Digital Commons Network^™

The Application, Construction, And Validation Of Hidden Markov Model Profiles For Carbonic Anhydrase Enzymes, Samuel F. Kaplan

Master's Theses

Carbonic anhydrases (CAs) catalyze the reversible hydration of CO2 and have evolved independently at least eight times, resulting in structurally distinct enzyme families (α, β, γ, δ, ζ, η, θ, ι). Traditional sequence alignment methods struggle to classify these convergently evolved proteins because their sequential similarity does not reliably indicate functional or evolutionary relationships. Many CA sequences in public databases are annotated generically without family assignments, and prior computational approaches have focused predominantly on the three well characterized families (α, β, γ), leaving the five recently discovered classes without robust classification tools. Family level assignment is often a prerequisite for …

Sea Level Trends Near Critical Levees In The Sacramento-San Joaquin Delta, Reyna Sanchez Gomez

Master's Theses

The Sacramento-San Joaquin Delta (Delta) levee system faces threats from rising sea levels, land subsidence, and deteriorating levees, all of which pose risks to California’s primary surface water supply. The purpose of this thesis is to assess relative sea level rise (RSLR) and estimate the spatially varying factors that influence water levels in the Delta. This thesis extends the work of Baranes et al. (2023) to the period 1975-2022 by appending recently acquired water-level records (1975-1982) to modern datasets (1982-2022) from 10 water-level stations. These water level datasets were digitized, quality-assured, and referenced to a common geodetic datum, as described …

Designing For Trust In Chat-Based Question Answering Systems: An Exchange-Based Retrieval Approach, Nathan Mccutchen

Master's Theses

Community chat platforms such as Discord and Slack support spontaneous, collaborative communication but make it difficult to retrieve previously discussed information. As conversations accumulate, valuable exchanges become buried, leading to repeated questions and sustained burden on experienced community members.

This work contributes a set of design requirements for question-answering systems operating over unstructured chat data, a Discord bot prototype implementing those requirements named Echo, and an empirical evaluation of how such a system affects user trust. Rather than encoding discrete question-answer pairs or generating synthetic responses with a language model, Echo indexes conversation topics for semantic retrieval and presents results …

Associations Between Nutrition-Related Chronic Disease And Food Insecurity: Data From The California State University, Elizabeth Ochoa

Master's Theses

Food insecurity is a growing public health concern consistently associated with elevated rates of nutrition-related chronic disease (NRCD) across the general population. Despite young adulthood being a critical window for dietary pattern formation, this relationship remains minimally explored among college students. This thesis examined associations between food insecurity and NRCD diagnosis, including hypertension, diabetes, hyperlipidemia, and cardiovascular disease, among undergraduate students across the California State University (CSU) system. Cross-sectional data were drawn from the Spring 2021 CSU National College Health Assessment, administered across all 23 campuses. After exclusions, the analytical sample comprised 13,762 students. Bivariate analyses assessed relationships between key …

Environmental Impact Of Preventative Fire-Retardant Applications On Soil Water Chemistry, Patrick C. Michelsen

Master's Theses

Between 1992 and 2012, 84% of all documented wildfires were started by humans. These fires often start around high-risk locations such as power lines and roadsides where fuel loads are near these potential human-caused ignition sources. Point source ignition sites that are surrounded by shrubs or grasslands are especially important because fires that occur within these biomes are responsible for far more destruction of property than forest fires. One strategy that is effective at mitigating the spread of fires from ignition sites that are within grassland or shrub biomes are preventative fire-retardant products (PFRPs). These PFRPs differ from traditional fire-retardant …

A Ship Between Worlds: Illicit Trade, Empire, And Enslavement In The Voyage Of The Nuestra Senora De Las Nieves, 1819-1820, Carly Eastham

Master's Theses

This study examines the illicit Spanish transatlantic slave trade to Cuba during the post-abolition era through a microhistorical analysis of the 1819 voyage of the schooner Nuestra Señora de las Nieves. Despite international efforts to suppress the trade following abolition treaties, this voyage illustrates how Spanish traders adapted their practices to continue trafficking enslaved Africans, fueling Cuba’s booming sugar economy amid shifting geopolitical and economic pressures. Drawing on primary documents seized by the British navy and analyzed alongside relevant secondary scholarship, this research situates the Cuban trade within the broader Atlantic world’s complex cultural, legal, and economic transformations.

