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The Impact Of Inter-Subunit Communication On F420h2:Nadp+ Oxidioreductase: A Kinetic Approach, Jamariya A. Howard

Chemistry & Biochemistry Dissertations - Archive

F₄₂₀H₂:NADP⁺ Oxidoreductase (Fno) catalyzes the reversible reduction of NADP⁺ to NADPH using reduced F₄₂₀ as the hydride donor. Both NADPH and the F₄₂₀ cofactor play significant roles in various metabolic pathways, including glycolysis and methanogenesis, particularly in methanogenic and sulfate-reducing archaea. These organisms play an essential role in global carbon cycling by converting carbon dioxide to methane through the methanogenic pathway, which is directly tied to energy production. This thesis investigates the hydride transfer mechanism of Fno from the extreme thermophile Archaeoglobus fulgidus, using fluorescence binding, steady-state and pre steady-state kinetics.

Chapter 1 outlines the structural and spectral characteristics …

Resveratrol Exerts Anti-Inflammatory Effects On Human Thp-1 Macrophages, Valeria B. Martinez

Chemistry & Biochemistry Theses - Archive

Inflammation is a natural biological response to harmful stimuli. It initiates a series of reactions that prompt defensive and curative mechanisms, ridding the body of offending agents and healing remaining injuries. Inflammation involves the intricate communication between cells, requiring complex signaling that mediates various pathways. This acute form of inflammation is vital for our survival, promoting a myriad of mechanisms that function to defend and heal. However, if this inflammatory response is not resolved, it results in a prolonged condition referred to as chronic inflammation. This persistent inflammatory state is incredibly harmful, damaging the host's healthy cells, tissues, and organs. …

Medical Ai: Solving Healthcare Challenges And Inspiring Ai Innovation, Xiaowei Yu

Computer Science and Engineering Dissertations - Archive

Artificial Intelligence (AI) is transforming healthcare by enabling large-scale analysis of medical data and integrating multimodal information for more comprehensive diagnostics. I present my work addressing fundamental and challenging problems in developing state-of-the-art AI models for medical data analysis, including multimodal brain data and other medical datasets. Additionally, I design brain-inspired AI models by integrating insights from organizational principles of brain networks. Specifically, my research tackles three critical aspects: (1) AI in Computational Neuroscience, where I design deep learning models for brain network analysis to uncover the organizational principles of brain networks; (2) Brain-Inspired AI, where I integrate superior brain …

3d Perception, Mapping, And Navigation For Mobile Cobot, Tuan T. Dang

Computer Science and Engineering Dissertations - Archive

Service robots are migrating from tightly controlled factory lines into offices, hospitals, and homes, where they must perceive, remember, and act amid people, clutter, and perpetual change. Humans solve this daily by forming compact, task-relevant “cognitive maps”: we sample just enough sensory detail to guide the moment, stitch those snapshots into a sparse topological scaffold, and continuously refine it as we move. Guided by that insight, this dissertation proposes a biologically inspired mapping framework that turns partial RGB-D observations into a hybrid temporal-spatial memory—locally metric for centimeter-scale navigation yet globally topological for room-to-building navigation. The system first distills raw depth …

Impact Of Glufosinate On Soil Microbial Community Dynamics, Sarobi Das

Biology Dissertations - Archive

The increasing global regulations of glyphosate due to its possible carcinogenicity and environmental hazards have necessitated the search for alternative herbicides. Glufosinate-ammonium offers a sustainable attribute due to its low toxicity and limited reported herbicide resistance cases. Despite its increasing agricultural importance, very limited studies are done on its environmental impact, especially on the soil systems. This thesis examines the ecological behavior of glufosinate in soil, precisely focusing on its effect on the dynamics of soil microbiome and the potential use of Bradyrhizobium japonicum USDA110 for bioremediation by reversing the effect of microbial dysbiosis. A series of 30-day mesocosm studies …

How Individual Traits Predict Distribution Patterns And Community Convergence, Zachary K. Lange

Biology Dissertations - Archive

One of the fundamental questions in biology is whether natural conditions lead species and communities toward predictable outcomes. Answering this question requires understanding how traits of individual organisms are connected to species- and community-level patterns. In Chapter 2, I examined how thermal physiology and environmental temperatures interact to determine the distribution patterns of Anolis lizards on the Greater Antilles. I combined lab-measured thermal traits (critical thermal minimum: CT_min, critical thermal maximum: CT_max, thermal preference: T_pref) with occurrence and abundance data from 21 species of Anolis lizards collected from extensive mark-resight surveys of communities across …

Parsimony, Parallelism, And Presentation: The Impact Of Presentation On Evaluation, Peter Mclemore

