Digital Commons Network^™

Post-Operative Delirium: A Neurocognitive Syndrome Expressed Through An Interactive Website Module Of Animations, Bailey Mikytuck

Theses

Post-operative delirium (POD) is a neurocognitive complication that can arise in patients who have undergone a surgical procedure. It is characterized by the onset of reduced attention or cognition, mood or personality disturbances, and hallucinations that occur between 10 minutes to multiple days after waking up from anesthesia. These symptoms may only be brief, but in some cases can lead to long-term cognitive impairment and dysfunction and have been associated with the development of dementias. It is estimated that rates of POD occurrence are between 13.2- 41.7% with major risk factors including being over the age of 65 and the …

Assessing Readiness, Perceptions, And Behaviors Of Midlife Adults To Adopt A Dietary Pattern Associated With Cognitive Benefits, Meghan E. Sullivan

Theses

Objective:  To explore the barriers and facilitators for following a brain-healthy dietary pattern by assessing readiness, cognitive dietary adherence, eating competence, quality of life, and health beliefs in midlife adults. Design: Quantitative cross-sectional online survey. Participants: Adults aged 30-60 years (N=189) recruited through social media, flyers, email, and text. Main outcome measures: Readiness to adopt a brain-healthy dietary pattern, eating competence, health beliefs, quality of life, and dietary adherence to a brain-healthy pattern such as the MIND diet. Analysis: Descriptive statistics, ANOVAs, Chi-Square, and correlations were conducted to explore associations among readiness, eating competence, health beliefs, quality of life, and …

Machine Learning-Based Determination Of Sex-Related Bladder Cancer Biomarkers, Joseph Pizzi

Theses

Bladder cancer exhibits sex-specific behavior, occurring more frequently in males but progressing to advanced stages more commonly in females. The activation of sex hormone receptors may explain these differences, but the exact genetic drivers remain poorly understood. Furthermore, current bladder cancer biomarkers have inconsistent sensitivities and specificities in practice, making early diagnosis a challenge. This study approaches bladder cancer biomarker discovery through machine learning techniques on gender and disease-stratified RNA-seq data. Training sets limited to differentially expressed genes were subjected to four different feature selection methods: differential gene expression analysis adjusted p-value, recursive feature elimination with support vector machine, logistic …

Visualizing Perception: Systems Of Perception And Cognition In Animal Species, Felicia Soto

Theses

Animal species utilize various modes of perception based on their individual adaptations and survival needs. The sensory organs of an organism serve as an interface between the present environment and the organism’s central nervous system (Dangles et. al, 2009). An organism will make decisions based on the information being perceived and processed by that individual's nervous system. Studies investigate the mechanisms of these interactions in a variety of ways, from studying physiology and functional morphology, to conducting observational studies of perception. These studies concerning perception and cognition in animals can help to uncover parallels between animal species, as well as …

Fish Community Composition Across Marine Habitats Around St. Croix, U.S. Virgin Islands, Assessed Using Underwater Video, Maya L. Seesholtz

Theses

Coral reef ecosystems support highly diverse fish assemblages that are strongly influenced by habitat structure and environmental conditions. Understanding how fish communities vary across habitat types is critical for effective monitoring and management. This study evaluated habitat-associated patterns in reef fish assemblages around St. Croix, U.S. Virgin Islands, using stationary underwater video data collected through the Southeast Area Monitoring and Assessment Program (SEAMAP) Caribbean.

A total of 37 video deployments were analyzed across coral (n=20), macroalgae (n= 9), and sand habitats (n=7), with seagrass (n=1) included for descriptive purposes only. Fish abundance was quantified using the MinCount metric, and taxon …

Targeting Rna Polymerase I In Ewing Sarcoma Treatment, Alexis Bruce

Theses

Ewing sarcoma is a rare and aggressive pediatric bone cancer with poor survival rates in patients, as low as 30% in advanced or recurrent cases. There are limited treatment options, making molecularly targeted therapy vital to explore. Through CRISPR scans of Ewing sarcoma cell lines, ribosome biogenesis was highlighted as a potential target. As RNA polymerase I is a key component of ribosome biogenesis, the cytotoxic ability of two RNA Polymerase I inhibitors, CX-5461 and BMH-21, were used on patient-derived Ewing sarcoma cells. The efficacy of the drugs on two cell lines was determined via measuring cell viability, migration potential, …

Hidden Diversity In A Clonal Endemic: Insights Into Clematis Socialis From A Population Genetics Perspective, Joanna M. Lapoint

