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Development Of Photolabile Coumarin Linker For Rna Synthesis And Crisprcas9 Applications, Ian Mcclain

Electronic Theses & Dissertations (2024 - present)

The scope of RNA-based therapeutics continues to expand as more siRNA, mRNA, and CRISPR-based treatments are approved for various medical applications. Purification of synthetic RNA drugs is inherently challenging and requires considerable time and resources. New cost-effective and efficient purification strategies will expedite drug development process and will lower the drug costs. In this thesis I describe two generations of photolabile linkers for the non-chromatographic purification of therapeutic RNAs. In addition, the photolabile linker was utilized for regulation CRISPR-Cas9 gene editing. In the first part of the thesis, I describe the first generation of the photolabile coumarin-based linker for non-chromatographic …

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 …

Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …

Analysis Of Δ¹¹B As A Seawater Ph Proxy: Comparing Ocean Circulation Inverse Model Output With Marine Calcifier Geochemistry, Jesse I. Dong

CMC Senior Theses

Increasing anthropogenic carbon flux into the oceans decreases seawater pH, alters dissolved inorganic carbon speciation, and reduces biogenic calcification. The marine calcifiers— specifically corals and coralline algae—incorporate elements from surrounding seawater into their carbonate structures, which preserve past records of ocean carbon chemistry. In particular, boron in biogenic carbonate is a potentially valuable proxy for historical ocean pH across human timescales. Within seawater, boron primarily exists as boric acid B(OH)3 and borate ions B(OH)4 - , where higher pH favors the formation of borate ions. Borate ions preferentially incorporate the heavier ¹¹B isotope over 10B. On the other hand, if …

Geovig And Purevig: Geometry-Aware Architectures For Efficient Computer Vision, Omar Ismail

Theses and Dissertations (Comprehensive)

Deploying deep learning models for medical image analysis on mobile devices requires a balance between inference latency, memory footprint, and delineating anatomical boundaries with high accuracy. While Convolutional Neural Networks (CNNs) and mobile Vision Transformers (ViTs) offer efficiency, they often struggle to model the irregular, non-local geometric structures inherent in biological tissues without incurring prohibitive computational costs. In this thesis, we introduce GeoViG (Geometric Vision Graph), an architecture that bridges the gap between efficient grid-based processing and explicit Geometric Deep Learning. GeoViG introduces a novel transition from high-resolution pixel grids to low-resolution dynamic graphs via a SpreadEdgePool operator, a geometry-aware …

Gender Differences In The Association Between Adverse Childhood Experiences And Drug Use: Findings From A Community-Based Survey In China, Hongyun Fu, Elizabeth Monk-Turner, Xiushi Yang

Department of Pediatrics Faculty Publications

Background

While adverse childhood experiences (ACEs) are widely recognized risk factors for behavioral health problems, including drug use, prior research has largely been conducted in Western countries, focused primarily on males, and relied on convenience samples without comparison groups of nonusers. Limited work has examined the impact of ACEs on drug use in non-Western contexts. This study examines gender differences in the relationship between ACEs and drug use in China, using data from a population-based probability sample survey.

Methods:

Cross-sectional data were collected in 2019 from one city in Yunnan Province in Southwest China and one city in Guangdong Province …

Identifying Relevant Covariates In Rna-Seq Analysis By Pseudo-Variable Augmentation, Yet Nguyen, Dan Nettleton

Mathematics & Statistics Faculty Publications

RNA-sequencing (RNA-seq) technology allows for the identification of differentially expressed genes, which are genes whose mean transcript abundance levels vary across conditions. In practice, RNA-seq datasets often include covariates that are of primary interest in addition to a set of covariates that are subject to selection. Some of these covariates may be relevant to gene expression levels, while others may be irrelevant. Ignoring relevant covariates or attempting to adjust for the effect of irrelevant covariates can compromise the identification of differentially expressed genes. To address this issue, we propose a variable selection method that uses pseudo-variables to control the expected …

