Digital Commons Network^™

Advancing Precision And Autonomy In Agriculture And Medical Imaging Through Ai And Computer Visions, Tan-Hanh Pham

Theses and Dissertations

Deep learning has revolutionized numerous fields by enhancing precision, automation, and decision-making capabilities. This dissertation explores its applications in agriculture and medical image processing, introducing novel methodologies to improve accuracy and efficiency in these domains. These fields hold critical societal importance -- agriculture underpins global food security and sustainability, while medical imaging drives advancements in diagnostics and personalized healthcare, both benefiting significantly from data-driven innovations. In agriculture, deep learning is applied to precision spray systems through droplet analysis. Specifically, a generative model is designed to create synthetic droplet images, addressing the challenge of limited training samples, which are expensive …

Comparative Analysis Of Regression And Random Forest Models For Player Performance Prediction In The Mls, Joshua Clement Madeti

Senior Honors Theses

Advanced technology and analytics have transformed the world and have benefited several industries throughout, the sport industry being one of them. Data is constantly generated during sports and requires post-game or post-season analysis which is crucial to team and player success. In this paper, the researcher will focus on the impact of analytics on soccer and soccer players. With over three billion active fans, soccer is the most famous sport in the world yet, when it comes to analytics, it is lagging. The thesis includes a comparative study of multiple linear regression and random forest regression to explore whether these …

Innovative Methods For The Design And Analysis Of Phase Ii Clinical Trials, Feng Tian

Dissertations and Theses (Open Access)

Drug development has become increasingly time-consuming, costly, and risky in recent years. There is significant potential for improving clinical trial designs, particularly for phase II trials, which play a critical role in the drug development process. Innovative methods are especially necessary for addressing key challenges in phase II trials in terms of dose-ranging study, patient population selection, and decentralized clinical trials (DCTs). This dissertation presents a comprehensive set of methodologies that address these critical issues with three projects. The first project introduces a Bayesian adaptive dose-ranging design that integrates both efficacy and toxicity data to evaluate each dose comprehensively. The …

Dual-Criterion Dose Finding Designs For Phase I Clinical Trials, Yunlong Yang

Dissertations and Theses (Open Access)

The primary objective of Phase I oncology trials is to assess the safety and tolerability of novel therapeutics. Conventional dose escalation methods identify the maximum tolerated dose (MTD) based on dose-limiting toxicity (DLT). However, as cancer therapies have evolved from chemotherapy to targeted therapies, these traditional methods have become problematic. Many targeted therapies rarely produce DLT and are administered over multiple cycles, potentially resulting in the accumulation of lower-grade toxicities, which can lead to intolerance, such as dose reduction or interruption. To address this issue, we proposed dual-criterion designs that find the MTD based on both DLT and non-DLT-caused intolerance. …

Development Of Lineal Energy Spectrum-Based Biological Effects Models For Protons, Joseph M. Decunha, Fada Guan, David Grosshans, Zhongxing Liao, Dragan Mirkovic, Oleg Vassiliev, Radhe Mohan

Dissertations and Theses (Open Access)

In this dissertation, methods are developed and described to allow for the rapid calculation of microdosimetric spectra (specifically, lineal energy) for protons. SuperTrack, a GPU-accelerated tool for calculation of microdosimetric spectra was developed and is capable of computing lineal energy spectra up to 5000x faster than using Geant4 directly. Proton lineal energy spectra generated by SuperTrack are indistinguishable from those generated by Geant4. With SuperTrack, large libraries of lineal energy spectra for monoenergetic protons spanning 0-300 MeV have been developed. The proton lineal energy spectra calculated by SuperTrack have been compared to experimental measurements made by a tissue equivalent proportional …

Novel Statistical Methods For Mediation Analysis With High-Dimensional Omics Mediators, Zhichao Xu

Dissertations and Theses (Open Access)

Mediation analysis is a widely used statistical method for examining how molecular traits, such as gene or protein expression, act as intermediaries linking an exposure to a health outcome. For example, it can help explain how smoking affects disease risk through molecular changes. The rapid progress in high-throughput omics profiling technologies and large-scale epidemiology consortia, such as the Trans-Omics for Precision Medicine (TOPMed) program from the National Heart, Lung and Blood Institute (NHLBI) and UK Biobank, now has resulted in an extensive accumulation of genomic data for biomedical research and analysis. At the same time, it poses significant methodological challenges, …

Identifying And Characterizing Transition Cells In Developmental Processes From Scrna-Seq Data, Yuanxin Wang

Dissertations and Theses (Open Access)

During the development of multicellular organisms, individual cells make distinct decisions about their cell types and states. Understanding the molecular mechanisms underlying cellular state transitions at different developmental stages provides deep insights into physiology, morphology and the etiology of diseases. Single-cell RNA-sequencing (scRNA-seq), which is widely used to study complex cell states and dynamic gene expression patterns, enables us to investigate molecular mechanisms of cellular state transitions. Currently, however, computational tools available for identifying cellular states and state transitions remain limited.

