Digital Commons Network^™

Cyber-Physical Security Through The Lens Of Ai-Enabled Systems, Zhiyuan Yu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cyber-physical systems (CPS), powered by emerging artificial intelligence (AI) technologies, have become integral to various critical domains such as the Internet of Things (IoTs), medical devices, and autonomous vehicles. A unique aspect of these systems lies in their interactions with the physical world, by perceiving environments through heterogeneous modalities (perception), processing digital data with human-in-the-loop intelligence algorithms (computing), and autonomously actuating controls that affect physical processes (actuation). While this intricate fusion of cyber and physical components has unlocked unprecedented capabilities, it has also introduced new security challenges. However, traditional security measures often fall short in addressing these multifaceted threats. This …

Chemical Reversal Of Beta-Lactam Resistance And Induction Of Hyper-Susceptibility In Pseudomonas Aeruginosa By Limiting Horizontal Gene Transfer Under Beta-Lactam Stress, Aimee Iradukunda

Dissertations - ALL

The emergence of antibiotic resistance poses a significant threat to global health, with certain bacterial strains evolving to resist multiple drugs. Urgent action is necessary to develop new antibacterial agents that effectively target these resistant strains; however, no new classes of antibiotics have been approved in recent decades. This research employs innovative biological tools to identify and highlight factors influencing resistance dynamics. Additionally, this study refines the novel approach by utilizing adjuvants to chemically repurpose existing antibiotics and improve their effectiveness against antibiotic-resistant strains. Pseudomonas aeruginosa, recognized for its adaptability, persistent infections—especially in cystic fibrosis patients—and widespread antibiotic resistance, serves …

Body Size Trends Of Late Devonian Dacryoconarid Tentaculitoids And Protocol Development For I/Ca Analysis In Corals By La-Icp-Ms, Ashley Prow-Fleischer

Dissertations - ALL

Paleoclimatology provides context for understanding the timescales and animal responses to environmental change under modern climate change scenarios. The key drivers of climate variability are identified using proxies for environmental conditions. Biological archives are especially useful for linking changing conditions to ecosystem responses. This dissertation establishes the foundation for utilizing dacryoconarid microfossils as biostratigraphic indicators of environmental change in the Paleozoic. It also presents a protocol for measuring iodine-to-calcium (I/Ca) ratios—an established proxy for localized hypoxia—in coral skeletons using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Studying Paleozoic microfossils presents challenges due to the high degree of induration of …

Deformations Of Thin Membranes In Incompatible Geometries And Interactions In Mechanical Hysteron Systems, Zachariah Schrecengost

Dissertations - ALL

Soft reconfigurable systems exhibit behaviors which are highly dependent on their geometries. Thin membranes can deform in a myriad of ways as they navigate geometries different from their own in an energy efficient manner. Behaviors in mechanical hysteron systems are influenced by the geometry of the interactions and global driving. This dissertation focuses on two different types of systems which are governed in part by their geometries: thin membranes in geometrically incompatible configurations and interacting mechanical hysterons. A thin membrane forced into a conflicting geometry with an incompatible metric will deform in highly non-trivial ways. These deformations are an attempt …

From Fables To Facts: Discovering The World Through Stories And Science, Lucille Helen Vanek

Graduate Student Portfolios, Professional Papers, and Capstone Projects

From Fables to Facts: Discovering the World Through Stories and Science examines the integration of narrative storytelling and hands-on scientific exploration as a means of cultivating environmental literacy, ethical reflection, and sustained engagement with the natural world. Grounded in environmental philosophy, aesthetics, and ethics, the project draws on theoretical insights from Holmes Rolston III, Marcia Muelder Eaton, Allen Carlson, Arnold Berleant, and C. Thi Nguyen to develop a multidimensional model of education that unites imagination, cognition, and participatory experience. Implemented in diverse Montana community settings—including libraries, early learning centers, science museums, and faith-based organizations—the program paired fables, parables, and literary …

Multi-Modal Mri For The Pre-Clinical Evaluation Of Hiv-Linked Changes In The Central Nervous System, Gabriel Gauthier

