Digital Commons Network^™

Removal Of Long- And Short-Chain Per- And Polyfluoroalkyl Substances From Surface Water Using Green Sorption Media–Nanofiltration Hybrid Processes, Md Touhidul Islam

Graduate Thesis and Dissertation post-2024

Per- and polyfluoroalkyl substances (PFAS) are a class of persistent environmental contaminants that pose significant risks to human health and aquatic ecosystems. This dissertation addresses the removal of both long- and short-chain PFAS from surface water through an integrated approach that combines green sorption media (GSM) with nanofiltration (NF). The research comprises laboratory-scale and field-scale studies designed to evaluate the effectiveness of novel recycled-material-based GSM formulations—namely, CPS and ZIPGEM—as pretreatment options to mitigate membrane fouling and enhance PFAS removal during NF. The study also investigates the adsorption mechanisms under varying water chemistry conditions, including pH, ammonia, and divalent cation concentrations. …

An Exploration And Evaluation Of Biologically Informed Variational Autoencoders For Scrna-Seq Data Analysis, Marjorie R. Principato

Graduate Thesis and Dissertation post-2024

Deep learning has been widely applied to the analysis of high-dimensional biological omics data, especially single-cell RNA sequencing (scRNA-seq). Incorporating biological information into the architecture of variational autoencoders (VAEs) has been shown to enhance model interpretability, allowing the model’s behavior to reflect the underlying mechanisms of the biological system used for its architecture. In recent years, several studies have employed these biologically informed VAEs to model large-scale single-cell transcriptomics data, with models correctly differentiating between cell states and identifying active pathways. However, systematic benchmarking and comparison of different biologically informed VAE architectures remain limited.

In this study, I evaluated and …

Pbwt-Based Methods For Biobank-Scale Haplotype Data Analysis, Pramesh Shakya

Graduate Thesis and Dissertation post-2024

Haplotype matching is the task of finding identical matching segments given a group of aligned genetic sequences. Haplotype matches play an important role as they represent biological phenomena. Long haplotype matching segments could indicate identity-by-descent segments showing some degree of genealogical relatedness between the individuals that the haplotypes belong to. Similarly, long segment matches that are adjacent to each other may indicate recombination events. Advanced genotyping technology has made it feasible for large numbers of individuals to be genotyped resulting in many biobanks across the world. This requires efficient algorithms that can analyze large amounts of genetic data.

In this …

Towards Robust Deep Learning: Label Noise Modeling, Algorithms, And Applications, Diego Fernando Linares Gonzalez

Graduate Thesis and Dissertation post-2024

This thesis investigates robust and hybrid deep learning with emphasis on improving accuracy and generalization in challenging real-world settings, including learning under noisy supervision and applications to complex scientific data.

In the first part, we address instance-dependent label noise by using a tensor factorization–based methodology that models the noise transition process as an instance-dependent decomposition. We also utilize low-rank block-term structures to capture class-specific and instance-specific correlations. Moreover, we include a robust loss function and rank regularization to achieve stable optimization during model training. We validated this with experiments on benchmark datasets, like Fashion-MNIST, CIFAR-10, and CIFAR-10N, demonstrating higher accuracy …

Insights Into Iapodian Lifeways: Phytolith And Starch Grain Analysis Of Animal And Human Dental Calculus From Croatia, Angelinne Moreno

Graduate Thesis and Dissertation post-2024

The Piplica hillfort is located near the village of Lovinac within the Lika region of Croatia. The Bronze Age is a pivotal period in Europe that encompasses changes in landscapes, social structures, and famously includes vast production of metals. The Bronze Age in Lika is characterized by changes in social, political, and economic lifeways; denser populations; expanded trade networks; and advancements in agriculture, husbandry, and metal-working. However, little is known about the Iapodes people, who inhabited the Lika region during the Late Bronze Age, and how they interacted with their environment.

