Digital Commons Network^™

Crab: A Novel Clustering Score Using Clustering With Rivals And Buddies For Unsupervised Learning, Allen Choi

Master's Theses

Unsupervised clustering algorithms today are used across a wide variety of fields such as biology, engineering, and industry in order to classify observations into groups where labels are not provided. This can provide important latent information regarding the observations within groups, as well as insight regarding the groups themselves. In order to judge the optimal number of clusters for an unsupervised clustering algorithm, many methods exist such as the Elbow Method and Silhouette Score; however, these methods come with drawbacks and are not necessarily flexible across many unsupervised methods. We present a novel clustering score framework relying on a resampling-based …

Marketing As Practice: Resolving The Hunt-Anderson Stalemate Through Practice Theory, Stephen A. Lemay, Martin Svendsen

Journal of Applied Marketing Theory

This paper revisits methodological debates in marketing theory, tracing the progression from Sidney Levy’s work on symbolic consumption to the Hunt–Anderson empiricist–relativist debate. We argue that this debate rests on a category error: marketing has been misclassified as either a science or an interpretive discipline. Drawing on contemporary practice theory, we reconceptualize marketing as a professional practice oriented toward creating and managing exchange relationships within cultural contexts. This perspective resolves the Hunt–Anderson stalemate, clarifies the epistemological foundations of Consumer Culture Theory (CCT) and Transformative Consumer Research (TCR), and generates distinct research questions and methods. Through comparative exemplars, we show how …

Alara+: Summit On Radiation And Orthopedic Risks In Fluoroscopic Laboratories: Endorsed By Acc, Acvp, Ase, Hrs, Scai, Sir, Snis, Svin, And Svs, Arash Salavitabar, Amit N. Vora, Dorothea Altschul, J. Fritz Angle, Chelsea Ballinger, Andrew Bojanowski, Anna E. Bortnick, Kyle Bugg, Emily Carpenter, Robert E. Foster, Joanna Ghobrial, Matthew Glogoza, Atul Gupta, James B. Hermiller, A. Kyle Jones, Summer L. Kaplan, Steven J. Kraus, Omar Khalique, Andrea Klein, Nick Morse, Preethi Ramchand, David G. Rizik, Lucy M. Safi, Cheryl C. Schultz, Kamala P. Tamirisa, R. Jay Widmer, Kristi Wilson, Jonathan X. Fang, Arnold Seto, Robert F. Riley

Department of Neurosurgery Faculty Papers

Occupational radiation exposure has a clear association with long-term health effects and has a particular impact on women, trainees, and supporting staff. There is a reliance on limited, traditional radiation protection and nonergonomic equipment, which carries associated orthopedic injury rates with adverse impacts on both individual career trajectories and health systems, and with significant challenges to widespread implementation of enhanced radiation protection devices. During the 2025 Society for Cardiovascular Angiography & Interventions Scientific Sessions in Washington, DC, a multidisciplinary Think Tank summit was convened and included representatives from multiple stakeholders, including other professional societies, advocacy groups, and industry partners. The …

Gobbling Activity And Use Of Structural Habitat At Nest Sites By Wild Turkeys (Meleagris Gallopavo) In Western Nebraska, Robyn M. Dausener

School of Natural Resources: Dissertations, Theses, and Student Research

Wild turkey (Meleagris gallopavo) populations in Nebraska have declined substantially in recent years. Understanding gobbling chronology and its environmental drivers may inform spring hunting season structure and management actions. I used autonomous recording units (ARUs) in two ecologically distinct regions of Nebraska, the northwestern (NW) Pine Ridge landscape, and the southwestern (SW) agricultural landscape, to quantify gobbling activity from 2023-2025. I paired gobbling data with nesting chronology, cumulative daily hunting pressure, weather conditions, and moon phase using Bayesian generalized additive mixed models. Gobbling peaked during mid-to-late April in both regions, preceding peak nest initiation and incubation, with no …

Association Of Insulin Resistance And Fracture Risk In The Osteoporotic Fractures In Men (Mros) Cohort, Jeonghoon Ha, Li-Yung Lui, Kristine Ensrud, Qian Xiao, Andrew R Hoffman, Joy Y Wu

Faculty, Staff and Student Publications

Context: Insulin resistance (IR) is more prevalent in men than in women, but evidence directly linking IR to fracture risk in older men remains limited.

Objective: To evaluate the association between insulin resistance (IR), estimated using the Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and the triglyceride-glucose (TyG) index, and fracture risk in older men.