Theses & Dissertations

Though the inception of anti-retroviral therapy (ART) has fundamentally changed the life expectancy of human immunodeficiency virus (HIV) patients, accessibility and outcomes vary enormously along demographic lines. Even for people living with HIV (PLWH) with perfect access and adherence to anti-retroviral drugs (ARVs), modern treatment plans are fundamentally unable to secure complete viral remission for patients. The cause of this perpetual infection is the persistence of viral reservoirs in the central nervous system (CNS), hidden beyond the reach of modern ARVs, leaving patients to deal with lifelong medication side-effects and risks of developing HIV-associated neurodegenerative disorders (HAND). Despite improving outcomes …

Intrinsic And Extrinsic Drivers Of Bioaerosol Decay: Investigating Pathogen Stability Of Bacteriophage Ms2, Sin Nombre Virus, And Sars-Cov-2 In Simulated Environments, Elizabeth A. Klug

Theses & Dissertations

The threat posed by a virus as a bioaerosol depends largely on its stability under various environmental conditions (relative humidity (RH), sunlight, ozone, etc.). This stability is typically studied through aerosol decay—how the virus' viability changes over time when exposed environmental conditions. The Goldberg rotating drum, a widely used tool for studying bioaerosols, has been the basis of such research (Goldberg et al., 1958). However, it has significant limitations, including an inability to measure initial pathogen infectivity loss and the use of small sample volumes. Additionally, it does not answer the question of what intrinsic factors (lipids, proteins, nucleic acids) …

Feasibility Analysis For The Implementation Of An Anaerobic Digestion System In The City Of Pittsburgh, Pa, Gianna L. Kolencik

Electronic Theses and Dissertations

The current study is investigating the feasibility of an anaerobic digestion system

in Pittsburgh, Pennsylvania, at the old State Correctional Institute (SCI-Pittsburgh)

located at 1922 Westhall St. This location is immediately upstream of the Allegheny

County Sanitary Authority (ALCOSAN) along the Ohio River. Municipal solid waste

from ALCOSAN may be used as the main form of feedstock. ALCOSAN produced

roughly 36,500 tons of dry sludge in the reporting year 2023-2024. Based on the volume

of dry sludge from ALCOSAN it is estimated that an anaerobic digestion system could

yield approximately 29,930,000 kWh of energy, which is enough to power over …

Creasing In Thick Hemispherical Shells As A Model For Foveal Formation, Indigo Skye Peppard

Undergraduate Honors Theses

This research experimentally investigates creasing behavior on the inner surface of hemispherical shells with the ultimate goal of modelling the formation of the foveal pit, a sharp surface deformation present in the retina of the eye of many animals. Creasing is a phenomenon observed in hyperelastic materials and is characterized by sharply localized surface deformations that appear at ~35% compressive strain. The foveal pits of anoles (small iguanian lizards) are funnel-shaped and resemble creases when cut along the central axis. Furthermore, during foveal pit formation the anole eye contracts around 35% along this same axis. Given these similarities we believe …

Impact Of Unconventional Gas Extraction On Tributaries Of Tenmile Creek, Greene County, Pennsylvania: A 12-Year Perspective, Christian L. Beall

Electronic Theses and Dissertations

Much of southwestern Pennsylvania has been central to a rapid increase in development for unconventional natural gas extraction in the past two decades. The continued monitoring of streams over their lifetime as extraction sites is pivotal to understanding the effects of fracking on local waterways and their ability to provide for wildlife and human use. Here, using multiple indices of biotic integrity (IBI), I perform analyses of fish and macroinvertebrate communities as well as water chemistry on two streams, Bates Fork (with shale wells) and Fonner Run (without), as part of a follow-up to work performed there from 2010-2012. Fish …

Bridging Cattle Farming And Technology: The Development Of Moomanager, Matthew Hayes

Honors College Theses

Small-scale cattle producers face persistent challenges in adopting digital tools for herd management, often due to barriers such as limited digital literacy, software complexity, and poor alignment with practical workflows. Existing literature highlights the potential benefits of mobile applications in agricultural contexts, yet adoption rates remain low among smaller operations. This thesis investigates how a streamlined, mobile-first application can address these adoption barriers while supporting essential farm management tasks. The study details the design and development of MooManager, a mobile application built with React Native and Supabase and structured around core features such as cattle tracking, beef sales logging, and …

Architecture Of Pseudomonas Aeruginosa Glutamyl-Trna Synthetase Defines A Subfamily Of Dimeric Class Ib Aminoacyl-Trna Synthetases, Michael K. Fenwick, Stephen J. Mayclin, Steve Seibold, Amy E. Derocher, Sandhya Subramanian, Isabelle Q. Phan, David M. Dranow, Donald D. Lorimer, Ariel B. Abramov, James M. Bullard

