Digital Commons Network^™

Seasonal Dynamics Of The Introduced Sponge Hymeniacidon Perlevis In The Elkhorn Slough, California, Usa, Jackson Hoeke

Master's Theses

Hymeniacidon perlevis is a cosmopolitan sponge with a seasonal life cycle We investigated seasonal and interannual dynamics of H. perlevis in Elkhorn Slough estuary, where it is an introduced species, and explored correlations between sponge cover and environmental conditions. We used sponge cover to estimate the potential effects H. perlevis on its environment and how those could vary across its seasonal life cycle. We found that successful recruitment is currently restricted to the upper estuary and while it varies annually, the frequency and density of sponge recruits have generally increased from 2007 to 2023. A seasonal life cycle was confirmed …

Comparing Shade And Impervious Surface Area With Extreme Heat And Environmental Equity: An Analysis Of The Urban Heat Island Effect In Santa Clara County, California, Jamsheed R. Mistry

Master's Theses

In the modern epoch of the Anthropocene, the rapid rise in urban sprawling has prompted a disproportionate exposure to extreme heat within underserved communities. As the global populace becomes increasingly urbanized, the inevitable formation of urban heat islands is becoming an imminent cause of concern for environmental and social justice. Due to an increase in urbanization, anthropogenic activities have not only increased the energy demand for cooling initiatives but also have increased the intensity of heat-related illnesses, such as heart attacks, dehydration, and respiratory diseases. Additionally, urbanization has yielded an unequal distribution of heat exposure and heat-related illnesses, particularly in …

Domain Specific Aspect Extraction For Product Design, Divyam Sobti

Master's Theses

As technology advances, computers become increasingly proficient at interpreting and translating human language into machine-understandable text. With the help of algorithms in natural language processing (NLP), machines can now translate textual data. These algorithms help identify and extract specific text components known as aspects. The aspects represent specific attributes or topics within textual data. For instance, an Amazon review states,“ This phone has good battery life but poor camera quality,” and attributes like ‘battery life’ and ‘camera quality’ represent aspects in the text. Aspect extraction is a pivotal process involving identifying and isolating key features or topics within text. This …

Application Of Agent-Based Simulation And Game Theory In Evaluating Implementation Of Whole Genome Sequencing In Treating Lung Cancer, Fateme Ghalenoei

Master's Theses

Cancer, particularly lung cancer, presents significant diagnostic and economic challenges globally. Timely diagnosis and cost management play pivotal roles in treatment success. A biomarker is any measurable molecule in blood, bodily fluids, or tissues, indicating the potential presence of an abnormal bodily process, condition, or disease. Biomarker testing is a laboratory test in oncology that is used in the selection of targeted cancer treatments and to help avoid ineffective treatments. Whole Genome Sequencing (WGS), is a biomarker test which while more comprehensive, comes at a higher cost. This study proposes an agent-based simulation model within a game-theoretic framework to examine …

A Broadband, Dual Polarized Antenna For The Radio Neutrino Observatory In Greenland, Danny Maas

Master's Theses

The Radio Neutrino Observatory in Greenland (RNO-G) is a multidisciplinary, multinational collaboration which uses antennas to detect neutrino interactions with arctic ice sheets. Neutrinos are formed from nuclear reactions; predominant sources include nuclear reactors, stars, supernovae, and the big bang. They rarely interact with normal matter and thus travel from origin to destination relatively unimpeded, with applications including tracking nuclear weapons tests and supernovae. Measurements of galactic neutrino flux can provide information about how the universe developed and its current evolution. Neutrino interactions produce signals from 100 to 1000MHz. Current RNO-G antennas operate over only a portion of this band; …

Modeling, Simulation, And Experimental Testing Of A Single-Legged Hopper, John Anthony Bennett

Master's Theses

Legged robots are well-suited for navigating unstructured terrain due to their ability to perform agile dynamic motions. Building on the efforts of Cal Poly's Legged Robotics Group, this project focuses on achieving stable forward hopping with a single legged robot.

