Digital Commons Network^™

Unveiling The Genomic Blueprint Of Two Pantoea Agglomerans Phages: Lia And Yaegar As Emerging Members Of The Chaseviridae Family, Leslie M. Ewool

Theses and Dissertations

Bacteriophages represent an essential component of microbial ecosystems and a promising resource for biocontrol. This study presents a comprehensive comparative genomic and evolutionary characterization of two novel bacteriophages that infect Pantoea agglomerans, Lia and Yaegar, belonging to the Loessnervirus genus within the Chaseviridae family. Both Lia and Yaegar possess double-stranded DNA genomes of approximately 54 kb with 44.4% GC content and 82 predicted open reading frames (ORFs). Functional annotation revealed distinct modules for replication, structural assembly, and lysis, but no genes associated with lysogeny, antibiotic resistance, or virulence. Average nucleotide identity (ANI) analysis indicated over 96% similarity between Lia, Yaegar, …

Toward Understanding Multi-Agent Decision Making In Complex Societies, Jonathan Skaggs

Theses and Dissertations

This dissertation investigates Multi Agent Decision Making (MADM) within Complex Societies (CS), systems of interdependent agents whose collective behaviors emerge from local interactions. Such emergent dynamics are nonlinear and difficult to predict, posing significant challenges towards understanding how individual decisions scale to societal outcomes. Existing approaches often fall short of capturing the combined attributes of CS, including asymmetry, decentralization, and adaptivity. To address this gap, we introduce new models and analyses of agent strategies that explain how cooperation and stability can arise in CS. Structured around three interrelated projects, this dissertation enhances our comprehension of MADM in CS. The research …

Fabrication And Evaluation Of Large Alumina Crucibles By Vat Photopolymerization Additive Manufacturing For High-Temperature Actinide Chemistry, R. Joey Griffiths, Christy Santoyo, Jean-Baptise Forien, Bradley Childs, Andrew J. Swift, Andrew Cho, Alexander Wilson-Heid, George Ankrah, Devin Rappleye, Aiden A. Martin, Jason Jeffries, Kiel Holliday

Faculty Publications

Additive manufacturing (AM) offers opportunities to advance the design and function of ceramic tooling in high temperature actinide pyrochemistry. In technical ceramics such as alumina, conventional forming techniques often restrict design flexibility and can limit experimental progress. In this study, we investigate the use of vat photopolymerization (VP) with commercial resins to fabricate large-scale alumina crucibles, reaching dimensions up to 125 mm, which is significantly larger than typically reported for dense VP ceramics. Notably, these additively manufactured components are produced using consumer-grade hardware, which limits process control, but offers significant upside in scalability and accessibility. Using microscopy and X-ray computed …

Navigating Structure, Function, And Stability: Bridging Immunotherapy And Protein Engineering In The Era Of Machine Learning, Christopher J. Haynie

Theses and Dissertations

The immune system is a remarkably adaptive network, yet it often fails to function optimally due to evasion strategies of pathogens or mutated cells. Many of these evasion strategies involve alterations in protein expression and function. Protein design is an area of computational biology with potential applications in improving protein function and therapeutic protein engineering. This thesis explores methods to enhance immune function and protein design across multiple scales, from molecular engineering of antibody fragments and chimeric antigen receptors (CARs) to cellular immune responses, and computational approaches for protein structure optimization. We characterize Thymidine Kinase 1-specific single-chain antibodies, highlighting both …

Chronosort: Revealing Hidden Dynamics In Alphafold3 Structure Predictions, Matthew J. Argyle, William P. Heaps, Corbyn Kubalek, Spencer Gardiner, Bradley C. Bundy, Dennis Della Corte

Faculty Publications

Protein function emerges from dynamic conformational changes, yet structure prediction methods provide only static snapshots. While AlphaFold3 (AF3) predicts protein structures, the potential for extracting dynamic information from its ensemble predictions has remained underexplored. Here, we demonstrate that AF3 structural ensembles contain substantial dynamic information that correlates remarkably well with molecular dynamics simulations (MD). We developed ChronoSort, a novel algorithm that organizes static structure predictions into temporally coherent trajectories by minimizing structural differences between neighboring frames. Through systematic analysis of four diverse protein targets, we show that root-mean-square fluctuations derived from AF3 ensembles can correlate strongly with those from MD …