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, “pipe strap” conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation …

Identification Of Subtypes Of Post-Stroke And Neurotypical Gait Behaviors Using Neural Network Analysis Of Gait Cycle Kinematics, Andrian Kuch, Nicolas Schweighofer, James M. Finley, Alison Mckenzie, Yuxin Wen, Natalia Sánchez

Physical Therapy Faculty Articles and Research

Gait impairment post-stroke is highly heterogeneous. Prior studies classified heterogeneous gait patterns into subgroups using peak kinematics, kinetics, or spatiotemporal variables. A limitation of this approach is the need to select discrete features in the gait cycle. Using continuous gait cycle data, we accounted for differences in magnitude and timing of kinematics. Here, we propose a machine-learning pipeline combining supervised and unsupervised learning. We first trained a Convolutional Neural Network and a Temporal Convolutional Network to extract features that distinguish impaired from neurotypical gait. Then, we used unsupervised time-series k-means and Gaussian Mixture Models to identify gait clusters. We tested …

Automation Of Javanese Shadow Puppets Using Machine Control, Kristian Rice, Yinson Tso, Mukhammadali Yuldoshev

Publications and Research

The virtualization of Javanese shadow puppetry (Wayang Kulit) offers a unique opportunity to preserve and revitalize traditional performance art through immersive digital platforms. This project explores the development of a virtual Wayang Kulit experience using real-time 3D engines like Unity/Unreal Engine while focusing on simulating the mechanics and aesthetics of shadow puppet performance. The puppets are designed using detailed 2D planes and rigged with skeletal systems to reflect the stylized motion of traditional puppetry. An aspect of this project is integrating an AI-driven control system that autonomously animates the puppets, learning from recorded puppeteer performances to replicate gesture, rhythm, and …

Evaluating Predictive Models For Predicting Total Score Of Beef Carcasses, Emmanuel Forson

Electronic Theses and Dissertations

The beef industry plays a vital role in global agriculture, with carcass quality and consumer preference being key determinants of market success. This thesis examines predictive modeling techniques for estimating the Total Score of beef carcasses, a composite measure representing yield and quality, primarily used by the Nebraska Cattlemen Association. Using data from the Nebraska Cattlemen’s Foundation Retail Value Steer Challenge (2000–2023), the study compares the performance of First Order Multiple Linear Regression (MLR) with three machine learning techniques: K-Nearest Neighbors (KNN), Random Forest, and Gradient Boosting Machine (GBM).

The analysis focuses on six key predictors: Hot Carcass Weight, Back …

Computational Design Of Potent Sirna For Braf Oncogene Silencing For Enhancing Cancer Therapy, Muhammad Hermawan Widyananda, Ricadonna Raissa

Karbala International Journal of Modern Science

The discovery of oncogenic BRAF mutations has prompted the development of inhibitors, yet resistance remains widespread. A more effective strategy involves targeting BRAF mRNA with siRNA to overcome resistance to BRAF inhibitors. This study aims to design potent siRNA for BRAF oncogene silencing using a computational approach. The full coding sequence of BRAF was retrieved from the NCBI database and potential siRNAs were predicted using the Ui-Tei, Reynolds, and Amarzguioui rules. Identified siRNAs were further analyzed using various prediction systems and parameters, including their interaction with the hAgo2 protein. The results identified that seven siRNAs (siRNA 23, siRNA 24, siRNA …

Praxly: An Online Ide For The Praxis Cs Test Pseudocode, Benjamin Saupp

James Madison Undergraduate Research Journal (JMURJ)

No abstract provided.