A comprehensive model of leg hopping is formulated, with leg dynamics during flight and stance phases derived using Euler-Lagrange equations. During the stance phase, a spring-mass system models the leg-ground interaction. The touchdown and lift-off conditions are formulated mathematically, and state mappings between phases are determined via momentum conservation. A two-phase hybrid controller is designed, incorporating trajectory planning during flight …

Identifying New Potential Breeding Pond Sites For The Dusky Gopher Frog In Southern Mississippi, Shelbie Kellum

Master's Theses

The main objective of this thesis was to identify potential new pond sites across southern Mississippi for the critically endangered dusky gopher frog (DGF). Ephemeral ponds are the preferred breeding habitat for the species, but they are quite rare in the region due to the diminishment of the longleaf pine ecosystem. This research addresses gaps in the current literature by providing a broad overview of dusky gopher frog breeding habitat identification. LiDAR derived datasets as well as tools within ArcGIS Pro were utilized in order to perform spatial analysis on sites of interest in south Mississippi. By using this methodology …

Assessing The Impacts Of Grazing By Piney Woods Cattle And Controlled Burning On The Herbaceous Layer In An East Gulf Coastal Plain Longleaf Pine Woodland, William Mcfarland

Master's Theses

Fire and grazing are two disturbances which influence vegetation composition and diversity in many ecosystems. In the southeastern United States, longleaf pine plant communities are adapted to frequent fires and are likely to have been grazed by bison in the past. Though bison have been extirpated from this region, Pineywoods Cattle, which were introduced by the Spanish in the 16^th Century, have been fulfilling a similar role in many of these communities. This study examines the effects that combined grazing and controlled burning have on plant diversity, biomass, and community similarity in a longleaf pine savanna in the East …

Understanding The Variability Of Circulation And Water Quality At Experimental Oyster Leases In The Mississippi Sound Using A High-Resolution Nested Modeling Approach, Shihab Hossain Saran

Master's Theses

Four 50-acre experimental oyster leases; two near Saint Louis Bay (StLB) and two near Pascagoula Bay (PB) were recommended to provide science-based guidance for oyster reef restoration efforts in response to continued limited productivity of oysters in the Mississippi Sound (MSS). Two-way nested simulations using ROMS within COAWST modeling framework have been run with improved forcings to analyze circulation, salinity and temperature variability within and around the lease areas under the extreme freshwater inflow from Bonnet Carré Spillway (BCS) openings and local rivers in 2019. High-resolution atmospheric forcing data is crucial because diurnal sea-land breeze affects salinity variability by increasing …

Exploring Overbank Sediment Deposition Variation In Heavily Modified Floodplains Of The Lower Mississippi River: A Sedimentological And Geophysical Analysis, Seth Fradella

Master's Theses

Since the 1930s, the Lower Mississippi River (LMR) has experienced large-scale modifications to the channel profile and surrounding floodplains through dams, dikes, revetments, dredging, and channel cutoffs. Although these changes have improved navigation and reduced flood risk, unanticipated changes to the major flood return period, individual flood severity and duration, and sediment regime have become increasingly apparent and sometimes problematic, such as the 2011 and 2018-2020 floods. Flood control levees along the LMR have reduced the natural floodplain area by 70-90%, resulting in heavily restricted overbank storage capacity of water and sediment. For the same flood events in recent history, …

Investigating The Response Of The Eastern Oyster (Crassostrea Virginica) To Low Dissolved Oxygen Conditions, Abiola Obafemi

Master's Theses

The Eastern oyster (Crassostrea virginica) requires dissolved oxygen (DO) of about 4 mg/L to support proper physiological function. Hypoxia and/or microxia occur when DO decreases to ≤ 2 mg/L. Salinity and temperature changes resulting from large-scale freshwater influx have been identified as key factors influencing the oyster populations in the Mississippi Sound. It is important to investigate the impacts of DO conditions on oyster mortality, biomass, size, and condition during these freshening events. Under controlled laboratory experiments, this thesis investigated 1) the response of oysters to microxic, hypoxic, and normoxic conditions 2) the response of oysters to combined hypoxia and …

Projected Range Shift Of The Atlantic Surfclam, Spisula Solidissima, And The Ocean Quahog, Arctica Islandica, Under Climate-Induced Benthic Warming: Forecasting Fishery Influence In The Mid-Atlantic Bight Throughout The 21st Century, Molly Mae Spencer