The Iapodes were only known from classical Greek written …

Better Models For Mosquito Control: Impacts On Nontarget Insects And Joint Species Distributions Of Mosquitoes, Jacob D. Hart

Graduate Thesis and Dissertation post-2024

Since its inception, mosquito control has been vital for limiting the spread of vector-borne pathogens. Modern control efforts balance the protection of public health and the prevention of environmental harm. We addressed this from two directions: the study of mosquito adulticide effects on nontarget insects, and fine scale distribution modeling of mosquitoes to better target control efforts. We first investigated the effects of ultra-low volume (ULV) pyrethroid applications on nontarget insects in Central Florida and found no statistically clear evidence of reduction in abundance or diversity. We reported a slight and statistically unclear reduction of night-flying Lepidoptera, and effective reduction …

Bridging Physiology, Data Science, And Genomics To Illuminate Photosynthetic Variation In Sunflower, Rebekah E. Davis

Graduate Thesis and Dissertation post-2024

Photosynthesis is a critical metabolic process in plants involving ‘light reactions’ that capture solar energy to produce ATP and NADPH, and ‘dark reactions’ where these molecules power the enzyme Rubisco to synthesize sugars in the Calvin-Benson cycle. These processes serve as the primary energy source for plant growth and reproduction, displaying significant variation across species and environments. In Helianthus, distinct differences in photosynthetic traits are observed between annual and perennial species. Notably, carboxylation rates, photon capture, and maximum photosynthetic rates show strong phylogenetic signal (Pagel’s λ = 0.99) and are significantly higher in annuals. Photosynthesis is modeled here as a …

Skeletal Embodiment Of Structural Violence: Testing Application Of The Weathering Hypothesis In Analyses Of Identified Sex, Jasper K. Shaw

Graduate Thesis and Dissertation post-2024

Structural violence refers to the experiences of inequality faced by marginalized sex, gender, race, and socioeconomic groups. Unequal access to healthcare, housing, and education can cause poor health that may affect how a decedent is analyzed by forensic anthropologists. This research hypothesizes that, due to gender- and sex-based marginalization, females will display greater rates of stress and correlated accelerated aging (i.e., weathering), than males. Computed tomography scans from 100 males and 99 females aged 20-69 years old and white and middle class, were sampled from the New Mexico Decedent Image Database (NMDID). Stress was assessed via cranial porosities, antemortem tooth …

Change Point Monitoring In High-Dimensional Factor Models, Mahdi Mirhosseini

Graduate Thesis and Dissertation post-2024

This dissertation presents the Factor-Augmented Detection (FAD) algorithm, a robust methodological framework for online change point detection in high-dimensional data streams, grounded in classical factor model analysis. To tackle the challenges of monitoring large-scale datasets, the FAD algorithm decomposes data into a parsimonious set of common factors and sparsely changing idiosyncratic residuals, facilitating independent, targeted analysis of low-dimensional factor dynamics and sparse high- dimensional residual evolution.

Following decomposition, structural changes in the factor components are identified using established multivariate sequential monitoring techniques, specifically the Multivariate Cumulative Sum (mCUSUM) and Multivariate Exponentially Weighted Moving Average (mEWMA) procedures. Simultaneously, sparse alterations in …

Exploring Senescence For Improved Diagnosis And Treatment In Head And Neck Cancer, Md Tanjim Alam

Graduate Thesis and Dissertation post-2024

Head and Neck Squamous Cell Carcinoma (HNSCC) comprises a heterogeneous group of malignancies originating from the mucosal epithelium of the oral cavity, pharynx, and larynx. Accounting for approximately 4.5% of global cancer incidence and mortality, HNSCC poses a persistent public health concern. Major risk factors include tobacco use, alcohol consumption, and infection with high-risk Human Papillomavirus (HPV) strains. Although conventional treatments such as surgery, chemotherapy, and radiotherapy have improved patient outcomes, therapeutic resistance and tumor recurrence remain significant challenges. A growing body of evidence implicates therapy-induced cellular senescence as a key mechanism in treatment resistance. Senescence is a stable state …

Targeting Il-6 Signaling And Release Pathways Modulates Inflammation And Restores Intestinal Epithelial Integrity And Function During Mycobacterium Avium Paratuberculosis Infection, Ala' Mahmoud Saleem Alhendi