Using An Old Assay In New Ways: Differential Scanning Calorimetry Characterization, Quantification, And Interaction Analysis Of Whey Proteins, Charity Conlin Jennings

Theses and Dissertations

Whey proteins including β-Lactoglobulin, α-Lactalbumin, Immunoglobulin-G, Serum Albumin, Lactoferrin, and Lactoperoxidase each have unique biological properties spanning anti-bacterial, anti-fungal, and anti-viral activities as well as deliver essential nutrients to the human body. In the past decade, there has been a large focus on extracting these individual proteins for their use in foods and supplements. In order to best extract these proteins and prepare them properly in foods and supplements, an understanding of how they behave and denature in different environments is necessary. However, there is insufficient knowledge of their thermodynamic properties and potential interactions in varying conditions. Additionally, there are …

Alphasperm Data, Seth J. Parks, Timothy G. Jenkins

ScholarsArchive Data

Data from a prospective cohort study of sperm DNA methylation, semen analysis, and DNA fragmentation in fertile and infertile men before and after treatment with a male fertility antioxidant supplement.

Evaluating Platinum, Gold, Glassy Carbon, And Graphite Anodes For Chlorine Evolution In Molten Calcium Chloride Salt, Cameron Vann, Shelssie Klvacek, Carlos Mejia, Devin Rappleye

Faculty Publications

The chlorine evolution reaction (CER) in molten CaCl₂ plays a critical role in high-temperature electrochemical processes, including chlorination, metal refining, and used nuclear fuel treatment. This study evaluates the performance of gold (Au), platinum (Pt), glassy carbon (GC), and graphite anodes for the CER under consistent electrochemical conditions. Anode performance was assessed based on chlorine (Cl₂) gas evolution, material robustness, and kinetic parameters. Cl₂ generation was directly confirmed using quadrupole mass spectrometry for Pt, GC, and graphite anodes. GC and graphite demonstrated stable and sustained CER activity. Pt and Au were shown to have significant mass …

Generative Ai In Chinese Esl Students’ Writing Processes: Stages, Methods, And Language Use, Runzhou Shan

Journal of Response to Writing

This paper explores how Chinese ESL students utilize Generative AI (Gen AI) in their writing processes, focusing on the stages of writing, specific methods of use, and language practices. The study was carried out in an English-medium instruction (EMI) environment at a Sino-American university in China. Data were collected through online surveys with 157 participants and follow-up interviews with nine students. Quantitative analysis of the survey data uncovered general patterns, while analysis of the interview data, using Polio & Freedman’s (2017) coding method to identify themes, provided detailed illustrations. Subsequent analysis indicates that students primarily engage with Gen AI in …

Fall 2025 Volume 11 Issue 2: Full Issue

Journal of Response to Writing

No abstract provided.

Resolution Of Physics And Deep Learning-Based Protein Engineering Filters: A Case Study With A Lipase For Industrial Substrate Hydrolysis, Spencer Gardiner, Peter Dollinger, Filip Kovacic, Jörge Pietruszka, Daniel Ess, Karl-Erich Jaeger, Gunnar F. Schröder, Dennis Della Corte

Faculty Publications

Computational enzyme design remains a powerful yet imperfect tool for optimizing biocatalysts, especially when targeting non-natural substrates. Using design tools we investigated Pseudomonas aeruginosa LipA, a lipase with a flexible lid domain crucial for substrate binding and turnover, aiming to enhance its hydrolysis of the industrially relevant substrate Roche ester. We generated an initial set of single-point mutations based on structural proximity to the active site and evaluated their effects using a computational pipeline integrating molecular dynamics (MD) simulations, density functional theory (DFT) calculations, and ensemble-based energy scoring. While we identified several active variants, attempts to rank them by activity …

When Evidence Is Shocking: The Value Of Struggling With Uncomfortable Ideas, Cortney Evans-Stout, Christin L. Porter

Family Perspectives

No abstract provided.

