Digital Commons Network^™

Stability Insights From Modeling Chronic Myelogenous Leukemia, Giovani Thai

Master's Theses

This thesis centers around a model for chronic myelogenous leukemia (CML) as it behaves under imatinib treatment, a common medication for CML patients, and the anti-leukemia immune response. The dynamics are represented with a system of nonlinear delay-differential equations first constructed by Kim et al. in 2008, capturing population changes of T-cells and various CML growth stages. We investigate stability in both the clinical and mathematical sense. Through numerical simulations, we computationally incorporate a supplementary treatment plan to determine its effectiveness in aiding immune response and medication in achieving remission and full elimination. The primary goal is to conduct a …

A Novel Fractional Order Model For Analyzing Counterterrorism Operations And Mitigating Extremism, Mutaz Mohammad, Isa Abdullahi Baba, Evren Hincal, Fathalla A. Rihan

All Works

This study examines the profound impact of terrorism on individuals and society by developing a fractional-order mathematical model to analyze and enhance counterterrorism efforts. The model accounts for the persistent and complex nature of extremist behavior, particularly emphasizing the importance of preventing violent extremism before it escalates into terrorism. Real-world data on terrorist activities in Nigeria – specifically from the Boko Haram insurgency – was used to calibrate and validate the model, ensuring its relevance and accuracy. The model reveals that the basic reproduction number (R0) plays a decisive role in determining the long-term success of counterterrorism strategies. Numerical simulations …

Characterization Of Sars-Cov-2 Replication And Transcription Complexes Via Structural And Evolutionary Approaches, Amelie Ghirardo, Ben Shabatian, Avishai Aghelian, Kyle Tau, Eleonora Gianti

Undergraduate Research

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused around 700M cases and over 7M COVID-19-related deaths recorded worldwide (World Health Organization, March 2025). Aiming to effectively combat this and other disease-causing Coronaviruses (CoV), unprecedented research efforts led to the development of new vaccines and antiviral therapies. Due to emergence of variants of concern (VOCs) with increased transmissibility, immune evasion from vaccination, and potential to resist the available treatments, SARS-CoV-2 continues to represent a major threat to global health. Hence, there is a pressing need to discover new antivirals with broad-spectrum efficacy against multiple SARS-CoV-2 variants and related CoVs. This project …

Computational Approach: 3d-Qsar, Molecular Docking, Molecular Dynamics Simulation Investigations, Drug- Like-Ness, And Dft Score Evaluation Of A Potential Novel And Retrosynthesis Of Some Tr-H Derivatives As Streptococcus Pneumoniae Drug., Belaidi Mustapha, Tchouar Noureddine, Djelilate Mohammed, Saleh Bufarwa, Dalal K. Thbayh

Karbala International Journal of Modern Science

Streptococcus pneumoniae is the main source of hospital-acquired pneumonia and meningococcal pneumonia in children, adults, and the elderly, especially the immunocompromised. Recently, it has attracted the attention of many research studies around the world as a potential target for remediation. TR-H are considered SP antibacterial agents, as they can inhibit. To describe their mode of action and to identify new antibacterial drugs against Streptococcus pneumoniae exhibiting the TR-H scaffold, the present work included 3D-QSAR, in- silico pharmacokinetic evaluation and molecular simulation modelling of TR-H. Using an atom-based method for quantitative structure-activity relationship (QSAR) study, a comprehensive 3D-QSAR model …

Evaluating San Francisco Urban Green Spaces And Policy To Inform Future Decision-Making: How Climate Change Adaptation Strategies Can Be Prioritized And Incorporated In Urban Park Design And Planning Through A Decision-Making Tool, Holley Anne Maassen

Master's Projects and Capstones

Amid the current climate crisis, enhancing urban green spaces (UGS), parks, and open spaces with climate change adaptation (CCA) as a strategic pillar in San Francisco’s urban planning is an essential strategic pillar to develop more resilient cities. However, in complex bureaucratic landscapes, integrating CCA strategies that meet project goals while ensuring inclusive stakeholder engagement presents a challenge. This project presents the identification, development, and application of a holistic decision-making tool (DMT) in the form of a Pugh matrix/decision matrix and with a focus on urban planning in San Francisco, California. Key decision-making criteria are identified and weighted through a …

Climate Change Impacts On Drinking Water Security: A Comparative Study In Australia’S Remote Central Australia And Torres Strait Islands, Nina Lansbury, Julia Bradford, Sandra J. Creamer, Geoffrey Evans

