Digital Commons Network^™

Signs Of Life: Interkingdom Communication And The Sympoietic Organism, Scott F. Gilbert

Biology Faculty Works

No abstract provided.

Analyzing Changes In Russian Olive Distributions Along The Missouri River In Response To Flooding, Zachary Schild

Dissertations and Theses

Russian olive (Elaeagnus angustifolia; RO) is an invasive, nitrogen-fixing tree that has spread across riparian ecosystems in the western United States, potentially hindering native tree recruitment, reducing species richness, and impacting wildlife. RO has established within the Missouri National Recreational River (MNRR) in part due to modified flow regimes following dam construction. This study aimed to map the spread of RO using high-resolution National Agriculture Imagery Program (NAIP) imagery (2010, 2012, 2018, 2022) and evaluate the effects of the 2011 and 2019 floods on RO distributions in the Missouri National Recreational River (MNRR). RO cover in this area has expanded …

Beyond The Square Pulse: Waveform Shape, Eeg Correlates, And The Pursuit Of Natural Sensation In Tens, Jason Whitson

Honors Undergraduate Theses

This study investigates the relationship between electrical stimulus characteristics of shape and charge on evoked sensations and electroencephalogram (EEG) data during multi-waveform transcutaneous electrical nerve stimulation (TENS) of the median nerve. Neuromodulation methods have traditionally had little control over the location and quality of their associated evoked sensation (e.g., electric, vibration, touch). This experiment utilized five unique stimulus waveforms during TENS stimulation. EEG data were collected concurrently to provide an introductory objective measure of the neural responses underlying these sensory changes. Eleven participants completed three tasks (thresholding, super-threshold stimulation, two-alternative forced choice) using a two-electrode TENS approach. Stimulus waveforms were …

Complexity Theory And Environmental Conservation Management: A Case Study With Coyote And Red Wolf Hybridization, Gretchen E. Mahalic

Honors Undergraduate Theses

Conservation biology and invasion biology are value-led scientific disciplines founded on environmental advocacy, operating at the intersection of research and action. Though these disciplines are known for their scientific veracity, unexamined values are often promulgated without scrutiny and drive decisions that work against good ecological outcomes. A case in point is that coyotes migrating into southeastern territory are framed as the greatest threat to the conservation of the endangered red wolf because hybridization is seen as diminishing their species integrity. Applying Val Plumwood’s ecofeminist account of dualistic frameworks, I will use this case to show how the vilification of the …

Investigating The Role Of Traditional Chinese Herbal Medicine For Cancer Symptom Management In Older Adults: A Rapid Review, Isabelle C. Karshner

Honors Undergraduate Theses

Background: Patients with cancer often experience symptoms related to disease, complications, and treatment. One potential method of alleviating these symptoms is traditional Chinese herbal medications (TCHM). This rapid review explores the role of traditional Chinese herbal medications in treating cancer-related symptoms in older adults.

Purpose: The purpose of this rapid review is to gain and provide a better understanding of the effects of TCHM on cancer-symptom management in the older adult population. This review explores the association between TCHM and effects on cancer symptoms in older adults, including interactions, toxicity, and signs/symptoms of TCHM use that may be useful information …

Synthesis And Characterization Of Succinate Dehydrogenase Inhibitors H2/Z14 And C6/Z96 In Order To Combat Small Cell Lung Cancer, Lauren M. Graves

Honors Undergraduate Theses

The use of ubiquinone inhibitors to combat cancer is a recent development in medicinal science and procedures to efficiently synthesize these drugs remain limited. C6/Z96 and H2/Z14, two succinate dehydrogenase inhibitors, have been previously tested in vitro against NSCLC with positive results. Their similarity to ubiquinone is what makes them a strong candidate for a succinate dehydrogenase inhibitor at the ubiquinone binding site. The heterocyclic scaffolds and substituents are proposed to bind strongly through a combination of electronics, hydrogen-bonding, and fit, allowing them to bind well and prove to be more favorable than ubiquinone when competing for the Q-site. By …

