Medicine and Health Sciences Commons^™

Segmented Profile Analysis (Sepa): Plane-Wise Decomposition Of Within-Person Variation Via Ipsatized Singular Value Decomposition, Se-Kang Kim, Joe Grochowalski

Faculty, Staff and Students Publications

Traditional profile analyses summarize multivariate person data with overall mean levels and relative patterns, but existing methods often blur these sources of variation or reduce each individual to a single best-fitting profile. Segmented Profile Analysis (SEPA) offers a unified, ipsatized singular-value decomposition (SVD) framework that decomposes individual profiles into orthogonal level (LE) and pattern (PE) effects and, crucially, introduces plane-wise segment profiles (summaries of each person's response pattern within each variable-contrast dimension) as primary person-oriented objects. Within each low-dimensional plane, SEPA defines a projected response pattern (segment profile), domain-person cosines that index variable-by-variable alignment, and plane-fit correlations that summarize how …

Rsv Can Infect The Human Nasal Epithelium Via The Basolateral Route And Shows Distinct Subgroup Infectivity And Basal Cell Tropism, Ashley Murray, Divya Nagaraj, Emily M Schultz, Gina Aloisio, Erin Nicholson, Sarah E Blutt, Vasanthi Avadhanula, Pedro A Piedra

Faculty, Staff and Students Publications

Respiratory syncytial virus (RSV) causes millions of lower respiratory tract infections (LRTIs) in young children, older adults, and immunocompromised populations every year. RSV infection initiates in the upper respiratory tract and can progress to the lower airways, resulting in bronchiolitis, pneumonia, and even death. RSV primarily infects epithelial cells apically, but we hypothesized that basolateral exposure of the respiratory epithelium could provide an alternative mechanism of infection that contributes to LRTI development. Using a human nose organoid-air-liquid interface (HNO-ALI) model, we performed apical and basolateral inoculations with contemporaneous RSV strains (RSV/A/Ontario [RSV/A/ON] and RSV/B/Buenos Aires [RSV/B/BA]) representing the two RSV …

Loss Of Atp-Dependent Citrate Lyase Drives Left Ventricular Dysfunction By Metabolic Remodeling, Shijie Liu, Seth T Gammon, Lin Tan, Yaqi Gao, Kyoungmin Kim, Mahmoud H Elbatreek, Adrian Arrieta, Ian K Williamson, Rebecca L Salazar, Janet Pham, Angela Davidian, Radhika Khanna Neicheril, Benjamin D Gould, Heidi Vitrac, Alia Sadiq, An Q Dinh, Evan C Lien, Francisca N De Luna Vitorino, Joanna M Gongora, Sara A Martinez, Melanie T Odenkirk, Anna K Boatman, Jessie R Chappel, Lawrence S C Czer, Evan P Kransdorf, David J Lefer, Blake M Hanson, Benjamin A Garcia, Erin M Baker, Matthew G Vander Heiden, Philip L Lorenzi, Heinrich Taegtmeyer, David Piwnica-Worms, James F Martin, Anja Karlstaedt

Faculty, Staff and Student Publications

Background: Metabolic adaptation and maladaptation are hallmarks of the failing heart and may be a target for therapeutic interventions. For example, sustained glucose oxidation during cardiac stress is associated with increased activity and abundance of ACL (ATP-dependent citrate lyase, Acly), which produces acetyl-coenzyme A (CoA) from citrate and CoA and supports de novo lipid synthesis. However, our understanding of how ACL supports cardiac metabolic adaptation and its potential to modulate disease pathophysiology has not yet been investigated.

Methods: We used human heart tissue samples from healthy donors and patients with nonischemic cardiomyopathy. Next, we used CRISPR (clustered, regularly interspaced …

Molecular Mechanism Leading To Human Coronary Atherosclerosis Assessed By Proteomic Analysis And Rna Sequences, Sarah J Parker, Chunhong Mao, David L Caudell, Austin Lyle Seals, Yizhi Wang, Thomas D Green, Joseph M Mcclung, Joshua T Maxwell, Jacolby T Roddey, Kiarash Shakeriastani, Chiung-Ting Wu, Yingzhou Lu, Do-Kyun Kim, Justyna Fert-Bober, Dongping Du, Archana Bhat, Niveda Sundararaman, Matthew Ayres, Rakhi Pandey, Saurabh Bhardwaj, Genesio M Karere, Dana Troxclair, Fannie Jackson, Gordon L Love, Richard Vander Heide, James Hixson, Jennifer E Van Eyk, Yue Wang, David Herrington

