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 …

Measurement And Control Of The Oxidation-Reduction Potential And Its Chemical And Sensory Consequences In Wines, William Jordan Wright

Master's Theses

The oxidation-reduction potential (ORP) is a measurement thought to reflect the overall ability of a solution to oxidize or reduce substances within that solution. In wine, there is no absolute agreement as to which substances control or dominate the ORP; however, oxygen, ethanol, iron-tartrate and copper-tartrate complexes, and glutathione are suspected to play key roles, while sulfur dioxide and phenolics may act as buffers. Anecdotally, some varieties of Vitis vinifera are prone to oxidation while others are prone to reduction, though the chemical basis of this remains unclear. The following works aim to further elucidate the influence of specific chemical …

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 …

A Scalable Iteration Of The Horizon Simulation Framework Using Multithreading Techniques, Jason E. Beals

Master's Theses

The Horizon Simulation Framework (HSF) occupies a unique space in the modern aerospace modeling landscape, enabling flexible, modular modeling of mission-level agent behavior through an object-oriented, hierarchical design. HSF's hallmark breadth-first search scheduling algorithm explores a "multiverse" of possible mission execution pathways, enabling exhaustive evaluation of schedule combinations against user-defined heuristics.

As aerospace systems become increasingly complex, HSF faces critical challenges in establishing verifiable, deterministic behavior. The framework's core scheduling algorithm had not undergone systematic validation, leaving questions about temporal consistency, state management correctness, and reproducibility across different program executions. Furthermore, the exponential growth of schedule combinations creates computational bottlenecks …

Empirical Comparisons Of Partial Dimension Reduction Algorithms In High-Dimensional Regression, Nathan Greenfield

Master's Theses

In high-dimensional regression problems, dimension reduction methods are often used to address the challenges of multicollinearity and estimation instability. Partial dimension reduction extends these ideas by applying dimension reduction to a subset of the predictors, while the remaining predictors are modeled without compression. This approach is particularly useful when it is important to retain variability and interpretability in certain predictors.

This thesis investigates the empirical performance of partial dimension reduction algorithms and introduces a novel algorithm, Iterative Partial Residual (IPR). Two algorithms are considered: a baseline algorithm, Marginal Residual (MR), and the proposed IPR method. Their predictive performance is evaluated …

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 …

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 …

Estimating Prey Capture Attempts And Activity Costs In Foraging Emperor Penguins (Aptenodytes Forsteri) Using Integrated Biologging Data, Taylor Rose Azizeh

Master's Theses

To forage efficiently in patchy and unpredictable prey landscapes, marine predators must optimize energy intake while minimizing costs. Central place foragers like emperor penguins face greater energetic constraints during demanding periods of high investment like chick-rearing. I used high-resolution tri-axial acceleration, depth, and GPS data from 25 birds from two feeding seasons (2019 and 2022) to quantify prey capture attempts and a proxy for energy expenditure (overall dynamic body acceleration; ODBA) across dive types (epipelagic, mesopelagic, benthic), phases (descent, bottom, ascent), and over time at-sea. While prey capture attempts per minute did not differ when looking across dive types alone, …

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 …

Latent Action Trajectory Optimization, Rahul Milind Kandekar

Master's Theses

Learning from demonstrations offers a path to bypass the sample inefficiency of reinforcement learning, but obtaining action-labeled expert demonstrations remains expensive and often impractical. Learning from Observations (LFO) addresses this by learning policies from observation-only demonstrations. Recent LFO work relies heavily on behavior cloning: VPT and LAPO use observation-only data combined with limited action labels to train BC policies, while AIME offers an alternative policy inference approach but requires the majority of its training data to have action labels. Through systematic experiments in the Lunar Lander environment, we investigate whether latent action methods can function when state and action dimensionalities …

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 …

Subculture And Identity As An Escape From The Societal Norms Of Power Imbalance And Authoritative Abuse, Sarah Goldberg

Master's Theses

By definition, a “bolthole” is an animal’s escape or burrow; or, a person’s escape or place of refuge. It also connotes construction, building, even sculpture - relating proletarian materials to themes of working-class labor and the need for escape. Through sculpture, installation, drawing, and oil painting, Bolthole as a body of work examines power imbalance as a societal norm, and identity and subculture as a rejection of the influence of capitalist institutions. Animal symbolism is used in combination with figurative work and portraiture, directly comparing power imbalances between humans to those in nature; such as predator and prey, parent and …