Theses

Clematis socialis (Kral) is a rare, federally endangered perennial species restricted to a small number of fragmented populations in Alabama and Georgia. The species exhibits extensive clonality and limited sexual recruitment, characteristics that complicate expectations regarding genetic diversity and population connectivity. Despite its conservation significance, genome-wide assessments of population structure have been lacking. We used genotyping-by-sequencing (GBS) to generate a genome-wide SNP dataset for 170 individuals sampled from six natural populations. Population structure and genetic differentiation were evaluated using Bayesian clustering, analysis of molecular variance (AMOVA), pairwise FST estimates, and network-based visualization. Analyses revealed strong genetic structuring among populations and …

Cellular And Molecular Characterization Of Ube3a Function In Cic-Dux4 Sarcoma, Jesse D. Walker

Theses

CIC-DUX4 sarcoma (CDS) is a rare and extremely aggressive soft tissue sarcoma that primarily affects children and young adults. CDS is characterized by an oncogenic chromosomal translocation. Current treatments for CDS are similar to those in other sarcomas like surgery, chemotherapy, and radiation. Treatments, however show that CDS responds poorly compared to other sarcomas, due to relapses of localized disease at high rates and short duration response of treatment, proving the importance of understanding CIC-DUX4’s complex role on how it regulates overall gene expression in CDS cells from a molecular approach.

UBE3A is a ubiquitin protein ligase that plays a …

The Indian River Lagoon Through The Lens Of An Artist: Examining The Impact Of Growth And Development On The Lagoon's Water Quality, Lisa K. Skelly

Theses

This project investigates the ecological degradation of the Indian River Lagoon, a vital estuary on central Florida’s east coast. The research focuses on the intersection of habitat loss and water quality degradation, specifically as they relate to anthropogenic factors such as land development and nutrient pollution. Furthermore, the study evaluates the effectiveness of environmental art in fostering environmentally conscious behavior. I translated these findings into a cohesive body of work, including ceramics, fiber arts, and oil painting, utilizing site-specific materials sourced from the lagoon. By integrating these organic elements, the work aims to showcase the estuary’s natural beauty while highlighting …

A Comparative Study On Performance Of Iot-Driven Ml-Enabled Forecasting Models For Efficient Air Quality Monitoring, Bara Ksiksi

Theses

Air pollution is one of the most critical environmental challenges affecting public health globally, responsible for approximately 4.2 million premature deaths annually according to the World Health Organisation. This thesis presents a comparative study of IoT-driven machine learning forecasting models for air quality monitoring in Abu Dhabi, UAE, introducing a zonal approach combined with satellite-based spatial validation. The primary objective is to evaluate forecasting performance across three distinct activity zones using ground station data from the Environment Agency Abu Dhabi (EAD), and to incorporate a spatial validation component using satellite imagery to assess the consistency of ground-based predictions at a …

A Computational Assessment Of Halobacterium Salinarum Glutamate Dehydrogenase Enzymes, Maaz Abdalla

Theses

Glutamate dehydrogenase (GDH) is a hexameric enzyme. GDH is involved in several pathways and cellular processes such as oxidation-reduction homeostasis, ammonia metabolism, lipid biosynthesis, insulin and lactate production, and acid-base equilibrium. The main objective of this thesis is to understand the structural and biochemical properties of this enzyme and why some organisms, for e.g., Halobacterium salinarum, have more than one GDH with different coenzyme specificities. The catabolism of glutamate is linked to NAD+ specific GDHs, meanwhile, NADP+ specific GDHs play an anabolic role in ammonia assimilation. Molecular docking and binding free energy calculations were employed followed by long-scale (500 nanoseconds) …

Comparative Evaluation Of Five Bacterial Strains For The Fermentation Of Camel Milk, Sifatun Nesa Ali

Theses

In this study, the comparative fermentation performance of lactic acid bacteria Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, Lb. helveticus, Lb. casei, and Lactiplantibacillus plantarum in Camel Milk (CM) and Bovine Milk (BM) was investigated. Fermentations were carried out at 42°C for 48 hours, and was monitored through bacterial growth, titratable acidity, pH evolution, proteolytic activity, microstructural properties, and rheological characteristics. Although comparable bacterial viability was observed in CM and BM, acidification kinetics varied significantly between CM and BM (p < 0.05). Proteolysis was significantly higher in fermented CM than in BM (p < 0.001), with consistently greater o-Phthalaldehyde Assay (OPA) values in CM across all strains during fermentation (p < 0.001). Scanning electron microscopy revealed more porous, loose protein matrices in fermented CM than in BM, which supports the rheological results showing weaker gel networks and lower rheological strength in fermented CM. Among the tested bacteria, Lb. casei demonstrated superior adaptability, enhanced viability, balanced acidification, and favorable rheological properties in both milks. Overall, the results of this thesis demonstrate strain-specific fermentation responses and support the possible suitability of different starter cultures for improving the technological performance of fermented camel milk products.