Faculty, Staff and Student Publications

Background and aims: Atherosclerosis results from cellular and extracellular changes in the arterial wall, preceded by molecular shifts that initiate disease and drive tissue conversion, yet these changes are not yet fully described. More data are needed concerning these early changes in the coronary artery molecular landscape that signify the initiation of atherosclerosis and the subsequent tissue pheno-conversion to atherosclerotic plaque. This report summarizes results from a large biorepository of human coronary artery tissue, applying state-of-the-art omics technology, advanced data analytic methods, and an arterial organoid model system to predict molecular dynamics and identify potential regulatory mechanisms that could interrupt …

Identification Of Acute Kidney Injury In African Children Hospitalized With Malaria: A Multinational Individual Participant Data Meta-Analysis, Caitlin Bond, Anthony Batte, Folake Afolayan, Nicholas M Anstey, Quique Bassat, Philip A Bejon, James A Berkley, Rhys D R Evans, Stuart L Goldstein, Michael T Hawkes, Olayinka Ibrahim, Peace Imani, Chandy C John, Kevin C Kain, Claire Liepmann, Kevin Marsh, Ruth Namazzi, Margaret Nakuya, Nicole O'Brien, Lere P Oluwadare, Robert O Opoka, Jonathan Sserunkuuma, Hunter Wynkoop, Andrea L Conroy, Malaria Associated Kidney Injury And Disease Consortium In Africa (Makid-Africa)

Faculty, Staff and Students Publications

Background: Historically, acute kidney injury (AKI) has been an underappreciated complication in children with severe malaria. We conducted an individual patient data meta-analysis to model the impact of AKI and its complications on inpatient mortality in African children hospitalized with malaria.

Methods: Studies were identified using MEDLINE, EMBASE, Scopus, and PubMed with no language restrictions, as well as through outreach at scientific meetings. Investigators were contacted about participation in the study. Eligible studies included African children hospitalized with Plasmodium falciparum malaria, a serum creatinine measurement, and mortality assessed. The primary exposure was AKI, defined using Kidney Disease Improving Global Outcomes …

Using Polygenic Risk Scores To Evaluate Definitions Of Self-Reported Sleep Phenotypes Across Cohorts, Annah B Wyss, Michael Brown, Xiang Li, Brian W Spitzer, Zhijie Huang, Heming Wang, Richa Saxena, Linda Gallo, Qibin Qi, Wassim Tarraf, Robert Kaplan, Melissa Lamar, Hector M González, Charles Decarli, Myriam Fornage, Jerome I Rotter, Stephen S Rich, Kent D Taylor, Xiuqing Guo, Alexis C Wood, Peter Y Liu, Susan R Heckbert, Chloé Sarnowski, Jan Bressler, Alanna C Morrison, Bing Yu, Pamela L Lutsey, Carmen R Isasi, Susan Redline, Tamar Sofer

Faculty, Staff and Students Publications

Study objectives: Since genome-wide association studies (GWAS) of sleep phenotypes have been conducted in differing populations and definitions of sleep phenotypes vary across studies, we investigated associations between several polygenic risk scores (PRSs) and potential sleep definitions among multiethnic cohorts.

Methods: Using data from four cohorts (HCHS/SOL, ARIC, MESA, BHS, N = 16 895), we considered multiple definitions of short and long sleep, insomnia, and excessive daytime sleepiness (EDS). PRSs were developed based on summary statistics from GWAS in European ancestry individuals from the UK Biobank (UKB) and from GWAS conducted in a multiethnic population from the Million Veteran Program …

Functional Divergence Of Capicua Isoforms Explains Differential Tissue Vulnerability In Neurological Disease, Hamin Lee, Esmeralda Villavicencio Gonzalez, Elias M Rivera, Mark A Durham, Ronald Richman, Elizabeth H-Y Chu, Kailey Xia, Hu Chen, Zhandong Liu, Surabi Veeraragavan, Binoy Shivanna, Huda Y Zoghbi

Faculty, Staff and Students Publications

Many neurological diseases impact specific brain regions despite widespread expression of the disease-related protein. Spinocerebellar ataxia type 1 (SCA1) primarily affects the cerebellum, though Ataxin-1 (ATXN1) is widely expressed. We previously showed that intensified interaction between mutant ATXN1 and Capicua (CIC) drives SCA1 pathogenesis in the cerebellum, whereas ATXN1 loss augments amyloid β production in the hippocampus and cortex. CIC, however, forms a complex with ATXN1 and its paralog, Ataxin-1-like (ATXN1L), yet knockout of either yields completely different phenotypes. To determine whether this could be due to CIC having two isoforms, we generated mice bearing either the long (CIC-L) or …

