Digital Commons Network^™

Patient Violence In The Emergency Department : The Potential Role Of Endogenous And Exogenous Factors, Laura Baker Graham

Dissertations

Patient Violence against nurses is a widespread problem resulting in both emotional and physical injury to the nurse. Emergency Department (ED) nurses are at an increased risk due to the volume and variety of the patients they serve, and the general chaotic environment of the ED; however, little research has been done examining the characteristics of patients who offend and the physical environment of the ED where the event happened. The aim of this three-article dissertation was to develop a more thorough understanding of the personal attributes (endogenous) of the individual patient and external (exogenous) factors of the emergency department …

Insights Into Female Urinary Microbiota Through Long-Read 16s Rrna Sequencing, Jerrin John

Dissertations

The human urinary microbiome—once thought to be sterile—is now recognized as a dynamic, low-biomass microbial community with potential implications for urinary tract health. Conventional short-read 16S rRNA gene sequencing targeting individual variable regions often lacks the taxonomic resolution needed to distinguish closely related species, while culture-based methods may miss fastidious or low-abundance taxa. We applied full-length 16S rRNA gene sequencing across all nine variable regions to daily urine samples collected from asymptomatic premenopausal female participants. Sequence data were processed with a modified DADA2 pipeline optimized for long reads to generate exact sequence variants. We compared species-level community profiles against both …

Including Conscientiously: How Charter School Educators Experience Inclusion Education Implementation, Joe A. Petty

Dissertations

This narrative inquiry examined how charter school educators experience inclusive education implementation while confronting ableist systems that maintain exclusion through seemingly neutral practices. This research emerged from my lived experience of how educational structures systematically marginalize disabled students while appearing progressive. The study investigated two research questions: how support structures and leadership practices either perpetuate or dismantle ableist assumptions embedded in educational practice, and how educators negotiate tensions between implementing evidence-based inclusive strategies and addressing environmental factors that create the need for those strategies.

Data collection employed semistructured interviews with eight credentialed educators across two Southern California charter school sites, …

Predictors Of General Education Teachers' Self-Efficacy For Educating Autistic Students: Enactive Mastery Experiences, Vicarious Experiences, Verbal/Social Persuasions, And Physiological And Affective States, Renette Portecop-Prentice

Dissertations

Problem

Autism is a complex neurodevelopmental condition that presents challenges not only for autistic individuals, but also for their families, healthcare providers and school professionals. A significant number of children with autism spend most of their school day in general education classrooms with teachers who may lack autism-specific training and are unfamiliar with evidence-based practices for supporting autistic students. This lack of training or relevant resources specific to autism may impact teacher self-efficacy for educating autistic students, which in turn may affect instructional decisions and student outcomes. Guided by Bandura’s theoretical framework, this study examined the relationships among autism-specific training …

Statistical Approaches In Evolutionary Biology: Using Threespine Stickleback Fish To Test Fisher's Geometric Model And Evaluate Methods For Handling Missing Data, Aaron Mathew Myrold

Dissertations

This thesis explores two distinct yet complementary aspects of evolutionary biology. The first chapter tests predictions from Fisher's geometric model of adaptation using a finely resolved fossil sequence of Gasterosteus doryssus spanning approximately 21,250 years. I analyze phenotypic changes in three armor traits during adaptation to a new environment and find that while step sizes follow the predicted exponential distribution—with many small steps and few large ones—they do not adhere to the model's temporal prediction that large-effect mutations should fix early in the adaptive walk. This discrepancy likely reflects adaptation from standing genetic variation rather than de novo mutation. The …

Genetic Architecture Of Complex Traits In African Ancestries Across Diverse Environments, Isadore Gregga

Dissertations

Given genetic and environmental diversity, genetic prediction based on African- ancestries individuals in the US or UK may not transfer well to other African diaspora regions. The Modeling the Epidemiological Transition Study (METS) is a longitudinal study of cardiometabolic health in five African-ancestry populations. We performed genome-wide genotyping in METS participants from the US, Jamaica, South Africa, and Ghana. We aimed to explore how genetic models for the transcriptome and body mass index (BMI) built using US- based African-ancestries populations perform in these four diverse populations. A subset of METS participants also had whole blood RNA-Seq data. For these, we …

Characterizing Niche Specialization In Staphylococcus Epidermidis, Sandra Jablonsk