Graduate Thesis and Dissertation post-2024

Like TNFα, IL-6 is upregulated in Crohn’s disease (CD) associated with Mycobacterium avium paratuberculosis (MAP) infection. Limited therapeutic response to anti-IL-6 therapy may be related to the dual role of IL-6. In this study, we investigated the effects and the signaling mechanism of IL-6 in intestinal epithelial integrity and function during MAP infection using an in vitro model that consists of THP-1, HT-29 and Caco-2 cell lines. Clinically, we determined that plasma samples from MAP-infected CD patients have higher IL-6 levels compared to controls (P-value < 0.001). In CD-like macrophages, MAP infection has significantly upregulated the secretion of IL-6 and the shedding of IL-6 receptor (IL-6R). Moreover, it resulted in significant upregulation of intestinal damage markers including CLDN2, NOX-1 and SERPINE1. Blocking IL-6 signaling exacerbated that damage and enhanced the levels of the damage markers. In HT-29 cells, MAP infection upregulated MUC2 expression, a protective response that was reversed when IL-6R was neutralized. More importantly, blocking IL-6 signaling during MAP infection rescued damaged Caco-2 cells from MAP-induced apoptosis. We also examined the role of monocarboxylate transporter 4 (MCT4), a proton-coupled lactate symporter, that facilitates the inflammatory shift in macrophages, and its impact on intestinal epithelial homeostasis during MAP infection. MAP infection increased lactate export and upregulated the expression of MCT4, TNFα, and IL-6 via TLR2. Inhibition of MCT4 during MAP infection using α-cyano-4-hydroxycinnamic acid (CHCα) significantly reduced TNFα and IL-6 and led to restoring baseline oxidative status, mucin level, and SERPINE1. It also enhanced tight junction protein TJP1 (ZO-1) expression. These findings emphasize the role of IL-6 in MAP-associated CD pathogenesis and explain the ineffective response to IL-6 therapies in CD patients. Moreover, our findings revealed the role of MCT4 in CD pathophysiology during MAP infection and highlighted MCT4 as a potential therapeutic target for effective CD treatment.

Wavefront Sensing Using Nonlocal Metasurfaces, Arturo Martin Jimenez

Graduate Thesis and Dissertation post-2024

Many laser applications require wavefront control to compensate for aberrations caused by system misalignment, component fabrication errors, and propagation through inhomogeneous atmospheres. Aberrations caused by atmospheric turbulence remain particularly challenging to measure due to the temporally fluctuating wavefront distortions and large transverse phase variations in the beam. Conventional wavefront sensors, like the Schack-Hartmann (SHWS) are effective at low turbulence levels, but require relatively bulky optical elements. This thesis investigates the use of metasurface optical elements for use in wavefront sensors both in the low-turbulence limit and in deep turbulence conditions. Such metasurface-based wavefront sensors can achieve the functionality of complex …

You And Me: Imagination As A Coping Mechanism For Childhood Trauma, Rachel B. Sacks

Graduate Thesis and Dissertation post-2024

You and Me is a two-dimensional (2D) animated short film about a young girl who suffers from an unknown illness. As she tries to rest, two otherworldly monsters transform her room into an unsettling nightmare. These monsters stem from her own distorted perceptions of the doctor and nurse caring for her. You and Me focuses on the difficulties that children navigating medical challenges face in communicating their fears with their caretakers. It is a film rooted staunchly in the subjective world of its protagonist. The art style deliberately combines conventionally appealing character design with surrealist imagery and evocative, unsettling lighting …

Digitally-Mediated Nature-Connectedness?: Listeners’ Emotional Responses To And Perception Of Digitized Nature Sounds, Marissa Salas

Graduate Thesis and Dissertation post-2024

• Faced with the potential closure or privatization of the U.S. National Park Service (NPS), it is important to reflect on the conservation efforts using soundscapes. This dissertation explores the gap between experts and lay listeners in listening to soundscapes through the digitally-mediated spaces (e.g. YouTube). In a pilot project conducted in 2024 that used facial emotional recognition software and a talk-aloud protocol, data on emotions was collected. Using NPS video recordings on its webpages, social media accounts and via other digital channels (YouTube, etc.) created by NPS experts, this project employed an innovative, interdisciplinary, mixed-methods experimental design to investigate …