Overcoming Igf1r-Mediated Resistance To Oncolytic Hsv1 And Radiotherapy Via Triple Combination Therapy, Alexandra A Miller, Min-Hye Noh, Jin Muk Kang, Jiyeon Kim, Lily Nguyen, Amanda S Kouaho, Grace Nguyen, Minxin Huang, Stephanie M Bean, Joshua Davis, Matthew P Mullarkey, Sunil Krishnan, Zhongming Zhao, E Antonio Chiocca, Tae Jin Lee, Ji Young Yoo

The Brown Foundation: Institute of Molecular Medicine

FDA-approved oncolytic herpes simplex virus-1 (oHSV) therapy has emerged as a promising viro-immunotherapy for solid tumors. However, tumor- and tumor microenvironment (TME)-associated adaptations following viral treatment, such as feedback immune suppression, neoangiogenesis, and enhanced tumor aggressiveness, often hinder complete tumor eradication. A deeper understanding of the molecular mechanisms underlying resistance to oHSV is crucial to enhancing its clinical impact. We recently discovered that oHSV induces Insulin-like growth factor 2 (IGF2) secretion, shaping an immunosuppressive TME. Similarly, radiotherapy (RTx) activates the IGF1/IGF1R and YAP1 signaling pathways, further promoting therapeutic resistance. In this study, we investigated how oHSV-induced Insulin-like growth factor 1 …

Quality Of Life And Depressive Symptoms In Older Adults: Findings From An Integrated Epilepsy Self-Management Data Set, Elaine T Kiriakopoulos, Farren Briggs, Nicole Fiorelli, Robin E Mcgee, Erica K Johnson, Barbara C Jobst, Ross Shegog, Refugio Sepulveda, Tanya Sprulli, Cam Escoffery, Rakale C Quarells, Molly Mcvoy, Sakshi Priy, Clara Adeniyi, Martha Sajatovic

Faculty, Staff and Student Publications

Background: In the U.S., about one million people with active epilepsy are adults aged 55+. Older adults with epilepsy (OAWE) experience complex health conditions that compromise quality of life (QOL). The contribution of depressive symptom dimensions to health-related QOL remains underexplored in OAWE.

Methods: We analyzed baseline data from 13 epilepsy self-management studies in the CDC-sponsored MEW-DB (Managing Epilepsy Well Database), including adults ages 55 and older (N = 198). The primary outcome was health-related QOL, assessed via the 10-item Quality of Life in Epilepsy scale (QOLIE-10), which was inverse rank normalized (mean = 0, SD = 1). Primary predictors …

Epilepsy-Associated Digenic Variants Affecting An Actin-Mitochondria-Glutamate Pathway Promote Seizure Susceptibility, Shenzhao Lu, Mengqi Ma, Shabab B Hannan, Mingxi Deng, Hu Chen, Zhijian Yu, Lindsey D Goodman, Haein Kim, Yun Zhao, Sandeep Kumar Dubey, Wen-Wen Lin, Xueyang Pan, Debdeep Dutta, Vishnu Anand Cuddapah, Jill A Rosenfeld, Xi Luo, Zhandong Liu, Joshua M Shulman, Hugo J Bellen

Faculty, Staff and Students Publications

Epilepsy affects approximately 50 million people worldwide, yet more than half of individuals with a presumed genetic cause still lack a molecular diagnosis despite the identification of over 1,000 monogenic epilepsy genes. This diagnostic gap is unlikely to be resolved by improved variant detection alone, suggesting that variants affecting the same biological pathway may combine to cause disease. By studying epilepsy-associated actin regulatory genes, we identified a conserved "actin-mitochondria-glutamate (AMG) pathway". We demonstrate that reduced actin polymerization promotes DRP1-mediated mitochondrial fission, increases reactive oxygen species (ROS) levels, and enhances glutamatergic transmission, leading to seizures. The glial innate immune pathway, a …

Strategies To Increase Attendance In Substance Use Disorder Group Treatment: Results From A Randomized Controlled Trial, Liliane Cambraia Windsor, Heather A Jones, Carla Ellis, Kennya Hooper, Andrea Rucker, Salma Musaad, Moses Okumu

Faculty, Staff and Students Publications

Background: Attendance in substance-use-disorder group-treatment is challenging with only 32% of patients attending at least one session (Substance Abuse and Mental Health Services Administration and Center for Behavioral Health Statistics and Quality. Treatment Episode Data Set (TEDS): 2023 admissions to and discharges from substance use treatment services reported by single state agencies, Bethesda, 2025). The present study tested a set of strategies to increase group session attendance in Community Wise, an innovative evidence-based group-intervention delivered in harm-reduction-community-based agencies and designed to reduce alcohol and substance use among people with substance-use-disorders living in predominantly Black and disinvested communities. We examined: (1) …

