Digital Commons Network^™

Granulomatous Cellular Signatures In Nontuberculous And Tuberculous Mycobacterial Infections, Brianna M. Doratt, Ethan G. Napier, Mahdi Eskandarian Boroujeni, Sarah Douglas, Michael H. Davies, Luiz Bermudez, Eliot Spindel, Erin F. Mccaffrey, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Mycobacterium tuberculosis (Mtb) and nontuberculous mycobacteria (NTM) are acid-fast bacilli that trigger granuloma formation, a hallmark immune response aimed at containing infection. While the biology of Mtb granulomas has been widely investigated, far less is known about granulomas caused by NTM infection, despite the increasing prevalence and clinical challenge of NTM cases worldwide. Because granulomas influence infection control, pathology, and treatment response, understanding their cellular organization and signaling is critical to improving therapeutic strategies. Therefore, we characterized granulomas formed following infection of rhesus macaques with Mycobacterium avium subsp. hominissuis (MAH) and compared them to granulomas from cynomolgus macaques infected with …

Inpatient Stroke Quality Improvement, Briyawna N. Wyatt

Doctor of Nursing Practice (DNP) Scholarly Projects - Archive

Inpatient nursing documentation for stroke care is essential for meeting quality metrics, maintaining continuity, and supporting timely decisions. Gaps can lead to inconsistent care, metric failures, and reduced staff confidence. This quality improvement initiative aimed to improve metric compliance, documentation consistency, and nursing knowledge and satisfaction. A three-part intervention included targeted education, a standardized documentation verification form, and ongoing feedback from stroke champions. Outcomes measured were metric compliance, knowledge (pre/posttests), documentation completeness (Venous Thromboembolism (VTE), education, Modified Rankin Scale), and staff satisfaction. Results showed significant improvement in nursing knowledge (p < .005), reduced metric fallouts, and better documentation across all indicators. Staff satisfaction increased by about 20%. Overall, combining education, standardized tools, and continuous feedback improved documentation practices, enhanced compliance with stroke metrics, and increased nursing knowledge and satisfaction, supporting better care processes and patient outcomes.

Role Of Estrogen Receptor Alpha In Modulating The Circadian System In Female Mice, Victoria Alvord

Theses and Dissertations--Biology

Circadian rhythms are approximately 24-hour cycles of physiology and behavior. Circadian rhythms of eating, or meal timing, are linked to cardiometabolic dysfunction in humans. Mistimed eating, such as breakfast skipping and eating late at night, increases the risk of obesity, diabetes, and cardiovascular disease in humans. Likewise, disrupted eating rhythms cause obesity in mice. This dissertation investigates how estrogens regulate eating behavior rhythms and tissue clock timing in female mice. Chapter 1 reviews three key components critical to this work. The first is an overview of the field of chronobiology and the function of the circadian system. The second is …

The Rhesus Macaque Model Of Mycobacterium Avium Infection Reveals That Age-Related Disease Is Due In Part To Chronic Inflammation And Lung Microbial Dysbiosis, Ethan G. Napier

Theses and Dissertations--Microbiology, Immunology, and Molecular Genetics

Aging is associated with dysregulated immunity and increased susceptibility to infection, a phenomenon dubbed as immunosenescence and characterized by reduced naïve T and B cell pools, altered innate immune function, and chronic low-grade inflammation. Nontuberculous mycobacterial (NTM) pulmonary disease (NTMPD) is an increasingly relevant chronic lung infection that disproportionately affects older adults (65+ years) and immunocompromised individuals. However, the host factors underlying increased disease severity in aged patients remain poorly defined. Literature suggests that effective control of NTM relies on coordinated innate and adaptive immune responses, particularly macrophage activation and Th1 cytokine signaling. Using a rhesus macaque model that closely …

Metabolism As A Regulator Of Sleep And Cortical Activity In Health And Alzheimer’S Disease, Nicholas J. Constantino