Macabre Therapeutics: An Exploration Into The Cathartic Nature Of Splatter Utilizing The Saw Franchise As Corpus, Rosalind E. Rohrbaugh

Graduate Thesis and Dissertation post-2024

This project positions splatter (a subgenre of horror films that centralizes gore) as applicable for sociopolitical critique and emotional catharsis, disrupting the narrative of splatter as a solely shock-based enterprise. The project utilizes the Saw franchise as a corpus, which reignited audience interest in extreme horror in 2004, rejuvenating splatter film releases since their stagnancy throughout the 1990s. This research seeks to answer why Saw captured the attention of audiences and returned the splatter subgenre to the 21st century, utilizing psychoanalytical film analysis, sociopolitical analysis, semiotics, content analysis, and archival research as methodology and drawing on Aristotle’s Catharsis and Rhetorical …

Inhibition Of Activin A Signaling Slows The Progression Of Barrett's Esophagus Induced Esophageal Adenocarcinoma, Lily A. Giardino

Graduate Thesis and Dissertation post-2024

In 2020, approximately 1.03 billion cases of Gastro-esophageal Reflux Disease (GERD) were reported worldwide, representing a significant global health burden. Chronic GERD is a potent initiator of Barrett’s Esophagus (BE), a precancerous condition in which the squamous epithelium is converted into columnar-like epithelium in the distal esophagus in response to reflux injury. Barrett’s Esophagus is the only known precursor to Esophageal Adenocarcinoma (EAC), a disease with a five-year survival rate of 21%. First line treatments focus on acid suppression and endoscopic mucosal resection but did not result in a decrease of EAC incidence highlighting the importance of new therapeutics. Previous …

Multi-Omics Analysis Of Streptococcus Pneumoniae Serotype 3 Using A Murine Infection Model, Jash Kamlesh Trivedi

Graduate Thesis and Dissertation post-2024

Streptococcus pneumoniae (SPN), a gram-positive encapsulated pathogen, inhabits the human nasopharynx asymptomatically but can cause severe infections, including invasive pneumococcal diseases (IPD). Although targeted by vaccines, serotype 3 (ST3) remains highly prevalent within the United States and globally. Sequence type 180 lineage within Clonal Complex (CC)180 is the predominant lineage of serotype 3 globally. Genetically, Clonal Complex 180 is divided into clade I and II, with clade II recently surpassing clade I in prevalence. However, the molecular mechanisms driving this shift remain poorly understood. Here, we employ a multi-omics approach, combining pangenome analysis and dual-RNA sequencing, to investigate genetic factors …

Comparing Inter-Rater Reliability For Two Coding Methodologies In Meta-Analysis Data Extraction, Christine D. Destefano

Graduate Thesis and Dissertation post-2024

Meta-analyses are critical tools for evidence-based policymaking, but their validity depends heavily on accurate data extraction from primary studies. While previous research has focused on procedural aspects of coding and reliability of effect size extraction, there remains a significant gap in understanding how to improve inter-rater reliability (IRR) for moderator variables that provide crucial context for meta-analytic findings. This study compared two methodological approaches for coding moderator variables: traditional low-inference coding and a novel drill-down questioning technique adapted from database development principles. Using a comparative analysis design, two independent coders extracted data from 18 primary studies included in a published …

The Impact Of Social And Political Capital On Black Male Educational Leaders Lived Experiences With Hiring Practices: A Convergent Parallel Mixed Methods Descriptive Study, Travis L. Brown

Graduate Thesis and Dissertation post-2024

According to Woodson and Pabon (2016, as cited in Bass, 2020) Black males represent less than 2% of the US public education workforce. This is concerning considering that many schools across the nation are becoming increasingly diverse. Scholars such as Bass (2020) have even cited that classrooms “may never completely rebound” (p. 356) from finding Black men to fill vacant teaching positions which could ultimately lead to a career in educational leadership. filling classrooms with available Black men in the profession. This study employed a convergent parallel mixed method design within a descriptive research framework to examine the impact of …