The case …

Opioid Use Knowledge And Attitudes Among U.S. Adults, Jadyn E. Knox

Master's Theses

The opioid epidemic remains a public health crisis, with overdose rates continuing to rise. Associations between individuals opioid use and knowledge of and attitudes toward opioid substances and overdoses have been investigated to inform educational interventions. However, many studies utilize college student or adolescent samples, and findings remain inconclusive. An assessment of opioid knowledge and attitudes across broader adult populations is lacking. Concurrently, replication literature in the social sciences is limited, therefore, the present study replicated and expanded upon Williams et al. (2013) and Vyas et al. (2023) studies. Reliability and validity of the Opioid Knowledge scale, Opioid Overdose Knowledge …

A Literature Review On Ethics In Medical Diagnostic Ai & Analysis Therein, Connor J. Turetzky

Master's Theses

Artificial Intelligence presents a very promising future in medicine. Being able to diagnose and recommend treatments quickly is vital in ensuring positive patient outcomes. However, the new technology is not without risk. In this narrative literature review, the risks of AI in terms of bias, ethics, and environmental impact will be explored through existing research. This paper will focus on research published between 2019 and 2026, highlighting the major ethical and systematic problems currently facing diagnostic AI. Historical bias in medical data has led to AI that share those biases, and humans inherit that bias creating a potential negative feedback …

Defining Limited English Proficiency: Implications For Assessment And Special Education Placement Decisions, Christine Vernon

Master's Theses

Problem

The problem addressed was the lack of a clear, consistent definition of Limited English Proficiency, despite its influence on funding, programming, assessment, and student placement. The purpose of the study was to clarify how LEP is constructed and used in educational literature and to explore its impact on assessment practices. This study examines the definition of Limited English Proficiency and its implications for educational assessment and special education placement decisions.

Methodology

An integrative literature review, guided by meta-narrative methodology and structural coding, was conducted using 119 peer-reviewed sources from APA PsycInfo, ERIC, and JSTOR (2001–2023).

Findings

Findings revealed that …

Assessing The Ecological Drivers Of Wildfire Hazard Mitigation Of Fuels In The California Home Ignition Zone, Christopher David Benterou

Master's Theses

Consecutive years of devastating home losses to wildfire indicate the need for home fuel reduction and construction improvements. Existing research correlates house survival with modifications to the home ignition zone (HIZ) and is required in high fire hazard areas of California (CA). Mitigations, designed to disrupt continuous fuel patterns, (e.g., separating surface and canopy fuels), can also introduce ecological changes that can alter overall code compliance. Previous compliance studies used respondent and agency-generated data, which may lack accuracy. Assessing additional house and ecological features (e.g., canopy cover and construction) would improve prediction of compliance, but these relationships are poorly studied. …

Exploring Math Word Problem Generation With Llms, Trung Hieu Vuong

Master's Theses

Math Word Problem (MWP) is an important building block for learning math. This type of problem is particularly useful for younger audiences because solving it involves two simultaneous skill sets: reading comprehension and mathematical reasoning. With publicly available large language models (LLMs), generating additional MWPs is readily achievable. While researchers have started using LLMs as MWP facilitators, there still exists a gap in studies about the diversity of MWPs generated by unmodified, publicly accessible LLMs. For that reason, our study focused on two goals: (1) to evaluate the diversity of MWPs generated by publicly available LLMs when provided with examples …

Developing A Vietnamese Text Summarization Large Language Model On Limited Hardware, Tin Pho

Master's Theses

Text summarization models have achieved significant growth during the last few years because of major Large Language Model (LLM) technological advancements. The application of LLMs are widely used in news distribution (TL;DR news), translation tools (DeepL Translate), or virtual assistants (ChatGPT, DeepSeek, Claude, etc.). However, the progress has not yet reached all languages equally. The Vietnamese language is used by more than 90 million people, but the language is not as highly developed for LLM as it has many homophones, five different tones that affect meaning of words, and irregular grammar compared to other languages (e.g. English, Spanish, etc.). Also, …