Theses and Dissertations--Neuroscience

Metabolic flexibility is essential for maintaining normal physiological function, enabling an organism to sense, flux, utilize, and switch fuel sources in response to changing energetic availability, demand, and cellular needs. Energetic demands are state-dependent, with wake and sleep exhibiting distinct metabolic profiles. Sleep is highly sensitive to changes in metabolism and requires metabolic flexibility to both transition into and maintain sleep stability. Alzheimer’s disease (AD) is increasingly recognized as a disease of altered metabolism yet is often framed as a disease of energetic failure. We instead define AD as a disease of metabolic inflexibility, characterized not by insufficient energy availability, …

Design And Advancement Of Analytical Frameworks For In Vivo Single-Photon Calcium Imaging To Characterize Temporal- And Treatment-Dependent Neural Adaptations To Opioid Exposure And Withdrawal In The Medial Prefrontal Cortex, Alexia R. Alsum Dr.

Theses and Dissertations--Pharmacy

Despite the availability of several approved medications for opioid use disorder (OUD), it remains a significant public health concern characterized by persistent neurobiological adaptations that drive relapse and impede successful recovery. The medial prefrontal cortex (mPFC), a region critical for executive control and decision-making, undergoes pronounced functional changes during chronic opioid exposure and withdrawal, yet the cellular mechanisms underlying these adaptations remain poorly understood. This dissertation aims to investigate longitudinal alterations in mPFC neural activity across opioid exposure and withdrawal using in vivo single-photon calcium imaging and newly developed computational frameworks.

Following standard preprocessing to extract and normalize calcium traces, …

Molecular Mechanisms And Metabolic Consequences Of Glucocorticoid Resistance, Genesee J. Martinez

Theses and Dissertations--Pharmacology and Nutritional Sciences

Glucocorticoids are vital steroid hormones that govern metabolism, stress responses, and immune functions through intricate, tissue-specific mechanisms, both genomic and non-genomic. These hormones bind to the glucocorticoid receptor (GR), which then acts as a transcription factor to modulate gene expression. Chronic elevation of glucocorticoid levels may lead to glucocorticoid resistance, resulting in adiposity, inflammation, and insulin resistance, thereby adversely affecting multiple metabolic tissues. Whether produced endogenously or administered exogenously, excessive, chronic glucocorticoid concentrations impair glucocorticoid signaling. Although there are two primary isoforms of the receptor, GR⍺ and GRβ, only GR⍺ interacts with glucocorticoids.Through the research conducted in this dissertation, we …

Expanding The Role Of Muscle Stem Cell Fusion In Muscle Under Hypertrophic Stimulus, Jensen Goh Zhong Sheng

Theses and Dissertations--Physiology

Muscle stem cells (MuSCs) are a unique stem cell population that can activate in response to both injury and growth stimuli. Studies on muscle regeneration have shown MuSC activation follows a uniform progression through proliferation, differentiation, and fusion. Therefore, to determine whether MuSC replication is a prerequisite for differentiation under hypertrophic stimulus, I used a lineage-tracking mouse model (Pax7^rtTA; TRE-H2B-GFP) to label MuSC nuclei and simultaneously tracked DNA synthesis via EdU incorporation. This dual-labeling approach allowed us to not only distinguish MuSC-derived nuclei but also demarcate which MuSC had proliferated prior to fusion. I then employed a mechanical …

Managing Dietary Nonstructural Carbohydrates In Insulin Dysregulated Horses: Pasture, Long-Stem Forage, And Restrictive Grazing Strategies, Morgan J. Askins

Theses and Dissertations--Veterinary Science

Insulin dysregulation (ID) is a complex endocrine disorder, impacting a large percentage of the equine population. ID is the defining characteristic of equine metabolic syndrome (EMS). Within the various classifications of EMS horses, the commonality is ID and their higher risk of laminitis. To mitigate insulin response and laminitis risk in ID horses, current management focuses on restricting pasture exposure and feeding low nonstructural carbohydrate (NSC) rations. Minimal studies have evaluated how ID horses respond to pasture of various NSC, long-stem forages, and restrictive grazing strategies. Providing horse owners and managers with improved nutritional management recommendations for ID horses with …

Equid Major Histocompatibility Complex (Mhc) Evolution & Genome Organization, Lauren C. Johnson