Magnetic Nanoparticles Tethered With Zn–Dpa For The Removal Of Bacteria From Red Blood Cell Suspension, Tochukwu P. Okonkwo, Rajendra P. Gautam, Jacob B. Limburg, Breckin L. Forstrom, Bowen J. Houser, Aaron Rappleyea, Tyler P. Green, Joseph P. Talley, Alexander D. Daum, Stacey J. Smith, Karine Chesnel, William G. Pitt, Roger G. Harrison

Faculty Publications

Bacterial infections continue to drive the need for more effective and rapid methods for bacterial analysis. To address this, magnetic nanoparticles (MNPs) have emerged as promising tools, especially when their surfaces are modified with bacteria binders. The bis-zinc–dipicolylamine (Zn–DPA) complex is known for its broad affinity to bacteria. We have synthesized MNPs via a thermal decomposition method, encapsulated them in silica, modified their surface with Zn–DPA, and tested their ability to remove bacteria. The MNPs retain their superparamagnetic properties and crystallite structure after being encapsulated. The MNPs coated with silica and Zn–DPA effectively bind and remove both Gram-positive and Gram-negative …

Beyond Earth: Strategic Pathways To A Multiplanet Civilization And The Case For Mars Settlement, Andrew Targowski

Comparative Civilizations Review

This research provides a comprehensive and interdisciplinary exploration of the transition toward a multiplanet civilization, with a special focus on Mars as humanity’s first major step beyond Earth. By addressing technological, political, economic, and ethical dimensions, it aims to inform policymakers, scientists, and the public about the feasibility, challenges, and philosophical implications of interplanetary expansion.

As humanity approaches the threshold of becoming a multiplanet civilization, it faces unprecedented scientific, technological, economic, and ethical challenges. This paper explores the rationale, methodologies, and critical considerations for establishing sustainable human settlements beyond Earth, with a particular focus on Mars. By analyzing advances in …

Towards The Systematic Cross-Civilizational Comparison: How Civilizations Work - Case 1: The Monotheistic Civilization, Liah Greenfeld

Comparative Civilizations Review

The purpose of this essay is to offer several hypotheses based on the concept of civilization and the conceptual scaffolding for the study of the cultural reality, proposed in the Spring 2024 CCR paper, regarding the three civilizations coexisting in the world today: the monotheistic, the Sinic, and the Indic. It introduces the modal dimensions along which civilizations may differ on the level of the individual mind — cognitive (pertaining both to the structure and contents of thought), moral, and emotional; and that of the society (separate institutions and institutional systems) and history.

Books Of Interest Fall 2025, Stephen T. Satkiewicz

Comparative Civilizations Review

Books that may be of interest to scholars of the comparative study of civilizations, and may add significantly to the body of scholarship in the civilizational field. These books are also available for book reviews in future editions of Comparative Civilizations Review.

The Fragrance Muse: Musk As A Symbolic Tapestry In Classical Persian Poetry, Akbar Shirini, Shen Xudong, Zhao Dan

Comparative Civilizations Review

This paper explores the symbolic representation of musk in classical Persian poetry, uncovering its role as a multifaceted emblem of Iranian cultural identity and human experience. Drawing on a qualitative analysis of primary texts from the Ganjoor archive and secondary sources, the study traces musk’s historical significance across China, Iran, and Islamic world. In China, musk is prized for its rarity, medicinal properties, and metaphysical roles; in Iran, it intertwines with mythology, Zoroastrian cosmology, and trade; in Islamic contexts, it holds commercial and therapeutic value, cherished by figures like Mohammad. Within Persian poetry, musk transcends its material origins, symbolizing blackness …

Effect Of Short-Chain Polymer Binders On The Mechanical And Electrochemical Performance Of Silicon Anodes, Fei Sun, L. Zurita-Garcia, Dean R. Wheeler

Faculty Publications

Polymer binders are crucial components in providing both mechanical support and chemical stability to the structure of porous Li-ion electrodes. Particularly in silicon anodes, the active material undergoes substantial volume expansion of up to 275%. Due to the mechanical constraint of the current collector, these silicon materials tend to expand in the normal direction while exhibiting substantial particle rearrangement and plastic deformation. Conventional rigid binders such as polyacrylic acid (PAA) and polyimide (PI), while providing satisfactory initial capacity, do not eliminate diminished long-term performance. Our research attempts to develop binder formulations that can accommodate sufficient flexibility for the substantial volume …

