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Loss Of Neuropeptide F (Npf) Signaling Reduces The Strength Of Circadian Rest-Activity Rhythms But Not Feeding-Fasting Rhythms, Katelyn Ann Wendt

Master's Theses

The circadian system governs crucial physiological and behavioral processes, dictating activities like movement, hormone release, and sleep patterns over a 24-hour cycle. Disruptions to these rhythms can lead to various health problems, including cardiometabolic dysfunction. Research has demonstrated the presence of circadian rhythms of feeding behavior in diverse organisms, but the specific molecules involved are not yet identified. Neuropeptide Y (NPY) influences metabolic activity in mammals, and its counterpart, NPF, affects locomotor activity and feeding in Drosophila melanogaster. Our study aims to investigate whether NPF, its receptor (NPFR), and NPF-expressing cells play a role in regulating circadian rest-activity and feeding-fasting …

Anthropogenic Litter In Freshwater Ecosystems: Effect On Ecosystem Processes And Spatial Distribution, Emily Johnson

Master's Theses

The rapid increase of plastic production and disposal into the environment has resulted in anthropogenic litter (i.e., trash; AL) becoming a global problem. In aquatic ecosystems, macro- and microplastics are long-lived, mobile, and interact with the physical and chemical components of aquatic ecosystems. Our objectives were to: (1) assess the impact of microplastic pollution on the ecosystem processes of ecosystem metabolism and N2 flux in an oligotrophic lake and (2) to assess the abundance and assemblage of anthropogenic litter in a large urban river. For objective (1), we added microplastics at a range of concentrations to littoral mesocosms. Ecosystem metabolism …

The Mechanisms Of Heterogenic Necrotic And Apoptotic Cell Death Fates In Human Epidermal Keratinocytes Following Uvb Exposure, Madeline Zoe Tara

Master's Theses

UVB radiation is a carcinogen that triggers inflammation and contributes to skin carcinogenesis. Although UVB exposure can induce apoptosis, this form of cell death is non-inflammatory and thus cannot explain the inflammatory response observed following UVB. Necrotic regulated cell death (RCD) pathways, namely necroptosis, pyroptosis, and PANoptosis, are inherently pro-inflammatory, and thus this study focused on characterizing these in irradiated human epidermal keratinocytes. Keratinocytes were irradiated, treated with cell death inhibitors, and analyzed for apoptotic and necrotic RCD markers using immunofluorescence (IF). Despite uniform UVB exposure, keratinocytes displayed heterogeneous cell death responses, and these findings were validated in ex vivo …

A Novel Approach To Treat Trastuzumab Resistant Her2+ Breast Cancer: Activation Pkcδ, Maria Grazia Mejia Monroy

Master's Theses

In the United States, approximately one in eight women will be diagnosed with invasive breast cancer in her lifetime and one in forty will die from breast cancer. From among all the different subtypes of breast cancer, HER2+ can be found in approximately 20% of breast cancer tumors. HER2 overexpression has been associated with an aggressive form of breast cancer, increasing the risk of metastasis or recurrent tumors in 50% of patients. The standard of care for HER2 positive breast cancer, trastuzumab, has been effective for some patients; however, others develop resistance over time, leading to disease progression and metastasis. …

Novel Electrospinning Techniques For Fabricating Scaffolds To Model Intracranial Atherosclerotic Disease In Tissue Engineered Blood Vessel Mimics, Isaac "Squeaky" Buentipo

Master's Theses

Novel Electrospinning Techniques for Fabricating Scaffolds to Model Intracranial

Atherosclerotic Disease in Tissue Engineered Blood Vessel Mimics

Isaac “Squeaky” Buentipo

Dr. Kristen Cardinal’s Tissue Engineering Lab at California Polytechnic State University specializes in fabricating customized vascular models, known as Blood Vessel Mimics (BVMs), for medical device testing. BVMs are simplified in vitro vascular models designed to bridge the gap between bench testing and in vivo evaluation of intravascular medical devices. BVMs are produced by combining a polymer scaffold with human vascular cells. Through novel scaffold fabrication techniques, such as silicone injection molding, silicone dip casting and electrospinning, the capabilities of …