Optimizing Duckweeds Harvesting Strategies To Maximize Nutrient Recovery And Its Role As A Phytosensor In Different Water Sources While Maintaining Sustainable Biomass Growth, Basma Ghannam

Theses

This thesis is concerned with determining the optimal water treatment and harvesting strategy for Lemna minor duckweed plants. The main objective of this thesis is to examine how duckweed plants grow in terms of biomass, photosynthetic activity, leaf morphology, chlorophyll and carotenoid content, and their efficiency in nutrient removal from different water sources. The methodology of the study included assessing duckweed in three water samples including tap water, saline water, and greywater and three harvesting strategies, including low, medium, and high harvesting intensities to assess their growth and nutrient removal efficiency. The results of the study showed that L. minor …

Breath-Based Detection Of Liver Cancer Biomarkers Using An Swcnt-Fet Nano-Biosensor: Quantumatk, Mohamed Mohieb Rashdan

Theses

Early detection of liver cancer remains limited by the slow pace and invasiveness of current testing methods. This study proposes a single-walled carbon nanotube field-effect transistor (SWCNT-FET) designed to detect hexanal—a volatile organic compound (VOC) elevated in liver cancer—directly from exhaled breath. The device is modeled in QuantumATK using a semi-empirical Extended Hückel Hamiltonian within the non-equilibrium Green's function (NEGF) framework, emphasizing realistic contact physics by employing metallic SWCNT electrodes instead of conventional metal films. Zigzag channels with (11,0) and (12,0) chiralities are examined to analyze how geometry and contact matching influence charge transport. Simulations include current–voltage (I–V) characteristics and …

Sampling And Counting Graph Structures With Triangle Motifs, Sherry Robinson

Theses

Understanding the structure of real-world networks often relies on identifying significant (i.e., occurring significantly more frequently than random) subgraph patterns, or motifs, such as triangles. To assess their significance, null models generate random samples from a constrained distribution of graphs, preserving selected properties while randomizing others. These models may either generate random graphs or sample structures from a fixed input graph. This thesis focuses on the latter, specifically the problem of sampling and counting graph structures that incorporate triangle motifs. While efficient algorithms exist for sampling classical structures such as matchings, extending these methods to higher-order motifs remains an important …

In-Context Retrieval For Molecules And Chemical Synthesis Pathways, Abhisek Dey

Theses

Contrastive learning methods require well-defined positive pairs, limiting their applicability to domains where complete, high-fidelity pairings are available. In practice, large-scale scientific corpora --including patents, publications, and web-scale data -- contain vast quantities of contextually relevant but incompletely paired samples that are discarded under standard training paradigms. In this work, we demonstrate that hard negative mining can be leveraged to construct pseudo-positive supervision signals from unpaired or partially paired data, enabling contrastive learning to exploit the full breadth of available corpora without sacrificing representational quality. Using a large-scale chemical drug patent corpus as a testbed, we train a cross-modal contrastive …

Testing The Intermediate Disturbance Hypothesis On Anthropogenic Pressure In Central Alabama, Gavin Terrell

Theses

Biodiversity is fundamental to maintaining ecosystem structure and function globally. Prior to the late 20th century, ecological theory generally predicted that biodiversity would be highest in systems experiencing minimal disturbance. However, Joseph H. Connell challenged this view with the Intermediate Disturbance Hypothesis (IDH), which posits that species diversity peaks at intermediate levels of disturbance and declines under conditions of both low and high disturbance. Although widely cited, the applicability of the IDH to natural systems remains debated, particularly in the context of anthropogenic disturbances and when diversity is measured beyond species richness alone.