Establishment Of An In Vitro Dss-Induced Epithelial Injury Model To Investigate Il-6 Signaling And Microbial Metabolite Mediated Barrier Recovery, Srijal Kunwar

Graduate Studies Theses and Dissertations 2026

Dextran sodium sulphate (DSS) is widely used in vivo to induce epithelial injury; however, the molecular effects of DSS on intestinal epithelial cells, that investigate inflammatory and metabolic repair mechanisms remain unclear. Here, we establish an in vitro DSS-induced epithelial damage model using differentiated Caco-2 cell monolayer. Exposure to 2.5%(w/v) DSS for 24 hours resulted in significant upregulation of pore forming protein Claudin-2(2.677-fold) and oxidative marker, NOX-1(1.866-fold), accompanied by increased ROS production confirmed via DHE staining. Increased epithelial permeability was observed by TEER analysis, without significant cytotoxicity. Surprisingly, ELISA analysis revealed significant downregulation of IL-6 (p-value …

Comorbid Psychosis In The General Population, Mariam Sankoh

Theses and Dissertations

Psychosis is a complex psychiatric phenotype characterized by substantial heterogeneity in symptom presentation, psychosis diagnosis, comorbidity patterns, and genetic architecture across diverse populations in the general population. Despite advances in psychiatric epidemiology and genomics, important gaps remain in understanding how psychosis symptoms and psychosis-related diagnoses manifest across racial and ethnic groups and how evolutionary genomic factors may contribute to disease risk and cross-ancestry genetic prediction. This dissertation, Characterizing Comorbidity in Psychosis in the General Population, integrates epidemiological, psychometric, and evolutionary genetic approaches to examine psychosis across diverse populations.

Aim 1 examined racial and ethnic differences in psychosis comorbidity patterns …

24-H Circadian Rest-Activity Rhythms And Physical Frailty In Older Adults: A Biopsychosocial Perspective On Sex Differences And Social Capital, Jisu Kim

Theses and Dissertations

Physical frailty is a prevalent geriatric syndrome characterized by age-related decline across multiple physiological systems. Physical frailty is associated with an elevated risk of adverse health outcomes, including chronic disease progression and all-cause mortality, representing a significant and growing public health concern. Disrupted circadian rest-activity rhythms (RARs) are increasingly recognized as clinically meaningful markers of physical frailty in older adults. However, the extent to which biological sex and social determinants of health (SDoH), particularly social capital, contribute to or modify the associations between RARs and physical frailty remains underexplored.

Therefore, this dissertation summarizes the existing literature on age-related changes in …

Self-Movement Cue Ability As A Potential Moderator For The Relationship Between Binge Drinking And Posttraumatic Stress Disorder Symptoms, Dominoe Anna Jones

Graduate Research Theses & Dissertations

Alcohol use disorder (AUD) has been found to co-occur in a range of 30% to 50% of individuals diagnosed with posttraumatic stress disorder PTSD. The current study aimed to assess whether this high comorbidity could be partially explained through a shared association with poorer function and reduced volume in the hippocampus. Self-movement cue processing, a behavioral ability previously shown to be associated with hippocampal functioning, was measured through a dead reckoning task (DRT) to test this hypothesis. The current study failed to replicate previous findings between alcohol use and DRT and alcohol use and posttraumatic stress symptoms (PTSS). Performance on …

Nutritional Niche Separation Amongst Sympatric Threatened Lemurs: The Role Of Micronutrients In Food Selection And Implications For Physiological Health, Maire K. O'Malley

Graduate Research Theses & Dissertations

Madagascar’s biodiversity is heavily affected by anthropogenic change and consequently, conservation management plans need to reflect current research to protect biodiversity. Primate nutritional ecology offers valuable insights into ecology, evolution, health, habitat requirements, social behavior, and conservation management strategies. Macronutrients (fat, carbohydrates, and protein) provide consumers with energy whereas micronutrients (vitamins and minerals) are essential to metabolic processes but are frequently overlooked. This study provides a novel examination of dietary niche separation by comparing mineral consumption between three sympatric species differing in feeding strategies: 1) Grey Bamboo lemur (Hapalemur griseus), a bamboo specialist, 2) Diadema sifaka (Propithecus diadema), a folivore, …