Dissertations

This thesis investigates the microbial diversity of Staphylococcus epidermidis (S. epidermidis) across various anatomical sites in the human body. While traditionally viewed as a benign skin microbe, S. epidermidis also inhabits the urinary, gastrointestinal, and respiratory tracts, raising questions about its genetic variation and adaptability in different environments. The research aims to compare strains of S. epidermidis isolated from the oral cavity, nostrils, urinary tract, and skin of healthy individuals to determine if they share a common ancestor or if they evolved independently in response to specific environmental factors. The study comprises three main aims. Aim 1 focuses on assessing …

Insights On The Cranial Anatomy And Osteohistology Of Cyonosaurus, Alexander Acker

Dissertations

This study investigates the cranial anatomy and life history of the small-bodied gorgonopsian Cyonosaurus. Previous research on gorgonopsians has disproportionately focused on larger members of the clade, leaving smaller forms relatively understudied. This gap has led to several unresolved questions, the most pressing of which concerns gorgonopsian ontogeny. Specifically, it remains unclear whether small-bodied gorgonopsians represent genuinely diminutive adult individuals or juveniles of larger species. The specimen NHCC LB1087 presents an ideal opportunity to address this issue and gain new insights into the biology of small-bodied gorgonopsians. The first chapter focuses on cranial anatomy. Due to the specimen’s preservation, many …

Interactions Between Microplastics, Biofilms, And Antimicrobials In Freshwater Streams, Ryan Thomas Krantz

Dissertations

Microplastics (MPs) are ubiquitous contaminants in freshwater ecosystems that could be hotspots for the interaction of antimicrobial compounds and surface-attached microbial biofilm communities. MPs and antimicrobials are both common in wastewater and urban freshwaters and MPs can adsorb contaminants like antimicrobials to their surface. Within aquatic habitats, MPs also support colonization by microbial biofilms. Therefore, we hypothesized that the adsorption of antimicrobials to MP surfaces would affect microbial communities colonizing MPs, altering their diversity, composition, and antimicrobial resistance. We investigated the effects of these interactions across two studies. The first study, discussed in Chapter 2, used a microcosm approach to …

Toward Measurable Explainable Ethical Ai: An Llm-Driven Data Analytics Study, Greg Bacon

Dissertations

Large Language Models (LLMs) have been a hot area for popular and research audiences. Users marvel subjectively at Artificial Intelligence (AI) outputs — so much that OpenAI delayed public release of Generative Pre-trained Transformer 2 (GPT-2) back in 2019, citing ``safety and security concerns.'' This research advances ethical and transparent AI through qualitative and quantitative measures between user intent and LLM responses in a way that aims to assist users with clear indications of good and poor alignment and of where to backtrack to minimize bias and hallucinations. The use case is recommending grant topics in a United States Department …

Novel Ai/Ml-Based Frameworks For Protein Conformation Selection In Drug Discovery Applications, Shivangi Gupta

Dissertations

Drug development is a lengthy, expensive process with a high failure rate. The urgency brought on by the COVID-19 pandemic has accelerated the integration of artificial intelligence (AI) and machine learning (ML) to enhance drug discovery by increasing target specificity, reducing toxicity, and optimizing formulation strategies. Building on this momentum, this dissertation introduces novel AI/ML-driven frameworks for protein conformation selection and classification, addressing critical challenges in modern drug discovery. However, designing such a novel AI/ML data-driven framework is a difficult task because most real-world biomedical datasets suffer from class imbalance issues, which can significantly skew AI/ML model training, resulting in …

Manganism And The Development Of A Green Sustainable Low-Threshold Spectrophotometric Test For The Monitoring Of Manganese In Consumable Water, Anna Merritt Holmes

Dissertations

Manganism, a neurotoxic disease from the hyperaccumulation of manganese, follows an etiology that parallels Parkinsonism. Non-occupational Manganism is acquired by the lifelong accumulation of manganese through water contaminated by natural and industrial sources. Biologically active manganese (II) eludes flocculation and filtration removal methods at water utilities. The U.S. Standard Methods For the Examination of Water and Wastewater persulfate testing method uses mercury sulfate, concentrated nitric and phosphoric acids, silver nitrate, and ammonium persulfate. The low detection limit of 210 µg/L is an order of magnitude greater than the World Health Organization (WHO) allowable limit of 10-50 µg/L. In 2004, the …

Design And Synthesis Of Crosslinkable Amphiphilic Pegylated Poly(Amino Acid) Copolymers For Spion Encapsulation, Adekunle Titus Akinmola

