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Doves And Symbiotic Bacteria: Whole-Genome Assembly And Phylogenomic Inference, Mariam Topchyan

Theses and Dissertations

Part 1

I examined a potential source of variation in phylogenetic inference, investigating whether handling single-nucleotide polymorphisms (SNPs) through different methods during reference-guided genome assembly of pigeon and dove species impacts phylogenetic reconstruction and inference. Specifically, I created a custom consensus base calling tool that handles allelic variation through two different approaches, either ignoring heterozygous sites by denoting them as an ambiguous character “N,” or using a pseudo-random choice between supported base variants. Through reference-guided assembly of 108 dove species, I generated two datasets of alignments using both consensus calling methods, created two trees from both datasets via supermatrix and …

Tate Speech: Radicalizing Rhetoric And Multi-Level Marketing Recruitment Strategies In The Manosphere, Carey J. Priebe

Theses and Dissertations

My study aims to uncover the discursive elements behind the gendered recruitment strategies that influencers in the manosphere use to pipeline men and boys into their multi-level marketing (MLM) companies. In the manosphere, male supremacy is presented as desirable and subversive, and MLMs take advantage of emotional and economic instability. My study examines the Twitter (X) account of the popular manosphere influencer Andrew Tate as I trace his rhetoric along a three-pronged gendered recruitment framework, a framework originally developed around women selling essential oils online and funneling their followers into radical alt-right politics. What are the similarities and differences in …

Characterization Of Outer Surface Protein C Of Borreliella Role In Host Tropism, Kathryn Mf Chambers

Theses and Dissertations

The Lyme disease spirochetes, Borreliella spp., are maintained in nature through a complex enzootic cycle involving Ixodes ticks and a diverse set of reservoir hosts. The outer surface protein C (OspC) of the bacterium is an essential virulence factor required for transmission from ticks and early infection of mammals. Deletion of ospC abolishes infectivity, yet the precise molecular mechanisms underlying OspC function remain incompletely defined. In this dissertation, I examined the contribution of OspC type identity to host specificity. OspC is highly diverse, with over 30 genetically stable types described. While intra-type sequences are conserved (>95% amino acid …

Learning To Deceive And Persuade: Predictive Agents With Language And Personality Diversity In Social Deduction Games, Aaron M. Shah

Theses and Dissertations

This thesis presents a novel multi-agent architecture that combines Joint Em bedding Predictive Architectures (JEPA), Free Energy Principle (FEP)–inspired planning, and language-based social interaction. The system is evaluated in a custom Werewolf-style hidden-role game, where agents must coordinate, persuade, or deceive under partial observability. Each agent encodes its belief state into a latent representation, predicts future trajectories under candidate actions, and selects votes or eliminations through a planner trained to minimize prediction error. To enable communication, agents are equipped with trainable mouthpieces. A lightweight SpeakerBandit selects from discrete templates using REINFORCE on judge-derived rewards, while a logit-bias head steers a …

A Fault-Tolerant Exchange-Coupled Spin-Ensemble Qubit At Elevated-Temperatures, Aniruddha Chakraborty

Theses and Dissertations

This thesis introduces a novel qubit architecture: the ferromagnetic exchange-coupled spin ensemble qubit (E-qubit), designed to address the noise-induced instability. In this work, the time evolution of the ensemble’s density matrix is studied using the Liouville–von Neumann equation. To benchmark against a single-spin qubit, the gate fidelity of an E-qubit is computed in the presence of thermal noise. Coherence time is also analyzed under identical thermal condition and a linear scaling is observed with qubit size . The results show that, at 6 K , the gate fidelity error (0.7 % ) of the seven- spin ensemble is an order …

Collaborative Robots For The Automation Of Additive Manufacturing Workflows, Logan Schorr

Theses and Dissertations

Collaborative robots have the potential to transform the world, being easier to program, safer around humans, and far cheaper than their industrial counterparts. This makes them uniquely qualified to operate autonomously in environments where the presence of humans is necessary, either as an operator themselves or as observers of active processes. One of the fields where collaborative robots have significant opportunity for utility is in metal additive manufacturing, in which near net-shape parts can be autonomously fabricated using materials like stainless steel, titanium, or nickel super-alloys. These processes, especially laser powder bed fusion and directed energy deposition, use a fine …

Still An Athlete? An Exploration Of Athlete Identity, Body Appreciation, And Psychological Flourishing In Middle-Aged Former Collegiate Athletes, Kelly Furr

