Biostatistics Commons^™

Topodino: Self-Supervised Topological Representation Learning For Neuronal Morphologies, Yasser Binbisher

Master's Theses

Neuronal cell types are categorized by transcriptomic identity, yet their morphological heterogeneity defies this classification. In response, researchers have adopted unsupervised graph representation learning as a tool to reveal morphological variation within single-class transcriptomic types. However, the complex geometry of neuronal morphology—especially long axons and dense dendrites—challenges graph neural networks, which struggle with message propagation across extended structures. To mitigate this, current approaches enforce sub-sampling on neuronal graphs and omit axons entirely, sacrificing critical biological features for computational efficiency. To overcome this trade-off, this thesis introduces TopoDINO, a self-supervised, topology-aware representation learning model designed to preserve the full hierarchical organization …

Socioeconomic Disparities In Breast Cancer Survival: Examining Potential Mediator Role Of Oncotype Dx(Odx) Test And Stage At Diagnosis Among Hr+/Her2- Breast Cancer Women, Pratibha Shrestha, Qingzhao Yu, Edward S. Peters, Edward Trapido, Mei Chin Hsieh, Tekeda Ferguson, Quyen D. Chu, Xiao Cheng Wu

School of Public Health Faculty Publications

Background: Women with a lower socioeconomic status (SES) have an increased risk of dying from breast cancer (BC) than those with a higher SES. The association of SES with BC survival may be partially mediated by factors such as Oncotype DX (ODX) testing and stage at diagnosis. This study aims to examine SES disparities in survival among HR+/HER2- BC women and to quantify the mediating effects of the ODX test and stage. Methods: We used data from the Louisiana Tumor Registry to identify women aged 20–90 years diagnosed with stage I–II in 2011–2014 and stage I–III in 2015–2017 HR+/HER2- BC …

American Society Of Hematology/International Society On Thrombosis And Haemostasis 2024 Updated Guidelines For Treatment Of Venous Thromboembolism In Pediatric Patients, Paul Monagle, Muayad Azzam, Rachel Bercovitz, Marisol Betensky, Rukhmi Bhat, Tina Biss, Brian Branchford, Leonardo R. Brandão, Anthony K.C. Chan, Vincent E.S. Faustino, Julie Jaffray, Sophie Jones, Hassan Kawtharany, Bryce A. Kerlin, Nicole Kucine, Riten Kumar, Christoph Male, Marie Claude Pelland-Marcotte, Leslie Raffini, Chittalsinh Raulji, Sarah E. Sartain, Clifford M. Takemoto, Cristina Tarango, C. Heleen Van Ommen, Maria C. Velez, Sara K. Vesely, John Wiernikowski, Suzan Williams, Hope P. Wilson, Et Al

School of Medicine Faculty Publications

Background: The American Society of Hematology (ASH) guidelines on treatment of pediatric venous thromboembolism (VTE) were published in 2018. In the last 6 years, there has been a 10-fold increase in the number of children involved in VTE treatment trials. Objective: The ASH Committee on Quality and Guidelines agreed to update the pediatric guidelines in conjunction with the International Society on Thrombosis and Haemostasis (ISTH). These ASH/ISTH evidence-based guidelines are intended to support patients, clinicians, and other health care professionals in the management of pediatric patients with VTE. Methods: ASH/ISTH formed a multidisciplinary guideline panel to minimize potential bias from …

Human Endogenous Retroviruses (Hervs) Associated With Glioblastoma Risk And Prognosis, Harun Mazumder, Hui Yi Lin, Melody Baddoo, Wojciech Gałan, Diana Polania-Villanueva, Chindo Hicks, David Otohinoyi, Francesca Peruzzi, Zbigniew Madeja, Victoria P. Belancio, Erik K. Flemington, Krzysztof Reiss, Monika Rak

School of Medicine Faculty Publications

Emerging evidence suggests expression from human endogenous retrovirus (HERV) loci likely contributes to, or is a biomarker of, glioblastoma multiforme (GBM) disease progression. However, the relationship between HERV expression and GBM malignant phenotype is unclear. Applying several in silico analyses based on data from The Cancer Genome Atlas (TCGA), we derived a locus-specific HERV transcriptome for glioma that revealed 211 HERVs significantly dysregulated in the comparisons of GBM vs. normal brain (NB), GBM vs. low-grade glioma (LGG), and LGG vs. NB. Our analysis supported development of a unique HERV scoring algorithm that segregated GBM, LGG, and NB. Interestingly, lower HERV …