Automatic Guitar Transcription Of Polyphonic Music, Ritwik Patil

Master's Theses

Transcribing guitar music automatically is a complex task due to polyphonic overlap, tuning variations, and diverse playing techniques. Current transcription systems focus on identifying note pitches and timing while ignoring performance techniques that describe how the notes are played, treating guitar recordings as generic polyphonic audio and producing MIDI-like outputs that lose important information about articulation and style. To address these challenges, we propose an end-to-end transformer model for automatic guitar transcription. The system uses a T5-based encoder-decoder architecture that processes the Constant-Q Transform (CQT) of stereo audio input. The stereo representation helps separate individual guitar parts within a mix …

Mobile Markets And Farmers’ Markets: Evaluating Food Accessibility For Underserved Communities In The Bay Area, Rajeshwari Rajesh

Master's Theses

Studies indicate including farmers’ markets, mobile markets, and other local food systems improve fresh food access for low-income communities, especially when paired with food assistance programs that offer financial incentives. This study aims to evaluate mobile markets and farmers’ markets in the Bay Area using the five dimensions of food access: accessibility, availability, acceptability, affordability, and accommodation. The study is based on primary data collected from 173 in-person surveys at six mobile and eight farmers’ markets in the Santa Clara and Contra Costa counties. Key survey participants were market shoppers participating in food assistance programs. A mixed research methodology included …

Game Genre, Gender, And Sense Of Community In Online Gaming, Patrick Brown

Master's Theses

Sense of community has been shown to improve quality of life in numerous ways. Previous research suggests sense of community can be felt even within groups that never meet in person. The current study explored the relation between game genre, gender status, and sense of community in online gaming groups. Additionally, discrimination was included as an additional outcome due to its close link with sense of community. A total of 189 college students (Mage = 20 years old) of diverse gender and ethnicity completed an online survey consisting of the Sense of Community Scale, Everyday Discrimination Scale, demographic questions, and …

Workplace Incivility And Well-Being: A Moderated Mediation Analysis Of Loneliness And Supervisor Support, Marie Rylance

Master's Theses

By building on previous research and addressing calls to examine the growing epidemic of loneliness, this study investigated how workplace incivility affects employee well-being and workplace outcomes, with attention to the roles of loneliness and supervisor support. Guided by the Conservation of Resources theory, workplace incivility was conceptualized as a resource-draining process that fosters stress states such as loneliness. A key contribution of this study was examining the process through which incivility impacts employees, by testing loneliness as a mediating mechanism and supervisor support as a potential moderator. Using data from 178 participants, regression and mediation analyses were conducted, as …

The Effects Of Educational Materials On Knowledge And Attitudes Toward Psilocybin, Lindsey Elise Wade

Master's Theses

Depression is one of the most prevalent and burdensome mental health conditions worldwide, affecting millions and contributing to over 700,000 deaths by suicide annually. Nearly half of patients with major depressive disorder fail to respond adequately to standard antidepressant treatments such as selective serotonin reuptake inhibitors (SSRIs). Psilocybin-assisted therapy (PAT) has emerged as a promising alternative for treatment-resistant depression (TRD), yet public understanding of this therapy remains limited. The present study examined whether a brief psychoeducational intervention could affect knowledge and attitudes toward PAT among members of the general public in the United States. Participants were randomly assigned to read …

Parameter-Efficient Multimodal Adaptation: Ocr-Integrated Lora For Textvqa And Captioning, Karthik Ganesh Malini

Master's Theses

Vision-Language Models (VLMs) have emerged as transformative technologies for multimodal AI, yet they face significant hurdles in processing text-rich images required for enterprise applications like document understanding, medical imaging, and industrial inspection. Current VLMs struggle with accurate text extraction and reasoning, often exhibiting high hallucination rates and poor Optical Character Recognition (OCR) token utilization. To address these limitations, this research presents a comprehensive framework for optimizing parameter-efficient Low-Rank Adaptation (LoRA) fine-tuning strategies on state-of-the-art architectures, including LLaVA-1.5 and BLIVA-FlanT5. Our methodology integrates enhanced OCR token utilization, faithful caption generation, and specific hallucination mitigation techniques. We employ a multi-dimensional evaluation protocol …

Bicultural Identity, Work-Life Balance And Mental Health Outcomes In Swana Students, Julie M. Salama