Theses and Dissertations

Collegiate athletes, upon retirement, are encouraged to develop other interests outside of sport to form a well-rounded identity. Yet middle-aged people often struggle to complete recommended strength training and exercise guidelines, and many continue to struggle with body appreciation and psychological well-being beyond adolescence and young adulthood. Using a cross-sectional survey design, 482 former NCAA athletes completed the Athlete Identity Measurement Scale (AIMS), Exercise Identity Scale (EIS), Body-Appreciation Scale (BAS-2), and Flourishing Scale (FS). The study used Structural Equation Modeling (SEM) to determine if athlete or exercise identity positively affects body appreciation and psychological flourishing through the mediating variable of …

Assessment Of Drivers Of Light Attenuation In Virginia Reservoirs, Jackson Barnett

Theses and Dissertations

Water clarity in aquatic ecosystems is crucial for submerged vegetation and algal dynamics. We investigated the factors influencing light attenuation (kd) by measuring total suspended solids (TSS), chlorophyll-a (CHLa), and chromophoric dissolved organic matter (CDOM) across thirteen stations located in seven reservoirs. Average kd was 1.69 m^-1 (range: 0.37-3.99 m^-1), with photic depths averaging 3.27 m (range: 1.15-12.43 m). TSS was the primary predictor of light attenuation (R² = 0.57, P = 0.003, SE = 0.053). Average TSS values for each site were multiplied by the slope of the kd-TSS relationship to find the proportion of kd …

The Trauma-To-Prison Pipeline: A Multi-Level Theoretical Framework Exploring The Intersection Of Inequality, Trauma, And Exclusionary Discipline, Dana Ainsworth

Theses and Dissertations

The school-to-prison pipeline (STPP) is a widely recognized and extensively studied metaphor used to describe the process by which school discipline policies increase the risk of juvenile justice system involvement, particularly among historically marginalized populations. While it has been instrumental in shaping educational policy, the STPP framework has not evolved to account for the critical impact of trauma on learning and behavioral outcomes. Furthermore, it overlooks the role of systemic inequality that increases trauma exposure and produces concentric patterns of marginalization.

Drawing on research across the fields of education, public health, sociology, and criminal justice, this study proposes a theoretical …

Self-Threat And The Anchoring And Adjustment Heuristic, Mattie V. Hedgebeth

Theses and Dissertations

Since its introduction in 1974, the anchoring and adjustment heuristic has been a topic of interest within the field of decision making. Although much work has examined factors that affect the process of the anchoring and adjustment heuristic, very little has been studied about how self-processes that may influence adjustment from an anchor. More specifically, the role of self-threat as a possible motivating factor in the adjustment process had yet to be explored. In my previous research, I explored how anchors that are threatening or flattering to one’s ingroup influences how they adjust from said anchor. Participants adjusted to an …

Investigating The Temperature Effects On Aedes Aegypti And Dengue Virus In Central Argentina: Perspectives From Mathematical Modeling, Morgan H. Jackson

Theses and Dissertations

Dengue virus (DENV) causes over 390 million infections and around 40,000 deaths worldwide each year. DENV is primarily transmitted by the mosquito Aedes aegypti, and both the life cycle of these mosquitoes and DENV transmission are significantly impacted by temperature. In the temperate region of Central Argentina, where dengue outbreaks first began in 2009, outbreaks only occur following new introductions of DENV from other regions. Due to the relationships between temperature and DENV and temperature and Ae. aegypti, the risk of an outbreak changes throughout the year. Here, we develop and analyze mathematical models for both mosquito population dynamics and …

Strength Imbalances And Shoulder Pain In Manual Wheelchair Users Stratified By Age Of Spinal Cord Injury/Disorder (Sci/D) Onset, Ashlyn M. Jones

Theses and Dissertations

Introduction The majority of manual wheelchair users (MWUs) with spinal cord injury or disorder (SCI/D) develop shoulder pain. In adults with SCI/D, there is evidence that upper limb strength imbalances are associated with shoulder pain. However, strength imbalances may indicate protective compensatory strategies, and other factors may be important contributors to pain. Currently, personalized prevention and management of pain is limited, little is known about joint strength imbalances and pain in children who use manual wheelchairs, and the effect of the age of SCI/D onset is poorly understood. The purpose of this study was to assess the effect of age …

Developing Bioinformatics Expertise Through The Annotation Of The Gut Microbiome Of Odontotaenius Disjunctus, Keidra E. Carter