Multilevel Network Governance For United Nations Sustainable Development Goals: The Role Of European Subnational Entities In Urban Resilience, Hasan Isgandar

Graduate Thesis and Dissertation post-2024

This dissertation investigates the role of subnational actors in European Union (EU) multilevel governance networks focused on reducing urban poverty and achieving the United Nations Sustainable Development Goals (SDGs). Focusing on the SDG #1 (No Poverty), SDG #11 (Sustainable Cities and Communities) and SDG #17 (Partnerships for the Goals) it examines the participation and impact of subnational actors in two case studies: Naples, Italy and Krakow, Poland. Using Social Network Analysis (SNA), the research investigates the configuration and performance of the networks created within the framework of the URBinclusion projects, which are part of the URBACT and Urban Innovative Actions …

Health Behavior In A Culture-Driven Society: Using Mixed Methods Research To Examine Medical Pluralism In Zimbabwe, Stephen Mhere

Graduate Thesis and Dissertation post-2024

This dissertation examined the role of cultural influences on health-seeking behaviors and healthcare choices among Zimbabweans, focusing on medical pluralism – where individuals simultaneously access traditional, faith-based, and allopathic medical systems. It applied the PEN-3 Cultural Model to examine Cultural Identity, Relationships and Expectations, and Cultural Empowerment. Using a convergent parallel mixed-methods design, data were collected via a Shona-language survey on WhatsApp. Multiple choice, closed-ended, and open-ended survey questions were texted to participants, and they responded by text or audio messages. Response data were collected from 137 study participants. Multinomial logistic regression was used for quantitative data analysis, while deductive …

Eating Disorder Patient Experiences With Best Practices During Psychiatric Treatment: An Exploratory Sequential Mixed Methods Study, Pamela L. Dow

Graduate Thesis and Dissertation post-2024

Eating disorders are among the deadliest mental health disorders and represent a significant financial burden to the U.S. healthcare system. However, little is known about eating disorder patients' experiences during psychiatric treatment. Informed by the Picker Principles of Person-Centered Care and recommendations from the American Psychiatric Association, this study explored eating disorder patient experiences with best practices during psychiatric treatment. First, 10 patients were interviewed about their treatment experiences with a psychiatrist. Themes were analyzed using iterative categorization in Dedoose and informed a quantitative survey to examine patient experiences with their psychiatrist performing best practices during eating disorder treatment. The …

Examining The Impact African American Male Teachers Have On The Math Scores Of Underserved Students, Demetrice Thomas

Graduate Thesis and Dissertation post-2024

This study contributed to a growing body of evidence emphasizing that teacher identity profoundly influences not only how students learn but also how they perceive themselves and their potential. As Gershenson (2022) noted, “Black teachers provide benefits to all students, fostering higher achievement and stronger aspirations,” highlighting the essential role of diverse educators in shaping student success. Consistent academic gains observed among students taught by African American male teachers reinforce the urgent need for educational systems to prioritize equity not only in student outcomes but also in diversifying the teaching workforce. Despite African American male teachers comprising less than 2% …

Cigarettes, Flesh, & Other Cravings, Gabrielle F. Decker

Graduate Thesis and Dissertation post-2024

Cigarettes, Flesh, & Other Cravings is a collection of short stories that explores themes of motherhood, death, and desire. Each character struggles with the friction between society's expectations and their desires for happiness, all through the lens of the surreal and the absurd. A destructive raccoon’s nightly visits unravel a woman’s sense of control. A teenager begins an internship with a conspiracy-obsessed clown. A minuscule old woman tumbles out of a chicken egg. A fissure in a kitchen floor births an imp. A Choose Your Own Adventure examines the illusion of choice. In Hell, torture is personalized. Cigarettes, Flesh, & …