Although trajectory-based methods such as Monocle and Slingshot assume that state transitions generate continuous expression profiles, they cannot distinguish …

The Stem Gender Gap: Can It Be Closed?, Makenna Roberts

Undergraduate Honors Capstone Projects

Despite increasing gender parity in many professional fields, women remain underrepresented in STEM industries, particularly in math-intensive areas such as engineering, computer science, and physics. This report explores the persistent gender gap in STEM through analysis of two data sources: gendered differences in the US national Scholastic Aptitude Test (SAT) performance and post-graduate employment patterns among scientists and engineers.

The first portion of the analysis examines SAT score data from 2018 to 2024, with a focus on high-performing test-takers. Using Python and R, data was extracted and visualized to compare male and female performance on the Math and Evidence-Based Reading …

Reevaluating The Drumian Carbon Isotope Excursion (Dice) In Western-Central Utah, Michelle M. Norman

Undergraduate Honors Capstone Projects

The Drumian Stage of the Cambrian Period is defined by the First Appearance Datum (FAD) of the cosmopolitan trilobite Ptychagnostus atavus in 504.5 Ma strata deposited on the slope and shelf of the Laurentia margin. The Drumian Global Stratotype Section and Point (GSSP), showing the best preserved example of P. atavus compared to global outcrops, is defined in the Drum Mountains of west-central Utah. Due to the inconsistent nature of fossil preservation, researchers have sought secondary proxies to identify Drumian-aged strata in the absence of age-diagnostic fauna. One key proxy is the Drumian Carbon Isotope Excursion (DICE), an ~-2.5‰ carbon …

Investigation Into The Effectiveness Of G-C3n4 For The Degradation Of Indigo Dye In Aqueous Solution Via Electrocatalysis, Rolando R. Barron Jr

Theses and Dissertations

Indigo dye (IUPAC 2-(3-hydroxy-1H-indol-2-yl)indol-3-one) is one of the most used dyes in the textile industry worldwide with more than 40,000 tons produced each year. It can elicit adverse physiological responses in humans including vomiting, diarrhea, and other gastrointestinal conditions, and it is toxic in large amounts. There is also evidence to suggest that indigo is a teratogen and genotoxic in aquatic life. Environmentally, the enormous amount of indigo used in the textile industry has caused rivers and waterways to run blue as well as severely impacting aquatic and plant ecosystems. The chemicals used in its synthesis are also …

Cranial Ontogeny Of The Extinct Dwarf Tapir Tapirus Polkensis; With Comparison To That Of The Extant Tapirus Bairdii (Tapiridae, Perissodactyla), Johannah Orendorff

Electronic Theses and Dissertations

Tapirus polkensis is the smallest known species of tapir to ever live, and the largest deposit of their fossils is currently located at the GFS in Gray, TN. Phylogenetics suggest that the extant T. bairdii may be the sister taxon to T. polkensis, although they differ greatly in their morphology. Variation exists among adult T. polkensis specimens, with patterns not present in T. bairdii. For this study, as series of 2D GMAs, with TPSs, were rendered on 10 skulls of T. polkensis and 48 skulls of T. bairdii, across both species’ ontogenetic series. Analyses confirmed that growth …

Molecular Insights: Advances In Single Molecule And Single Particle Detection For Analysis Of Chemical, Physical, And Biological Phenomena, James Ethan Batey

Chemistry & Biochemistry Undergraduate Honors Theses

This thesis is focused on recent advancements made in the field of chemical imaging, optical microscopy, and recent developments that have improved spatial, temporal, or spectral resolution or have made certain techniques more accessible and cost effective for their wider adoption. This thesis is organized based on the systems of interest we studied with each new technique. Although, it is important to note that many of the methods here can be used with a multitude of systems even if not explicitly mentioned. The first chapter of this thesis will discuss the current state of chemical imaging, common terminology, and important …