Master's Theses

Southwest Asian and North African (SWANA) college students navigate academic demands alongside immigration-salient stressors that may shape their mental health and academic performance. This study examined generational status (Gen 1 vs. Gen 2+), identity conflict, ethnic identity, and work–life balance (WLB) in overall GPA and major GPA, and mental health outcomes of depression (PHQ-9), and anxiety (GAD-7) among SWANA students (N = 35). Two one-way MANOVAs found no generational differences for academics (overall/major GPA) or mental health (PHQ-9/GAD-7). Identity conflict was unrelated to GPA or symptoms but was positively associated with ethnic identity, while WLB was negatively correlated with depression …

A Functional Mri Meta-Analysis Encoding In Alzheimer’S Disease, Joanne Ha

Master's Theses

Alzheimer’s disease (AD) is the most common form of dementia and is characterized by episodic memory impairment. Numerous functional magnetic resonance imaging (fMRI) studies have examined brain activity differences between individuals with AD and age-matched controls during memory encoding. However, small sample sizes and methodological variability across studies have limited the ability to draw meaningful conclusions regarding brain activity underlying encoding impairments. We conducted a meta-analysis to identify consistent patterns of hyperactivity and hypoactivity in AD during episodic memory encoding. Using PubMed to identify studies that met our inclusion criteria, 1,002 studies were screened; ultimately, seven studies were included in …

I Can’T Believe It’S Not Social: Investigating The Relationship Between Loneliness, Parasocial Relationships, And Potential Moderators, Hannah I. Suozzi

Master's Theses

Increased loneliness trends coincide with increased media use. Media is turned to as a source of comfort and distraction from the real world. There is cause to believe that people also use media as a way to form parasocial relationships (PSRs), one-sided relationships audiences form with media figures (i.e., celebrities, influencers, and fictional characters). The connection between loneliness and PSR is thought to be moderated by social vulnerability, particularly the need to belong (NTB) and ethnicity. The medium from which PSRs originate lacks empirical study. To address the limitations, this study analyzed data collected from San Jose State University students …

A Methodology To Reconstruct The Extent And Dynamics Of Historic Wildfires (1850-1950) In The Santa Cruz Mountains Of California, David Vásquez Ospina

Master's Theses

This thesis reconstructs the extent and dynamics of historic wildfires in the Santa Cruz Mountains of California between 1850 and 1950 using qualitative archival evidence from historical newspapers, maps, and related documents. A systematically coded database of 225 reports, consolidated into 155 unique wildfire events, was developed to analyze temporal and spatial patterns, ignition sources, vegetation types, suppression strategies, and impacts on communities and infrastructure. Historical rainfall records from the Boulder Creek station were integrated using water-year totals, three-year rolling averages, and standardized precipitation indices to examine how multi-year dryness relates to fire occurrence and size. Linear regressions show only …

Building A Data-Driven Security Ai Framework Using Machine Learning Models, Christopher Chan Vi

Master's Theses

This research project explores a modern approach to Intrusion Detection System (IDS) anomaly detection by leveraging Artificial Intelligence (AI), Machine Learning (ML), Large Language Models (LLM), and Explainable AI (XAI). The purpose is to assess the effectiveness of these technologies in enhancing the understanding of intrusion events. This research study addresses the challenges of threshold determination and the interpretability of anomaly detection results. The proposed solution involves an LLM-based framework with XAI capabilities, integrated with a Retrieval Augmented Generation (RAG) architecture, to provide clear explanations for detected anomalies, utilizing both custom and pre-trained datasets. The study navigated inherent challenges, including …

Fully Integrated Slippage Detection System For Lower Limb Amputees, Christopher E. Miglio

Master's Theses

Lower limb amputees face significant challenges in maintaining a proper prosthetic fit, as improper fit can lead to slippage at the limb-socket interface, resulting in discomfort, pressure sores, and long-term musculoskeletal complications. To address this issue, a fully integrated slippage detection system was developed to monitor an amputee’s daily activities and slippage occurrences to understand their prosthetic fit over time. The system consists of a prosthetic sock embedded with Interlink 406 flexible piezoresistive force-sensing resistors (FSRs). The sock, worn directly on the residual limb, continuously measures pressure at the limb-socket interface. Sensor data from six FSRs is sampled at approximately …