Methods And Applications Of Coherent Analog Photonic Processing, Andrew B. Klein

Graduate Thesis and Dissertation post-2024

Photonic processing is a compelling approach to address the increasing computational requirements of neural networks, promising increased processing speed and better energy efficiency for operations such as matrix-vector multiplication. However, in practice the limitations of photonic hardware necessitate that these systems adopt fixed-point encoding rather than the floating-point standard used by digital electronics. The reduction in accuracy incurred by this requirement must be managed and addressed for real world applications. In this work, we present a reconfigurable, scalable, and parallelizable photonic multiplier cell using coherent balanced photodetection of analog signals to produce signed multiplications. This style of system outperforms other …

The Multifaceted Roles Of Propionic Acid In Autism Spectrum Disorder And Crohn’S Disease, Piotr P. Lagod

Graduate Thesis and Dissertation post-2024

Short chain fatty acids (SCFAs), including propionic (PPA) and butyric (BA) acid, exert a variable and organ-specific effect on the body. They are by-products of human microbiota metabolism and are often used as a food preservative. Studies have shown that PPA and its producers are elevated in autism spectrum disorder (ASD) patients and their mothers. Our lab previously demonstrated that PPA alters neural stem cell differentiation in favor of glia. In this work, we utilized an in vivo mice model, in which dams and their offspring were fed a PPA-rich diet. In the brain, we observed a significant increase in …

Molecular Basis For The Disaggregase Activity Of Protein Disulfide Isomerase, Antonio Mele

Graduate Thesis and Dissertation post-2024

Protein disulfide isomerase (PDI) is an essential, multifunctional, and promiscuous protein with a modular abb’xa’c domain arrangement. Conformational flexibility and the independent, yet coordinated, functionality of PDI domains facilitate protein folding, redox regulation, and the maintenance of cellular homeostasis. Previous investigations have shown that PDI can inhibit amyloid β peptide aggregation, associated with Alzheimer's disease, and is required for cholera toxin disassembly, the rate-limiting step in Vibrio cholerae pathogenesis. However, the precise mechanistic details underlying these interactions remain to be elucidated. Using molecular and biophysical approaches, this study has begun to establish substrate-induced unfolding, or conditional disorder, of PDI as …

Encapsulation Of Phytochemicals Through Polymer-Catechin Nanoparticles Self-Assembled Via Tea-Steeping, Sawyer S. Chang

Graduate Thesis and Dissertation post-2024

The brewing of teas has been an integral pillar of human food culture for millennia. These beverages have always aimed to extract the phytochemicals from berries, leaves, and many other food products. Leaves from Camellia sinensis are used to prepare green, black, white, oolong, and pu’er teas that are highly regarded for their organoleptic properties. Moreover, many of the widely regarded health benefits are ascribed to the high polyphenolic content within the teas. It has been established that polyphenols can interact with hydrophilic polymers, through hydrogen bonding, to form stable small particle suspensions. In this work, polymer-catechin nanoparticles were synthesized …

Catching Light Finding Encouragement Through Art And The Role Of Women In Impressionism, Vlada Evtushenko

Graduate Thesis and Dissertation post-2024

Catching Light is a two-dimensional (2D) animated film about the importance of human connection through the tale of an artist rediscovering their passion for painting through the support of a fellow artist. Catching Light is told through the lens of the period in art history when the artists, who eventually came to be known as 'Impressionists', broke free from the traditions of the Academy. The story highlights how the Art Academy restricted and discriminated against people based on social class and gender, and its disrespect towards the craft of paintmaking. By setting this story in the late 19th century, Catching …

Development Of Human Neuronal Microphysiological Models And Subsequent Integration Into Multi-Organ Platforms For Evaluation Of Therapeutic Efficacy And Off-Target Toxicity, Aakash Patel

Graduate Thesis and Dissertation post-2024

Microphysiological systems are a rapidly growing field of research for modeling of physiological processes and disease in an in vitro environment. The translatability and cost effectiveness of these platforms make them a valuable tool for drug discovery, allowing investigation of both efficacy and off-target toxicity either as a replacement or supplement to traditional animal models. Neurological disorders in particular are often difficult to emulate in an animal model, making the development of these models a highly useful area of research for both elucidation of brain function, as well as neurological disorders. Taking these models and integrating them into a multi-organ …