Ruth Gatrell, Myrna J. Layton

Faculty Publications

Ruth Josephine Barton was born on December 23, 1921, in Farmington, Utah. Her parents were Lloyd and Edna (Cottrell) Barton. When the Bartons married, Edna already had a five-year-old daughter, Helen, from a previous marriage. Ruth was the first of two children born to Edna’s second marriage. The family was living in Mount Pleasant, Utah, but returned to the home of Edna’s father, Edward Cottrell, for the birth of the baby. She was named Ruth for the biblical heroine, and Josephine because she shared a birthday with the prophet Joseph Smith. A younger sister, Laura Jean, joined the family in …

Engineering Protein Linkers For Optimized Telsam-Darpin Fusion And Crystallization With Electric Field-Based Polymer Orientation, Maria Jose Pedroza Romo

Theses and Dissertations

Fusing a variant of the sterile alpha motif domain of the human translocation ETS leukemia protein (TELSAM) to a protein of interest significantly enhances crystallization and diffraction quality. TELSAM is a pH-dependent, polymer-forming crystallization chaperone that, when covalently fused to a protein, forms a well-ordered crystal lattice. However, the success of this method depends on two factors: 1) the design of the linker connecting TELSAM to the target protein, which influences both crystal packing and target orientation, and 2) the prevention of TELSAM polymer flipping, a phenomenon that disrupts lattice periodicity and impairs structure determination. To address the first challenge, …

Cost-Effectiveness Model For Reservoir Sediment Management Economics, Connor Ronald Hale

Theses and Dissertations

Reservoir sediment deposition poses a challenge to sustainable water supplies around the world. Sediment management has proven to be an expensive endeavor. Two models have been developed to guide economic analysis for reservoir sediment management, namely the Reservoir Sediment Economics Model (RSEM) and the Reservoir Conservation Model 2 (RESCON 2). While these are helpful tools for benefit-cost prefeasibility studies, they rely heavily on sometimes elusive estimations of the benefits of water supply. In this study, a new method for economic analysis is proposed that foregoes benefit-cost analysis in favor of a cost-effectiveness approach. The Sediment Management Cost-Effectiveness Model ranks sediment …

Magnetic Ordering And Dynamics In Assemblies Of Magnetite Nanoparticles Throughout The Superparamagnetic Transition, Johnathon Michael Rackham

Theses and Dissertations

Magnetic nanoparticles are used in nanotechnologies and biomedical applications, such as drug targeting, hyperthermia treatment, MRI contrasting agents, and bio-separation of compound solutions. Magnetite (Fe3O4) nanoparticles stand to be effective in these roles due to the non-toxic nature of magnetite and its strong magnetization. To this end, a greater understanding of the magnetic behavior of the individual magnetite nanoparticles is needed when a collection of them is used. This research seeks to discover the local magnetic ordering and dynamics of fluctuations of ensembles of magnetite nanoparticles at various stages of the magnetization process, throughout the superparamagnetic blocking transitions, and for …

Seating Charts, Connections, And Fostering Community, Mckenna B. Chow

Theses and Dissertations

This thesis explores how fostering stronger connections in the high school ceramics classroom can create a more inclusive and collaborative community. I regularly changed seating charts to encourage new relationships and strengthen classroom culture as part of this effort. Historically, seating charts have enforced uniformity and promoted specific behaviors. My research challenges these traditional purposes and proposes that seating arrangements can instead serve a more meaningful and enduring goal: promoting connection and ensuring that all students feel seen. I found that while seating charts can contribute to this goal, achieving genuine connection and inclusivity also requires several additional factors to …

Executive Functioning And Mental Health In Emerging Adults: Type 1 Diabetes Status As A Moderator, Hannah Margot Mcdaniel

Theses and Dissertations

Emerging adults (ages 18-26) with type 1 diabetes mellitus (T1DM) are especially vulnerable to diabetes management challenges when taking on increased disease responsibility during this critical period of development. They may experience higher cognitive and psychological demands compared to peers. The study examined whether having T1DM moderated the association between executive functioning (EF) and mental health symptoms (i.e., depression, anxiety, stress, and disordered eating) in emerging adults. Exploratory analyses investigated the associations between EF, disease management, and mental health symptoms. Participants were 35 emerging adults with T1DM and 35 healthy controls. Participants completed questionnaire measures of mental health and performance-based …

Remote Running Gait Analysis Using Smartphone Video And Monocular Pose Estimation: A Feasibility Study, Luke Vankeersbilck