Self-Efficacy In Juvenile Probation Officers: An Examination Of Training, Eva K. Ott Hill

Master's Theses

The role of juvenile probation officers (JPO) has significantly changed in the past two decades. Rather than a focus on compliance, juvenile probation officers are tasked with using evidence-based practices focused on rehabilitation. Training is a key tool as it equips juvenile probation officers with the skills they need to implement new evidence-based practices and programs. Juvenile probation officers’ confidence in their ability to complete their changing job tasks should increase when they receive training. The current study examines how training impacts perceived self-efficacy among juvenile probation officers in Connecticut. The study seeks to understand what aspects of training impact …

Exploring Synthetic Data Generation For Machine Learning And Statistical Analysis, Aditi S. Gajjar

Master's Theses

In the data-driven machine learning and statistical analysis world, real-world data availability is often constrained by privacy concerns, access restrictions, or resource limitations. To address these challenges, synthetic data provides a groundbreaking solution, enabling academics and data scientists to generate artificial datasets that mimic real-world data for model development and testing in a controlled, privacy-preserving environment. The syntheticDatasets package represents an R-based counterpart to Python's widely-used Scikit-learn dataset generators, adapted to meet the needs of statisticians, educators, and data scientists primarily working in the R programming ecosystem.

This thesis explores the design and implementation of the syntheticDatasets package, focusing on …

Performance Enhancement For Rufa: Rapid Urban Forest Assessment, Nicholas Tan

Master's Theses

Urban forests are crucial to the livability and resilience of cities, offering critical ecosystem benefits such as air quality enhancement, temperature regulation, and biodiversity. Managing said urban forests is essential to ensure their sustainability and adaptability to rapidly changing environmental and climate conditions. The Rapid Urban Forest Assessment (RUFA) tool was developed to address the need for a standardized approach to evaluating and comparing urban and community forestry programs. By analyzing and aggregating tree-specific data across California, such as canopy cover, tree counts, and diversity scores, RUFA assigns a comprehensive urban forestry score for each city. This score allows for …

An Analysis Of Neuroidal Memory Formation Within D. Melanogaster, Jerry Chang

Master's Theses

The Neuroidal model poses a neurobiologically plausible theory for modeling the brain. This symbolic network has been shown to capture realistic memorization behaviors using the JOIN algorithm. The model has also been recently improved by incorporating Watts-Strogatz small-worlds within its base structure. From the efforts of neuroscience researchers, we have access to the Drosophila melanogaster (D. melanogaster) fruit fly’s connectome, which has been found to also contain small-worlds in this thesis. By synthesizing the Ocellar Ganglion (OCG) region of Drosophila, we compare a digitized version of a real-world brain with an instance of the Neuroidal model. In this thesis, we …

Educational Methods For Fostering Sustainability Competencies: A Toolkit For Integration Of Sustainable Education In Engineering, Clara Hallgarth

Master's Theses

This thesis proposes a framework to assist in developing educational activities targeting the longitudinal growth of sustainability skills, knowledge, and attitudes (cumulatively known as competencies), contextualized in a Toolkit for engineering educators. This framework is applied to three civil engineering classes in a teaching-oriented university to demonstrate potential applications and limitations. Sustainability integration in higher education institutions has been recognized as increasingly important as complex sustainability challenges continue to develop and arise. Sustainable education, a pedagogical framework and collection of educational methods, has been shown to produce students with the key sustainability competencies needed to address sustainability challenges and promote …

Abiotic Stress Impacts On Macrophomina Root Rot And Nano-Encapsulated Citrus Oils To Control Fruit And Foliar Pathogens Of Strawberry, Marina J. Gutierrez

Master's Theses

Disease remains one of the major constraints to the productivity and economic success of the California strawberry industry. The most important soilborne pathogen is Macrophomina phaseolina, causing Macrophomina root rot (MRR). The most economically significant airborne pathogens include Botrytis cinerea, causing Botrytis fruit rot (BFR), and Podosphaera aphanis, causing powdery mildew (PM).

Disease severity of MRR is highly dependent on environmental factors. Therefore, understanding which abiotic stressors contribute most to disease development is crucial for effective management. A two-year field experiment at Cal Poly, SLO (2024 and 2025) evaluated the effects of drought stress, two elevated chloride …