Master's Theses

The Atlantic surfclam, Spisula solidissima, and ocean quahog, Arctica islandica, are biomass dominant bivalve species on the eastern North American continental shelf, both supporting lucrative commercial fisheries in the Mid-Atlantic with a combined value of $53.6 million in ex-vessel revenue per year. Rapid climate change is expected to modify the geographic range of these bivalve populations across the Mid-Atlantic Bight (MAB), suggesting transformative consequences for the surfclam fishery. This study forecasted future distributions of the two species from years 2016 – 2095, based on projected bottom water temperatures and a temperature-dependent population dynamics model, to project subsequent fishery-based indicators …

Investigation Of The Microbiome Of A Recirculating Aquaculture System (Ras) For Crassostrea Virginica Larvae, Isabelle Townsend

Master's Theses

Recirculating Aquaculture Systems (RAS) offer control over physicochemical and biological factors impacting aquaculture success. One understudied facet of RASs is the water microbiome. Oyster larval microbiomes are shaped by their aquatic microbiomes. Understanding the dynamics of and the factors shaping RAS microbiome may provide insights to how the microbiome can be a tool for optimizing larval production. This study’s goals were to investigate the microbiome stability of a RAS rearing oyster larvae across time and space, determine impacts of larval presence on the microbiome, and examine connections between larvae production outcomes and microbiome stability. Water samples were collected weekly from …

Effects Of Extreme Starvation On The Fasting-Adapted Western Rattlesnake (Crotalus Oreganus), Brandon R. Kong

Master's Theses

Ambush-hunting snakes have long been of great interest in the biology of fasting and starvation, as they are adapted to withstand well over a year without taking a meal. Well-justified ethical constraints have limited our understanding of their biology at the limits of these abilities. Unfortunate circumstances, in which the California Department of Fish and Wildlife confiscated over 50 Western Rattlesnakes (Crotalus oreganus) from an animal hoarder that had long neglected them, culminated in the euthanized animals ending up in the hands of our lab. Some of these snakes were extremely starved, being only one-half to one-third of …

Biometric Assessment Of Spotted Seatrout (Cynoscion Nebulosus) From Recreational And Commercial Fisheries In Mississippi, Usa, Nimah Folake Osho-Abdulgafar

Master's Theses

Quantitative stock assessments for Mississippi’s Spotted Seatrout use length-, age-, and sex-composition data from fishery-independent sources as proxies to estimate biostatistical characteristics of fisheries harvests due to lack of sector-specific data. In Chapter 2, I examined the age, length, and sex composition of Spotted Seatrout from three fishery-dependent sectors. Between April and December 2023, I collected 210 fish (n = 19, 124, and 67 from private, charter, and commercial sectors, respectively). The length ranged between 373-535mm, 285-523mm, and 345-568mm TL, with mean ± SD lengths of 453 ± 51mm, 393 ± 57mm, and 442 ± 53mm TL, respectively. Age ranged …

Development Of A Flow Cytometry Method For The Identification And Enumeration Of Enterococcus Faecalis, Riza Magbitang

Master's Theses

A multi-color flow cytometry method coupled with fluorescent staining was developed to detect and quantify E. faecalis concentrations in coastal waters as an alternative to the traditional membrane filtration method. The developed method was used to characterize E. faecalis during batch growth and yielded consistent results across the various physiological states of the cells. Additionally, the application of propidium iodide (i.e., a viability stain), afforded the method the ability to differentiate between cells with intact and compromised cell membranes, which raises the potential of quantifying cells that are in viable-but-non-culturable (VBNC) state. Initial field test using natural seawater samples spiked …

Adaptable Quantum Education Platform Using Learning Objects, Krishna Puja Anumula

Master's Theses

In recent years, the need to make classroom learning more interactive and engaging has become increasingly important. The lack of workforce in interdisciplinary fields such as quantum networking and quantum internet requires a new approach that addresses every learner’s individual needs. To address this challenge, this thesis introduces an adaptive learning platform rooted in the theory of learning objects and Kolb’s experiential learning model. The platform aids educators and learners in designing and utilizing various learning objects for quantum networking and quantum internet.