“Do You Even Lift, Bro?”: Correlates Of Muscle Dysmorphia Symptomatology In Filipino Male University Students, Pamela Paula C. Pioquinto

UNLV Theses, Dissertations, Professional Papers, and Capstones

Muscle Dysmorphia (MD) is a subtype of Body Dysmorphic Disorder (BDD) and is marked by the desire to increase muscularity and reduce body fat. MD is typically more prevalent among younger male populations, and it often drives comorbid disorders, including substance abuse, eating disorders, and social anxiety. Despite the growing literature on MD, it remains understudied in certain racial/ethnic populations, such as Filipinos. Acculturation, defined as the process in which an individual adopts, acquires, and adapts to a new cultural environment as a result of immigration, influences body image by reshaping an individual’s perceptions of beauty and muscularity standards. Guided …

Two-Sample Bi-Directional Causality Between Two Traits With Some Invalid Ivs In Both Directions Using Gwas Summary Statistics, Siyi Chen

School of Public Health Faculty Publications

Mendelian randomization (MR) is a widely used method for assessing causal relationships between risk factors and outcomes using genetic variants as instrumental variables (IVs). While traditional MR assumes uni-directional causality, bi-directional MR aims to identify the true causal direction. In uni-directional MR, invalid IVs due to pleiotropy can violate assumptions and introduce biases. In bi-directional MR, traditional MR can be performed separately for each direction, but the presence of invalid IVs poses even greater challenges. We introduce a new bi-directional MR method incorporating stepwise selection (Bidir-SW) designed to address these challenges. Our approach leverages public genome-wide association study (GWAS) datasets …

The Impact Of Maternal Age On The Expression Of Transgenerational Plasticity In Daphnia Pulicaria, Calvin Nguyen

2025 Spring Honors Capstone Projects - Archive

Transgenerational plasticity refers to heritable, non-genetic changes in phenotype that persist across multiple generations and can enhance offspring survivability in variable environments. In Daphnia, increasing maternal age has been associated with maladaptive plasticity. To investigate this relationship, six clones were collected from two Wisconsin lakes and acclimated to laboratory conditions through a common garden rearing process. For each clone, ten replicates were generated and evenly divided between young (clutches 2–4) and old (clutches 5–8) maternal age groups. Offspring were exposed to three dietary treatments for three experimental generations: one fed only green algae, one fed only cyanobacteria (a nutritionally …

Innovative Methods For The Design And Analysis Of Phase Ii Clinical Trials, Feng Tian

Dissertations and Theses (Open Access)

Drug development has become increasingly time-consuming, costly, and risky in recent years. There is significant potential for improving clinical trial designs, particularly for phase II trials, which play a critical role in the drug development process. Innovative methods are especially necessary for addressing key challenges in phase II trials in terms of dose-ranging study, patient population selection, and decentralized clinical trials (DCTs). This dissertation presents a comprehensive set of methodologies that address these critical issues with three projects. The first project introduces a Bayesian adaptive dose-ranging design that integrates both efficacy and toxicity data to evaluate each dose comprehensively. The …

Dual-Criterion Dose Finding Designs For Phase I Clinical Trials, Yunlong Yang

Dissertations and Theses (Open Access)

The primary objective of Phase I oncology trials is to assess the safety and tolerability of novel therapeutics. Conventional dose escalation methods identify the maximum tolerated dose (MTD) based on dose-limiting toxicity (DLT). However, as cancer therapies have evolved from chemotherapy to targeted therapies, these traditional methods have become problematic. Many targeted therapies rarely produce DLT and are administered over multiple cycles, potentially resulting in the accumulation of lower-grade toxicities, which can lead to intolerance, such as dose reduction or interruption. To address this issue, we proposed dual-criterion designs that find the MTD based on both DLT and non-DLT-caused intolerance. …

Novel Statistical Methods For Mediation Analysis With High-Dimensional Omics Mediators, Zhichao Xu

Dissertations and Theses (Open Access)

Mediation analysis is a widely used statistical method for examining how molecular traits, such as gene or protein expression, act as intermediaries linking an exposure to a health outcome. For example, it can help explain how smoking affects disease risk through molecular changes. The rapid progress in high-throughput omics profiling technologies and large-scale epidemiology consortia, such as the Trans-Omics for Precision Medicine (TOPMed) program from the National Heart, Lung and Blood Institute (NHLBI) and UK Biobank, now has resulted in an extensive accumulation of genomic data for biomedical research and analysis. At the same time, it poses significant methodological challenges, …