Theses and Dissertations

Introduction: Running is a common form of exercise that comes with many health benefits; however, many people stop exercising because of the high injury risk. Running injury is connected with biomechanical risk factors. Yet, these risk factors often show inconsistent and conflicting results across studies, largely due to small sample sizes limiting statistical power. Low subject numbers may be partly due to the time requirements of traditional motion capture. Monocular pose estimation offers a promising alternative by using machine learning to track body landmarks from a single camera. This study evaluated the feasibility of remotely collecting running biomechanics data using …

Under The Sea And Into The Future With Darwin, Verne, & Wells: Evolutionary Ideas In Early Science Fiction Literature And Atomic Age Adaptations, Suzette K. Forston

Theses and Dissertations

In the latter half of the nineteenth century, Charles Darwin's theories challenged traditional ways of thinking about the world so dramatically that his writings inspired the formation of a new genre: science fiction. Two pioneering authors, Jules Verne and H. G. Wells drew from Darwin's writings in their classic novels, 20,000 Leagues Under the Seas (1870) and The Time Machine (1895). Though the two authors are often compared because they were both early science fiction authors, they approached Darwinian theory in different ways. Verne uses a more extrapolative approach and focusing on specific details of Darwin's texts to tell a …

Circadian Influences On Glycemic Control In 24-Hr Fasts Initiated At Different Mealtimes, Elizabeth Z. Gipson

Theses and Dissertations

This study investigated whether the timing of a 24-hour fast influences indicators of glycemic control throughout the duration of the fast or upon refeeding. Twenty-four adults who have overweight or obesity (13 female, 11 male) completed this randomized crossover study involving three 24-hour fasts initiated at either 8:00 am, 1:00 pm, or 6:00 pm followed by a 75 g oral glucose tolerance test (OGTT) which lasted 2 hours. Continuous glucose monitors (CGMs) were employed to track interstitial glucose throughout each fast and OGTT. Plasma samples for insulin, glucagon, glucagon-like peptide-1 (GLP-1), and glucose-dependent insulinotropic polypeptide (GIP) were collected at the …

Refugee Families: Parental Traumatic Stress And Child Outcomes A Scoping Review, Britta Sedig

Theses and Dissertations

This scoping review synthesizes recent literature (2019-2024) to explore mechanisms linking parental trauma to child mental health outcomes within refugee families. Guided by a systemic and relational focus, 20 studies were identified and analyzed, revealing five central themes: intergenerational transmission of trauma, parenting practices as mediators, parent-child dyadic attachment, family functioning and conflict, and post-migration and acculturative stress. Findings highlighted associations between parental trauma-related symptoms and refugee children's emotional and behavioral concerns. Parenting practices were frequently linked to child wellbeing, with some studies identifying risk factors like harsh discipline and emotional unavailability, and others noting protective roles of intentional caregiving. …

Recreation Effects On Soil Carbon, Biocrust Presence, Soil Stability, And Invasive Species In Indian Creek, Bears Ears National Monument, Elisabeth M. Currit

Theses and Dissertations

Desert ecosystems perform essential ecosystem services, including playing a crucial role in the global carbon cycle. Because of this, it is important to understand how recreational activities, common in desert environments, impacts dryland ecosystems' ability to perform ecosystem services. The growing popularity of outdoor recreation in Western US poses a threat to desert ecosystems, and unregulated activities can harm soil health, particularly the presence and functioning of biological soil crusts (biocrusts). This study uses the Indian Creek Special Recreation Management area in Bears Ears National Monument, Utah, USA, as a case study for recreation impacted desert ecosystems. It examines the …

Coding For Nonstandard Channels: A Capacity-Oriented Approach, J Daniel Harman

Theses and Dissertations

This work addresses the issue of coding for non-standard channel models with an emphasis on capacity-oriented channel analysis and system design. The first channel studied is the Wyner wiretap channel. Channel sounding results were obtained to calculate the capacity for the multi-antenna case of the Wyner wiretap channel to ascertain the potential for secure communication via secrecy coding. The second channel studied is an asymmetric binary crossover erasure channel (ABCEC) with a short-blocklength constraint. The capacity for this channel was derived, and linear codes were chosen and tested. Another study was conducted on the ABCEC within a degraded wiretap channel …