Journal of the Australian Indigenous HealthInfoNet

Aboriginal and Torres Strait Islander communities are well adapted to the many different environments in which they have lived for thousands of years. However, their environments and communities are highly vulnerable to impacts of anthropogenic climate change, including increasing threats to the security of drinking water supplies. Climate change is intensifying the significant social and economic disadvantage Australia’s Aboriginal and Torres Strait Islander communities face from poverty, poor housing, and poor health including high exposure to infectious and other diseases. Lack of sufficient safe, clean, drinking water could force Aboriginal and Torres Strait Islander people to leave their homelands, adding …

Chemical Reversal Of Beta-Lactam Resistance And Induction Of Hyper-Susceptibility In Pseudomonas Aeruginosa By Limiting Horizontal Gene Transfer Under Beta-Lactam Stress, Aimee Iradukunda

Dissertations - ALL

The emergence of antibiotic resistance poses a significant threat to global health, with certain bacterial strains evolving to resist multiple drugs. Urgent action is necessary to develop new antibacterial agents that effectively target these resistant strains; however, no new classes of antibiotics have been approved in recent decades. This research employs innovative biological tools to identify and highlight factors influencing resistance dynamics. Additionally, this study refines the novel approach by utilizing adjuvants to chemically repurpose existing antibiotics and improve their effectiveness against antibiotic-resistant strains. Pseudomonas aeruginosa, recognized for its adaptability, persistent infections—especially in cystic fibrosis patients—and widespread antibiotic resistance, serves …

Identification And Preclinical Assessment Of Novel Therapeutic Modalities In Environmental Exposure-Induced Lung Disease, Aaron D. Schwab

Theses & Dissertations

Environmental lung diseases are preventable respiratory conditions either caused or made worse by inhaled environmental exposures. Contemporarily, environmental lung diseases are most associated with workplace exposures given specific occupational processes aerosolize inflammatory agents that can be inhaled at high concentrations. Although a considerable amount is known regarding immunoglobulin (Ig)E-mediated responses to environmental exposures, little is known about non-IgE mediated respiratory conditions resulting from lipopolysaccharide (LPS)-enriched organic dust exposure(s). Chronic respiratory diseases such as asthma, hypersensitivity pneumonitis, chronic obstructive pulmonary disease (COPD), and pulmonary fibrosis have all been identified as environmental lung diseases caused or exacerbated by such environmental dusts. Therapeutic …

Intrinsic And Extrinsic Drivers Of Bioaerosol Decay: Investigating Pathogen Stability Of Bacteriophage Ms2, Sin Nombre Virus, And Sars-Cov-2 In Simulated Environments, Elizabeth A. Klug

Theses & Dissertations

The threat posed by a virus as a bioaerosol depends largely on its stability under various environmental conditions (relative humidity (RH), sunlight, ozone, etc.). This stability is typically studied through aerosol decay—how the virus' viability changes over time when exposed environmental conditions. The Goldberg rotating drum, a widely used tool for studying bioaerosols, has been the basis of such research (Goldberg et al., 1958). However, it has significant limitations, including an inability to measure initial pathogen infectivity loss and the use of small sample volumes. Additionally, it does not answer the question of what intrinsic factors (lipids, proteins, nucleic acids) …

A Modified Sir Model Used To Investigate The Relationship Between Congenital And Adult Syphilis, Kaleesta R. Waysman

Honors Thesis

A complex SIR model integrating the relationship between adult and congenital syphilis was developed. The goal of the project was to determine the specific population(s) or control strategies that should be enforced, altered, or removed to decrease the number of children experiencing clinical sequelae due to congenital syphilis. Early clinical sequelae include hydrops fetalis, preterm birth, central nervous system infection, hepatosplenomegaly, hyperbilirubinemia, cholestasis, hemolytic anemia, snuffles, osteochondritis, and lesions or rashes in the palms and soles. Late clinical sequelae include interstitial keratitis, hearing loss, Hutchinson teeth, saber shins, Clutton joints, mulberry molars, and saddle nose. After implementing real-world data into …

Synthesis Of Sensitive Oligodeoxynucleotides Containing Acylated Cytosine, Adenine, And Guanine Nucleobases, Komal Chillar, Rohith Awasthy, Marina Tanasova, Shiyue Fang