Dissertations

The development of polymeric micelles for biomedical applications has been of significant interest due to their potential for targeted delivery for therapeutic and diagnostic agents. This dissertation focusses on the synthesis, characterization, and application of amphiphilic PEGylated poly(amino acid) block copolymers as nanocarriers for superparamagnetic iron oxide nanoparticles (SPIONs) in magnetic particle imaging (MPI). Series of novel diblock and triblock copolymers were synthesized through ring-opening polymerization of amino acid N-Carboxyanhydrides (NCAs) to afford HO-PEG77-b-p(L-Leu)m and HO-PEGx-b-p(Allyl-L-Gly)10-b-p(L-Leu)n. These polymers were further functionalized to yield their folate conjugates through dicyclohexylcarbodiimide (DCC) coupling. NMR and FTIR were used to verify the chemical structures …

Evolution Of Bacteria: The Subsequent Relationships Between Different Species And Their Hosts, Helen Appleberry

Dissertations

To explore the relationship between two recently identified bacterial species (S. anginosus and S. urinae), three aims were designed. First, niche ranges were identified via two metagenome databases. Different niche ranges were identified between the two groups. S. urinae was more specific to the urogenital tract. S. anginosus appeared to be present across human anatomical niches. Secondly, specific genes to the S. urinae group were identified. This gives insight into the genomic and phenotypic differences previously identified. Thirdly, a temporal study was created to view S. urinae in female urine over 8 weeks. This showed stability in the urinary microbiome …

Analyzing The Population Structure Of The Rhizobia Associated With Astragalus Lentiginosus, Joshua Adam Melnick

Dissertations

Legumes are an incredibly diverse and agriculturally important family of plants. They have a special relationship with symbiotic bacteria known as rhizobia which fix nitrogen into ammonia within nodules on their roots. Astragalus is the largest plant genus on Earth, and the species Astragalus lentiginosus is extraordinarily diverse, consisting of approximately 40 varieties. However, the rhizobia of A. lentiginosus have never been studied. In this study, root nodules were extracted from 17 varieties of A. lentiginosus to obtain rhizobial strains and metagenomes. A. lentiginosus primarily associates with rhizobia from the genera Mesorhizobium and Allomesorhizobium. There was little evidence of horizontal …

Exploring The Ecological Relevance Of Biotic And Abiotic Stressors In Structuring Legume Microbial Communities, Cian Dotson

Dissertations

Heavy metal hyperaccumulation is prevalent throughout plant evolution, particularly in the legume family (Fabaceae), and acts as a presumed chemical defense against herbivory. However, heavy metal hyperaccumulation can have non-target impacts on other biological interactors including plant-microbe interactions. This information is important given the interest in utilizing hyperaccumulating plants for phytoremediation of anthropogenically contaminated soils. Here we employ a greenhouse experiment manipulating selenium level along with 16S rRNA gene amplicon sequencing methods to explore the effect of selenium on the prokaryotic microbiome of the selenium hyperaccumulator Astragalus crotalariae and non-accumulator Astragalus lentiginosus var. borreganus. Regardless of hyperaccumulator status, both plant …

Deciphering The Source Of Escherichia Coli In Urinary Tract Infections: A Comparative Metagenomic Analysis Of The Female Urogenital Microbiome, Alexis Annabel Avalos

Dissertations

In 2019, there was a 140.19% increase in deaths due to urinary tract infections (UTIs) compared to 1990, worldwide. One of the common uropathogens known to associate with UTIs in females is Escherichia coli. The prevailing belief is that E. coli in the bladder originates in the rectum, passing its way from the perineal, to the vagina, and finally into the bladder. Known as the Fecal-Perineal-Urethral (FPU) hypothesis, this “origin story” has been supported by several studies that have relied on genotyping or serotyping isolates collected from the bladder and rectum. Most notably, culturing isolates from samples has been central …

Selecting For Lysis In A Temperate Phage Population, Haley Atkins

Dissertations

The ongoing evolutionary arms race between bacteria and bacteriophages (phages) is a prime example of Red Queen hypothesis, where continuous adaptation drives survival. This study focuses on Escherichia coli-infecting temperate phages, which dominate natural environments and contribute to bacterial resistance mechanisms. Despite their prevalence, temperate phages are less suited for phage therapy due to their lysogenic life cycle, where they integrate into bacterial genomes instead of lysing the host. In contrast, obligately lytic phages, which directly lyse bacterial cells, are ideal for therapeutic use but occur less frequently in nature. This research aims to select for lytic behavior in temperate …

Refining Cross-Population Polygenic Risk Scores Across Diverse Populations, Mansi Patel