Utilizing Machine Learning Techniques For Computer-Aided Covid-19 Screening Based On Clinical Data, Honglun Xu, Andrews T. Anum, Michael Pokojovy, Sreenath Chalil Madathil, Yuxin Wen, Md Fashiar Rahman, Tzu-Liang (Bill) Tseng, Scott Moen, Eric Walser

Mathematics & Statistics Faculty Publications

The COVID-19 pandemic has highlighted the importance of rapid clinical decision-making to facilitate the efficient usage of healthcare resources. Over the past decade, machine learning (ML) has caused a tectonic shift in healthcare, empowering data-driven prediction and decision-making. Recent research demonstrates how ML was used to respond to the COVID-19 pandemic. This paper puts forth new computer-aided COVID-19 disease screening techniques using six classes of ML algorithms (including penalized logistic regression, random forest, artificial neural networks, and support vector machines) and evaluates their performance when applied to a real-world clinical dataset containing patients’ demographic information and vital indices (such as …

Changepoint Analyses Confirms Global Tropical Cyclone Frequency Decline, Michael Wehner, Thomas Fisher, Norou Diawara, Robert Lund

Mathematics & Statistics Faculty Publications

Changes in tropical cyclone frequencies as the climate warms is a topic of significant current debate [1, 2]. There is no accepted theory of how tropical cyclogenesis might respond to a warmer ocean-atmosphere system as multiple controlling factors exist [3–7]. Anthropogenic warming of surface ocean temperatures due to increased greenhouse gas concentrations [8] increases the potential for tropical cyclogenesis [9–11]; however, realized cyclogenesis also requires an initial local disturbance [12–16] to develop. Most multi-decadal tropical cyclone permitting climate models (i.e. resolutions of 15-50km) exhibit frequency decreases in warmer climates, despite the increase in tropical cyclogenesis potential [17–25]. In this paper, …

31p Solution Nmr Investigation Of Abasic Dna, Clarissa R. Krimmel

Graduate Theses/Dissertations

Base excision repair (BER) mechanisms fix single base lesions in DNA, such as T:G mismatches. During the base excision repair mechanism, an abasic site (AP site) is formed as an intermediate. AP sites are unstable and highly mutagenic; they can stop DNA replication. This research investigates how the conformational properties of abasic sites in DNA affect the binding recognition of enzymes involved in DNA repair mechanisms, including BER. Three different abasic sequences are being analyzed for this research project. A second project looks at the effects of a naturally occurring purine derivative, hypoxanthine, on the DNA backbone. These hypoxanthine lesions …

Remediation Impacts Metal Concentrations And Metal Tolerant Bacteria In Soils Of The Missouri Tri-State Mining District, Ophelia R. Pettington

Graduate Theses/Dissertations

After over 100 years of Zn and Pb mining in the Tri-State mining district (TSMD), former mines continue to be sources of metals. Metal contaminated soils can be remediated using plant-microbe interactions. Plants manipulate their microbiome and recruit microbes to increase metal tolerance. Remediating bacteria are site-specific and identifying native microbes can accelerate remediation efforts. Studies relating microbes and metal concentrations in remediated areas in the TSMD are scarce. I collected root and bulk zone soils associated with Andropogon virginicus from remediated and non-remediated sites in Webb City, MO. I used 16S rRNA gene amplicon sequencing to evaluate the bacterial …

Improving Human Dimensions Of Conservation Planning: Challenges And Opportunities For Sustainable Conservation Outcomes, Vivian Hulugh

Electronic Theses and Dissertations

Conservation planning is important to ensure both ecological and social benefits of natural resources, including the maintenance of functional ecosystems and stable wildlife populations as well as the provision of resources that communities rely on. Yet, the integration of the human dimensions of conservation planning remains limited in practice. This thesis examines conservation planning in South Dakota and within Joint Venture (JV) partnerships, using qualitative methods to identify challenges and opportunities for more effective and coordinated planning. In chapter one, I examine how collaboration, public participation, and the use of climate information are integrated conservation planning in South Dakota and …