The platform enables educators and learners to build their own lessons and lesson plans using learning objects …

Automated Concrete Bridge Deck Inspection Using Unmanned Aerial Systems Collected Data: A Machine Learning Approach, Rojal Pokhrel

Master's Theses

Many national infrastructures, particularly bridges, are becoming older and older day by day. Their safe operation and maintenance require routine monitoring and inspection. There are lots of bridge inspection specifications and manuals to guide inspectors to give the proper recommendations about the bridge structure and safety. These manuals and specifications require bridge inspectors to manually inspect the bridge and recommend maintenance and repair tasks referring to the specific criteria available in the manuals. In time, the application of technology makes many Unmanned Aerial Systems (UAS) advancements during the phase of data collection. For the image processing and analysis of collected …

Neurogenomics Of Competition And Parental Care In A Socially Polyandrous Shorebird, Tessa Mathur Patton

Master's Theses

Despite sharing largely similar genomes, females and males of the same species exhibit morphological, physiological, and behavioral differences. Sex-role reversal stems from a unique case of sexual selection in which females compete for mates and males conduct the majority of parental duties. We examined the extent to which aggression and parenting may be mediated by different neurogenomic mechanisms by comparing females versus males in the northern jacana (Jacana spinosa), a sex-role reversed shorebird. We hypothesized that sex differences in neural transcriptomic profiles explain sexual dimorphism in behavior. We conducted RNA-Seq in two brain regions within the social behavior network: the …

Digimindready: Enhancing Military Readiness Through Edge Ai-Driven Wellness, Education, And Digital Discipline Via Privacy-First Mhealth Innovation, Md Mehedi Hasan

Master's Theses

Military personnel often find themselves in intense situations that require high focus. Successfully engaging in these dangerous missions means they must efficiently control cognitive load, manage overwhelming stress, and stay focused through distractions to perform at their best. Military training significantly focuses on human performance, which benefits military readiness. The 21st century has introduced unanticipated challenges to all, such as the adverse effects of excessive screen time, external distractions, and over-reliance on technology without being aware of digital discipline. Militaries are no exception. These challenges have become an emerging threat to military personnel's cognitive, emotional, and physical well-being. On top …

Neuroinflammation And Gut Barrier Function Post Traumatic Brain Injury, Anne Sullivan

Master's Theses

Traumatic Brain Injury (TBI) is a major cause of morbidity and mortality that afflicts millions of people in the United States annually. TBI mice had significantly increased expression of the pro-inflammatory cytokines and decreased expression of tight junction proteins CLDN5, CLDN12, and OCLD in brain lesion tissue. TBI mice exhibited a significant accumulation of FITC in the middle and distal part of the small intestine compared to sham mice. TBI mice exhibited an increase in pathogenic bacteria Enterobacteriaceae and a decrease in beneficial bacteria lactobacillus. TBI mice exhibited a trend toward an increase in permeability compared to no treatment. These …

Investigating Car T Cell Persistence, Functional Phenotype, And The Associations With Clinical Response In Cd19 Car T Cell Treated Patients, Oliwia Bochnacka

Master's Theses

CAR T cell therapy is the adoptive transfer of autologous T cells genetically engineered to express an artificial T cell receptor. In the clinic, CAR T cells have been most effective in treating hematological malignancies and there have been many efforts to continue improving both the safety and efficacy of CAR T cells. Using patient blood samples from the Loyola CD19 CAR T clinical trial, we studied CD19 CAR T persistence and the cell surface phenotype to identify how CD19 CAR T cells change over time in the blood of treated patients and determine whether there were trends associated with …

Development Of An Advanced Step Counting Algorithm With Integrated Activity Detection For Free Living Environments, Paige M. Dolan

Master's Theses

Physical activity plays a crucial role in maintaining overall health and reducing the risk of various chronic diseases. Step counting has emerged as a popular method for assessing physical activity levels, given its simplicity and ease of use. However, accurately measuring step counts in free-living environments presents significant challenges, with most activity trackers exhibiting a percent error above 20%. This study aims to address these challenges by creating a machine learning algorithm that leverages activity labels to improve step count accuracy in real-world conditions. Two approaches to balancing data were used: one employed a simpler oversampling technique, while the other …

A Screening Life Cycle Analysis Of One-Way And Reusable Crate Designs – Estimating Environmental Impacts Via Lca Software, Nicolas R. Corona

Master's Theses

A comparison analysis conducted via COMPASS life cycle analysis software has indicated that a one-way crate design, rather than a reusable crate design, is in fact the more environmentally friendly packaging system. These results can be interpreted differently, however, as the manufacturer of said crate designs must confirm what impact indicators they would like to reference as environmental goalposts. The conducted analysis provides insight into what the environmental impacts of each packaging system look like as packaging at all three system levels has been identified as a means of reducing environmental impacts globally. As such, the manufacturer of said crate …

Engineering An Injectable Hydrogel With Self-Assembling 3d Vasculature, Kendyl Cohn

Master's Theses

This research developed methods for culturing self-assembling capillaries in an injectable gel as a potential method for vascularizing tissue-on-a-chip models to mimic physiological drug delivery. Additionally, a mathematical model was developed as a tool for understanding nutrient delivery and comparison of potential delivery systems. Organs-on-a-chip provide novel platforms for studying biology and physiology in 3D, allow exploration of tissue engineering on a manageable scale, and serve as models for drug screening and drug-delivery testing.