Understanding The Impact Of Ransomware On Biotechnology, Tswvyim Vang

Electronic Theses, Projects, and Dissertations

Biotechnology encompasses the use of research on both biology and technology to create products that can advance in areas such as healthcare and agriculture. Because of the technology and products that arise from the use of biotechnology, the industry is especially targeted by cyber-attacks. A prominent type of cyber-attack that is utilized by cyber criminals on biotechnology is ransomware. The goal of this project is to determine the impact of ransomware on biotechnology. The research questions posed are: Q1) What are real examples of ransomware attacks that have occurred on biotechnology companies and what patterns can be identified by these …

Constructing Binary Encoding Matrices From Joined Graphs, Joshua Avalos

Electronic Theses, Projects, and Dissertations

Codes and technology are part of our daily lives and allow the modern world to function, and for us to have conveniences in our lives such as smartphones that can be used to privately call people on the other side of the planet, and for secure access to the internet. In this thesis we will explore the construction of binary codes created by vertex-edge incidence matrices of planar graphs. The Hamming (7,4) code was an incredible code that allowed the detection and correction of errors after receiving them through a transmission. We will explore the possibility of the creation of …

Silver Nanoparticles In Ammonia Sensing And Photovoltaics, Madhuka Liyanage

All Dissertations

Nanocomposite films (NCF) containing silver nanoparticles (AgNPs), separated by thin layers of silica/poly-4-vinylpyridine/polyvinylpyrrolidone, were fabricated via drop casting, spin coating, dip coating on glass substrate and drop casting on nylon filter membranes. The more uniform films were produced by drop casting on nylon filter membranes due to their solvent wicking properties. The films demonstrate electrical conductivity that varies in response to moist ammonia and water vapors. The changes in conductivity are attributed to hydrogen bonding between ammonia and water molecules with the silica/polymer layers, as well as the direct adsorption of ammonia onto the silver surface. Notably, NCFs with polyvinylpyrrolidone …

Qualitative And Quantitative Analysis Of New Psychoactive Substances And Related Metabolites Using Liquid Chromatography-Ion Mobility-Mass Spectrometry (Lc-Im-Ms), Ralph Aderorho

All Dissertations

The increasing prevalence of novel psychoactive substances (NPS) in illicit drug markets has posed significant challenges for forensic and clinical toxicology, primarily due to the structural similarity and diversity among these compounds. This dissertation investigates the application of advanced liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS/MS) techniques, using the high-resolution Structures for Lossless Ion Manipulations (SLIM) platform and the drift tube ion mobility spectrometry (DT-IMS), for the qualitative and quantitative analysis of various types of synthetic opioids, synthetic cannabinoids, psychedelics and xylazine. By combining IMS separations with mass spectrometry and targeted chemical derivatization, this work enhances the ability to distinguish and characterize …

Learning Through Online Participation: From Breakout Rooms To Discord, Makayla Moster

All Dissertations

For software development teams, teamwork is an essential part of their day-to-day lives. However, due to the aftermath of the COVID-19 pandemic, more companies have allowed employees to have more hybrid and remote work options than before. As more companies are adopting hybrid and remote workstyles, we need to ensure that we are preparing the next batch of young software developers to conduct teamwork in remote and hybrid settings. In this dissertation, I address the tools students use for teamwork and how to improve their teamwork inside and outside of the classroom. I present my research on improving student experiences …

Toward The Application Of Natural Language Processing In Electronic Health Record Analysis For Taxonomy Development, Latoya Mcdonald

All Dissertations

Electronic health records (EHRs) are pivotal resources for nurse practice because they increase the timeliness and reliability of patient information at the point of care and support access by multiple healthcare providers and the individual patients themselves. However, it is widely recognized that data extraction from EHRs is challenging due to the variability in the language used in clinical care notes and the lack of standardized terminology across healthcare systems. The broad objective of this dissertation is to develop taxonomy-based classification models for nursing care by applying feature engineering approaches to EHRs that include nursing care of ostomy patients following …

Development Of Small-Molecule Inhibitors For Bacteroides, Naegleria, And Toxoplasma Microorganisms And Synthesis Of N-Heterocycles From Thiolated Ene-Ynes And Azodicarboxylates, Samuel Kwain

All Dissertations

Humans and microorganisms are intricately interconnected, with microbes constituting an essential component of human biology and ecology. This interdependence necessitates a delicate balance between leveraging beneficial microbes and mitigating the impact of harmful ones. The human gut microbiome, home to trillions of microorganisms, predominantly comprises commensal species that support health. However, dysbiosis within this ecosystem has been linked to serious diseases. For instance, an overrepresentation of Bacteroides species is associated with Type I diabetes mellitus (T1D) and various chronic gut disorders, including ulcerative colitis, inflammatory bowel disease, celiac disease, and colorectal cancer. Similarly, Naegleria fowleri, a free-living amoeba, causes …

A System And Method For Measuring Spatially Varying Surface Appearances With A Study Of Feathers, Jessica Baron-Lis

All Dissertations

Real-world materials, particularly biological structures such as feathers exhibit complex appearances that vary spatially across their surfaces. The field of computer graphics provides a means of understanding such surfaces through material modeling which uses both analytical models and data acquired from light-surface interactions. There are many efforts within the past decade in measuring materials for graphics, but common limitations in these works include not accounting for spatially varying properties and reliance on neural networks and synthetic datasets.