Connecting Classroom Physics To Real-World Research: A Citizen Science Approach In Ap Physics 1, Heather M. Landgarten

West Chester University Graduate Theses, Dissertations, and Final Projects

Advanced Placement (AP) Physics 1 emphasizes evidence-based reasoning, quantitative modeling, and scientific inquiry. However, secondary science instruction often remains focused on procedural problem solving and standardized assessment rather than authentic scientific practice. This study examined the integration of citizen science projects into an AP Physics 1 curriculum to provide students with authentic research experiences while reinforcing physics concepts during the post-AP examination instructional period.

Using a classroom-based mixed-methods pre–post design, students participated in citizen science activities through publicly available research platforms, including Zooniverse. Students collected and classified authentic scientific data, analyzed real-world datasets, developed research questions, compared observations with theoretical …

A Dual-Emission Polymer-Dots/Gold-Nanoclusters Nanohybrid For Ratiometric Fluorescence Detection Of Hg²⁺, Sha Wu

Dissertations and Theses

Heavy metals, such as Hg, Cd, Pb, and Cr, become a serious environmental problem because they are highly toxic, bioaccumulation, and long-term persistence, required a high sensitivity and selectivity detection method. Although laboratory testing instruments, such as inductively coupled plasma mass spectrometry, offer high sensitivity, their practical application is limited because they rely on large-scale equipment and complex sample pre-treatment processes. Single-emission fluorescence probes are simpler but can be affected by variations in probe concentration, excitation intensity, and measurement conditions. In this study, a dual-emission nanohybrid that consists of poly(9,9-di-n-hexylfluorenyl-2,7-diyl) (PDHF) and bovine serum albumin (BSA), termed as PDHF-Pdots/BSA-AuNCs nanohybrid, …

Ai-Assisted Surface-Enhanced Raman Spectroscopy For Cardiovascular Diagnostics: From Plasmonic Materials To Clinical Translation, Anju Joshi, Gymama Slaughter

Center for Bioelectronics Publications

Raman spectroscopy (SERS) has emerged as a powerful analytical technique, offering molecular fingerprint specificity and ultrasensitive detection of cardiac biomarkers. Recent advances in plasmonic nanostructures, surface functionalization strategies, and flexible sensing platforms have significantly improved the analytical performance of SERS-based biosensors. In parallel, the integration of artificial intelligence (AI) and machine learning has enabled robust interpretation of complex spectral datasets, facilitating automated biomarker classification and improved diagnostic accuracy in heterogeneous biological environments. Despite these advances, the field remains fragmented, with limited integration between nanomaterial design, biomarker selection, and data-driven analysis, and persistent challenges related to reproducibility, standardization, and clinical validation. …

Image-Derived 3d Hepatic Lobule Modeling Of Acetaminophen-Induced Hepatotoxicity, Rebecca Lauren Strauss

Selected Full-Text Master Theses 2021-

The liver’s highly structured vascular microarchitecture governs blood perfusion, metabolic zonation, and the spatial distribution of xenobiotic toxicity. Current computational models of hepatic drug metabolism often oversimplify this geometry, limiting their ability to capture realistic flow dynamics and cellular injury patterns. This study develops a multiscale computational framework to predict acetaminophen-induced hepatotoxicity using image-derived, three-dimensional hepatic lobule geometries. The model integrates computational fluid dynamics (CFD) with a mechanistic cellular injury module to simulate the interplay between perfusion, metabolism, and hepatocellular viability.