A Systematic Literature Review Of Cvid Reveals Pervasive Detrimental Noninfectious Manifestations, Robert B Lindell, Samir U Sayed, Jose S Campos Duran, Sydney A Sheetz, Apoorva Babu, Montana S Knight, Andrea A Mauracher, Ceire A Hay, Peyton E Conrey, Julie C Fitzgerald, Nadir Yehya, Stephen T Famularo, Teresa Arroyo, Richard Tustin, Hossein Fazelinia, Edward M Behrens, David T Teachey, Lisa R Forbes Satter, Alexandra F Freeman, Jenna Re Bergerson, Steven M Holland, Jennifer W Leiding, Scott L Weiss, Mark W Hall, Deanne M Taylor, Rui Feng, E John Wherry, Nuala J Meyer, Sarah E Henrickson

Faculty, Staff and Students Publications

BACKGROUND

Sepsis is a leading cause of morbidity and mortality in critically ill children, yet heterogeneous immune responses complicate the development of targeted therapies and the host immune factors driving sepsis pathobiology remain unclear.

METHODS

We integrated deep immune phenotyping, plasma proteomics, single-cell transcriptomics, and phosphoflow cytometry in a prospective cohort of 88 critically ill children to elucidate the mechanisms underlying immune heterogeneity.

RESULTS

Unsupervised clustering of plasma cytokines identified 3 immunologic subgroups, including a high-severity group (“Group C”) characterized by hypercytokinemia driven by IL-6 and IFN-γ. Group C exhibited distinct alterations in immune cell frequency and activation, with a …

Tau Seeds Induce Neurofibrillary Tangle Formation Across Brain Regions Via Individual-Specific Connectivity, Audrey J Weber, Bernard Ng, Kelsey M Greathouse, David A Bennett, Shinya Tasaki, Chris Gaiteri, Jeremy H Herskowitz

Faculty, Staff and Student Publications

The spread of tau pathology across the cerebral cortex is closely tied to cognitive decline in Alzheimer's disease (AD). To investigate mechanisms underlying tau spread, we measured bioactivity of tau seeds from inferior temporal gyrus (ITG) and superior frontal gyrus (SFG) synaptosomes in 128 individuals and demonstrated that tau seed bioactivity associates with tau phosphorylation, neurofibrillary tangles (NFTs), and cognitive impairment. Incorporating genotype data from the same individuals within a Mendelian randomization framework showed that tau seeds in ITG induce NFTs locally as well as drive tau seeds and NFTs in SFG. Integrating antemortem functional magnetic resonance imaging data from …

Metabolic Syndrome Is Associated With Increased Mortality In Patients With Breast Or Prostate Cancer, Jessica P Hwang, Ning Zhang, Mercy W Misoi, Sabhi Gull, Zayd A Razouki, Justin R Gregg, Natalia I Heredia, Sharon H Giordano

Faculty, Staff and Student Publications

We investigated the association of metabolic syndrome (MetS) with mortality in patients with breast and prostate cancer. Breast and prostate cancer cohorts were created retrospectively using the SEER-Medicare database. Patients with first primary breast or prostate cancer diagnosed in 2008-2019 were identified using ICD-O-3 site and histology codes. Among those, patients with MetS were identified using ICD-9/10-CM codes, CPT/HCPCS codes, and prescription drug use from Medicare claims files. We defined continuous enrollment from 12 months before through 12 months after diagnosis, exposure during the first 12 months after diagnosis, and survival follow-up starting 12 months after diagnosis. We used multivariable …

Deep Learning Single-Cell Analysis For Cytologic Evaluation Of Oral Potentially Malignant Disorders, Michael P Mcrae, Kritika S Rajsri, Nadarajah Vigneswaran, A Ross Kerr, Spencer W Redding, Martin H Thornhill, Craig Murdoch, Paul M Speight, Nancy Ruel, Rachelle Wolk, Ryan R Ruff, John T Mcdevitt

Faculty, Staff and Student Publications

Oral potentially malignant disorders (OPMDs) such as leukoplakia and erythroplakia may harbor dysplasia or progress to oral squamous cell carcinoma (OSCC), yet visual inspection alone is unreliable for risk assessment. Cytology offers a minimally invasive adjunct, but conventional approaches depend on manual feature extraction and subjective review. Herein we report a deep learning (DL) object detection model that directly classifies four cell phenotypes: differentiated squamous epithelial (DSE) cells, small round (SR) cells, leukocytes, and lone nuclei. The DL model produced cytology-derived parameters that correlated strongly with histopathologic diagnoses across 692 subjects with OPMDs, OSCC, and healthy controls, including declining DSE …