Feasibility Of Corn Stover For Biogas Production In Northwestern Illinois: A Case Study Of Jo Daviess And Carroll Counties, Anthony Amotoe-Bondzie

Masters Theses

The growing demand for renewable energy and sustainable waste management has intensified interest in agricultural residues such as bioenergy feedstocks. This study evaluated the feasibility of converting corn stover into biogas through anaerobic digestion (AD) in Jo Daviess and Carroll Counties, Illinois, with consideration of the Savanna Industrial Park as a potential centralized processing hub. Although corn stover represents one of the largest biomass resources in the United States, this research identifies a critical gap between theoretical availability and practically recoverable feedstock. Using a mixed-methods framework, the study integrates biomass quantification, methane yield modeling, economic analysis, and policy assessment. Results …

Epigenetic Modifications In Dedifferentiated Liver Cells To Restore Lost Liver Function, Shreya Sharma

Masters Theses

The goal of the study is to investigate whether the epigenetic modifications can enhance the restoration of liver gene expression in dedifferentiated hepatoma cells or not. For the study, we used dedifferentiated H11 hepatoma cell lines which overexpress one of a panel of introduced candidate liver-enriched transcription factors H11-HNF1a, H11-CREB3L3, H11-CREG1, H11- HHEX, H11-HNF6, and H11-IGFBP1. The cells were treated with the DNA methyltransferase inhibitor 5-azacytidine and the histone deacetylase inhibitor sodium butyrate, both individually and in combination. Gene expression analysis was determined by RT-qPCR, which revealed that while transcription factor overexpression alone produced limited activation, epigenetic modulation, particularly Histone …

Evaluating Planting Methods For Native Seed Production And Exploring Granivory In The Northern Great Plains, Allison Dollen

Electronic Theses and Dissertations

Temperate grasslands have faced immense losses due to land use change in the last 150 years and less than half of the overall grasslands that once covered North America remain today. A portion of historic and remaining U.S. grasslands are located within the northern Great Plains (NGP) region which is home to over 1,600 species of native plants and provides many ecosystem services and economic benefits. Initiatives to restore grasslands and their ecosystem services are currently underway, but barriers such as limited native seed supply and granivory hinder restoration efforts. My first chapter addresses knowledge gaps in planting methods for …

A Marine Science Career In The Eastern Caribbean: Witnessing Four Decades Of Change, Hazel A. Oxenford

Gulf and Caribbean Research

Reflecting back on a long and rewarding career from 1980—2023 at the University of the West Indies, based on the small island of Barbados, this paper tracks the many and often remarkable changes in the marine environment, in attitudes and policies, and available opportunities that have influenced my journey as a marine scientist in an ever—changing but resilient Caribbean. From free—access fisheries to degraded stocks, from coral to algal dominated reefs, from flyingfish to Almaco Jacks, from sandy beaches and clear water to a Sargassum crisis — these are just some of the fundamental changes in the marine environment that …

An Exploratory Analysis Of The Role Of Sex In Load Carriage, Rachel E. Perez, Dustin R. Slivka, Brent C. Ruby

Graduate Student Theses, Dissertations, & Professional Papers

Axially loaded weight may impose a metabolic demand equivalent to that of fat mass (FM) during load carriage. Males (M) typically have a lower body fat percentage than females (F), resulting in metabolic demand differences during load carriage that may be mitigated by accounting for FM in pack loads. PURPOSE: To determine whether normalizing pack load to FM equalizes metabolic cost across sexes during load carriage. METHODS: Twenty-eight participants (14M, 23 ± 5 y, 1.81 ± 0.07 m, 78.7 ± 10.0 kg, 12.7 ± 5.4% body fat, VO₂peak 4.18 ± 0.54 L·min^-1; 14F, 22 ± 4 …