Theses and Dissertations--Veterinary Science

The evolution of modern horses has a well-documented fossil record and has long been of interest to the genetics community. Although non-caballine equids (e.g. zebras, donkeys, and asses) can hybridize with horses, the resulting offspring are typically infertile. Despite these reproductive barriers, genomic analyses reveal regions of high sequence similarity among equid species. This dissertation investigates the role of historical introgression in the evolution of modern Equus species. The first chapter re-evaluates earlier findings derived from a limited horse population and a single reference genome. The variants of the identified regions were pushed through Ensembl’s Variant Effect Predictor to assess …

Between The Rails: Experiential Education And Its Impact On Compliance And Consistency In Racetrack Surface Management, Heather Mackenzie

Theses and Dissertations--Community & Leadership Development

Recent regulatory requirements within the Thoroughbred racing industry have increased expectations for consistent collection and reporting of racetrack surface data. Despite clear standards, implementation in daily operations remains inconsistent, highlighting a gap between regulation, knowledge, and practice. This study examined the impact of an experiential education curriculum on racetrack personnel’s self-efficacy and reporting consistency.

Using a quantitative design, data were collected through pre- and post-surveys measuring self-efficacy and records of the number of days surface data were entered. Descriptive statistics, paired-samples t-tests, and effect size analyses were used. Results showed a statistically significant increase in self-efficacy (p < .001) with large effect sizes, indicating meaningful gains in confidence and comfortability. Reporting consistency did not show a statistically significant change (p = .885).

Overall, experiential education …

Understanding Knowledge And Perceptions Of The Beef Industry On A Land-Grant University Campus, Allison E. Reaves

Theses and Dissertations--Community & Leadership Development

A well-researched phenomenon in the agricultural industry is the effects of constant innovation coupled with an increasing divide between producer and consumer. This issue has been presented as especially prevalent within animal agriculture and the beef industry, a predominant concern considering Kentucky’s agricultural commodities. This study (n = 31) utilized a mixed-methods approach to understand the knowledge, perceptions, and behavior of beef consumers on a land-grant university campus. Methodologies included Python’s DeepFace emotion recognition, semi-structured interviews, and the JMALI agricultural literacy assessment. Findings revealed participants to be below expected agricultural literacy levels of high school graduates (M=11), with no …

Non-Invasive Detection Of Intracranial Pressure, Andrei V. Nesterenko

Honors Undergraduate Theses

Intracranial pressure is a critical metric used when managing tumors, strokes, TBIs, hydrocephalus, and other operative conditions. Traditional methods for continuous ICP monitoring, intraparenchymal catheters, epidural transducers etc., are invasive and carry a high risk of infection. Previous attempts to create accurate, easy to use, and non-invasive ICP monitoring techniques have been unsuccessful. In this study, we investigated the utility of supraorbital and posterior auricular photoplethysmography to monitor changes in ICP during orthostatic tilt and hyperventilation, which increase and decrease ICP respectively.

Through a continuous 5-minute recording on a tilt-table we characterized SOA and PAA waveforms in 12 participants (ages …

Adolescent Binge-Like Feeding And Neuroinflammation: Effects Of Intermittent Palatable Diet Access On Microglial Activation In The Brain In Adolescents, Jaimie T. Yu

CMC Senior Theses

Binge eating disorder (BED), one of the most common eating disorders in the United States (Definition & Facts for Binge Eating Disorder - NIDDK, n.d.), is characterized by recurrent episodes of consuming large quantities of food in a short period of time accompanied by a sense of loss of control. The intermittent access (INT) model reliably produces binge-like eating in adult rodents, with animals showing episodic hyperphagia upon time-limited access to a high-fat, high-sugar (HFHS) diet. In adult female rats, INT access produces elevated meal size and reduced satiety ratio relative to controls (Maske et al., 2020), and promotes microglial …

Microbial Community Structure In Global Soils, Matthew Jabro

CMC Senior Theses

Soil harbors the most diverse microbial communities on Earth, yet whether predictable community types exist across biomes and whether taxonomic composition encodes habitat of origin remain open questions at global scale. This thesis addresses both questions by applying unsupervised clustering and supervised classification to transformed 16S ribosomal RNA (rRNA) amplicon profiles from two independent datasets: the global topsoil survey of Bahram et al. (193 samples) and the Earth Microbiome Project (EMP) soil subset of Thompson et al. (2,209 samples). Application of a sample clustering method based on a mixture of Gaussian Graphical Models (MixGGM) identified 19 clusters in the topsoil …