Uncovering Phenotypic Expansion In Axin2-Related Disorders Through Precision Animal Modeling, Nathalie M Aceves-Ewing, Denise G Lanza, Paul C Marcogliese, Di Lu, Chih-Wei Hsu, Hirokazu Hashimoto, Matthew Gonzalez, Audrey E Christiansen, Tara L Rasmussen, Alex J Ho, Angelina Gaspero, Cher Sha, Mary E Dickinson, Bo Yuan, Brian J Shayota, Stephanie Pachter, Xiaolin Hu, Debra Lynn Day-Salvatore, Laura Mackay, Oguz Kanca, Michael F Wangler, Lorraine Potocki, Jill A Rosenfeld, Richard Alan Lewis, Hsiao-Tuan Chao, Brendan Lee, Lauren Blieden, Barry N Wasserman, Dorine A Bax, Nicola K Ragge, Sukyeong Lee, Undiagnosed Diseases Network, Baylor College Of Medicine Center For Precision Medicine Models, Shinya Yamamoto, Hugo J Bellen, Lindsay C Burrage, Jason D Heaney

Faculty, Staff and Students Publications

Purpose: Heterozygous pathogenic variants in AXIN2 (HGNC 904) cause oligodontia-colorectal cancer syndrome (ODCRCS). We identified five individuals with de novo, heterozygous variants (NM_004655.4:c.196G>A p.(Glu66Lys), c.197A>G p.(Glu66Gly), and c.199G>A p.(Gly67Arg)) in AXIN2. Common phenotypes among these individuals included ectodermal dysplasia, global developmental delay, microcephaly, and limb, ophthalmologic, and genitourinary abnormalities.

Methods: Structural modeling was performed to predict the impact of these variants on AXIN2. A prime editing N1 screen of mouse embryos was performed to test whether the p.Glu66Lys variant produces a phenotype. Drosophila models were used to test the effect of this variant on Wnt signaling.

Results: …

Unbiased Avidity-Based Isolation Of Antigen-Specific T Cells, Amanda Montoya, Meredith L Frank, Peixin Jiang, Hui Nie, Minying Zhang, Emily Bontekoe, Jared K Slone, Ludovica L Posta, Sofia Rosy Caterina Sorice, Tina Cascone, Maura Gillison, Don L Gibbons, Jianjun Zhang, Eleonora Dondossola, Lydia Kavraki, Pamela L Wenzel, John V Heymach, Alexandre Reuben

The Brown Foundation: Institute of Molecular Medicine

Background: Cancer immunotherapies have significantly improved treatment efficacy and patient survival by exploiting antigen-specific T cells to eliminate cancer cells. However, current approaches for identifying and isolating antigen-specific T cells typically require prior knowledge of target antigens, limiting discovery, and reducing the ability to consistently detect rare tumor-reactive T cells. We therefore sought to develop an unbiased platform for the identification and enrichment of antigen-specific T cells using naturally processed and presented tumor antigens.

Methods: We developed ATTACH (Assessment of T cells Tethered to Antigen Class I Histocompatibility), a microfluidic platform that applies controlled shear stress and leverages tumor cells …

Thanks For The Signal-Now What? Program Director Perspectives On How Preference Signals Are Shaping General Surgery Residency Recruitment, John M Woodward, Connie Y Gan, Darci C Foote, Tasha Posid, Nicole M Santucci, Noosha D Deravi, Caitlin Silvestri, Kirstyn E Brownson, Erika Simmerman Mabes, Rondi Gelbard, Milanie Milan, Nina Zhao, Dylan R Nieman, Martha Godfrey, Benjamin D Ferguson, Joseph C L'Huillier, Colleen Mcdermott, Prajjwol Luitel, Olabisi Sheppard, Jennifer H Chen, Emma G Burke, Jenny M Guido, Ladonna Kearse, Jonathan Davies, Trenton Foster, Sarah Lund

Faculty, Staff and Students Publications

Objective: We aimed to explore general surgery program director (PD) experiences with and perspectives on preference signaling in a 15-signal system.

Design: We performed qualitative analysis of de-identified transcripts from semi-structured interviews of general surgery PDs.

Setting: General surgery PDs across the United States.

Participants: All general surgery PDs in the spring of 2025 were invited to participate. Fifteen PDs volunteered to participate in semi-structured interviews (73% university-based, 53% programs with < 8 residents/class).