This study evaluated the predictions of the …

Alabama Prairie Reconstruction: Comparing Management Pathways For A Southeastern Landscape, Cecelia R. Geyer

Theses

Southeastern prairies are highly biodiverse yet increasingly threatened by land-use change, fire suppression, and habitat fragmentation. These disturbance-dependent systems rely on periodic fire and grazing to maintain plant diversity and ecosystem function. This study evaluates prairie restoration strategies by testing predictions from the Intermediate Disturbance Hypothesis and the Patch Mosaic Burn Hypothesis. The study site was divided into three treatments: prescribed burned only (B), prescribed burned with mowing (BM) to simulate grazing, and an undisturbed control (C). A standardized mix of native plant seeds was broadcast across all treatments. Ecosystem health and function were evaluated using plant community diversity and …

Towards Reliable And Trustworthy Deep Learning Through Explainability And Interpretability, Dipkamal Bhusal

Theses

Deep neural networks achieve state-of-the-art performance across many domains, yet their deployment in high-stakes settings is constrained by two challenges: opaque decision-making and vulnerability to adversarial manipulation. This thesis investigates explainability and interpretability as principled mechanisms for improving the reliability and trustworthiness of deep learning models. First, we develop new post-hoc explanation methods that improve feature attribution and concept-based explanations. These methods provide faithful decision cues by modeling meaningful feature interactions and extracting faithful coherent concepts, enabling more reliable understanding of why a model predicts a given label. Second, we show that explanation quality is not solely a property of …

Defining Her2 Associated Proteogenomic Features In Breast Cancer And Extending To Gynecologic Cancers, Maya Anand

Theses

HER2 amplification is a well-established driver of breast cancer and serves as the primary basis for clinical classification and treatment selection. However, this framework assumes that HER2-driven tumor biology is defined solely by ERBB2 amplification or overexpression. The goal of this study was to evaluate whether HER2-associated signaling is represented as a pathway-level activation state and whether this framework could help identify tumors with clinically relevant HER2 activity beyond current routine classification methods. HER2-associated transcriptional programs were identified across three independent breast cancer cohorts, resulting in conserved gene sets (P76 and P25). Amplification-independent HER2 activation was assessed using the HER2 …

Leveraging Volatile Ecram Dynamics For Short-Term Plasticity In Neuromorphic Circuits, Sean Borkholder

Theses

Short Term Plasticity (STP) is fundamental for information processing and computational efficiency within biological neural systems. STP has previously been implemented at the circuit level using complex designs with high power and area overheads, resulting in designs that are not scalable in neuromorphic systems. Electrochemical random-access memory (ECRAM) devices naturally exhibit STP behavior through volatile ion dynamics, creating transient conductance modulation.  In previous ECRAM implementations, this behavior was seen as an undesirable artifact of device programming when implemented as a Compute in Memory (CIM) device; however, this thesis proposes leveraging the volatile  behavior to instead act as a computational resource. …

Medical Detection Dogs: A Visual Exploration Of Canine Olfactory Anatomy & Volatile Organic Compounds As Applied To Non-Invasive Biomedical Detection, Kirsten Santiago

Theses

Medical detection dogs provide a non-invasive early method of disease and medical alert detection that is underrepresented in the medical visualization sector. The domesticated dog, or Canis familiaris, is known for its loving nature and has become an important member of many households, but they are also incredibly intelligent with a capacity for specialized training. Dogs have a specialized olfactory system, allowing them to detect scents with high acuity (Guest & Otto, 20). Volatile organic compounds or VOCs are molecular substances associated with metabolic processes that are often a result or byproduct of certain diseases and can be influenced by …

Horizontal Gene Transfer In Neisseria, Wen Ting Dong

Theses

Antibiotics are a special category of drugs that help treat bacterial infections by killing bacteria or hindering their growth and replication. Antibiotics are greatly significant in modern medical practices, providing an effective treatment for bacterial infections as well as enabling organ transplants, open surgeries, and chemotherapy to be possible. Unfortunately, cases of antibiotic resistance were observed shortly after the introduction of antibiotics. The appearance and spread of these resistant strains poses a significant threat to public health safety. The Centers for Disease Control (CDC) estimates there are 2,868,700 antibiotic-resistant bacterial and fungal infection cases per year in the United States, …

Mediators Of The Dead: Funerary Strategies And Material Practice In The Final Jōmon Period, Celeste Marie Tran

Theses

Shakōki-dogū are prehistoric clay figurines from Japan’s Final Jōmon period, characterized by enlarged, goggle-eyed features. In both scholarship writing and museum display texts, generalized thematic labels or iconographic readings sometimes reduce the corpus’s internal variability. This study examines a focused set of Final Jōmon shakōki-dogū from northern Honshū (Tōhoku) and Hokkaidō (Figures 2–6) through their formal and material evidence—shape, surface treatment, and condition—read alongside published excavation reports and catalogue records. It asks what these figurines can be shown to do, as prehistoric artworks, within death-related practice when interpretation is anchored to observable features and documented context, rather than to a …

Art Therapy In The Art Classroom, Sherry Williams

Theses

The integration of art therapy practices within the art classroom provides a transformative framework for supporting the emotional and psychological well-being of students. Research into these strategies demonstrates that creative practices allow students to manage stress and anxiety while fostering mindfulness, reflection, and self-expression. Art educators can create safe and supportive environments by incorporating therapeutic activities such as drawing mandalas, doodling, and engaging in collaborative projects. These methods prioritize the creative process over technical achievement, allowing students to communicate complex feelings that may be difficult to articulate verbally. 