A Complete Diploid Human Genome Benchmark For Personalized Genomics, Nancy F. Hansen, Nathan Dwarshuis, Hyun Joo Ji, Arang Rhie, Hailey Loucks, Glennis A. Logsdon, Mitchell R. Vallger, Jessica M. Storer, Juhyun Kim, Eleni Adam, Nicolas Alternose, Dmitry Antipov, Mobin Asri, Sofia Barreira, Stephanie C. Bohaczuk, Andrey V. Bzikadze, Sara A. Carioscia, Andrew Carroll, Kuan-Hao Chao, Yanan Chu, Arun Das, Peter Ebert, Adam English, Mark Fleharty, Laura E. Fleming, Giulio Formenti, Andrea Guarracino, Gabrielle A. Hartley, Katharine Jenike, Jenna Kalleberg, Yu Kang, Robert King, Josipa Lipovac, Mira Mastoras, Matthew W. Mitchell, Shloka Negi, Nathan D. Olson, Keisuke K. Oshima, Luis F. Paulin, Brandon D. Pickett, David Porubsky, Jane Ranchalis, Desh Ranjan, Mikko Rautiainen, Harold Riethman, Robert D. Schnabel, Fritz J. Sedlazeck, Kishwar Shafin, Mile Sikic, Steven J. Solar, Alexander P. Sweeten, Winston Timp, Justin Wagner, Dongahn Yoo, Ying Zhou, Erik Garrison, Evan E. Eichler, Michaeel C. Schatz, Andrew B. Stergachis, Rachel J. O'Neill, Karen H. Miga, Steven L. Salzberg, Sergey Koren, Justin M. Zook, Adam M. Phillippy

School of Medical Diagnostics & Translational Sciences Publications

Human genome sequencing typically relies on mapping reads to a reference genome to call variants, but this approach introduces technical biases, excluding duplicated and structurally polymorphic regions of the genome. To overcome this, we present a telomere-to-telomere genome benchmark with near-perfect accuracy across 99.4% of the diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), which were absent from prior benchmarks. We annotated genes and repeats on both haplotypes, including 19,956 protein-coding genes on the maternal haplotype and 19,190 on the paternal haplotype, and developed new methods to measure the accuracy of …

Predicting Tilt In Esports: A Psychophysiological Approach To Understanding Player Emotional Regulation, Nathan Rhea

University of the Pacific Theses and Dissertations

Emotional regulation and stress management are important to both casual and competitive esports players. When players become dysregulated, they experience a phenomenon known as “tilt” within the gaming community, where they often lose control of their emotions and their performance declines. This study aimed to investigate whether a psychophysiological variable in heart rate variability could predict tilt in college-age esports players. Additionally, the relationship between heart rate variability and emotions predicted by the Tiltometer system with gameplay performance and winning or losing was tested.

This study used a quantitative correlational research design. Participants for this study were college-age players (N=23) …

Chromnet: A Multi-Task Learning Framework For Cross-Cell Type Prediction Of 3d Chromatin Interactions Using Epigenetic Signals, Bin Wang, Shaokai Wang, Liqing Ding, Hongdong Li, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

The 3D organization of chromatin plays a fundamental role in gene regulation, cellular function, and disease mechanisms. However, current experimental techniques, such as Hi-C, remain costly and labor-intensive, limiting their application in large-scale and disease-related studies. To address this challenge, ChromNet is presented, a multi-task learning framework that integrates epigenetic signals across diverse cell types to enable high-precision prediction of chromatin architecture. By incorporating noise perturbation and auxiliary classification tasks, ChromNet improves the identification of topologically associating domains (TADs) and cell-type-specific chromatin structures, demonstrating superior generalization performance. Notably, ChromNet accurately predicts chromatin interactions in acute myeloid leukemia (AML) samples by …

A Comprehensive Overview Of Neurophysiological Correlates Of Cognitive Impairment In Amyotrophic Lateral Sclerosis, Seyyed Bahram Borgheai, Brie E. Achorn, Alyssa H. Zisk, Sarah M. Hosni, Karl E. G. Richter, Frank S. Menniti, Yalda Shahriari