Feathers from modern birds present diverse appearances due to how light interacts with their unique hierarchical microstructures. Variations in those structures lead to …

Efficient Fully Bayesian Approach To Brain Activity Mapping With Complex-Valued Fmri Data, Zhengxin Wang, Daniel B. Rowe, Xinyi Li, D. Andrew Brown

Mathematical and Statistical Science Faculty Research and Publications

Functional magnetic resonance imaging (fMRI) enables indirect detection of brain activity changes via the blood-oxygen-level-dependent (BOLD) signal. Conventional analysis methods mainly rely on the real-valued magnitude of these signals. In contrast, research suggests that analyzing both real and imaginary components of the complex-valued fMRI (cv-fMRI) signal provides a more holistic approach that can increase power to detect neuronal activation. We propose a fully Bayesian model for brain activity mapping with cv-fMRI data. Our model accommodates temporal and spatial dynamics. Additionally, we propose a computationally efficient sampling algorithm, which enhances processing speed through image partitioning. Our approach is shown to be …

Single Valued Neutrosophic Hypersoft Set Based On Merec-Moosra Mcdm Methods For Evolution Of Sustainable Strategies For The Circular Supply Chain Based On The Beverage Industry, Alaa Salem, Rayan Hussein, Ahmed Abdelmouty, Mohamed Abouhawwash

Neutrosophic Systems with Applications

Corporate enterprises around the world are facing increasing pressure to operate sustainably due to rising environmental concerns such as climate change, resource scarcity, and ecological degradation. In response, circular supply chain (CSC) practices have emerged as a promising solution, especially within the manufacturing and beverage sectors. CSC focuses on reusing materials, minimizing waste, and creating value from products that have reached the end of their lifecycle. This study investigates the challenges and opportunities of applying circular supply chain management (CSCM) in the beverage industry, which is known for generating significant waste due to high production volumes. The research identifies key …

Harnessing Edna Metabarcoding To Monitor Species Diversity In Restoration Sites: Insights From Laikipia, Kenya, Cornelius Okello, Nina Wambiji, Susana W. Kihia, Nehemiah Ongeso, Samuel Mwakisha Mwamburi, Anthony Wandera, Marie Estelle Demory, Margaret Awuor Owuor

All Peer-Reviewed Publications

Restoration of degraded arid and semi-arid lands (ASALs) dryland ecosystems gained traction globally with the enactment of the Bonn Challenge and UN Decade of Restoration. This has been domesticated in Kenya's context by The Forest and Landscape Restoration Implementation Plan (FOLAREP). However, effectively monitoring restored ecosystems is crucial but challenging because of data gaps and technical hurdles, highlighting the need for innovative approaches to assess and restore biodiversity. This study aimed to pilot soil environmental DNA (eDNA) metabarcoding to detect species compositions rapidly, evaluate population structures and abundances, and characterize taxonomic groups. The results from this study serve as a …

Atomic Level Characterization For The Transport Cycle Conformational Pathways Of Multidrug Resistance Protein 1 (Mrp1), Samuel Wamwere Mwatha

Graduate Theses and Dissertations

The multidrug resistance-associated protein 1 (MRP1/ABCC1) is an ATP-binding cassette (ABC) transporter that mediates the cellular efflux of endogenous and xenobiotic substrates, including therapeutic drugs. Its overexpression is a major contributor to multidrug resistance in cancer, which tends to result in negative clinical results. Even with considerable progress made in structural biology, the intricate details of how membrane lipid composition affects the conformational changes and functional switches of MRP1 still lack explanation.