Methods were first developed for co-culture of endothelial cells and fibroblasts (3T3s or HDFs) in 2D, evaluating culture time, seeding density and ratio of HUVECs and …

Thermal Preconditioning Effects On Perforation Propensity Of Transvenous Implantable Cardiac Leads Used For Pacing And Defibrillation, Diane Muff

Master's Theses

Thermal preconditioning to simulate shipping, handling and storage conditions did not affect distal tip stiffness values for permanently implantable cardiac leads used for pacing and defibrillation. Leads that were subjected to extreme temperatures and temperature cycling did not show changes in buckle force values compared with control specimens which were maintained at ambient room conditions. Absolute differences between all measurements were small, generally under 0.05 N and were attributable to measurement variability.

Buckle force values are used to assess the propensity of leads to perforate the heart, a rare but potentially serious complication of implantable pacing and defibrillation systems. Since …

Providing Cadence Feedback In Real-Time To Guide Cardiovascular Workouts, Levi O. Rash

Master's Theses

Cardiovascular workouts offer numerous health benefits, yet beginners often find it challenging to initiate them. Existing wearable technologies, although providing valuable feedback such as heart rate zones, often disrupt the workout flow and distract users due to the need for interaction with the wearable display. In response, we propose an alternative feedback mechanism: cadence, measured in steps per minute. This feedback mechanism uses multiplicative control to produce the correct cadence for the user’s target heart rate (HR). To model the HR and cadence relationship, a first-order system was used. The prototype implementation of this system was completed in Arduino, using …

Shuffled Faster Than Nyquist Signaling For Spectrally Efficient And Secure Wireless Communication, John Gharib

Master's Theses

This thesis investigates the implementation and performance of Shuffled Faster than Nyquist (SFTN) signaling, a communication method that enhances spectral efficiency and provides physical layer security (PLS) in wireless communications. In Faster than Nyquist signaling, the Nyquist inter-symbol interference (ISI) criterion is exceeded, thereby increasing spectral efficiency. By varying the transmission rate of symbols above the Nyquist rate, SFTN signaling is able to obfuscate the timing of transmitted symbols with ISI. The work in this thesis evaluates the performance of SFTN in Additive White Gaussian Noise (AWGN) channels and the MATLAB 802.11ax fading channels. Results show that while SFTN signaling …

Liquefaction Case Histories From Oceano, California During The 2003 San Simeon Earthquake, Hayden Brake

Master's Theses

On December 22nd, 2003, the Mw=6.5 San Simeon earthquake occurred 12 kilometers east of San Simeon, California, causing damage to buildings, roads, and other infrastructure throughout the central coast. The community of Oceano, 80 kilometers southeast of the epicenter, experienced damage to foundations, roads, and utilities due to liquefaction and lateral spreading. The unique geologic environment in Oceano caused a local amplification of ground motions, liquefaction, and lateral spreading. This study entailed developing ten liquefaction case histories from Oceano during the 2003 San Simeon earthquake. Four of the ten case histories are liquefaction cases and six are non-liquefaction cases, with …

Pain Points: Cluster Analysis In Chronic Pain Networks, Iris W. Ho

Master's Theses

Chronic pain is a pervasive health issue, affecting a significant portion of the population and posing complex challenges due to its diverse etiology and individualized impact. To address this complexity, there is a growing interest in grouping chronic pain patients based on their unique treatment needs. While various methodologies for patient grouping have emerged, leveraging graph-based approaches to produce and evaluate such groupings remains largely unexplored. Recent studies have shown promise in integrating knowledge graphs into exploring patient similarity across different biological domains, indicating potential avenues for research. Additionally, there is a growing interest in investigating patient similarity networks, highlighting …