Theses and Dissertations

Next-generation sequencing (NGS) technologies have revolutionized biological research by generating unprecedented volumes of genomic data, necessitating advanced bioinformatics tools and specialized expertise to fully interpret complex microbial communities. This study outlines an integrated workflow to characterize the gut microbiome of the wood-feeding beetle Odontotaenius disjunctus. Prokka is employed for functional annotation to identify protein-coding genes and other genomic features, while Kaiju is used for taxonomic classification. DIAMOND is then applied to locate and validate the taxonomic assignments generated by Kaiju by aligning sequences within the contigs to a comprehensive protein database, proGenomes. Functional analysis revealed that the contigs encode proteins …

Financial Health Literacy Of Community-Dwelling Older Adults: A Qualitative Research Study, Kimberly Davis

Theses and Dissertations

Background: Financial health literacy (FHL) is an emerging concept with unique application to older adults. Multiple complexities converge in older age that create increased financial vulnerability (e.g., retirement, chronic disease). However, low financial and health literacy are common in older adults, impacting their ability to self-manage. The AWV’s focus on prevention offers an opportunity to incorporate a proactive approach to financial-related assessment. This study will explore the perceived value of assessing FHL in primary care settings and the financial-related barriers and facilitators to implementing the personalized prevention plan.

Methods: The conceptual framework was guided by the Individual and Family Self-Management …

The Role Of Context Sensitivity On The Association Between Racial Discrimination And Emotional Dysfunction Among Black American Adolescents, Summer C. Bryant

Theses and Dissertations

Black adolescents are at an increased risk of experiencing racial discrimination due to a developmental period marked by increased time away from parents and caregivers and increased time with peers (Fisher et al., 2000). Empirical research has shown that Black adolescents’ experiences of racial discrimination are associated with emotion dysfunction (Benner et al., 2018; Seaton et al., 2009; Sellers et al., 2006). Although previous research has identified racial factors such as racial socialization and racial identity as protective factors by reducing the impact of racial discrimination on Black adolescents’ emotion dysfunction (Gibson et al., 2021; Neblett et al., 2008), we …

Swarming Segregation: Leveraging Swarm Intelligence And Regionalization As Instruments For School District Desegregation, Jeffrey Wooten

Theses and Dissertations

Even after Brown led to the South briefly having the most diverse schools in the nation, schools throughout the Northeast have remained the most segregated in the nation for decades. While federal jurisprudence has made compelling desegregation pursuant to the Equal Protection Clause more challenging, New Jersey has a particularly favorable landscape to address severe segregation. With a highly diverse, densely populated public enrollment, favorable state constitutional precedent, and a history of successfully compelling desegregation, New Jersey is fertile ground exploring regional desegregation. Scholars, judges, and even plaintiffs in ongoing litigation (Latino Action Network v. N.J.) have called for New …

The Art Belongs To The Artists, Deborah M. Weissman, Louis A. Pérez

Faculty Publications

This Article examines the rights of detainees interned at the Guantánamo Bay Naval Station to claim ownership of cultural work produced during their imprisonment. Through a series of arbitrary policies, the U.S. government alternately punished detainees for creating works of art, confiscated paintings and drawings, and otherwise denied detainees’ rights to control their creative works. This Article suggests the need to understand these policies as acts akin to plunder—that is, as a practice long associated with colonialism as a means through which the artifacts of the material culture of conquered peoples were expropriated and claimed as “trophies” of conquest. It …

More Information Or More Frequent Information? A Proposal For Quarterly 1099s, Kathleen Delaney Thomas

Faculty Publications

Third-party information reporting enhances tax compliance. When substantial information reporting is present, the compliance rate reaches 94 percent, compared to just 45 percent when there is little or no information reporting. Accordingly, policymakers have expanded information reporting requirements over the past several decades to enhance revenue collection. More recently, Congress has expanded information reporting requirements for third-party settlement organizations (“TPSOs”) by significantly lowering the reporting threshold from $20,000 to $600 as well as eliminating the requirement for 200 or more transactions. While such a shift will subject more taxpayers to information reporting, it will also create additional burden on the …

Suspending The Truancy Paradigm, Barbara A. Fedders, Lucy Carlson, Max Parker

Faculty Publications

In the aftermath of the COVID-19 pandemic, school absences have skyrocketed. While racially minoritized, disabled, and low-income students have historically been, and remain, most likely to experience absence, white and affluent students’ rates of attendance have also declined. To respond to this new universality of student absenteeism, some policymakers have begun to seek alternatives to what we term “the truancy paradigm.”