Identifying And Characterizing Transition Cells In Developmental Processes From Scrna-Seq Data, Yuanxin Wang

Dissertations and Theses (Open Access)

During the development of multicellular organisms, individual cells make distinct decisions about their cell types and states. Understanding the molecular mechanisms underlying cellular state transitions at different developmental stages provides deep insights into physiology, morphology and the etiology of diseases. Single-cell RNA-sequencing (scRNA-seq), which is widely used to study complex cell states and dynamic gene expression patterns, enables us to investigate molecular mechanisms of cellular state transitions. Currently, however, computational tools available for identifying cellular states and state transitions remain limited.

Although trajectory-based methods such as Monocle and Slingshot assume that state transitions generate continuous expression profiles, they cannot distinguish …

New Bayesian Methods For Longitudinal Data Analysis With Complex Dependence Structures., Anish Mukherjee

Electronic Theses and Dissertations

Longitudinal data in real-world settings are frequently found to be heterogeneous and exhibit intricate spatio-temporal dependence structures. Analyzing such complex data to obtain reliable estimation while quantifying uncertainty necessitates using sophisticated Bayesian methodology. In this work, we present novel Bayesian methods developed to address these challenges. We often observe heterogeneity in longitudinal data, where the mean and variance for certain profiles meaningfully differs from the rest. Some profiles may also exhibit outliers at a limited number of measurements. Using a standard mixed effects model, which assumes homogeneity, can lead to overestimating the residual variance and inefficient estimation. In this work, …

Clinicogenomic Insights For Prostate Cancer Progression, Kelvin Ofori-Minta

Open Access Theses & Dissertations

Prostate cancer (PrCa) remains a critical challenge in precision oncology due to several reasons including its apparent heterogenous condition, recurrence following treatment and rapid progressive forms. Therefore, identifying patients at risk of progression is essential to fast-track therapeutic decisions and improve outcomes. Despite recent advances in genomic and molecular profiling, conventional PrCa risk assessment tools heavily rely on a few clinical parameters, neglecting the prognostic potential of genomic biomarkers in the presence of clinical biomarkers. This study presents a computational pipeline to harmonize and evaluate the prognostic value of clinicogenomic profiles of patients in modelling progression free survival (PFS). PFS, …

Joint Modelling Of Longitudinal Egfr Trajectory And Time To Acute Kidney Injury In Lung Transplant Patients, Samiha Zakir

Theses and Dissertations

Progressive declines in estimated glomerular filtration rate (eGFR) often precede acute kidney injury (AKI), yet the relationship between eGFR trends and AKI risk remains unclear. This study investigates longitudinal eGFR changes and their association with AKI in 459 lung transplant patients followed for up to 7 years (n = 6419). We applied a piecewise linear mixed-effects model to evaluate eGFR trajectories and a Cox proportional hazards model to assess time to AKI. A joint model was used to explore the interplay between longitudinal and survival processes. Key covariates included gender, age at transplantation, antibody-mediated rejection (AMR), and pre-transplant eGFR. Males …

Sexually Transmitted Infection (Sti) Incidence And Risk Factors Among People With Hiv (Pwh): Insights From A 13-Year Cohort Study In South Carolina, Salome-Joelle Gass, Shujie Chen, Jiajia Zhang Ph.D., Bankole Olatosi

Faculty Publications

The Ending the HIV Epidemic (EHE) initiative aims to reduce new HIV infections by 90% by 2030 in the United States (US). However, rising sexually transmitted infection (STI) rates exacerbate the bidirectional infection risk between HIV and STIs. Most research on STIs among people with HIV (PWH) has focused on high-risk groups, resulting in limited data on broader populations. This study addresses that gap by examining the incidence and risk factors for gonorrhea, chlamydia, and syphilis in a statewide cohort of PWH in South Carolina. Data from South Carolina’s HIV and STI surveillance systems were linked, and all PWH aged …

Environmental Risk And Alpha-Gal Syndrome (Ags) In The Mid-Atlantic United States, Brandon D. Hollingsworth Ph.D., Margaret Wiener, Dana A. Giandimenico, Scott P. Commins, Ross M. Boyce

