Nirav S Shah, Sarah Shizuko Morimoto, Joyce K Lee-Iannotti, William D S Killgore, Brigid Dwyer, William Stringer, Carmen Isache, Jennifer A Frontera, Jerry A Krishnan, Ashley O'Steen, Melissa James, Barrie L Harper, Kanecia O Zimmerman

Faculty, Staff and Student Publications

Importance: Treatment for cognitive dysfunction due to postacute sequelae of long COVID (ie, symptoms of fatigue, malaise, weakness, confusion that persist beyond 12 weeks after an initial COVID infection) remains a significant unmet need.

Objective: To test evidence-based rehabilitation strategies for improving cognitive symptoms in persons with long COVID.

Design, setting, and participants: This was a 5-arm, multicenter, randomized clinical trial of 3 remotely delivered interventions conducted between August 17, 2023, and June 10, 2024. The study took place at 22 trial sites and included the screening of individuals with cognitive long COVID.

Interventions: Participants were randomized to 1 of …

Improving Remote Monitoring Compliance For Pediatric And Adult Congenital Electrophysiology Patients With Cardiac Implantable Electronic Devices (Cieds), Christine Meliones

Doctor of Nursing Practice Final Project Abstract

Improving Remote Monitoring Compliance for Pediatric and Adult Congenital Electrophysiology Patients with Cardiac Implantable Electronic Devices (CIEDs)

Purpose

The purpose of this scholarly project was to implement a quality improvement (QI) project to improve patient safety by improving cardiac implantable electronic device remote monitoring (RM) which has traditionally failed to achieve published benchmarks.

Background

The project was implemented at a healthcare institution in Houston, Texas. The practice area includes pediatric and adult patients with cardiac implantable electronic devices (CIEDs) in an outpatient setting. Current compliance with 14-day post-implementation enrollment (44%) and ongoing compliance (60%) did not meet published benchmarks.

Methodology …

Utilizing A Suction Catheter As A Makeshift Tracheostomy Tube In A Premature Infant: A Case Report., Ashwini V Bandi, Shaina W Gong, Gabriela G Cruz, Alicia S Lore, Kunal Shetty, Sancak Yuksel

Faculty, Staff and Student Publications

One of the most challenging aspects regarding pediatric tracheostomy tube placement is the size selection, particularly in preterm infants. We present the first reported case of a makeshift tracheostomy tube using a 6-French suction catheter in a 31-week-old premature infant in an emergent situation. This approach holds promise as a potentially life-saving intervention for extremely small preterm infants. Furthermore, this case emphasizes the size discrepancy between the premature neonatal airway and the smallest tracheostomy tubes available. Further research is warranted to allow for more diverse clinical solutions that can accommodate similar cases in acute settings.

Ventilation-Perfusion Scan: A Functional Imaging Approach To Regional Lung Disease In Primary Ciliary Dyskinesia, Gabriel Román-Ríos, Gabriel Rosario-Ortiz, Marcos J Ramos-Benitez, Ricardo A Mosquera, Wilfredo De Jesús-Rojas

Faculty, Staff and Student Publications

Introduction: As a rare genetic disorder defined by defective ciliary motility, Primary Ciliary Dyskinesia (PCD) leads to chronic respiratory complications. A founder variant in the RSPH4A [c.921+3_921+6delAAGT] gene, common in Puerto Rico, impairs ciliary function and contributes to progressive lung disease. Today, the clinical value of ventilation/perfusion (V/Q) scans in PCD has not been thoroughly investigated as well as pulmonary function tests (PFTs) and chest imaging. To explore the role and clinical utility of V/Q scans in PCD.