We define the truancy paradigm as the range of coercive and often punitive interventions deployed by states and school districts to enforce compulsory attendance statutes. This paradigm, we argue, wrongly assumes (a) that strict enforcement of compulsory attendance laws …

Using Preformed Particle Gels To Control Transport In Geothermal Reservoirs: Mathematical Modeling, Philip Winterfeld, Baojun Bai, Yu Shu Wu

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

We are developing swellable Preformed Particle Gels (PPG), which can control preferential fluid and heat flow through fracture networks to increase the performance of EGS reservoirs. Part of this development is a mathematical model and numerical simulator to simulate PPG treatments by considering coupled thermal-hydraulic-mechanical effects, and gel swelling kinetics and plugging efficiency, from which an optimized gel treatment design and operation can be achieved. The starting point for our mathematical model is the TOUGH2-CSM formulation and code. The TOUGH2-CSM fluid and heat flow formulation is based on the TOUGH2 one for multiphase, multicomponent, and multi-porosity systems, with the latter …

Predictive Modeling For Optimal Gel Treatment Design In Brownfields Using Ensemble Machine Learning And Data Upsampling Via Generative Ai, Munqith Aldhaheri, Baojun Bai, Mingzhen Wei

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Efficiently designed gel treatments play a vital role in extending the lifespan of brownfields through rejuvenating oil production. Recently, a three-mode mathematical methodology named the VCR approach has been proposed for designing effective treatments. To optimize this approach, it is crucial to determine the appropriate design mode systematically rather than relying solely on the intuitive judgments of field operators. This study introduces an advanced methodology for predicting the optimal design type of gel treatments using 12 reservoir and production variables. The methodology integrates ensemble machine-learning (EML) models with historical data from 65 field projects across 11 countries (1985-2020). The Random …

Identifying Potential Risk Areas Close To The Oil And Gas Pipelines Due To Subsidence In Qazvin Plain, Mahmoud Rajabi, Sanaz Vajedian, Ryan Smith, Neil Grigg, Hossein Nahavandchi, Mehdi Goli

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Surface displacement caused by natural and anthropogenic activities poses a significant risk to subsurface pipelines, particularly in areas experiencing subsidence. Stress and strain induced by deformation can lead to pipeline buckling and potential vulnerability. This study applies a multidisciplinary approach integrating interferometric synthetic aperture radar (InSAR) deformation analysis, well data, and geological context to assess the risk to oil and gas pipelines in Iran's Qazvin plain. The focus is on evaluating the impact of an unconfined aquifer, which has a lower risk of subsidence compared to a confined aquifer, on pipeline infrastructure. We analyzed multitemporal Sentinel-1 data collected between 2014 …

Individual Design Task Final Report Security Design, Ciarrah Bell

Honors Academy

"The Environmental Services Campus project is a comprehensive development designed to support the City of Springfield’s Environmental Services operations, with a focus on functionality, sustainability, and safety. The campus includes administrative office space, staff parking, a maintenance vehicle garage, and educational facilities aimed at community outreach. A component of the project is establishing site-wide security that not only protects personnel and assets but also integrates seamlessly with the architectural and environmental goals of the facility.

The primary focus of the Security IDT is the development and implementation of a comprehensive security strategy for the entire site. This includes designing and …

The Effects Of Explicit And Systematic Phonics Instruction On Student Achievement, Teagan Dougherty

Masters Theses

The purpose of this study was to examine how explicit and systematic phonics instruction impacts student achievement, and to explore how instructional strategies are effectively implemented in the classroom. To guide the study, two research questions were developed: (1) How does explicit and systematic phonics instruction impact student achievement in vowel teams and r-controlled vowels? (2) What are teacher perceptions of explicit phonics instruction and how are they implemented in the classroom? This was a mixed-methods study. Data was collected from 18 second-grade students and one classroom teacher. Quantitative data was gathered using weekly pre and posttests addressing various phonics …

Enhancing Sunflower Regeneration: Molecular And Genetic Insights From Helianthus Eggertii, Owen West

Masters Theses

In vitro plant regeneration, particularly through organogenesis and somatic embryogenesis, is essential for plant transformation and crop improvement, especially in recalcitrant species like sunflower. In this study, we explore the genetic and molecular mechanisms underlying regeneration in Helianthus eggertii, a wild sunflower species with high regeneration potential. Global gene expression profiling, conducted using Oxford Nanopore sequencing across multiple time points and genotypes, identified sixty-three core differentially expressed genes (DEGs) critical to regeneration. These DEGs are associated with critical biological processes such as cell proliferation, transcriptional regulation, and photosynthesis. Among them, a sunflower WUSCHEL-related homeobox transcription factor (WOX4) showed preferential expression …

Spatiotemporal Variability In Invasive Carp Spawning Activity In Two Midwestern River Basins, Braden A. Whisler