Michigan Tech Publications

Background/Objective: Oligodeoxynucleotides (ODNs) containing base-labile modifications such as N4-acetyldeoxycytidine (4acC), N6-acetyladenosine (6acA), N2- acetylguanosine (2acG), and N4-methyoxycarbonyldeoxycytidine (4mcC) are highly challenging to synthesize because standard ODN synthesis methods require deprotection and cleavage under strongly basic and nucleophilic conditions, and there is a lack of ideal alternative methods to solve the problem. The objective of this work is to explore the capability of the recently developed 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) method for the incorporation of multiple 4acC modifications into a single ODN molecule and the feasibility of using the method for the incorporation of the 6acA, 2acG and 4mcC modifications into ODNs. Methods: …

Architecture Of Pseudomonas Aeruginosa Glutamyl-Trna Synthetase Defines A Subfamily Of Dimeric Class Ib Aminoacyl-Trna Synthetases, Michael K. Fenwick, Stephen J. Mayclin, Steve Seibold, Amy E. Derocher, Sandhya Subramanian, Isabelle Q. Phan, David M. Dranow, Donald D. Lorimer, Ariel B. Abramov, James M. Bullard

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, “pipe strap” conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation …

Compartmental Disaggregation: Bridging Simulation And Sampling Methods For Synthetic Population Data Generation, Dylan Mack

McKelvey School of Engineering Graduate Student Theses & Dissertations

As agent-based models (ABMs) grow increasingly widespread in public health, their associated challenges have become all the more significant. Lauded for their ability to capture population heterogeneity, nonlinear dynamics, and emergent behaviors, disease ABMs are also computationally expensive and often require detailed inputs that describe each agent at the individual-level, known as synthetic population data. Current approaches for synthetic population data generation generally fall into one of two categories: sampling or simulation. These methods are both feasible only under restricted conditions and suffer from challenges surrounding data availability and computing power. This thesis proposes compartmental disaggregation, an intermediate method for …

Shortage To Surge - Studying The Post-Covid-19 Guitar Retail Market, Jed H. Kim

Data Science Undergraduate Honors Theses

The COVID-19 pandemic was one of the most catalyzing events of the 21st century, leading to supply chain disruptions, lifestyle changes, and a massive shift towards digital technologies. During the COVID-19 lockdown, many people had more free time, and over 16 million individuals learned to play guitar in the first 2 years of the pandemic. According to a study by Fender, 62% of these new guitar learners cited the pandemic as their primary reason for learning the instrument. However, pandemic policies and supply chain disruptions meant that many guitar retailers were unable to satisfy demand, and backorders accumulated. After the …

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 …

Comparison Of Rt-Qpcr And Rt-Ddpcr On Assessing Model Virus In Wastewater, Wafa Youssfi

Graduate Theses and Dissertations

There is an increasing demand for quantifying viral loads in diverse wastewater systems using polymerase chain reaction (PCR). This study evaluates the performance of two commonly used workflows: reverse transcription quantitative PCR (RT-qPCR) and reverse transcription droplet digital PCR (RT-ddPCR) in wastewater. We compared the two methods by measuring the viral ribonucleic acid (RNA) of a model virus Phi6 in samples collected from various treatment stages at the Westside Wastewater Treatment Facility in Fayetteville, AR. RNA was extracted from real and synthetic wastewater samples and analyzed in parallel using both RT-qPCR and RT-ddPCR. Findings reveal that both methods demonstrated similar …

Alphamissense Predictions And Clinvar Annotations: A Deep Learning Approach To Uveal Melanoma, David J. Taylor Gonzalez, Mak B. Djulbegovic, Meghan Sharma, Michael Antonietti, Colin K. Kim, Vladimir N. Uversky, Carol L. Karp, Carol L. Shields, Matthew W. Wilson

Wills Eye Hospital Papers

OBJECTIVE: Uveal melanoma (UM) poses significant diagnostic and prognostic challenges due to its variable genetic landscape. We explore the use of a novel deep learning tool to assess the functional impact of genetic mutations in UM.

DESIGN: A cross-sectional bioinformatics exploratory data analysis of genetic mutations from UM cases.

SUBJECTS: Genetic data from patients diagnosed with UM were analyzed, explicitly focusing on missense mutations sourced from the Catalogue of Somatic Mutations in Cancer (COSMIC) database.