Psychology Theses - Archive

In professional and academic settings, support for creative ideas often hinges on how effectively those ideas are communicated in writing. This study examined how two sentence-level rhetorical features—parsimony and parallelism—influence the evaluation, support, and recall of written proposals featuring creative restaurant concepts. Using a 2×2 within-subjects design, 211 undergraduates reviewed proposals manipulated to vary in parsimony (high vs. low) and parallelism (high vs. low). Participants rated each proposal on quality, originality, elegance, support, and completed a recall task. Contrary to expectations, proposals with low parsimony and low parallelism received the highest evaluations across all three creative indicators (i.e., quality, originality, …

Developing The Rural Older Adult Dementia Prevention-Health Behaviors (Road-Hb) Questionnaire: A Mixed Methods Approach To Instrument Development, Jessica Cassidy

Social Work Dissertations - Archive

Older adults living in rural communities are at heightened risk of dementia; however, preventative strategies can reduce these risks. To facilitate dementia prevention efforts in rural communities, this methodological study developed the Rural Older Adults Dementia prevention–Health Behaviors questionnaire (ROAD-HB) by applying a lifespan approach to the Health Belief Model (HBM). The questionnaire contained three embedded instruments and was constructed following a stage development design involving item pool processes with community and expert review panels. Convergent mixed methods were used to assess the ROAD-HB’s validity, including a pretest in 36 older adults from two rural Northeast Texas counties and cognitive …

Understanding The Sociodemographic Correlates Of Early Social Security Retirement, Erica D. Robinson

Social Work Dissertations - Archive

Using data from the Health and Retirement Study (HRS), a nationally representative sample of Americans aged 50 and older, this study employed logistic regression analysis guided by intersectionality theory and the Intersectionality-Based Policy Analysis (IBPA) framework to examine the influence of marital status, ever having children, educational attainment, self-reported health, and race/ethnicity on receiving Social Security retirement benefits early (before reaching the Social Security Administration’s full retirement age (FRA)) among women. Individuals’ monthly and total lifetime Social Security retirement amounts, as well as longevity, are influenced by when they begin receiving Social Security retirement payments. Findings revealed that reporting excellent/ …

Excitation And Polarization Of Isolated Neurons By High-Frequency Sine Waves For Temporal Interference Stimulation, Iurii Semenov, Vitalii Kim, Giedre Silkuniene, Andrei G. Pakhomov

Bioelectrics Publications

The capacity of temporal interference (TI) stimulation to target deep brain regions without affecting nearby surface electrodes remains uncertain. Using artifact-free optical recording, we compare excitation patterns and thresholds in hippocampal neurons stimulated by “pure” and amplitude-modulated sine waves, representing TI waveforms near electrodes and at the target, respectively. We show that pure 2- and 20-kHz sine waves induce repetitive firing at rates that increase up to 60–90 Hz with stronger electric fields. Beyond this limit, action potentials merge into sustained depolarization, resulting in an excitation block. Modulating the sine waves at 20 Hz aligns firing with amplitude “beats” and …

Personality And Victimization: The Relationship Between The Big Five Personality Traits And Victimization In Adulthood, Cameron Kan

Criminology & Criminal Justice Theses - Archive

Myriad risk factors have been found to predict victimization. Research, however, has yet to examine the impact of personality—if any—in the likelihood of victimization in adulthood. The current study attempts to fill this gap in the literature by being the first to examine the effects of the Big Five personality traits, also known as the Five Factor Model, on adult victimization in a nationally representative sample (Add Health). Results reveal that scoring high in extraversion is related to a 12 percent increase the in rate of victimization controlling for a host of temperamental and criminological covariates. Depressive symptoms, criminal behavior, …

Assessing Stress, Anxiety, And Burnout In Undergraduate Veterinary Technology Students, Dean Ann Daughaday-Provine

Murray State Theses and Dissertations

Academic stress, anxiety, and burnout can negatively impact the mental health and well-being of students pursuing degrees in veterinary medicine. This quantitative study was designed to investigate the effects of academic stress, anxiety, and burnout on undergraduate students enrolled in Veterinary Technology programs. This study gained critical insight from current students transitioning through a rigorous curriculum of standards designed by the American Veterinary Medical Association (AVMA). The AVMA Committee on Veterinary Technician Education and Activities (CVTEA) has established standards, outlined in policies and procedures, to ensure the quality of assessments and enhancements in veterinary education within accredited Veterinary Technology programs.