Evaluation Of Antibiotic Testing Protocols For Biofilm-Forming Escherichia Coli In A Microfluidic Platform, Caleb R. Telander

Master's Theses

Catheter-associated urinary tract infections remain an ongoing clinical problem due to biofilm persistence and antibiotic resistance. Standard antibiotic susceptibility testing cannot accurately reproduce flow conditions and the spatial complexity of the in vivoenvironment and is thus questionable in relevance to device-related infections. This study examines a microfluidic device designed to simulate physiologically relevant wall shear stress and antibiotic gradients in Escherichia coli biofilms. The polydimethylsiloxane-based system integrates a 16-well culture chamber with a gradient generator. Biofilm growth was observed using fluorescence microscopy of green fluorescent protein-labeled bacteria. Simulations performed using COMSOL Multiphysics software estimated the appropriate range of wall …

Balance Assessment Of Disc Golf Players By A Smartphone, Joshua Paul Kannankunni

Master's Theses

Disc golf is an underrepresented sport in biomechanics research, even though it could have effects on gait and balance. Forward and side lunges performed while throwing discs can improve static and dynamic balance. The purpose of this study was to explore the effects of playing disc golf on various static and dynamic balance metrics. Static and dynamic balance experiments were done on 20 disc golf players and 20 control participants to record their RMS of acceleration during the double leg, tandem, and single leg static poses, as well as their gait speed, cadence, stride length, right step length, left step …

Effects Of Spirulina And Nannochloropsis Supplementations On The Meat Quality And Sensory Properties Of Broiler Carcasses, Shreyash S. Patel

Master's Theses

Microalgae are a promising feed ingredient due to their high content of proteins, lipids, polysaccharides, vitamins, pigments, and enzymes. This study evaluated the effects of algae as a dietary supplementation on the appearance, quality, and sensory attributes of broiler carcasses. In each of experiment I and II, a total of 54 Ross-708 broilers were randomly obtained from the pool of 270 broilers in the 18 floor pens of soybean-mealbased diets at 0, 2.5%, and 5% Spirulina (Experiment I) and Nannochloropsis (Experiment II) supplements in the Poultry Unit at California Polytechnic State University (Cal Poly, San Luis Obispo, CA). Broiler carcasses …

Opensim Analysis Of The Aymara Indigenous People Performing Ancestral Tasks: Exploring Trends Of Muscle Activity With Tiwanaku Skeletal Indicators, Noah M. Taylor

Master's Theses

The Tiwanaku civilization (AD 500-1100) of the Andean highlands exhibited occupational specialization in communities, with archeological evidence suggesting the existence of labor- and residential-communities, or “taskscapes”, based on an individual’s livelihood. Prior bioarcheological studies have examined Tiwanaku skeletal remains for musculoskeletal stress markers, osteoarthritis, and cross-sectional geometry to infer activity patterns. Their descendants, the Aymara Indigenous people, currently live in the same highlands and until recently lived a lifestyle like their ancestors. Over the past 20 years, the global quinoa demand has risen, thrusting the Aymara into globalization and moving them away from the traditional tasks previously performed. This study …

Acoustic And Hemodynamic Analysis Of Phantoms: Roughness And Flow Dynamics, Ethan Erik Olof Sundberg

Master's Theses

The purpose of this study was to determine whether different vascular phantoms, with and without a surrogate arm, could serve as effective analogs to the human brachial artery for assessing endothelial dysfunction, an early indicator of cardiovascular disease, particularly atherosclerosis. Atherosclerosis is characterized by plaque buildup and endothelial damage, which precede more severe clinical events and are often detectable through changes in vascular function. A 40” water tower was used to simulate diastolic pressure, enabling water flow through each phantom. Strain gauge pressure transducers were placed at both ends of the phantoms to measure pressure drop, while a microphone captured …

A Manufacturing Process For Interdigitated Microelectrodes On Glass Wafers, Wyatt W. Warfield

Master's Theses

This study presents work done to optimize the process parameters to produce interdigitated electrodes on a borosilicate wafer. Using designed experiments and statistical analysis, the error in pattern transfer was minimized using for key process steps including exposure time, develop time and post exposure bake duration. Similarly, statistical analysis was used with profilometry data to fine tune the develop times. Qualitative analysis was used to assess thin film deposition. The resulting process produced wafers with improved pattern transfer and adequate film adhesion