Methods: Retrospective evaluation of pulmonary function tests, chest imaging, and Tc-99m DTPA ventilation and Tc-99m MAA perfusion scans in ten patients with …

Racial And Ethnic Disparities In Clinical Characteristics And Outcomes In Adults With Encephalitis: A Retrospective Study, Sienna Wu, Rodrigo Hasbun, Ralph Habis, Jordan Benderoth, Ivany Patel, Ashutosh Gupta, Megan Goyal, Arun Venkatesan, John C Probasco, Paris Bean, Ashley Heck, Laya Rao, Rajesh K Gupta

Faculty, Staff and Student Publications

Background and objectives: This study aims to assess whether adult patients with encephalitis from different racial and ethnic backgrounds exhibit significant differences in clinical presentation, diagnostic findings, and outcomes.

Design and methods: A retrospective cohort study was conducted by utilizing the electronic health records of encephalitis patients in the greater Houston and Baltimore areas. Patients were categorized by race/ethnicity into White or ethnic minority (including Black, Hispanic, and Asian patients). Data was analyzed for the presence of significant differences in clinical characteristics between the two groups.

Results: Among 599 patients, 312 (52.1%) were White and 287 (47.9%) were of an …

Accelerating Ai Innovation In Healthcare: Real-World Clinical Research Applications On The Mayo Clinic Platform, Yue Yu, Xinyue Hu, Sivaraman Rajaganapathy, Jingna Feng, Ahmed Abdelhameed, Xiaodi Li, Jianfu Li, Xiaoke Liu, Liu Yang, Nilüfer Ertekin-Taner, Phil Fiero, Soulmaz Boroumand, Richard Larsen, Maneesh Goyal, Clark C Otley, Nansu Zong, Vijay H Shah, John D Halamka, Cui Tao

Faculty, Staff and Student Publications

Artificial intelligence (AI) holds promise for healthcare, but real-world implementation remains difficult. The Mayo clinic platform (MCP) addresses this by providing scalable, multi-institutional, de-identified data and analytical tools. Through four research projects, we demonstrate MCP's ability to support efficient cohort identification, AI model development, and real-world evidence generation. MCP enables broader accessibility and standardization compared to institutional EHRs, positioning it as a powerful platform for advancing translational research and precision medicine.

The Ai-Native Health Science Institution Innovation Theater Vs. Structural Redesign, Jiajie Zhang, Martin J Citardi, Xiaoqian Jiang, Sean Savitz

Faculty, Staff and Student Publications

Academic health institutions face a new constraint: cognitive labor. Many adopt AI through additive initiatives that risk becoming "innovation theater"-visible activity without structural change. We argue this reflects a mismatch between rapid AI advances and slower institutional evolution. AI-native institutions treat AI as infrastructure, requiring governance, shared platforms, and workforce readiness. The challenge is not adoption but redesign; those that fail risk widening gaps and accelerating irrelevance.

Frame: Fast Reference-Based Ancestry Makeup Estimation Tool, Pramesh Shakya, Ardalan Naseri, Degui Zhi, Shaojie Zhang

Faculty, Staff and Student Publications

Motivation: The availability of large-scale genetic data presents a unique opportunity to study the genetic ancestries of individuals, which requires an efficient and scalable method. The existing global ancestry methods are accurate, but they cannot scale to large genetic datasets. Identity-by-descent (IBD) segments are DNA segments shared by individuals such that they are inherited from a common recent ancestor without recombination. These IBD segments, which reflect co-ancestry, provide an efficient alternative for inferring genetic ancestry.

Results: We introduced a reference-based global ancestry inference method called FRAME (Fast Reference-based Ancestry Makeup Estimation). FRAME utilizes partial local ancestry information estimated through IBD …

Digital Commons@Tmc 2025 Highlights, Alice Sherwood

TMC Library Newsletter (2015-)

No abstract provided.

Lunch & Learn Webinar Series, Sandra Y. Desjardins, Jenny Stockton

TMC Library Newsletter (2015-)

Take your CINAHL searches to the next level in this hands-on library training. Learn practical techniques for effectively combining subject headings, keywords, and filters to create strong, efficient search strategies that support evidence-based research and clinical decision-making.

Register here to attend the session.