Transcription Factors – Insights Into Abiotic And Biotic Stress Resilience And Crop Improvement, Roopali Bhoite, Olive Onyemaobi, Tanushree Halder, Manisha Shankar, Darshan Sharma

Grain and Other Field Crops Research Articles

Numerous crop traits are controlled by multiple gene-networks. These gene-networks play a crucial role in crop evolution, disease prevention, stress adaptation and other fundamental processes in different organisms. Transcription factors (TFs) are master regulators of gene-networks and therefore have been targets for genetic improvement in crops since the dawn of agriculture. Enhancement of quantitative traits through plant breeding often involves manipulation of several TF sites and altered RNA expression. Advancements in OMICS technology have significantly expanded our understanding of transcription factor (TF) binding sites in plants and their roles in various biological processes. This progress has facilitated the validation of …

Synthesis, Stability, And Lumiinesent Properties Of Nayf₄:Yb³⁺, Er³⁺ Upconversion Rare-Earth Nanoparticles, Moshira Ibrahim

Graduate Thesis and Dissertation post-2024

Upconversion nanoparticles (UCNPs), particularly those based on Sodium Ytterium Floride ( NaYF₄) doped with Lanthanide ions, have emerged as promising multifunctional materials owing to their exceptional capacity to convert near-infrared (NIR) light into visible or ultraviolet light through multiphoton excitation processes. Their remarkable resistance to photobleaching, minimal toxicity, and customizable emission characteristics render them ideal candidates for applications in both environmental monitoring and biomedical fields. This thesis investigates the synthesis, structural characterization, and functional performance of NaYF₄:Yb³⁺,Er³⁺ upconversion nanoparticles s, with a focus on its applicability in fog. In response to the limitations of conventional fog detection technologies under low-visibility …

Computational Methods For Population Genetic Inference Using Identity By Descent And Local Ancestry, Yuan Wei

Graduate Thesis and Dissertation post-2024

Identity by descent (IBD) and local ancestry are essential for population genetic inference, such as understanding genealogical relationships and demographic history through genomic data. With the availability of large and high-resolution datasets, new opportunities and computational challenges are brought for efficient and accurate methods to infer IBD segments and local ancestry. This dissertation presents three computational methods designed to assist in population genetic inference. First, RaPID-Query is introduced to efficiently query IBD segments for individual haplotypes over a large genotype dataset. This method is based on the positional Burrows-Wheeler transform (PBWT) algorithm and utilizes a random projection approach. RaPID-Query is …

Algorithms And Benchmarking For Parallel Identity-By-Descent Segment Detection, Kecong Tang

Graduate Thesis and Dissertation post-2024

As genomic biobank initiatives continue to grow, the availability of large-scale genotype datasets, encompassing hundreds of thousands to millions of individuals, has transformed genetic research and biomedical discovery. However, the sheer volume of this data presents major computational barriers. Efficient and scalable methods are urgently needed to process and extract meaningful signals from biobank-scale data using modern multi-core architectures. One central task in this domain is the detection of identity-by-descent (IBD) segments, which underpins a range of applications including genealogical inference, disease mapping, phasing, and population structure analysis.

This dissertation addresses these challenges by presenting a sequence of contributions that …

A Numerical Assessment Of Shock-Raindrop Interaction: An Investigation Of Cavitation Dynamics Driven By Internal Pressure Wave Focusing, Reed Forehand

Graduate Thesis and Dissertation post-2024

This dissertation investigates the formation and evolution of cavitation within liquid droplets subjected to shock wave interactions, with emphasis on internal pressure wave focusing as a fragmentation mechanism. A numerical framework is developed in which high-resolution Volume-of-Fluid (VoF) simulations resolve shock transmission into spherical, cylindrical, and cubic water droplets across a range of flow conditions. The resulting pressure histories at droplet centers are extracted and post-processed using the Rayleigh–Plesset equation to model the dynamics of spherical vapor bubbles.

The modeling framework is validated against established benchmarks, including canonical shock tube behavior, shock-droplet interaction studies, and experimental cavitation observations. A series …

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 …

Lowering The Barrier For Reading Primary Literature In Stem, Sebastian G. Alvarado, Maral Tajerian

Open Educational Resources

Building Bridges of Knowledge (BBK) is a cross‑CUNY initiative that integrates artificial intelligence (AI) and open educational resources to lower the barrier to primary literature and enhance research‑focused pedagogy. Recognizing that scientific papers are often dense and inaccessible to newcomers, we developed a suite of AI‑assisted instructional materials and activities to help students interpret complex data and methodology. A central component is the use of large language models (LLMs) and tools such as Scite.ai to provide citation‑context analytics and personalized research support. These tools allow students to filter literature by supportive, neutral, or contrasting citation statements and to troubleshoot laboratory …

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 …