Results: PDs highlighted that signals saved time when utilized as a screening tool, which gave PDs more time for holistic review of applications. PDs also felt signaling increased equity …

Promoting Equity For Children And Adolescents Through Implementation Processes In Health And Social Care: A Scoping Review, Michelle Gooey, Heather Morris, Rebecca Madill, Callie Walsh-Bailey, Ahlia Griffiths, Melissa Savaglio, Claire Blewitt, Amanda O'Connor, Sara Holton, Helia Khalesi, Sofia Grage-Moore, Maria Fernandez, Echezona E Ezeanolue, Allison Metz, Ana Baumann, Helen Skouteris

Faculty, Staff and Student Publications

Background: Despite the many existing implementation methods, theories, and frameworks, implementation science is insufficiently closing the research-to-practice gap. Bridging this gap is critical to achieving healthy and thriving communities globally, and requires implementation processes that promote equity and reach diverse populations, especially those most in need. The aim of this scoping review was to identify, thematically analyse, categorise, and provide examples of implementation processes described in equity-focused literature, with a focus on health and social care interventions for children and adolescents from birth to 18 years of age.

Methods: A comprehensive search of literature was undertaken across six electronic databases …

Pneumococcal Colonization In Pediatric Patients Undergoing Hematopoietic Cell Transplantation, Liset Olarte, Jennifer E Schuster, Ibrahim Ahmed, Kristina G Hulten

Faculty, Staff and Students Publications

Despite the increased risk of invasive pneumococcal disease among pediatric hematopoietic cell transplant (HCT) recipients, pneumococcal colonization has not been evaluated in this population. We prospectively assessed longitudinal pneumococcal colonization in 22 pediatric HCT recipients from conditioning therapy to 100 days post-HCT. A higher likelihood of pneumococcal colonization was observed in the late post-HCT period (weeks 9-14) compared with the early post-HCT period (weeks 1-8), with odds increasing with each additional week after conditioning.IMPORTANCEThis is the first study to longitudinally evaluate pneumococcal colonization in pediatric hematopoietic cell transplant (HCT) recipients from the onset of conditioning therapy to 100 days post-HCT. …

Tau Pathology In Epilepsy: Emerging Mechanisms And Translational Opportunities, Arjune Sen, Xin You Tai, Aristea Galanopoulou, Maria Thom, Eleonora Aronica, Lucy Vivash, Martin Hardmeier, Action Amos, Stephan Rueegg, Matthias Koepp, Yaroslav Winter, Christoph Helmstaedter, Jeffrey L Noebels, Hilal A Lashuel, Terence J O'Brien

Faculty, Staff and Students Publications

The onset of epilepsy in adulthood occurs most commonly after 55 years of age. Given the ageing global population, this disorder represents an increasing burden on healthcare and society. The bidirectional link between epilepsy and dementia is a focus of intense research with underlying tau pathology highlighted as a potential mechanistic link. In this review, we examine the evidence for tau-related neurodegenerative processes in epilepsy beginning with how changes in biochemical and structural properties of the tau protein can lead to abnormal phosphorylation and pathological aggregation. We consider the role of tau in seizure occurrence and cognitive difficulties in experimental …

Longitudinal Genomic Surveillance Of Sars-Cov-2 In A University Microcosm Reflects Global Evolutionary Trends, Sankar Prasad Chaki, Melissa M Kahl-Mcdonagh, Benjamin W Neuman, Loni A Taylor, Rebecca S B Fischer, Blake M Hanson, Marlisa S Hardy, Jo Ann Culpepper, Eric Boerwinkle, Kurt A Zuelke

Faculty, Staff and Student Publications

SARS-CoV-2 transmission has declined, yet ongoing viral evolution continues to pose public health challenges. This study conducted long-term (2020-2024) genomic surveillance within a large and globally diverse university community. Viral genomes obtained from clinical (n = 1,786) and surveillance (n = 888) testing samples were classified under clade, lineage, and variant systems, and compared with global genomic data sets. Local patterns broadly paralleled global evolutionary trends, including the phased emergence of major variants, episodic introductions of new lineages, and shifts in dominant clades. Lineage diversity peaked during fall semesters and was highest among undergraduate-aged individuals, with similar distributions …

Single-Nucleotide Rna M6a Mapping In Bovine Preimplantation Development Reveals Site-Specific Regulation Of Rpl12 At Zygotic Genome Activation, Rajan Iyyappan, Yichi Niu, Yang Li, Hao Ming, Kinga Pajdzik, Noah R Rakestraw, Piyush K Jain, Chuan He, Chenghang Zong, Zongliang Jiang