METHODS: We identified missense mutations frequently observed in UM using the COSMIC database, assessed their potential pathogenicity using AlphaMissense, and visualized mutations using AlphaFold. Clinical …

Implementing And Evaluating An Ai-Powered Visual Decision Support System To Improve Antibiotic Usage Among Physicians With A Built-In Early Warning System, Akua Sekyiwaa Osei-Nkwantabisa

Theses and Dissertations

The widespread misuse and excessive prescription of antibiotics have played a pivotal role in the emergence and proliferation of antibiotic-resistant bacteria, posing a critical global public health crisis. Addressing this challenge necessitates innovative solutions that enhance antimicrobial stewardship. This study presents the development and implementation of a visual decision support system designed to monitor and optimize antibiotic usage among healthcare providers. The proposed system integrates advanced machine learning algorithms with real-time data analytics to provide a dynamic, evidence-based decision support tool. Specifically, a neural network model was developed after evaluating multiple machine learning approaches, including Random Forest, Logistic Regression and …

Network-Based Attacks In Cloud Computing In 2020-2024, Yaswanth Sai Manikanta Anguluri

Electronic Theses, Projects, and Dissertations

As the use of cloud technologies has increased in the past five years, the number of network attacks is also increasing. During 2020 to 2024, there are lot of changes in cloud technologies which led to various network attacks in the cloud computing environments from 2020 to 2024. This study investigates the evolution of network-based attacks in cloud environments from 2020 to 2024. Data was collected from Kaggle website to analyze the trends of the evolution of network-based attacks. The research questions are: (Q1) How do the trends change in network-based attack from 2020 to 2024 and why? (Q2) Which …

Navigating The Challenges Of Coccidioides Surveillance: Insights From The Environment Of El Paso County, Texas, Tanzir Hossain

Open Access Theses & Dissertations

Coccidioidomycosis, or Valley fever, is a fungal infection resulting from the inhalation of spores from the Coccidioides species (C. immitis and C. posadasii), native to arid areas of the Western Hemisphere. Coccidioidomycosis presents considerable health hazards and can be fatal. It affects between 206,000 and 360,000 individuals annually, leading to 700 to 1,100 fatalities in the United States alone. In response to these issues, extensive research has concentrated on therapeutic goals for this infectious disease. Nonetheless, more limited research has focused on the environmental detection of its causative fungi, which is crucial for forecasting treatment needs and formulating preventive strategies. …

Machine Learning And Protein Engineering Approaches To Understanding Kinesin-5 Activity, Jason Eden Sanchez

Open Access Theses & Dissertations

Cancer is a term describing a collection of diseases that result in uncontrolled cell growth. Cancer has manifold etiologies and underlying cancers are rouge biochemical pathways involving many different proteins. In the current work, two approaches are used to enhance knowledge of kinesin-5, a potential cancer target involved in cell division. Kinesin-5 promotes cell division by cross-linking and separating microtubules in dividing cells. The first approach uses machine learning (ML) to identify small molecule inhibitors for kinesin-5. Though decades of research have uncovered classes of small-molecules which inhibit kinesin-5 in vitro and in vivo, no candidates have reached phase III …

Mathematics-Ai Based Phylogenetic Analysis Of Influenza Virus Mutation Data, Emilee Walden

Mathematical Sciences Undergraduate Honors Theses

The influenza virus is one of the most common viral infections each year and can mutate rapidly. Viral mutations pose significant threats to public health by increasing infectivity and strengthening vaccine resistance. To track these evolving patterns, agencies like the CDC annually evaluate thousands of virus strains to understand viral mutagenesis and evolution in depth. Therefore, a computational method for analyzing high-dimensional, noisy virus data could aid in the rapid identification of antigens essential for an effective influenza vaccine for the upcoming season. Through the integration of genomic analysis, clustering, and dimensionality reduction methods, this study specifically aims to develop …

Exploring The Evolution Of Global Warming Discourse: A Twitter-Based Analysis Across The United States, United Kingdom, And India, Trevor Christensen

Honors Projects in Data Science

Global warming has gained increasing attention over the past decade, with public discourse intensifying on social media platforms, particularly on Twitter. This increased discussion stems from political controversies surrounding climate change and the rise in extreme weather events. This study explores the evolution of global warming discourse on Twitter, with a focus on the United States, United Kingdom, and India. This research used a dataset of historical tweets ranging from 2010 to 2023 containing the keyword "global warming." Using natural language processing (NLP) techniques such as emotion analysis, word cloud visualization, and topic modeling (LDA), approximately twenty-eight million tweets were …

The Attitudes And Perspectives Of Laboratory Professionals On The Use Of Machine Learning Combined With Maldi For Viral Identification: A Qualitative Study, Grace Johnson

Honors Projects

The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with machine learning (ML) has been proposed by numerous studies as a novel approach for viral identification. However, the development and implementation of this instrumentation is still in its early stages, and laboratory professionals' perspectives on its feasibility, accuracy, implementation, and effect on current laboratory operating procedures remain underexplored.