Neuroimaging Correlates Of Differences In Learning From Repeated Probabilistic Outcomes, Allison E. Rudolph

CMC Senior Theses

Learning from experience requires integrating feedback over time, yet individuals vary widely in how effectively they extract structure from probabilistic environments. This study examined how such variability relates to neural responses in the ventral striatum (vStr), caudate nucleus, hippocampus, and medial prefrontal cortex (mPFC). Seventy-four participants across childhood, adolescence, and adulthood completed a modified Iowa Gambling Task during fMRI scanning, choosing whether to play or pass on four machines differing in expected value and variance. Behavioral learning slopes, calculated across six runs for each machine, were used to classify participants as learners or non-learners. Learners showed clearer improvement over time …

Evaluating Soil And Plant Health In A Wide-Row Maize (Zea Mays L.) Production System Integrated With Perennial Cover Crops And Turkey (Meleagris Gallopavo), Sovika Bhattarai

All Graduate Theses, Dissertations, and Other Capstone Projects

In regions dominated by intensive maize (Zea mays L.) production systems, such as the US Midwest, sustainable agricultural practices such as cover crops and livestock integration are gaining interest for their potential to improve soil, plant, and environmental health. Traditionally, annual cover cropping systems (ACCs) have been used to maintain soil quality and crop performance without compromising ecosystem services. However, the high establishment and management costs of ACCs highlight the need for alternative approaches, such as perennial cover crops (PCCs). Grown as companion crops with maize, PCCs provide extended soil cover and can improve soil biochemical properties (e.g., total C …

Investigating Primary Motor Cortex Involvement In Mouse Vocal Communication, Elena N. Duryea Waidmann

Student Theses and Dissertations

Vocal communication is used to transmit a range of information to other individuals. While many vocalizations are innate, some species can learn to change their vocal output. This is termed vocal-learning, and it is a rare trait and a necessary building block for human spoken language and songbird song. Comparative work in humans and songbirds suggests that convergent genetic and neural specializations may drive these learned vocal behaviors. Two key features of these advanced vocal learners are: i) specialized primary motor regions in the forebrain with activity tied to vocalization; and ii) dense monosynaptic projections from the primary motor cortex …

Spatiotemporal Patterns Of Migratory Songbird Habitat Use: An Analysis Of Environmental Drivers At The Net Level, Garrett Kucharski

Dissertations, Master's Theses and Master's Reports

Many eastern North American migratory songbirds are declining at alarming rates, and growing evidence suggests that events occurring away from the breeding grounds, particularly during migration, can be major drivers of these trends. Stopover sites are a key component of migration because they are where birds rest, refuel, and recover before continuing long-distance movements, yet the ecological factors that shape how broadly different species use stopover habitat remain unresolved. From both an applied perspective, identifying habitat attributes associated with use by the greatest diversity of migrants will help land managers prioritize and restore stopover sites, actions that may contribute to …

Fluctuation Of Organochlorine Concentrations In Bull Sharks At Different Life Stages, Mackenzie R. Phillips

Dissertations, Master's Theses and Master's Reports

For Carcharhinid species such as the bull shark (Carcharhinus leucas), the maternal offloading of nutrients is essential for pup development and growth, however, significant amounts of OCs are also transferred. As a top predator in aquatic food webs, bull sharks can potentially bioaccumulate high concentrations of pollutants such as dichloro-diphenyl-trichloroethane (DDT) that biomagnify through aquatic food webs. These pollutants are also hydrophobic and fat soluble and therefore pose toxicity risks to developing young bull sharks. In this study, liver tissues collected from juvenile bull sharks inhabiting Florida’s coastal waters were analyzed for a suite of organochlorine pesticides (OCs) …

Computational And Ai Frameworks For Identifying Key Regulatory Genes And Their Target Genes In Plants And Humans, Md Khairul Islam

Dissertations, Master's Theses and Master's Reports

This dissertation presents computational and AI-driven frameworks for identifying key regulatory genes and their downstream targets across plant and human biological systems. Three studies address distinct challenges in genomic regulation using advanced machine learning and bioinformatics approaches.