Faculty, Staff and Students Publications

RNA N6-methyladenosine (m6A) is a key regulator of gene expression during early embryogenesis. Using SAC-seq (m6A-selective allyl chemical labeling and sequencing), an antibody-independent m6A profiling method, we generated the first single-nucleotide-resolution m6A map of bovine oocytes and preimplantation embryos. We observed both coordinated and uncoupled relationships between m6A modification and expression of protein-coding and noncoding genes. Integrative analysis of the transcriptome, m6A epitranscriptome, and translatome revealed dynamic m6A remodeling, particularly in ribosomal protein genes. Functional interrogation of a specific m6A site within the RPL12 transcript demonstrated that loss of this modification reduces protein synthesis, disrupts translation-related gene expression, impairs zygotic …

Gene Transcriptional Expression Of Cerebral Blood Flow Alterations In Parkinson’S Disease: A Transcription-Neuroimaging Association Study, Jiaqi Cui, Qiane Yu, Haifeng Ran, Kexin Huang, Jie Hu, Tijiang Zhang

Faculty, Staff and Student Publications

Aim: Despite the intimate link between cerebral blood flow (CBF) alterations and Parkinson's disease (PD) pathogenesis and cognitive decline, the precise pathophysiological mechanisms driving this relationship remain elusive. This study seeks to correlate changes in CBF with regional gene expression to advance mechanistic understanding of the disease.

Methods: CBF group differences were first determined from ASL data in 53 PD and 40 healthy controls (HC) and subsequently correlated with cognitive scores (Dataset 1). A coordinate-based meta-analysis of published literature provided a second set of CBF differences (Dataset 2). Transcriptomic data from the Allen Human Brain Atlas were then correlated with …

Reducing Communicable-Disease Risk After Earthquakes: Vaccination And Prevention Lessons For Venezuela's Doublet, Alfonso J Rodriguez-Morales, Ivan Arturo Rodríguez-Sabogal, Adriana Sucari, Wendy Moncada, Lili Vanessa Hernández-Serrano, Florencia Escarrá, Pasesa Pascuala Quispe-Torrez, Francisco Javier Membrillo, Tomás Orduna, Susana Lloveras, Tânia S S Chaves, Miguel M Cabada, Cecilia Perret, René Echavarría, Ana F Ribeiro, Melinda Tanabe, Fernando Bazzino, Maximiliano Ramirez, Baruch Diaz, Karen Mirna Loro Morejón, Karen Daly, Reinaldo Rosas, Maria Belen Lopez, Cristina Miranda, Marisa Liliana Fernandez, Yasemin Özsürekçi, Wasin Matsee, Yenddy Carrero, Cristian Biscayart, Sergio Cimerman, Maria L Avila-Aguero, Roberto Debbag, Jose Brea, Alejandro Risquez, Jaime David Acosta-España, Rolando Ulloa-Gutierrez, Carlos Espinal, Carlos N Torres-Martinez, Marta González-Sanz, Aula Abbara, Jill Weatherhead, Bernal Cordero, Virgilio Lezcano, Amanda Guerrero, Herberth Maldonado, Luis Cuellar, Ines Ceron, Yori Roque, Melisa Florentin, Rosa Infante, Ana Carvajal, Lily M Soto-Ávila, Marbelys Hernández, Hector Villaroel, Gianmary Miozzi, Rafael Navas, Moraima Hernández, Carlos Pérez-Vega, Manuela Mérida, David A Forero-Peña, Juan-Carlos Navarro, Claudia Beltrán-Arroyave, Mario Masana

Faculty, Staff and Students Publications

No abstract provided.

High-Order Brain Interactions During Ketamine-Induced State Changes: A Functional Marker Of Response In Late-Life Treatment-Resistant Depression?, Krisha Shah, Rubén Herzog, Alan C Swann, Brittany O'Brien, Rahul Balakrishnan, Sanjay J Mathew, Nicholas Murphy

Faculty, Staff and Students Publications

Ketamine is a fast-acting intervention for treatment-resistant depression (TRD), yet only a subset of patients show robust clinical response, and the underlying neural mechanisms remain unclear. High-order interactions (HOI) derived from multivariate information theory provide a framework for examining nonlinear dependencies among brain regions beyond pairwise connectivity. One such metric, the O-information, captures the balance between synergistic and redundant interactions across three or more variables. In this secondary analysis of a randomized, double-blind, midazolam-controlled trial (NCT02556606), we examined EEG-derived HOI in 30 late-life veterans with TRD following a single 40-minute intravenous infusion of ketamine (0.1, 0.25, 0.5 mg/kg; n = …

Aberrant Ciliogenesis Induced By Enhanced Bmp Signaling Causes Heterotopic Ossification, Hiroyuki Yamaguchi, Jianbo Wang, Fangfang Yan, Jiarui Bi, Radbod Darabi, William R. Lagor, Zhongming Zhao, Aris N. Economides, Yuji Mishina, Yoshihiro Komatsu