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 …

Stream Behavior Characterization Of Marin County Coastal Watersheds And Their Influence On Salmonid Habitat, Ellie L. Murdoch

Master's Theses

Coastal watersheds in California are increasingly affected by climatic variability, threatening stream behavior, ecological function, and salmonid habitat suitability. This study evaluated streamflow behavior of seven watersheds in Marin County, California, with detailed analysis of Corte Madera, Olema, and Redwood watersheds, which are not influenced by reservoir releases. Using USGS stream gauge records, PRISM climate data, SSURGO soils, and geologic and vegetation information, streamflow metrics critical to salmonid life cycles were quantified for water years 2014 to 2023. Watersheds with greater storage capacity, such as Redwood, exhibited muted hydrologic responses, including delayed flow activation, lower peak flows, slower recession rates, …

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 …

A Novel Microfluidic Device For Preclinical Testing Of Chemotherapeutics, Kaija Saleh Ogan

Master's Theses

This work demonstrates the feasibility of a novel microfluidic tumor model that reproduces physiologically relevant nutrient gradients and endothelium–tumor interactions, validating its potential as a preclinical test platform. Finite element simulations of glutamine diffusion and fluid dynamics aligned with experimental tracer studies, and co-cultures supported directed endothelial migration toward tumor spheroids, confirming the device’s ability to mimic in vivo–like behavior.

Current preclinical models often fail to capture the complexity of the tumor microenvironment (TME), limiting their predictive value for therapeutic testing. Nutrient availability and angiogenic signaling are critical drivers of tumor progression, yet they are poorly represented in traditional …

Muscle Impulse Transducer: Research, Pre-Pilot Experiments, And The Design Of A Pilot Study For Quadriplegic Spinal Cord Injured Subjects For The Development Of A Novel Device, Marta Oreglia

Master's Theses

Paralysis due to spinal cord injury is a challenging condition that affects millions of people around the world. The Muscle Impulse Transducer (MIT) is a novel, wearable device that can be used to improve grip strength in the hand by using functional muscle impulses as a trigger for stimulus delivery to weakened or paralyzed nerves, to induce contraction of a paralyzed or paretic muscle. The MIT is still in development, with proof of concept [1], and functional prototypes [2] achieved. In this thesis, research was conducted on the best methods for functional electrical stimulation, EMG data collection, and nerve stimulus …

Using Noninvasive Calibrated Cuff Plethysmography To Observe The Effects Of Lifestyle Habits On Arterial Compliance, Joshua M. Whitaker

Master's Theses

Cardiovascular disease remains as a leading cause of death for both sexes and across all racial backgrounds. Continuing to research causes, early predictors, and preventative actions are paramount to ensuring that cardiovascular disease starts to decrease in its activity. Endothelial dysfunction is the earliest known predictor of cardiovascular disease, therefore investigating early detection methods of endothelial dysfunction can improve health outcomes. This study revolves around a non-invasive calibrated cuff device that uses the principles of segmental plethysmography and oscilliometry to measure arterial compliance of baseline and induced hyperemic conditions in human subjects to determine how well arteries vasodilate in response …

Analyzing Patterns In Hofstede’S Cultural Dimensions Towards Individual Ai Receptiveness For Affective Experiences, Maggie Yang

Master's Theses

The use of artificial intelligence (AI) has significantly advanced efficient decision-making, with trust in algorithmic decisions shown to vary by cultural upbringing [1]. As AI becomes increasingly embedded in everyday life, it is essential to examine how cultural values affect trust in AI in subjective contexts that extend beyond purely quantitative analysis, like the personal interpretation of art. This work utilizes Hofstede’s cultural dimensions to investigate potential patterns in receptiveness towards AI predictions during art interpretation, providing insight into individual susceptibility to bias in AI-assisted affective analysis.

The study leveraged a cultural dimension survey and a custom Java program connected …

Associations Between Feed Efficiency And Feeding Behavior In Yearling Angus Bulls In A Competitive Environment, Amelia Katz

Master's Theses

Feed efficiency in beef cattle is a complex trait shaped by physiological, behavioral, and social factors that influence how animals access and utilize feed resources. This study examined feed efficiency classification and how it is influenced by feeding behavior, competitive interactions, and bunk approach patterns in yearling Angus bulls housed in a drylot over two years. Bulls were grouped into high and low feed efficiency categories using residual feed intake and feed conversion ratio within pen and year (n = 40 per year; n = 40 per treatment). Continuous electronic monitoring quantified feeder visitation, feeding duration, intake, and rate. A …

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 …

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 …