Realistic vascular reconstruction was achieved from histopathology liver slices, and the resulting geometry was meshed and solved using ANSYS …

Deep Learning For Eeg-Based Emotion Recognition With Temporal And Spectral Interpretability, Shruti Rameshbhai Shingala

Selected Full-Text Master Theses 2021-

Electroencephalography (EEG)-based emotion recognition has emerged as a critical component of affective computing and clinical neuroscience. Existing approaches to this problem primarily reduce the multi-dimensional EEG time series to a single averaged feature vector, thereby discarding the temporal structure of the emotional response. The present work addresses three identified gaps in the literature: the absence of temporal interpretability, the uniform use of frequency bands, and the use of single-scale temporal feature extraction. A deep learning architecture, MST-Mamba-Asym, is proposed, comprising four components: Asymmetry Attention, which encodes hemispheric asymmetry by computing signed left–right channel differences, FreqBandAttention, which learns differential weights across …

Superelectrophile Promoted Synthesis Of Heterospirocycles, Mariam A. Adegbenro

Graduate Research Theses & Dissertations

Spirocycles are important scaffolds with a wide range of applications in material science as well as in medicine. The introduction of a heteroatom into the spirocyclic framework can improve its electronic, photophysical, and structural properties. Various reports have been published on the incorporation of atoms other than carbon into the spirocycle. The work outlined in this dissertation involves the development of synthetic methodologies for the synthesis of hetero-spirocycles via superacid-promoted cyclization reactions. These concepts are summarized in Chapter 1.

Chapter 2: Aromatic imines were prepared from 9-fluorenone and azafluorenones, and these substrates were reacted in the Brønsted superacid, triflic acid, …

Supramolecular Self-Assemblies Of Ru( Ii ) Phototherapeutics: Biological Activity Of Micro- And Nano-Particles Acting As Reservoirs, Jérôme Laisney, Sarah M. Kriger, Dmytro Havrylyuk, Jason M. Unrine, David K. Heidary, Edith C. Glazer

Chemistry Faculty Publications

Ruthenium( II) coordination complexes have many appealing properties as prodrugs, but can suffer from poor aqueous solubility and short circulation times, drastically decreasing efficiency in vivo. Nanoformulations using a variety of carriers, such as inclusion in polymers/lipids or adsorption on inorganic nanoparticles have been applied to overcome this limitation, but unfortunately, these approaches raise additional concerns regarding the fate of the carriers, with potential long-term toxicity and accumulation in vital organs. Here, we present an alternative delivery strategy with formation of pure and polymer-supported supramolecular self-assemblies of Ru(II) complexes acting as ‘‘reservoirs’’. A facile preparation of size-controlled particles was achieved …

Characterization And Antimicrobial Activity Of Lignin-Derived Compounds In Ground Hurd Tissue Of Cannabis Sativa L. (Hemp) Cultivars, Jourdan E. Lakes, Anjam Sadik, Robert C. Pearce, Barbara L. Knutson, Stephen E. Rankin, Bert C. Lynn, Michael D. Flythe

Chemistry Faculty Publications

Objectives: Characterize lignin-derived compounds from the hurd of 10 fiber/grain Cannabis sativa L. cultivars and investigate the antimicrobial activity of select compounds on the wasteful ruminant bacterium, Acetoanaerobium sticklandii SR.   Methods: Hurd was processed using an aqueous ethanol solvent system and analyzed via GC-MS to identify and characterize lignin derivatives. Antimicrobial activity of the hurd and three monomers was assessed using solid (hurd) and liquid medium (monomers) bioassays against SR.   Results: 27 compounds were identified, most as monomers but a few were dimers, ethylated derivatives, and organic acids. There were approximately equal G- and S-units with substantially fewer H-units. Several …

A Critical Perspective On The Society Of Environmental Toxicology And Chemistry's Adherence To Founding Principles— Opportunities For The Future, Barnett A. Rattner, Annegaaike Leopold, Carys L. Mitchelmore, Glenn W. Suter, Mark S. Johnson, Adriana C. Bejarano, Lawrence A. Kapustka, Niranjana Krishnan, Derek C. G. Muir, Beatrice O. Opeolu, Martha Georgina Orozco-Medina, April Reed, Bruce W. Vigon, Adam R. Wronski