This study aimed to investigate laboratory professionals’ attitudes and opinions regarding the use of MALDI-TOF-MS coupled with machine learning for viral identification, focusing on perceived benefits, barriers, and factors that would affect participants’ opinions on implementation.

A qualitative descriptive research …

The Dialogue Dilemma: The Role Of Patient-Clinician Communication For Low-Income People Who Smoke And Manage Multiple Conditions, Monique T. Cano, Michael R. Lindstrom, Ricardo F. Muñoz

School of Mathematical & Statistical Sciences Faculty Publications

Introduction: Adults from low-income backgrounds who smoke face significant health disparities related to tobacco use, often at disproportionately high rates. These individuals are more likely to endure multiple mental and physical (MP) health conditions, which can negatively influence their self-rated health (SRH). The quality and effectiveness of patient-clinician communication (PCC) can influence how patients perceive their own health. Understanding how PCC influences SRH among low-income adults who smoke and suffer from multiple MP conditions is essential for clinical care as multimorbidity is on the rise. This study examines how PCC may influence the health perceptions of low-income adults who smoke …

Evaluating The Causal Effect Of Receiving Transthoracic Echocardiography On 28-Day Mortality In Mimic-Iii Intensive Care Unit Patients With Sepsis, Monserrath Velez, Jack O'Connor, Nicholas Della Pesca, Rio Baliga

Research & Creative Achievement Day

❏ Sepsis (an infection associated with vital organ dysfunction) is an emergent

medical condition estimated to occur in about 30% of intensive care unit

(ICU) patients[1] and is responsible for 20% of all deaths worldwide[2]

❏ Transthoracic echocardiography (TTE; an imaging modality that uses

ultrasound technology to record heart structure and function) is widely used in

medical treatment [3]

❏ 28-day mortality (whether or not a patient dies within 28 days after receiving a

treatment) is a measure considered to closely approximate ICU mortality[4]

Objectives

❏ Assess and quantify the causal effect of receiving a TTE on …

Synthesis Of Novel Five-Membered Heterocycles As Bioactive Agents, Subrata Roy

Student Theses and Dissertations

This dissertation outlines the synthesis of various types of heterocyclic small molecules across three chapters. The first chapter discusses the efficient synthesis of seventy-one fluorinated pyrazole molecules and thirty-five 3,4-dihydroxy and 4-hydroxy phenyl-substituted thiazole molecules. These molecules were designed and synthesized for their potential antibacterial properties. The second chapter discusses the synthesis of fused thiazole molecules with enone-based steroidal natural products. This chapter reports on sixty-five novel fused thiazole molecules distributed across three libraries featuring different steroidal natural products: ethisterone, bisnoralcohol, and diosgenin. These molecules were designed and synthesized as potential anticancer agents. The third chapter comprises the development of …

Application Of Analytical Methodologies To The Analysis Of Food Flavoring Agents: Part Ii, James Daniel, Kexin Li, Anaaya Monroe, Melissa C. Rhoten

Spring Showcase for Research and Creative Inquiry

No abstract provided.

Modeling Droplet Levitation Over A Heated Liquid Surface, Jacob E. Davis

Mathematics Theses and Dissertations

Research into the interactions between droplets and liquid surfaces is of importance for a number of practical applications. These applications range from spray cooling techniques in engineering, to infectious disease transmission, to the distribution of aerosolized pharmaceuticals and various challenges in particle transport in multiphase flows. In this study, we focus on the dynamics of a slowly condensing droplet, suspended above an evaporating liquid layer. The key objective of the present study is to formulate comprehensive mathematical models that describe the phenomena of diffusion and heat transfer occurring within this system. Using this, we model the flow around the droplet …

Quadratic Stochastic Processes: Algebraic Structures And Their Applications, Taimun Saleh Qaisar

Dissertations

This research focuses on the algebraic structures of the Quadratic Stochastic Processes (𝑄𝑆𝑃𝑠). In this work, we first study 𝜉𝑎- Quadratic Stochastic Operators (𝑄𝑆𝑂𝑠) linked to the partition P3. We simultaneously discuss the dynamics of the obtained 𝑄𝑆𝑂𝑠. Moreover, algebraic structure of the associated genetic algebra is studied. Further, we build Quadratic Stochastic Processes (𝑄𝑆𝑃𝑠) using the given Markov processes. Consequently, we obtain an ordinary differential equation for the resultant Quadratic Stochastic Processes (𝑄𝑆𝑃𝑠). Besides, we apply the solution of this ordinary differential equation for the option pricing problem. Thereafter, we construct Quadratic Stochastic Processes (𝑄𝑆𝑃𝑠) in three-dimensional space by …