Optimizing Microfluidic Murine Fibroblast And Human Epidermal Keratinocyte Cell Culture In 70Μm Microwells, Christian Navarro

Master's Theses

Cell culture is an essential technique utilized in biotechnology and medicine to remove systemic influences to study cellular behavior and morphological development of individual cell lines. However, conventional cell culture is two-dimensional and static meaning it can’t easily mimic in vivo conditions such as multicellular cell to cell interactions, fluid perfusion, or 3D structures which might alter cellular behavior and morphology. Microfluidic cell culture allows for the incorporation of in vivo conditions such as perfusion and chemical gradients allowing for more physiologically accurate models. The goal of this study is to develop a protocol for testing a microfluidic chip designed …

Effectiveness Of Nutrition Education On Male Student Veterans From Cal Poly, San Luis Obispo University, Keith S. Kim

Master's Theses

This pilot study evaluated the effectiveness of a 13-week nutrition education intervention designed to improve dietary patterns, physical health, and mental health outcomes among 10 student male military veterans at California Polytechnic State University, San Luis Obispo. The intervention, grounded in the Dietary Guidelines for Americans, 2020–2025, included a one-time educational presentation and periodic recap videos to reinforce key messages. Outcome measures included dietary intake, body mass index (BMI), handgrip strength, depressive symptoms (via the Beck Depression Inventory), and post-traumatic stress disorder (PTSD) symptoms (via the PCL-5). Results revealed no statistically significant changes in dietary patterns, BMI, handgrip strength, …

Density-Based And Model-Based Clustering With Tidyclust In R, Brendan S. Callender

Master's Theses

Clustering is a fundamental technique in unsupervised learning that can be used to find hidden patterns and structures within unlabeled data. The tidyclust package in R provides a unified interface for applying various clustering techniques to data. This paper outlines the addition of density-based clustering with DBSCAN, and model-based clustering using Gaussian mixture models (GMMs) to the tidyclust package. DBSCAN can be performed using the db_clust() function and makes use of the dbscan package implementation as its engine. GMMs can be fit using the gm_clust() function which makes use of the mclust package implementation. This paper highlights the changes made …

When Trees Disappear: Understory Successional Implications Of Sudden Oak Death And High-Severity Wildfire In Big Sur, California, Sam J. Balthazard

Master's Theses

The rapidly emerging disease sudden oak death, caused by the non-native pathogen Phytophthora ramorum, is transforming coastal California forests by driving extensive mortality of tanoak (Notholithocarpus densiflorus) and increasing fire severity. As a novel disturbance, sudden oak death and its interaction with wildfire may catalyze unexpected shifts in successional trajectories and reconfigure forest understory communities. Furthermore, how tanoak influences the forest understory and how its decline might reshape understory dynamics remain poorly understood. We hypothesize that disease alone and the compounding disturbances of disease and wildfire alter successional dynamics, and that the potential functional extinction of N. …

Comparing The Effectiveness Of Low Impact Image Analysis To Traditional Vegetation Sampling In A Branford Marsh, Peter T. Porrello

Master's Theses

The growing need for non-intrusive research methods has led to a surge in passive data collection, such as audio recorders, data loggers, and camera traps, in the ecological field. This improves the capacity to observe fragile habitats without causing any harm and gives researchers new perspectives on the natural world. A non-invasive cable camera system is suggested as a means of gathering data to lessen these ecological disruptions. By taking images of the salt marsh's surface, this technique will minimize plant destruction and lower CO2 emissions brought on by foot traffic through the marsh, whilst producing data that is on …

Design Principles For Robotic-Controlled 3d Printing Of Soft Tissue-Mimicking Materials, Karina Mealey

Master's Theses

Geometrically and physically accurate 3D models are emerging as essential tools for surgeons in pre-operative planning and training, but current methods of producing these models are not sufficient. Existing solutions have downsides such as high costs, long and tedious production times, high complexity resulting in a lack of scalability, or an inability to meet material requirements for accurately simulating human tissue.