Soft Modular Robots: From Modular Tensegrity Structures To Bioinspired Sea Robots, Luyang Zhao

Dartmouth College Ph.D Dissertations

The rapid advancement of robotics necessitates systems capable of adapting to complex, unstructured environments. Soft robots, with their flexibility and compliance, excel in delicate interactions, making them ideal for medical applications and search-and-rescue missions. Modular robots, on the other hand, offer reconfigurability, enabling diverse task-specific adaptations in dynamic settings. Despite their individual advantages, the integration of soft and modular robotics remains underexplored. This proposal aims to develop soft modular robots that combine the adaptability of soft robotics with the versatility of modularity. These systems will be capable of autonomously transitioning between locomotion, manipulation, and infrastructure assembly across land, water, and …

Improving The Reproducibility Of Deep Learning Software: An Initial Investigation Through A Case Study Analysis, Nikita Ravi, Abhinav Goel, James C. Davis, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

The field of deep learning has witnessed significant breakthroughs, spanning various applications, and fundamentally transforming current software capabilities. However, alongside these advancements, there have been increasing concerns about reproducing the results of these deep learning methods. This is significant because reproducibility is the foundation of reliability and validity in software development, particularly in the rapidly evolving domain of deep learning. The difficulty of reproducibility may arise due to several reasons, including having differences from the original execution environment, incompatible software libraries, proprietary data and source code, lack of transparency, and the stochastic nature in some software. A study conducted by …

Treatment Wastewater Of Oil Refinery By Fe2o3 Nps Produce By The Novel Alishewanella Jeotgali Strain Haq8., Hawraa Qays Al-Assdy, Wijdan Hussein Al-Tamimi, Asia Fadhile Almansoory

Karbala International Journal of Modern Science

Metal oxide nanoparticles like iron oxide (Fe₂O₃) exhibit strong reactivity and photolytic features in wastewater treatment and serve as an effective adsorbent for water purification due to its substantial surface area and affinity for different functionalized groups. Iron oxide nanoparticles) IONPs) are currently applied to treat oil-contaminated water. Fe₂O₃NPs were produced using an extracellular approach utilizing the Alishewanella jeotgali strain HAQ8. IONPs were characterized using UV-vis, FT-IR, XRD, AFM, SEM-EDX, and Zeta potential. λ max for the synthesized nanoparticles observed at (358) nm. The bands at 485 cm⁻¹ in the FT-IR spectrum confirmed the formation of …

Responsibility To The Land: Perspectives Of Farmers On Climate Change And Land Transition, Meira A. Smit

Environmental Studies Honors Projects

Agriculture is a defining aspect of Minnesota and Wisconsin’s culture and identity, characterized by family farms, rolling hills blanketed with crops, and cows. Interspersed are small scale diversified farms and a growing number of emerging and young farmers. Another cultural mainstay is talking about weather, a ubiquitous conversation of Midwesterners. As weather events such as erratic rainfall, drought, and pest pressure become both more common and volatile, and long-term weather patterns shift from “normal”, it is important to ask farmers what they think about it. Adapting to changes and planning for resilience are what farmers have always done, yet increasing …

Dynamic Riskscapes For Prey: Disentangling The Impact Of Human And Cougar Presence On Deer Behavior Using Gps Smartphone Locations, Heather N. Abernathy, Mark A. Ditmer, David C. Stoner, Kent R. Hersey, Kathryn A. Schoenecker, Pat J. Jackson, Kristin N. Engebretsen, Julie K. Young, George Wittemyer

Wildland Resources Faculty Publications

Prey species adjust their behavior along human-use gradients by balancing risks from predators and humans. During hunting seasons, prey often exhibit strong antipredator responses to humans but may develop tolerance in suburban areas to exploit human-mediated resources. Additionally, areas with high human activity may offer reduced predation risk if apex predators avoid such locations. This study examined mule deer Odocoileus hemionus behavioral responses to risks from humans and their primary predators, cougars Puma concolor, contextualized by differences in risk levels between study sites, individual risk exposure, and human habituation. We framed our investigation using three non-mutually exclusive hypotheses: (H1) …

Improving User Retention And Learning Through Interactive Tutorial Systems, Prakhyat Chaube

2025 Spring Honors Capstone Projects - Archive

The onboarding experience in software applications is crucial for user engagement and retention. Traditional static tutorials often fail to provide adaptive, role-specific learning, leading to user frustration and drop-off. This project introduces an interactive tutorial system tailored for students and tutors using the CSE Student Success Center App at the University of Texas at Arlington. Designed to enhance usability and accessibility, the system personalizes onboarding experiences through guided, role-based learning paths and real-time feedback. By streamlining the learning curve, the tutorial system fosters greater user confidence and engagement, ensuring a more intuitive transition into the application. User evaluations indicate a …

Spatio-Temporal Analysis Of Human-Carnivore Conflict In The Tarangire-Manyara Ecosystem, Tanzania, Sophie Carpenter