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

The Society of Environmental Toxicology and Chemistry (SETAC) is a global organization whose mission is the advancement of environmental science and management through collaboration, leadership, communication and education. On SETAC's 45th anniversary, the following question was raised: Are the 1979 founding principles of SETAC, multidisciplinary approaches to solving environmental problems, multisector engagement and scientific objectivity, still useful, adequate and effective in fulfilling its mission? In a special session held at the 45th Annual Meeting in Fort Worth, Texas, United States, a critical evaluation of the founding principles was initiated by reviewing SETAC's history and ongoing activities, and recommendations were made …

Comparison Of Push-Pull Air Curtain To Overhead Downdraft Systems On Aerosol Containment And Distribution In Controlled Environments, Manal Mutairi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Abstract

Comparison of Push-Pull Air Curtain to Overhead Downdraft Systems on Aerosol Containment and Distribution in Controlled Environments.

This dissertation looks at the ongoing issue of tiny airborne particles created during medical and dental procedures and evaluates ways to reduce the risk of exposure for healthcare workers and patients to these particles. The first study focuses on the size, how long particles stay in the air, and how far they travel from common medical procedures that create aerosols, showing that tiny particles (less than 5 µm) can stay in the air long enough to escape basic droplet controls. As a …

Deep Learning-Based Co-Current Upward Gas-Liquid Two-Phase Flow Regime Identification In An Annular Conduit, Joshua Robert Macomber

Graduate Theses, Dissertations, and Problem Reports (ETD)

Flow regime identification in co-current upward gas-liquid flow through annular conduits remains a significant challenge in petroleum engineering, with major safety and operational implications. It is also important across industries involving the transport of multiphase fluids. Misidentifying flow regimes can introduce major operational risk, yet regime boundaries in annular gas-liquid flow are often visually complex and context dependent.

The objective of this study was to evaluate the utility of convolutional neural network (CNN) classifiers for flow regime identification. The CNN was trained using annular flow image dataset published by Texas A&M University. The dataset consists of approximately 947 RGB images …

Operationalizing Cyber-Routine Activities Theory For Senior Cybercrime Prevention: An Evaluation Of The Shield Training-The-Trainer Program, Kyung-Shick Choi, Insun Park, Mijin Kim, Ji Yae Bong

International Journal of Cybersecurity Intelligence & Cybercrime

Older adults face growing risks of cyber-enabled fraud, yet scalable, evidence-based prevention programs remain limited. Guided by Cyber-Routine Activities Theory (Cyber-RAT), this study evaluates the pilot implementation of the Seniors Harnessing Internet Education for Lasting Defense (SHIELD) Training-the-Trainer program, designed to prepare law enforcement officers and community leaders to deliver cybercrime prevention education to older adults. A key innovation of SHIELD is its integration of interactive game-based simulations, which allow participants to practice verification, refusal, and reporting behaviors in realistic cybercrime scenarios. Following the December 2025 pilot session in Boston, semi-structured interviews were conducted with 12 participants from law enforcement, …

Assessing Forest Health And Small Mammals After A Limited Suppression Wildfire In Colville National Forest, Samantha J. Kennel

EWU Masters Thesis Collection

In the face of a wildfire crisis, there is a growing need to expand the pace and scale of forest treatments, including the strategic use of wildfire as a management tool. However, ecological outcomes remain uncertain in forests shaped by more than a century of fire suppression. The 2022 Thor Fire, a managed wildfire in the Colville National Forest, Washington, provides an opportunity to evaluate forest health in a relatively understudied system. Using a control–impact design, I established 100 monitoring plots in burned and adjacent unburned forests to assess how wildfire and fire severity influence forest structure, fuels, and tree …