The first study introduces DyGAF (Dynamic Gene Attention Focus), a dual-attention transformer framework that identifies and ranks disease-relevant biomarker genes by simultaneously modeling independent molecular responses and interdependent regulatory network behavior. Two attention models provide complementary perspectives on gene importance and are fused through a novel combination metric. Applied to COVID-19 nasopharyngeal swab profiles, the attention-weighted representations achieved 94.23% classification accuracy, high sensitivity, …

Identifying Controls On The Biodegradation Of Dissolved Organic Matter To Inform Microbial Fuel Cell Applications, Lily N. O'Hagan

Dissertations, Master's Theses and Master's Reports

Microbial fuel cells (MFCs) harness dissolved organic matter (DOM) biodegradation to generate power. To evaluate effects of DOM source, nutrients (nitrate and phosphate), and oxygen on DOM biodegradation, we conducted 4-day DOM biodegradation experiments with water and sediments from the Chesapeake Bay. Compared to soil-derived DOM, algal-derived DOM composition changed more and nearly doubled carbon dioxide (CO₂) production, peak CO₂ rates, and carbon removal, indicating MFC site selection should target regions with algal-rich DOM. Aerobic conditions increased CO₂ production by ca. 16%, doubled peak CO₂ rates, and reached peak rates 1 hour faster than anaerobic …

Mitochondrial Efficiency: Bridging Early-Life Environment And Organismal Performance, Kayla E. Lichtner

Master’s Theses

Mitochondria operate at the forefront of organismal-environmental interactions. Despite remarkable diversity in mitochondrial function both within and among species, all mitochondria serve a universal role in facilitating the flow of energy between organisms and their environment. Energetic efficiency, the way in which organisms assimilate and transform environmental substrate into physiological currency, is a major determinant of organismal performance. Although previous studies have shown that early-life environment can have lasting effects on metabolism, the underlying mechanisms driving the emergence of mitochondrial phenotypic variation remain poorly understood. Leach’s storm-petrels (Hydrobates leucorhous) provide a valuable opportunity to investigate longitudinal hypotheses of …

Overview And Methods Of Molecular Paleontology: A Review, Shelby Touchstone

Williams Honors College, Honors Research Projects

Molecular paleontology—the study of ancient biomolecules preserved in fossils and sediments, including ancient DNA, lipids, and proteins—has motivated researchers since the 1950s, inspiring both scientific inquiry and broader cultural imagination. Think Jurassic Park. This honors thesis presents a comprehensive review of the history, current state, and methods of the field of molecular paleontology. Drawing on peer-reviewed literature and scholarly resources accessed through databases such as EBSCO and Bierce library, this review examines key techniques such as Next Generation Sequencing and amino acid racemization and will go over limitations and controversies in the field. It will also explore potential new …

Red Clover Isoflavones And Establishment In The Context Of Tall Fescue Toxicosis Mitigation In The Mid-South, Jonathan L. Stephens

Theses and Dissertations--Plant and Soil Sciences

Low levels of red clover (Trifolium pratense L.) have been shown to mitigate tall fescue (Lolium arundinaceum (Schreb.) toxicosis symptoms. This is because of the presence of plant-produced compounds known as isoflavones. Production of a red clover supplement on a commercial scale would require industrial-level processing of raw plant material into granules or pellets. The first study of this thesis evaluated the impact of drying temperature on bioavailability of isoflavones. Drying temperatures up to 104°C had minimal impact on isoflavone concentrations. Additionally, varietal differences in isoflavone concentrations were documented. The second study of this thesis evaluated optimal establishment …

Early Microglial Response To Amyloid Plaques Drives Sleep Loss In Alzheimer’S Disease, Nicholas J. Constantino, Riley E. Irmen, Matthew J. Lanning, Sierra M. Turner, Clair C. Ashley, Caitlin M. Carroll, Evan M. Neary, Dave Rubinow, J. Andy Snipes, Shannon L. Macauley

Physiology Faculty Publications

Introduction: Sleep disruption is an early feature of Alzheimer's disease (AD), but the cellular mechanisms linking amyloid pathology to sleep loss remain unclear.