Dissertations

Large biobanks containing whole genome sequences connected to the deidentified electronic health records of hundreds of thousands of individuals are increasingly available to researchers. This has facilitated the development of polygenic risk scores (PRS), which use machine learning to predict risk of disease and other phenotypes from millions of genetic variants. Due to Eurocentricity of available genetic data, PRS have primarily been trained in populations of European descent. Differences in allele frequencies, effect sizes, and linkage disequilibrium patterns between populations can limit the transferability of PRS across different populations. Given that most data are from European genetic ancestry populations, we …

The Impact Of Lactobacillus Supplementation On Gut Microbiome Composition And Phage Induction In Mice, Kimia Boreiri

Dissertations

The mammalian gastrointestinal (GI) tract harbors a dense and dynamic community of microbes known as the gut microbiota, which plays vital roles in digestion, immunity, and overall health. Among these, probiotic bacteria such as Lactobacillus strains have garnered attention for their ability to influence microbial community structure and host physiology. This study investigated the effects of five Lactobacillus strains, Lactobacillus casei R1A482, Lactobacillus casei O3, Lactobacillus rhamnosus GG, Lactobacillus gasseri ATCC 33323, and Lactobacillus paragasseri UMB1065, on the gut microbiome of Swiss Webster mice over a six-week feeding period. To reduce stress, mice were fed Lactobacillus strains using gelatin pellets …

Decoding The Origins Of Infection: A Machine Learning Framework, Nirupama G. Shanbhag

Dissertations

Many infections can be attributed to a specific microorganism. For example, while there can be many causes of urinary tract infections (UTIs), such as the bacterial species Klebsiella pneumoniae or Enterococcus sp., the most widespread cause for UTIs is uropathogenic Escherichia coli. Generally, diseases or infections that are the result of a single pathogenic organism are more easily understood. Other diseases, such as irritable bowel disease (IBD), cannot be attributed to one member in the community; rather, it is a result of dysbiosis of the microbial community (microbiota) of the gastrointestinal tract, a combination of an overgrowth of problematic members …

Role Of Coronavirus Envelope Protein On Infectivity, Garrett E. Zaagman

Dissertations

Coronaviruses infect a wide range of hosts and have caused recent human pandemics. While much has been learned, gaps remain in understanding viral assembly and egress, particularly the role of the envelope (E) protein in specific infectivity. To study this, recombinant MHV viruses were created with E gene deletions and HiBiT-tagged spike (S) proteins to monitor virion release. In mouse cells, MHV∆E S-HiBiT secreted less spike and fewer infectious particles, indicating reduced specific infectivity. Comparisons between human HeLa-CEACAM and mouse DBT cells showed species-specific support for virus production. TMED10, a host membrane protein, was tested as a potential E-interacting partner …

Anti-Inflamatory Mechansim Of Bacillus Subtilis Derirved Exopolysaccharide, Adrian Taylor Ibarra

Dissertations

Exopolysaccharides (EPS) secreted by the commensal bacterium Bacillus subtilis exhibit potent anti-inflammatory properties, yet the underlying molecular mechanisms remain incompletely understood. We hypothesized that EPS reprograms antigen-presenting cells toward a tolerogenic state by modulating TLR4–MyD88 signaling. To test this, we began using a chemically defined, high-yield EPS production and purification protocol that largely eliminates protein and DNA contaminants, thus improving functional reproducibility across experiments using this new method. In vitro, EPS engaged TLR4 on murine dendritic cells (DC2.4) without inducing classical NF-κB activation, seen by LPS stimulation. Rather, EPS treatment upregulated inhibitory molecules, PD-L1 and PD-L2 while leaving activation markers, …

Investigating The Mechanism Of Resistance To Ido1 Enzyme Inhibitor Treatment In Human Glioblastoma, Kyla Shivakumar Hatton

Dissertations

Glioblastoma (GBM) is the most common and most aggressive form of adult cancer in the central nervous system, with GBM accounting for the majority of all malignant brain tumors. GBM is currently considered to be an incurable form of cancer, with over 14,000 patients diagnosed in the United States last year. Given the success of immunotherapy for treating other types of cancer, our group has investigated the possibility of therapeutically neutralizing immunosuppressive indoleamine 2,3 dioxygenase 1 (IDO1) in patients with GBM. Canonically, IDO1 is an immunosuppressive cytoplasmic enzyme that catalyzes the first step in metabolizing L-tryptophan into L-kynurenine (ie. ↓L-Trp→↑L-Kyn). …