Relationships Between Benthic Macroinvertebrate Communities And Environmental Conditions In Headwater Tributaries Of The Pend Oreille Lake Watershed, Idaho, Devlin Mee

EWU Masters Thesis Collection

Benthic macroinvertebrates are widely used indicators of stream condition, and their communities respond to thermal and land-use conditions in headwater streams. This study characterized macroinvertebrate biomass, community composition, and diversity across forested headwater tributaries of the Pend Oreille lake watershed in northern Idaho, and examined their relationships with summer temperature, land development, and road proximity. Samples from thirteen streams collected in 2024 were identified to genus, measured, and converted to estimated biomass using published length–mass regressions; ten streams had recovered temperature loggers. Because environmental variables were characterized once per stream, all analyses were conducted at the stream level.

Estimated total …

From Physical Correlation To Emotional Connection: The Role Of Passive Haptics On Empathy In Virtual Reality, Jemely Robles

Dartmouth College Master’s Theses

Virtual reality is increasingly explored as a tool for cultivating empathy, and haptic feedback as a tool for enhancing immersion. This paper investigates the effects of combining the two.  Fifty-two participants experienced a custom-built VR scene in which a character was shown packing up a room. Participants were assigned to either a haptic condition, receiving passive haptic feedback corresponding to the character's actions, or a non-haptic control condition that did not receive any haptic input. Trait empathy was measured beforehand, and state empathy and engagement were measured after the experience. Thematic analysis was conducted on post-study interviews, and headset recordings …

Artem: Enhancing Large Language Model Agents With Spatial-Temporal Episodic Memory, Cassandra Hui Ming Tan, Budhitama Subagdja, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

Current large language models (LLMs) exhibit significant deficiencies in episodic memory tasks including encoding, storing, and retrieving specific information from temporally dependent events over a long period of time. Recent approaches to handle memory tasks in LLMs, such as in-context learning, retrieval-augmented generation (RAG), and fine-tuning, may resolve the long-term retention issues, but are still inadequate to handle tasks requiring chronological awareness of the stored information. We introduce Agentic Retrieval with Temporal-Episodic Memory (ARTEM), a hybrid LLM-based agent architecture integrating LLMs with a self-organizing neural network named Spatial-Temporal Episodic Memory (STEM), designed to handle episodic memory tasks. Our approach employs …

Memoryart: Enhancing Llms Via Multi-Memory Models With Adaptive Resonance Theory For Healthcare Agents, Renke Dai, Hebin Hu, Jiahui Zhang, Yilin Kang, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

Though promising in healthcare consultation applications, large language models (LLMs) face critical limitations in retaining and utilizing long-term memory across multiturn interactions. In particular, existing memory enhancing paradigms are constrained by limited context windows and embedding-based retrieval, often failing to maintain task relevance and still suffering from memory prototype collapse in multi-turn healthcare consultation. To address these challenges, we propose a cognitively-inspired memory framework named MemoryART, which is grounded in Adaptive Resonance Theory (ART)—a cognitive and learning theory of how humans and animals adapt to dynamic environments. MemoryART employs three memory modules—working memory, episodic memory, and semantic memory to support …

Synthesis And Characterization Of Succinate Dehydrogenase Inhibitors H2/Z14 And C6/Z96 In Order To Combat Small Cell Lung Cancer, Lauren M. Graves

Honors Undergraduate Theses

The use of ubiquinone inhibitors to combat cancer is a recent development in medicinal science and procedures to efficiently synthesize these drugs remain limited. C6/Z96 and H2/Z14, two succinate dehydrogenase inhibitors, have been previously tested in vitro against NSCLC with positive results. Their similarity to ubiquinone is what makes them a strong candidate for a succinate dehydrogenase inhibitor at the ubiquinone binding site. The heterocyclic scaffolds and substituents are proposed to bind strongly through a combination of electronics, hydrogen-bonding, and fit, allowing them to bind well and prove to be more favorable than ubiquinone when competing for the Q-site. By …