The objective of this work is to develop principles for a low-cost, easy-to-use 3D printing system capable of prototyping with soft tissue-mimicking materials. To pursue this goal, a MyCobot280 robot arm was used as the mechanism to explore the …

The Application Of Lidar For Classifying Wildland Fuels, Madison Muschetto

Master's Theses

Accurate vegetation classification is critical for modeling wildfire behavior, particularly in fire-prone ecosystems where fuel type influences fire spread and intensity. This study evaluates the effectiveness of UAV-based aerial LiDAR, supplemented by multispectral imagery, for classifying grass, shrub, and tree vegetation types across a grass-dominated landscape. Using canopy height thresholds, vertical profile analysis, LiDAR predictions were compared against field-verified vegetation observations at 80 survey points. Results showed that LiDAR classified grass with high accuracy but was less reliable for detecting shrubs and trees, especially under canopy cover. Misclassifications were most common beneath tree canopies and in areas where low-stature shrubs …

Topodino: Self-Supervised Topological Representation Learning For Neuronal Morphologies, Yasser Binbisher

Master's Theses

Neuronal cell types are categorized by transcriptomic identity, yet their morphological heterogeneity defies this classification. In response, researchers have adopted unsupervised graph representation learning as a tool to reveal morphological variation within single-class transcriptomic types. However, the complex geometry of neuronal morphology—especially long axons and dense dendrites—challenges graph neural networks, which struggle with message propagation across extended structures. To mitigate this, current approaches enforce sub-sampling on neuronal graphs and omit axons entirely, sacrificing critical biological features for computational efficiency. To overcome this trade-off, this thesis introduces TopoDINO, a self-supervised, topology-aware representation learning model designed to preserve the full hierarchical organization …

"The Effect Of Methylobacterium Symbioticum On The Growth And Yield Of Dent Corn And Romaine Lettuce", Sinead Carney

Master's Theses

Nitrogen (N) is an essential nutrient for plant growth and is often a limiting nutrient in cropping systems. An estimated half of applied N fertilizers are lost from cropping systems by processes that can be environmentally destructive, such as leaching and volatilization, and cause economic loss for growers. Effective N biofertilizers offer a means to mitigate the need for high inputs of synthetic N. The objectives of this study were to determine the effects of leaf inoculation with the N-fixing bacteria, Methylobacterium symbioticum, in combination with different rates of urea-N fertilizer on the physiology and yield of dent corn …

From Tree To Shrub? The Fate Of Tanoak Through Fire And Nonnative Disease, Jacqueline Rose

Master's Theses

Invasive plant pathogens have killed an uncountable number of trees and disrupted ecosystem processes throughout the world. Newly introduced pathogens may interact with historically occurring disturbances in unexpected ways to cause amplified mortality and change to ecosystem processes. Here, I examine the a natural experiment created by three wildfires in Big Sur, a portion of the central coast of California impacted by the nonnative pathogen Phytophthora ramorum, to forecast the future of a species susceptible to the pathogen. Using a plot network which spans the length of Big Sur, I track the survival of individual tanoak (Notholithocarpus densiflorus) stems and …

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 …

Structural Color Pigments For Waterborne Coatings, Kyle William Liston

Master's Theses

Structural colors offer unique alternatives to conventional pigments, utilizing their microstructures to produce vibrant colors. These pigments offer an alternative source for colorants without the need for less environmentally friendly conventional pigments. In keeping with the sustainability approach, the use of waterborne coatings was chosen over solvent-based coatings. Here we report the synthesis of brushite platelet, silica supraball, and inverse opal pigments. Brushite platelets were produced through a condensation reaction, while silica supraballs were synthesized via the Stöber process and assembly was attempted using an oil-in-water emulsion. Inverse opal was produced through the templating of silica on poly(methyl methacrylate) (PMMA) …

Functionalization Of A Calcium-Based Squaric Acid Metal Organic Frameworks With Amine-Based Polymers For Enhancing Post Combustion Carbon Capture, Corinne D. Watson

Master's Theses

The primary driver of climate change is the release of carbon dioxide (CO₂) from fossil fuel combustion. Global climate change has resulted in sea level rise, adverse weather patterns, and countless other negative global effects. Several carbon-reduction frameworks emphasize the transition to clean energy sources; however, other strategies must be concurrently pursued to immediately and effectively reduce atmospheric carbon dioxide point source emissions. Metal organic frameworks (MOFs) are a promising new technology for post-combustion carbon dioxide capture. The materials are synthesized using organic linker molecules and metal ion joints. Notably, there are several challenges with various types of …