Methods: Electroencephalography/electromyography (EEG/EMG) recordings, quantitative EEG analysis, and sleep deprivation were performed in APPswe/PSEN1dE9 (APP/PS1) mice at different stages of pathology relative to normal aging. Amyloid burden and microglial density were quantified with whole-brain light-sheet microscopy. CSF1R-mediated microglial depletion explored effects of microglia on sleep loss.

Results: Amyloid plaques caused non–rapid eye movement (NREM) sleep loss that did not worsen with increased plaque burden. Aging reduced REM sleep and eliminated sleep rebound. Amyloid pathology was associated with …

Agricultural Evidence Synthesis At A Critical Juncture: Quality Gaps And Implications For Evidence-Based Agriculture, Chao Cai, Jane Yatcilla, Justyna Czader, Sylvie Brouder, Jeffrey Volenec

Libraries Faculty and Staff Scholarship and Research

Systematic reviews and meta-analyses have become essential tools for synthesizing evidence to guide agricultural policy and practice, yet whether these syntheses are themselves conducted with sufficient rigor has rarely been systematically assessed. This study provides a field-wide assessment of reporting quality in agricultural evidence synthesis, examining whether existing reviews are conducted with sufficient transparency and rigor to support the policy and practice decisions they are meant to inform. We drew a random sample of 244 systematic reviews and meta-analyses from a bibliometric dataset of 1,709 articles published between 1997 and 2023, evaluating reporting quality using a 12-indicator rubric across four …

The Forensic Implications Of Hydrochloric Acid (Hcl) Exposure On Dna Preservation In Human Teeth, Shaelyn Lee Zimmerman

Graduate Student Theses, Dissertations, & Professional Papers

Identity is a human right, and forensic anthropological methods are often aimed at returning identity to decedents. Three main pathways are used for the identification of human remains: fingerprints, dental records, and DNA analysis. Identification efforts may be hindered when perpetrators attempt to obscure the victim’s identity. In cases where corrosive substances, such as hydrochloric acid (HCl) are used, dental comparison and fingerprinting often fail and genetic analysis becomes the best chance of achieving personal identification.

Previous studies have shown teeth are an excellent source of DNA. Large, multi-rooted teeth, such as molars, are often preferred because they contain the …

Labor Savings From Mechanical Rice Transplanting In Bangladesh, India, Nepal, And The Philippines: A Systematic Review And Meta-Analysis, Rodrigo S. David

ASEAN Journal on Science and Technology for Development

Rice production in South and Southeast Asia faces serious challenges, including acute labor shortages and rising wages, which threaten regional food security. Mechanical rice transplanting offers a promising solution; however, evidence on labor savings, especially region-specific data, remains inconsistent. This systematic review and meta-analysis aimed to quantify labor savings from mechanical versus manual transplanting across Bangladesh, India, Nepal, and the Philippines.

Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, a systematic search was conducted across four major scientific databases (2000–2026) using Boolean search terms for mechanical transplanting and labor outcomes. Of 284 initial records, 52 met eligibility …

Climate And Seasonal Influences On Indo-Pacific Sea Level: Insights From 30 Years Of Satellite And Tide Gauge Data, Karlina Triana

ASEAN Journal on Science and Technology for Development

We analyze Indo-Pacific sea-level variability using monthly satellite altimetry (1993–2025) validated against records from 16 tide-gauge stations. Cross-comparisons show strong agreement, especially in the western Pacific, confirming the reliability of altimetry for regional assessments. Seasonal SLA variability is largest in the Bay of Bengal and South China Sea and reflects monsoonal forcing, whereas interannual fluctuations in the eastern Indian and western Pacific oceans are dominated by ENSO and modulated by PDO. Harmonic decomposition isolates annual and semi-annual cycles, and an EOF/PCA framework identifies the leading modes: EOF1 (30.8%) captures basin-scale interannual variability and EOF2 (20.9%) reflects the seasonal cycle. Spectral …