Computer Science Faculty Publications

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that leads to the gradual loss of motor control, typically resulting in paralysis and death within 3 to 5 years of diagnosis. ALS shares neuropathological and genetic associations with fronto-temporal dementia (FTD), a neurodegenerative condition primarily impacting cognitive functions. These two conditions are increasingly viewed as manifestations of a single molecular disease process that affects distinct brain systems, impacting motor neuronal pathways in ALS and fronto-cortical functions in FTD. However, this simple dichotomy belies the complexity of these conditions. In particular, patients with primary motor ALS can also experience significant cognitive …

Attention-Based Multi-Omics Fusion For Drug Synergy Prediction, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Drug combination therapy in disease management gained popularity in the last few decades. Computational modeling of such combinations is an active area of research in the drug discovery domain. While earlier approaches solely emphasized on the structural features of participating drugs for designing synergistic models, they lack other crucial factors directly linked with drug administration - omics expressions. As differential omics expression is a downstream consequence of the administered drug combinations, utilizing such expressions while designing synergistic models promises robust and dynamic modeling. In this work, we propose SynergyLM that fuses multi-omics features with drug embeddings to build an omics-aware …

Identifying Rna Splicing Changes During Alcohol Withdrawal Using An Optimized Rna-Seq Analysis Pipeline, Yasaswi Veera, Luana Martins De Carvalho, Amy Lasek

UROP Posters

Alcohol use disorder (AUD) causes long-lasting changes in brain gene expression and RNA splicing, particularly in the ventral hippocampus. This study analyzes RNA-Seq data from rats exposed to chronic alcohol and withdrawal to identify transcript-level and splicing alterations. An optimized RNA-Seq pipeline using STAR, FeatureCounts, edgeR, and WGCNA improved efficiency by 25-40% while maintaining consistency across 25 datasets. Results reveal changes in neural signaling and stress-response pathways associated with withdrawal. This work provides both biological insight into AUD and a reproducible computational framework for transcriptomic analysis.

The Myopia Epidemic: Integrating Genetic, Environmental, And Epigenetic Pathways To Define A Critical Window For Intervention, Pranavika Balaji

UROP Posters

Myopia, or nearsightedness, has increased rapidly worldwide and is now a major public health concern caused by both genetic and environmental factors. Current understanding shows that too much near work, limited time spent outdoors, and prolonged screen use contribute to abnormal eye growth in individuals who may already have a genetic predisposition. At the molecular level, epigenetic changes and shifts in DNA activity, often influenced by environmental conditions, affect the signaling pathways that regulate eye development and may help explain why myopia is increasingly common among children. This paper synthesizes recent environmental, genetic, and epigenetic research to explain how these …

The Importance Of Hippotherapy: Improving The Lives Of The Disabled Through Alternative Therapy, Jennifer N. Stapleton

UROP Posters

For centuries, horses have been suggested as “healers” and “helpers,” although it wasn’t until the 1900s that horseback riding was scientifically proven as a treatment and rehabilitation method. The exploitation of hippotherapy, the implementation of the three-dimensional pelvic movement stimulated by the oscillation and gait of the horse to combat symptoms of diseases and disorders, has since become a flourishing field of study, but one that is often overlooked. Benefits of hippotherapy often include increased motor neuron function, facilitating proper anatomical alignment, and reducing spasticity. This research analyzes the diverse and dynamic nature of treatment that hippotherapy facilitates, exploring the …

Determining Genes Involved In Recovery From Chemotherapy In 4t1, Emt6, And Eo771 Breast Cancer Cells, Akash Jagdeesh, Joseph Landry Ph.D.