This thesis employs long-timescale, all-atom molecular dynamics (MD) simulations to study the influence of various lipids on MRP1 lipid bilayer environments. Both inward-facing and outward-facing conformations of MRP1 …

Biophysical Studies Of Nucleic Acid - Small Molecule Recognition, Andrea Conner

All Dissertations

The presented work is a collection of studies performed to examine small molecule recognition of nucleic acids. Recognition of nucleic acids was examined using two types of small molecules: aminoglycosides and Hoechst dyes. Chapter One focuses on established experimental techniques (i.e. absorbance, isothermal titration calorimetry, flow cytometry, cell microscopy, etc.) in small molecule recognition of nucleic acids. The emphasis of studies in the group has been on two focus areas. (i) Thermodynamic characterization of mixed A-form and B-form DNA or RNA conformation with aminoglycosides, particularly neomycin-class. (ii) Characterization of new Hoechst-morpholine (HT-MO) derivatives’ interactions with nucleic acids.

Focus area (i) …

Synthesis Of Nanoparticles In Silicate Matrix And Stimuli Responsive Nanocomposite Polymer Films, Dimuthu Edirisinghe

All Dissertations

Interactions between aqueous metal ions and soluble silicates lead to the formation of insoluble metal silicate complexes that form nanoparticles via condensation polymerization. Metal silicates function as nanoreactors, effectively condensing metal ions into nano-sized particles that can undergo further chemical transformations. Core-shell nanostructures present an intriguing strategy for integrating materials with different properties. The silicate shell around the silver nanoparticles can be successfully infused with other metal ions, enabling subsequent reactions to tailor their properties. Silver nanoparticles exhibit strong interactions with light, surpassing other chromophores, including noble metal nanoparticles, due to their highly efficient surface plasmonic resonance. The unique optical …

Strengthening The Bonds Between Us: An Empirical Investigation Of Morale In Human-Ai Teams And The Socially Supportive Ai Teammates Who Empower It, Rohit Mallick

All Dissertations

This dissertation investigates how artificial intelligence (AI) can be designed to improve the collective emotion within a team. A team's collective emotion, or morale, describes how motivated, optimistic, and enthusiastic the group is in accomplishing its goals. We conducted four studies that compared different social support strategies that AI teammates can provide to the team. Study 1A found that AI teammates who communicate with emotions can better motivate human team members and promote awareness of team dynamics and environmental changes. Study 1B found that human teammates become more motivated and happier when their AI teammates express joy and are close …

Thermal Performance Drifts Between The Egg Parasitoid Telenomus Remus And The Fall Armyworm May Threaten The Efficacy Of Biological Control Under Climate Change, Macdonald Mubayiwa, Honest Machekano, Brighton M. Mvumi, Winnifred A. Opio, Bame Segaiso, Frank Chidawanyika, Casper Nyamukondiwa

All Peer-Reviewed Publications

The fall armyworm, Spodoptera frugiperda J.E. Smith, is a significant global agricultural pest known for its rapid invasion and devastating impact on crops. While pesticides may be effective for controlling the pest in the short-term, they cause several socioeconomic and ecological costs that highlight the need for more sustainable management strategies. Telenomus remus (Nixon) is a promising egg parasitoid for its biological control. For the parasitoid to provide effective ecosystem services, it should be able to survive and coexist within the same ecological niches as its host. However, there is limited information regarding the potential responses of T. remus to …

Analyzing Sleep Staging And Cognitive Transitions Using Fmrl Time Series Analysis, Qingwen Zeng

Arts & Sciences Graduate Student Theses and Dissertations

Understanding sleep stages and their underlying cognitive transitions is essential for advancing our knowledge of brain function. While sleep staging has traditionally relied on electroencephalogram (EEG), this study explores the feasibility of classifying sleep stages using only functional Magnetic Resonance Imaging (fMRI) data. We investigate the use of Hidden Markov Models (HMM) and Hierarchical Dirichlet Process Hidden Markov Models (HDP-HMM) to capture temporal brain-state dynamics from task-free fMRI recordings. A series of pipelines—including sliding window, two-stage majority filtering, and prototype-based mapping via the Hungarian algorithm—were implemented to align model-inferred states with EEG-defined sleep stages. Among the twelve tested pipelines, the …

Random Processes With High Variance Produce Scale Free Networks, Josh Johnston

Boise State University Theses and Dissertations

The degree distribution of a real world network --- the number of links per node --- often follows a power law, so some hubs have many more links than traditional graph generation methods predict. For years, preferential attachment and growth have been the proposed mechanisms leading to these scale free networks, exemplified by the Barabási–Albert model. This dissertation provides an alternative model using a randomly stopped linking process, showing that mixtures of geometric distributions can lead to power laws, an intuition suggested by the Central Limit Theorem for distributions with infinite variance. Having a collection of Bernoulli trials with high …