Studies On The Effects Of Cap Management On The Oxidation–Reduction Potential, Phenolic Composition, And Sensory Properties Of Red Wines, Dallas J. Parnigoni

Master's Theses

Cap management during alcoholic fermentation of red wines plays a critical role in modulating the phenolic and volatile extraction from grape solids, influencing the homogenization of chemical and temperature gradients, while imparting oxygen to the must. Different cap management alternatives are also thought to influence the evolution of the oxidation-reduction potential (ORP). It is critical to understand how different cap management protocols affect these variables to design a cap management protocol tailored to wine style and varietal. This thesis investigated the effects common commercially applied cap management protocols, as well as the efficacy of novel, automated gas mixing protocols as …

Data Driven Analysis Of Samara Seed Kinematics And Dynamics, Shashwat Sparsh

Master's Theses

Samara Seeds are a class of fruit most famously belonging to the Acer species and are characterized by their single-bladed geometry and their auto-rotation response during descent. This steady-state auto-rotation response is the subject of aerodynamic analysis which aim to quantify the performance. The period prior to the beginning of steady-state auto-rotation is classified as the transition regime and has not been the subject of intense scrutiny.

This thesis employs a data-driven approach to analyzing the kinematic and dynamic response of these seeds during both the transition and auto-rotation stages of flight to quantify the performance with respect to the …

Spatial And Functional Metrics For Analyzing Seedling Roots, Irina Ivchenko

Master's Theses

To study the complicated structure of a maestro pea seedling root, we investigate three spatial metrics and one functional metric. The spatial metrics are fractal dimension which measures the complexity, convex hull area which measures the occupied space, and Euler characteristic which topologically describes the shape of the root. We discuss the successes of various metrics and the possible limitations they bring to analysis. As a functional metric, we study the rhizosphere: the volume radially around the root branches from which the plant accesses nutrients and water. We investigate the relationship of the rhizosphere to the root, and propose how …

The Effects Of Sirulina And Nannochloropsis Supplementation On Broiler Performance, Intestinal Morphology, And Gut Microbiology, Emily Beckerman

Master's Theses

The poultry industry is constantly searching for new nutritional strategies and better feed conversion ratio to enhance broiler growth and productivity. Microalgae have been shown to improve broiler performance and health depending on species and supplementation levels. The objective of this study was to determine the effects of Spirulina supplementation (Experiment I) and Nannochloropsis supplementation (Experiment II) on broiler production performance, intestinal morphology, and gut microbiology. In Experiment I, a total of 270 broiler chicks (one-day-old Ross 708) were obtained from a local hatchery after vaccinating against Newcastle, Marek’s disease, and Infectious Bronchitis. They were weighed and sorted into 18 …

Understanding The Habitat Associations Of Nearshore Rockfishes Inside And Outside Of Marine Protected Areas Using Hook-And-Line Data, Kaila Raeanne Fritch

Master's Theses

Habitat is an important driver in shaping the distribution of a range of species. For demersal fish species, benthic habitat characteristics can drive distribution and community structure. Understanding the relationship between habitat and species distribution in important, especially for exploited species such as rockfishes (Sebastes spp.). Increased data on the relationship between rockfish and benthic habitat characteristics could enhance marine protected areas (MPAs) and management practices which are used to protect rockfishes along the U.S. West Coast. To address this, we used hook-and-line, catch-and-release data that were collected inside two MPAs on the central coast of California, and …

Filling Gaps In Scientific Data Sets Using Physics Informed Neural Networks: A Case Study In Velocity Fields, Ellen Saunders

Master's Theses

Gaps in scientific data sets are a persistent issue for researchers in a variety of fields, and while nothing makes up for missing out on real data, well-simulated synthetic data can be a useful tool. In the world of image processing, machine learning techniques have become quite sophisticated at taking an image with a missing component and filling in that space with something believable. The aim of this thesis is to take machine learning techniques similar to what gets used in image processing and repurpose them to infill gaps in scientific data sets in a realistic manner. This thesis compares …