UROP Posters

Breast cancer is one of the most common types of cancer, and often has poor prognosis. Traditional treatments for breast cancer include chemotherapy, which involves a chemical attack on all growing cells within the body. However, these treatments are not 100% effective, and patients might experience recurrence in their cancer months or years after achieving remission. Cancer cells can evade chemotherapy through five mechanisms: senescence, quiescence, cytoprotective autophagy, and apoptosis/necroptosis suppression. Prior studies have conducted CRISPR screens and experiments involving inhibition of epigenetic regulators, to alter the regulation of genes that can contribute to breast cancer chemotherapy resistance. This study …

Genomic Determinants Of Appetite Regulation And Their Role In Obesity Risk, Timothy J. Renier

Dartmouth College Ph.D Dissertations

Over 40% of US adults and 20% of children live with obesity. It is related to increased risks of diseases including type II diabetes and cancer, is a source of harmful stigma, and impairs child development. Appetitive traits describing patterns of food approach and avoidance behaviors may serve as windows into the underlying pathophysiology of obesity. As both obesity and appetitive traits are heritable, common genetic drivers of obesity may lead to phenotypic obesity through appetitive traits as a disease mechanism. Additionally, GLP-1 receptor agonists (GLP-1RAs) have been shown to exert their profound clinical effects in part by modulating appetite. …

The Serotonin 1b Receptor In Psilocybin’S Therapeutic-Like Mechanisms: From Behavior To Network Reorganization, Sixtine Fleury

Dartmouth College Ph.D Dissertations

Mood disorders represent a substantial and growing global health crisis, with ~10 million adults in the US meeting criteria for a major depressive disorder (MDD). Current first-line treatments such as SSRIs require long-term daily administration and fail a significant proportion of patients, driving renewed interest in rapid-acting alternatives. Psilocybin, a serotonergic psychedelic, shows growing clinical evidence of efficacy in treating depressive and anxiety disorders, often producing therapeutic effects persisting weeks to months following a single dose. Yet, the neural mechanisms underlying these enduring effects remain poorly understood and have been largely attributed to the serotonin 2A receptor (5-HT2AR) based on …

External Validation Of A Knowledge-Based Clinical Toxicology Consultant For Diagnosing Single Exposures, Hugo Lerogeron, Joel D. Schipper, Jay L. Schauben, Laurent Guéguen, Valentine Lacotte, Kim An Nguyen

Publications

Introduction

Clinical prediction models assist healthcare providers in estimating disease likelihood using multiple patient-specific factors. While these models are increasingly used, few undergo the essential process of external validation, which limits their clinical utility. In toxicology, timely diagnosis is crucial and expertise scarce, making knowledge-based systems an excellent choice to support medical decision making. A knowledge-based system developed using data from the Florida Poison Information Center Network has shown promise but lacks external validation. This study aims to evaluate its performance using data from the Lyon Poison Information Center to assess its generalizability

Methods

To externally validate the Florida diagnostic …

Federated And Explainable Spiking Neural Networks For Fair And Privacy-Preserving Nail Disease Diagnostics, Ch Pavani Reddy, Krishnanaik Vankdoth

Mansoura Engineering Journal

Automated nail disease diagnostics provide a non-invasive pathway for identifying underlying systemic health conditions; however, conventional centralized deep learning approaches often raise concerns related to privacy, fairness, and interpretability. Although the original NeuroNail-SNN framework demonstrated an energy-efficient and edge-ready diagnostic solution, its broader clinical adoption remained limited by unresolved trust, transparency, and ethical considerations. In this study, we propose the Federated and Explainable NeuroNail-SNN, which extends the original spiking neural architecture by integrating federated learning (FL), explainable artificial intelligence (XAI), fairness evaluation, and uncertainty quantification within a unified framework. Federated learning enables decentralized model training across hospitals and mobile clinics …

Health And Nutrition In The First 1000 Days Of Life, Yaojiang Shi, Qi Zhang, Yiliang Zhu, Jingchun Nie

Health Behavior, Policy & Management Faculty Publications

Malnutrition and health issues remain persistent global crises, with developing regions bearing the brunt of the burden. According to the World Health Organization, nearly half of under-five deaths in low-and middle-income countries are linked to malnutrition, while stunting, wasting, and micronutrient deficiencies impair the development of millions of children annually. The studies in this special issue focus on countries facing distinct yet interconnected challenges: Sub-Saharan African nations grapple with high rates of stunting and maternal high-risk fertility behaviors; China confronts rural-urban disparities in dietary diversity and grandparenting practices; Colombia struggles with intersectional inequalities driving infant mortality; and Zambia faces unique …