Developing Chemically Defined Serum-Free Medium For Leukemic Blast And Stem Cell Expansion, Carmen Eva Finley

Dissertations

The relapse and chemotherapy resistance are the major challenges of acute myeloid leukemia (AML) treatment, driven by a rare population of leukemia stem cells (LSCs). LSCs are unique types of cells which evade standard chemotherapies and can regenerate AML post-treatment. Targeting LSC therapy remains limited, in part due to the lack of reliable in vitro AML culture systems to grow LSCs for drug discovery. This study aimed to engineer a chemically defined, serum-free 2D in vitro culture condition that supports either the expansion of leukemic blasts (LBs) or primary human LSCs by optimizing current protocols for hematopoietic stem cells (HSCs) …

Investigating Whether Txnrd2 Is A Therapeutic Target Against Triple Negative Breast Cancer Using African American-Derived Models, Keacha Chang

Dissertations

Despite similar breast cancer incidence rates, African American (AA) women experience a 40% higher mortality rate compared to Caucasian American (CA) women. This disparity is multifactorial and particularly pronounced in the Chicago area. AA women are twice as likely to be diagnosed with triple-negative breast cancer (TNBC), often at a younger age and with more aggressive disease. TNBC is a heterogeneous subtype lacking targeted therapies and is associated with the poorest prognosis among breast cancer types. Therefore, there is an urgent need for novel therapeutic strategies for TNBC, especially those tailored to AA patients. The thioredoxin pathway is essential for …

Capturing Diverse Adolescents’ Social Contexts: The Development Of An Ethnic-Racial Microaffirmations Scale For Peer Interactions, Maria Radulescu

Dissertations

The development of a strong and positive sense of ethnic-racial identity (ERI) has been identified as an asset for ethnically and racially marginalized adolescents. Peer interactions during the adolescent years can support ERI development. In particular, a subtle micro-level form of peer support—microaffirmations—may be protective for ERI processes. However, the field of microaffirmations is very small, and there is no scale that captures adolescents’ experiences of ethnic-racial microaffirmations from their peers. The current study developed an ethnic-racial peer microaffirmations scale based on extant literature and feedback from 4 focus groups with 22 sophomore high school students. Findings indicated that 5 …

“What’S Happening In The Gulf Of Maine?”: Middle School Students’ Engagement In Climate Science Through Data Visual Representation And Reflections, Grace Ocular

Dissertations

This study examined how middle school students engaged with science concepts while working with data visualizations during a field trip learning experience. Fifty-one teams of 2–4 students from 35 schools participating in the LabVenture program were video- and audio-recorded. Students completed two activities: one using a frequency table of marine species illustrating threats to Maine’s lobster population, and another using maps depicting changes in Gulf of Maine sea surface temperature. After each activity, students annotated the visualization, discussed their claims, and recorded short reflections. Transcripts were coded for science-related talk, and annotations and gestures were also analyzed. Findings indicate that …

The Bacterial Sensing Nuclear-Oligomerization Domain 2 Receptor In The Brain: Location And Potential Function, Julia Smyth

Dissertations

Nucleotide-binding oligomerization domain-2 (NOD2) is a cytosolic receptor, activated by bacterial peptides that initiates innate immune responses through nuclear factor-κB (NF-κB), mitogen-activated protein kinase (MAPK), and Caspase-1 pathways. While the role of NOD2 in inflammation outside the central nervous system (CNS) is well-established, especially in the gastrointestinal system, its expression and function in the brain remain poorly defined. Previous genetic studies suggest a link between NOD2 and neurological and psychiatric conditions, including stroke, Parkinson’s disease, and schizophrenia. However, information regarding NOD2 expression, localization, and function in the CNS is limited. In this work, we investigated NOD2 expression, localization, and regulation …

Evaluation Of Bacteriophage Infection Of Enterococcus Faecalis In A Monolayer, Alexandria Osborn

Dissertations

Enterococcus faecalis is one of the first colonizers of the human gastrointestinal tract, and it plays a role in the intestinal immune development at the very early stages of life. However, it is also an opportunistic pathogen, capable of translocating across the mucosal barrier to cause systemic infections. E. faecalis is also linked to infections including endocarditis, recurrent urinary tract infections (rUTIs), bacteremia, wound infections, meningitis, root canal infections, intra-abdominal and pelvic infections, and septicemia. Persistent enterococcal opportunistic infections have been associated with the production of virulence factors and sharing of antibiotic resistance genes, thus making E. faecalis difficult to …