Faculty Publications

Alpha-gal syndrome (AGS), commonly referred to as the tick bite red meat allergy, has been reported worldwide with the number of suspected cases in the United States increasing from 24 in 2009 to over 34,000 in 2019. Within the US, AGS is associated with the bite of two tick species, Amblyomma americanum and Ixodes scapularis, and has particularly high incidence rates in the mid-Atlantic region. Because AGS is associated with tick bites, the risk of developing AGS is affected by the environment individuals visit. Despite this, as well as the numerous studies associating the environment with Am. americanum, …

Diabetes: Non-Invasive Blood Glucose Monitoring Using Federated Learning With Biosensor Signals, Narmatha Chellamani, Saleh Ali Albelwi, Manimurugan Shanmuganathan, Palanisamy Amirthalingam, Anand Paul

School of Public Health Faculty Publications

Diabetes is a growing global health concern, affecting millions and leading to severe complications if not properly managed. The primary challenge in diabetes management is maintaining blood glucose levels (BGLs) within a safe range to prevent complications such as renal failure, cardiovascular disease, and neuropathy. Traditional methods, such as finger-prick testing, often result in low patient adherence due to discomfort, invasiveness, and inconvenience. Consequently, there is an increasing need for non-invasive techniques that provide accurate BGL measurements. Photoplethysmography (PPG), a photosensitive method that detects blood volume variations, has shown promise for non-invasive glucose monitoring. Deep neural networks (DNNs) applied to …

Human Capital And Lifetime Income Gains Of Scaling-Up Small-Quantity Lipid Nutrient Supplements Among Children Under 2 Years: A Modelling Analysis, Nandita Perumal Phd, Goodrarz Danaei, Günther Fink, Mark Lambiris, Christopher R. Sudfeld

Faculty Publications

Undernutrition in early childhood is associated with adverse health and developmental outcomes later in life and remains a persistent global public health problem. Providing small-quantity lipid nutrient supplements (SQ-LNS) to children aged 6-24 months improves child growth and neurodevelopmental outcomes, but the potential long-term benefits to human capital have not been previously estimated. We estimated the potential returns to schooling and lifetime income attributable to increasing coverage of SQ-LNS for children < 2 years of age from 0% to 50% or 90% per five-year birth cohort in five countries (Bangladesh, Burkina Faso, Ethiopia, Pakistan, and Uganda) with a high burden of undernutrition. Random-effects meta-analyses were used to estimate the effect of SQ-LNS on child development using evidence from randomized controlled trials, and to estimate the returns to lifetime income as a function of change in development based on a de novo meta-analysis of observational economic studies. Gains in school years attributable to scaling-up SQ-LNS to 90% coverage ranged from 0.14 million school years (95% uncertainty interval [UI]: 0.064, …

Ahr Activation At The Air-Blood Barrier Alters Systemic Microrna Release After Inhalation Of Particulate Matter Containing Environmentally Persistent Free Radicals, Ankit Aryal, Ashlyn C. Harmon, Alexandra Noël, Qingzhao Yu, Kurt J. Varner, Tammy R. Dugas

School of Public Health Faculty Publications

Particulate matter containing environmentally persistent free radicals (EPFRs) is formed when organic pollutants are incompletely burned and adsorb to the surface of particles containing redox-active metals. Our prior studies showed that in mice, EPFR inhalation impaired vascular relaxation in a dose- and endothelium-dependent manner. We also observed that activation of the aryl hydrocarbon receptor (AhR) in the alveolar type-II (AT-II) cells that form the air-blood interface stimulates the release of systemic factors that promote endothelial dysfunction in vessels peripheral to the lung. AhR is a recognized regulator of microRNA (miRNA) biogenesis, and miRNA control diverse signaling pathways. We thus hypothesized …

Predicting Capture And Survival Probabilities Of The Arizona Tiger Salamander: A Comparison Of Capture-Recapture Models, Brittney Nelson

Scholars Week

Capture-recapture models are essential tools for estimating population dynamics in ecological studies. A fundamental component of these models is the capture history matrix, which records individual detection over time and serves as the basis for estimating survival and capture probabilities. This presentation explores three statistical approaches to these estimations: the Cormack-Jolly-Seber (CJS) model, the Hidden Markov Model (HMM) for CJS, and the Bayesian CJS model. The CJS model provides a likelihood-based framework for estimation, and the HMM CJS incorporates latent states into the model to account for uncertainty in detection. The Bayesian CJS extends this same analysis by integrating prior …