Faculty, Staff and Student Publications

Bone morphogenetic protein (BMP) signaling is a principal driver of heterotopic ossification (HO), yet how aberrant BMP activity structurally reprograms cellular signaling machinery to develop HO remains unclear. Here, we identify BMP signaling as a direct upstream regulator of ciliogenesis that coordinates a multi-stage, pro-osteochondrogenic signaling relay during HO. Using a conditional gain-of-function BMP mouse model (Acvr1Q207D/+), we demonstrate that enhanced BMP signaling promotes primary cilium biogenesis and axonemal elongation through canonical Smad1/5/9-dependent transcriptional activation of intraflagellar transport (IFT) Ift20, a core component of the IFT machinery. Rather than operating via a singular downstream cascade, these elongated …

Multiplexed Plasmon-Enhanced Lateral Flow Assay For Early Diagnosis Of Acute Kidney Injury, Heng Guo, Yuxiong Liu, Ravi Jada, Ying Liu, Carissa Ng, Aquiles Payte, Jiaying Xu, Connor Malone, Jie Zhao, Kedhareswara Sairam Pasupuleti, Arda Aidan Arikan, Sameer Thadani, Srikanth Singamaneni, Ayse Akcan Arikan, Limei Tian

Faculty, Staff and Students Publications

Early diagnosis of acute kidney injury (AKI) remains a major clinical challenge due to the delayed and insensitive nature of conventional markers such as serum creatinine. Urinary protein biomarkers, including neutrophil gelatinase-associated lipocalin (NGAL) and cystatin C (CysC), provide earlier and complementary information on kidney injury, but their clinical translation is limited by the lack of rapid, quantitative, and multiplexed point-of-care (POC) diagnostic tests. Here, we report a multiplexed plasmonic-fluor-based lateral flow assay (p-LFA) that enables sensitive, quantitative, and simultaneous detection of NGAL and CysC. By harnessing ultrabright plasmonic-fluor nanolabels and ratiometric fluorescence analysis, the p-LFA achieves picogram-per-milliliter analytical sensitivity …

Advancing Bioinformatics With Language Models: Components, Applications, And Perspectives, Jiajia Liu, Mengyuan Yang, Yankai Yu, Haixia Xu, Tiangang Wang, Kang Li, Xiaobo Zhou

Faculty, Staff and Student Publications

Large language models (LLMs) are deep learning-based artificial intelligence models that have achieved remarkable success in natural language processing. Typically composed of neural networks with billions of parameters, they are trained on massive unlabeled datasets using self-supervised or semi-supervised learning. Beyond language, LLMs hold immense potential for addressing complex bioinformatics challenges. This review provides a comprehensive overview of transformer-based model applications in genomics, transcriptomics, proteomics, drug discovery, and single-cell analysis. We discuss critical components, including tokenization strategies for diverse biological data, transformer architectures, attention mechanisms, and pretraining approaches. We also survey currently available foundation models and their downstream applications across …

Bi-Allelic Loss-Of-Function Variants In Tmem63b Cause Syndromic Surfactant Dysfunction Disorder, Sock Hoai Chan, Audra N Iness, Jill A Rosenfeld, Mir Reza Bekheirnia, Lindsay C Burrage, Matthew Hoi Kin Chau, Chaerish Eint Myet Chae Htoo, Eric C Kao, Shamika Ketkar, Wan Wan Lim, Xi Luo, Rifhan Mazlan, Elizabeth Mizerik, Kein Seong Mun, Kalyani R Patel, Lorraine Potocki, Christina K Rapp, Xavier Roca, Ana Saianda, Ignacio Iglesias-Serrano, Everlyn C Siew, Donald Yuhui Sim, David R Spielberg, Sok-Kun Tae, Jing Xian Teo, Julian Warfsmann, Fan Xia, Child-Eu Registry, Saumya S Jamuar, Ee Shien Tan, Matthias Griese, Weng Khong Lim, Meow-Keong Thong, Keren Machol

Faculty, Staff and Students Publications

Transmembrane protein 63B gene (TMEM63B) encodes a mechanosensitive ion channel expressed in alveolar type II epithelial cells, where it mediates stretch-induced surfactant secretion. While heterozygous gain-of-function variants in TMEM63B have been associated with developmental and epileptic encephalopathy, no human disorder has previously been linked to bi-allelic loss-of-function variants. Here, we report five individuals from four unrelated families with childhood interstitial lung disease and bi-allelic predicted loss-of-function variants in TMEM63B. Affected individuals presented with early-onset respiratory distress, chronic hypoxemia, and diffuse parenchymal lung abnormalities on chest imaging. One individual died in infancy, two underwent bilateral lung transplantation, and two require oxygen …