Masters Theses

Across the United States, fisheries managers and agencies continue to battle the spread of invasive bigheaded carp (Hypophthalmichthys spp.). Although previous research has identified environmental parameters such as temperature and flow to be triggers of spawning activity, many of these studies focus on larger rivers, rarely focusing on the specific thresholds or timing of when a spawning event takes place. I utilized the differing hydrology of the Illinois and Wabash Rivers and their tributaries to examine the differences in environmental parameters needed to trigger bigheaded carp reproduction. Three mainstem sites and three tributaries of both basins were sampled …

Assessing Ecological And Food Web Responses To Small-Scale Stream Restorations In Urban And Agricultural Streams, Sydney Mcandrews

Masters Theses

Urban and agricultural streams across the Midwestern United States are vulnerable to elevated pollution, eutrophication, habitat simplification, and losses of sensitive species. Instream habitat restoration is increasingly used to mitigate the impacts of rapid land-use change. This study synthesizes habitat and biological responses from a 2020 urban stream restoration in the Saline Branch (Urbana, Illinois) and evaluates food web responses from both the Saline Branch and a 2010 restoration in Kickapoo Creek (Charleston, Illinois), an agricultural stream. In the Saline Branch, four years of fish and three years of habitat and macroinvertebrate pre-restoration surveys were compared to three years of …

Sustaining Substance Use Recovery Housing For People Taking Medications For Opioid Use Disorder: Diverse Funding, Strategic Partnerships, And Charging Rent, I Niles Zoschke, Kathryn R Gallardo, Danielle Gillespie, Hannah L N Stewart, Serena A Rodriguez, Sheryl A Mccurdy, J Michael Wilkerson

Faculty, Staff and Student Publications

Introduction: Opioid use disorder is a U.S. epidemic, and recovery housing plays a critical role by providing stable, supportive environments that promote long-term recovery. However, little is known about the sustainability of recovery homes, particularly those serving people taking medications for opioid use disorder.

Methods: We applied thematic analysis to interviews with 29 staff and operators from 10 recovery homes serving people taking medications for opioid use disorder across five Texas cities.

Results: Operators relied on diverse funding sources, leveraged strategic partnerships and professional certifications, and planned to charge rent when public funding ended. Staff and operators balanced financial sustainability …

Prediction Of Preterm Birth Among Infants With Orofacial Cleft Defects, Katherine L Ludorf, Renata H Benjamin, Mark A Canfield, Michael D Swartz, A J Agopian

Faculty, Staff and Student Publications

Objective: To develop risk prediction models for preterm birth among infants with orofacial clefts.

Design: Data from the Texas Birth Defects Registry for infants with orofacial clefts born between 1999-2014 were used to develop preterm birth predictive models. Logistic regression was used to consider maternal and infant characteristics, and internal validation of the final model was performed using bootstrapping methods. The area under the curve (AUC) statistic was generated to assess model performance, and separate predictive models were built and validated for infants with cleft lip and cleft palate alone. Several secondary analyses were conducted among subgroups of interest.

Setting: …

Corrigendum: Phenotypic Variation In Disease Severity Among Hospitalized Pediatric Patients With Covid-19: Assessing The Impact Of Covid-19 In The Epico Study, María Camila Sossa-Alarcón, Mónica Paola Gutiérrez, Natalia Becerra, Luz Yessenia Ortegon, María Camila David, Melisa Naranjo Vanegas, Gabriela Friedrich, Pablo Vásquez-Hoyos, María Lucía Mesa-Rubio, Luis Miguel Navarro-Ramirez, Sergio Moreno-Lopez, Olga Lucía Baquero, Luz Marina Mejía, Juan Gabriel Piñeros, Sonia Restrepo-Gualteros, Carlos Álvarez-Moreno, Alejandro Díaz-Díaz, Iván Gutierrez-Tobar, Andrés Camilo Mesa, William Ricardo Bachiller Tuta, Clara Esperanza Galvis Diaz, Martha Africano, José Manuel Nieto, Paola Marsela Pérez Camacho, Claudia Beltrán-Arroyave, Rosalba Vivas Trochez, Irati Gastesi, Cinta Moraleda, Alfredo Tagarro García, Blanca Herrero, Lourdes Calleja, Carlos Grasa, Paula Rodriguez, Susana Melendo, Antoni Soriano-Arandes, Irene Gómez Pastrana, Sonsoles García García, Victoria Fumado, Andrea Ramírez Varela

Faculty, Staff and Student Publications

This corrects the article "Phenotypic Variation in Disease Severity Among Hospitalized Pediatric Patients With COVID-19: Assessing the Impact of COVID-19 in the EPICO Study", 1607246.