Environmental Studies Honors Projects

Livestock depredation by large carnivores significantly threatens human livelihoods across the globe, with severe ecological and socioeconomic implications. Economic costs of livestock depredation impact the tolerance for carnivores among communities living alongside wildlife, often straining human-carnivore coexistence. Using geographic and temporal attributes from livestock depredation records (n=406) collected between 2004 and 2023, we identified spatiotemporal patterns of depredation by African lions, leopards, and spotted hyenas in the Tarangire-Manyara Ecosystem in northern Tanzania. We found significant interactive relationships between the number of attacks reported and the season, time, and site of attack; with these interactions differing between the carnivores. To better …

Evaluation Of Tree Legumes Species At Different Agroclimatic Zones Of Indonesia, Mas'ud Panjaitan, R Jessop, W W. Stur

IGC Proceedings (1977-2023)

The population of Indonesia is over 145 million and more than 56 % of them earn their living from agriculture (Bi. Stat. Ind., 1983). A major problem in the development of improved animal production has been the shortage of feed and the generally low nutritive value of tropical forages which limit livestock pro­duction in Indonesia (Asian Agriculture Survey, 1969). The production of feed of adequate quality for ruminants is an important consideration particularly for small holders. In many situations, nitrogen fixing legume trees can be used as a high protein feed supplement which improves the utilization of grasses and crop …

Utilization Of Native Mediterranean Fodder Trees By Dairy Goats, M Meuret

IGC Proceedings (1977-2023)

Few data are available on utilization of fodder trees and shrubs by lactating goats. In most cases, predictions of animal performances on the basis of recommendations obtained from standard reference trials, do not correspond with production results achieved on the farm. Using measurements in digesti­bility cages and on rangelands (chromic oxide marker), we recorded intake, apparent digestibility of diets and perform­ances of goats well used to rangelands and browsing fresh oak foliage (Quercus ilex and Quercus pubescens).

Phenols As Defensive Compounds In Birch (Betula Spp.) Metabolism Of Platyphylloside In Goats, Rabbits And Hares, R T. Palo, G Iason, P G. Knutsonn

IGC Proceedings (1977-2023)

Herbivores of the boreal forest like moose (Alces alces), hares (Lepus spp.) and birds (Tetranoidae) use birch as a major feed source. The tree is of medium preference to the animals and is low in available nutrients for most of the year. Apart from a high amount of lignified cell walls it also contains con­siderable amounts oflow molecular phenolic substances (Palo, 1984). A herbivore feeding on birch could thus be excepted to ingest large amounts of phenols. These are in general enough fat soluble to enter animal cells expected to ingest large amounts of …

Rumen Degradation Of Various Grass Species At Different Stages Of Growth, L J. Halliday

IGC Proceedings (1977-2023)

The species and cultivars sown depends on the farming sys­tem practiced. These developing swards are however, always invaded by native species including Agrostis, Paa and Festuca spp. which are generally referred to as 'weed' grasses. While the merits of Lolium spp. are well documented (Minson et al. 1960; Norton, 1982) information on the weed grasses is limited (Hag­gar, 1976). The potential for milk and meat production is dependent on the supply of utilizable nutrients to the animal's tissues which in turn is largely governed by the ability of rumen microbes to degrade plant cell walls. Although the degradability of dry …

Feed Evaluation Using Mobile Dacron Bags And Influences Of The Diet Composition, H Anzola, F N. Owens

IGC Proceedings (1977-2023)

The Mobile Nylon Bag (MNB) technique has been used successfully in protein nutrition studies with swine (Sauer et al., 1983) to determine amino acid availability from protein in specific feedstuffs. Canadian researchers also have tested this technique to predict site of digestion in ruminants (Kirkpatrick and Kennelly, 1987). Differences in small intestinal digestion may explain why animal responses differ to dietary protein sources which have similar ruminal escape values (Owens, 1986). The MNB holds promise to appraise the intestinal avail­ability of undegraded dietary protein though further develop­mel).t and testing are needed. The objective of this experiment was to examine the …

Forage Quality Of Coast Cross 1 Bermudagrass On Intestinal Digestion Of Dietary Amino Acids, G Coto, Hanna Meier, Patrica Malgarez

IGC Proceedings (1977-2023)

The aim of this work was to study the digestibility of dietary amino acids found in the fibrous material, considering the qual­ity of the forage offered as the sole feeding source.