While art teachers are not licensed therapists, they can effectively implement therapeutic …

Engineering Human Microphysiological Models To Investigate Bacterial Extracellular Vesicle–Driven Endothelial And Blood–Brain Barrier Dysfunction, Louis P. Widom

Theses

Pathogenic bacterial extracellular vesicles (BEVs) are nanoscale particles derived from bacteria that contain pro-inflammatory cargo. During bacterial infections, BEVs provoke the host inflammatory response and may cause widespread damage. Furthermore, antibiotic treatment can boost BEV production and thereby increase the number of toxic signals traveling through the circulatory system. This is especially dangerous in brain blood vessels since evidence suggests that BEVs may destabilize the protective blood–brain barrier (BBB), resulting in neuroinflammation associated with cognitive decline and development of neurological disorders. Our understanding of BEV interactions with the host remains limited, necessitating the development of in vitro models to better …

The Usability And Influence Of Comprehensive Sports Nutrition Handouts For Adolescent-Aged Female Athletes, Chloe Brassie

Theses

Objective: This study aimed to examine the usability and influence of comprehensive sports nutrition handouts for adolescent-aged female athletes. Design: Cross-sectional online survey incorporating post retrospective-pre self-assessment Participants: Adolescent female athletes between 13 and 17 years of age Methods: Participants received a series of digital nutrition handouts every day for seven days and completed an online survey. Variables: Age, sport, engagement, knowledge, behavior, features of interest, and experience with nutrition education. Analysis: Quantitative data were analyzed with descriptive statistics and qualitative data were examined using thematic analysis. A Wilcoxon signed-rank test assessed the change in responses for both knowledge and …

Inflection Points In Academic Career Trajectories: Statistical Modeling And Interactive Visualization, Aicha Malouche

Theses

This thesis examines the temporal structure of academic career trajectories, with a particular focus on identifying non-linear patterns of research productivity and moments of maximum acceleration in scientific impact. Situated within the broader context of bibliometric evaluation, the study responds to long-standing limitations of aggregate and linear career models that obscure heterogeneity across disciplines and national research systems. Drawing on theories of cumulative advantage, life-cycle productivity, and structural stratification, the research seeks to clarify how and when elite researchers experience peak growth in impact over the course of their careers. The study is guided by four research questions: (1) when …

Stimuli-Responsive Chemotherapy For Glioblastoma: Sequence-Dependent Synergy Of Cold Atmospheric Plasma And Ultrasound With Cationic Lipo-Doxo, Alessandro Cazzolla

Theses

Glioblastoma (GBM) is an aggressive, infiltrative astrocytic tumour in which pharmacotherapy remains constrained by the blood-brain barrier (BBB) and the heterogeneously altered blood brain tumour barrier, with additional limitations imposed by active efflux and the complexity of the tumour microenvironment. In this setting, externally addressable strategies that modulate transport and uptake at the site of disease are required. A stimuli-responsive chemotherapy platform was developed in which Lipo-DOXO was combined with two non-invasive physical modalities, low-frequency ultrasound (US) and cold atmospheric plasma (CAP), to enhance intratumoural delivery while limiting off-target effects. Liposomes were produced by thin-film hydration followed by a controlled, …

Microplastics In St. John, United States Virgin Islands Sediments: Methodological Approaches And Variability Of Microplastics Concentrations And Accumulation Rates, Henry B. Arbaugh, Sarah C. Gray, Dimitri Deheyn

Theses

Sediment samples were collected from a near shore and reef site in Coral Bay, St. John, United States Virgin Islands (USVI) from 2007-2016, using tube sediment traps. These samples provide an opportunity to study microplastics (MPs) in an area where no previous MP studies have been performed. Most sedimentary MP studies utilize benthic samples which can only measure MP concentrations (#MP/g or #MP/mL sediment), while sediment traps can provide MP accumulation rates (#MP/cm²/day) as a function of time. However, the methods used for extracting MPs from benthic samples have not been tested using sediment trap samples whose characteristics, …