Methods: Data from 5994 men (≥65 years) in the MrOS cohort were analyzed. A total of 5416 participants were included in the HOMA-IR analysis and 5384 in the TyG index analysis. Fractures were self-reported and confirmed radiographically. Participants were grouped into quartiles based on IR …

Global Youth Development: Challenges And Remedies, Raymond Chimezie

Faculty Publications and Presentations

Young people have enormous potential for growth and innovation, but not all have access to resources and opportunities to explore, achieve their dreams, and contribute immensely to society. Absence or limited opportunities and resources pose great challenges to young people’s aspirations. Through a review of literature and study of some countries young people globally face challenges, though at varying degrees like unemployment, limited access to healthcare, social services, and education; lack of professional support, skills acquisition and retraining, and political exclusion; judicial inequity, loneliness, and poor parenting. There still exist policies, structures, or regulations that encourage racial and ethnic or …

Age And Sex Affect The Prevalence And Severity Of Periodontal Conditions In An Academic Setting, Karo Parsegian, Nikolaos Soldatos, Tonia C Carter, Nikola Angelov, Neel Shimpi, Krishna Kumar Kookal, David K Okano, Effie Ioannidou

Faculty, Staff and Student Publications

Background: The aim of the present study was to examine whether age and sex affected the prevalence and severity of periodontal conditions in patients attending an academic dental clinic.

Methods: Electronic health record (EHR) data on the demographic characteristics and periodontal conditions of patients presented for a comprehensive periodontal evaluation were extracted from the institutional dental EHR database. Retrospective analysis of independent associations of age, sex, and other subject characteristics with periodontal conditions was determined using multinomial logistic regression. The null hypothesis stating that age and sex were not associated with the increased prevalence and/or severity of periodontal conditions was …

Cytosignal Detects Locations And Dynamics Of Ligand-Receptor Signaling At Cellular Resolution From Spatial Transcriptomic Data, Jialin Liu, Hiroaki Manabe, Weizhou Qian, Shion Orikasa, Javid Ghaemmaghami, Yichen Wang, Yichen Gu, Angel Ka Yan Chu, Gaurav Gadhvi, Yuxuan Song, Patrick Mcclinden, Vibha N Lama, Noriaki Ono, Joshua D Welch

Faculty, Staff and Student Publications

Cells communicate through ligand-receptor (LR) signaling interactions, but identifying when and where these interactions are active remains challenging. We developed CytoSignal to infer the locations and dynamics of cell-cell communication at cellular resolution from spatial transcriptomic data. Here we show that our cellular resolution, spatially resolved signaling scores enable several important analyses-identifying spatial gradients in signaling strength, quantifying the locations of contact-dependent and diffusible interactions, detecting signaling-associated genes and identifying differential signaling across multisample data. Additionally, we can predict the temporal dynamics of a signaling interaction at each spatial location. We experimentally validate our results in situ by proximity ligation …

Marine Heatwaves And Fish Reproduction: Endocrine Responses In The Eurythermal Sheepshead Minnow (Cyprinodon Variegatus), Isabel Villafuerte

Master's Theses

Marine heatwaves associated with climate change are increasing in frequency and severity, posing significant threats to fish populations in shallow habitats such as estuaries and salt marshes. Because temperature is a primary regulator of fish reproduction, understanding how heatwaves affect reproductive physiology is critical for anticipating the biological consequences of ongoing climate change for coastal fishes. Here we examined how simulated heatwave conditions affect the reproductive hypothalamic-pituitary-gonadal (HPG) endocrine axis in the estuarine sheepshead minnow (Cyprinodon variegatus), a eurythermal fish well suited to studying thermal stress responses in estuarine environments. Adult sheepshead minnows acclimated to a daily oscillating …

A Polygon Approach For Satellite Coverage Computation Problems, Caleb I. Arbreton

Master's Theses

During celestial body observation mission planning, predicted sensor coverage is a key analysis tool used by designers to inform concept of operations. It enables trade studies by applying a metric to assess how well different sensor, satellite, and constellation configurations can observe a mission's region of interest. The effectiveness of the studied components is then paramount in determining whether they are justified in the system architecture. Coverage computation becomes more difficult as sensor types and regions of interest (RoIs) deviate from simple shapes, and as problem formulations seek higher-fidelity results. These simplifications include: conical camera sensors, RoIs represented as simple, …

Dot Product Engine Based Neuromorphic Hardware For Continuous-Time Biomedical Signal Classification, Sanjeev Srinivasan

Master's Theses

Accurate diagnosis of pathological conditions from biomedical signals, such as electrocardiograms (ECGs) is often performed offline, making it time-consuming, costly, and inefficient, especially when abnormal patterns are rare and long-term monitoring generates large amounts of data. To address this, this work proposes a compact, scalable, and programmable neuromorphic system designed for real-time preliminary arrhythmia detection and classification using ECG signals, that can be extended to other biomedical signals. The proposed design processes ECG signals using a delta modulation-based spike encoder, followed by classification with a dot-product engine (DPE) based spiking neural network (SNN) processor and winner-take-all (WTA) circuit. The architecture …

Effects Of Hot Water Dipping And Sub-Zero Saline Chilling On The Microbial Safety Of Broiler Carcasses And Recycled Chilling Water, Elen Zhu

Master's Theses

Broiler meat became the most widely consumed meat within the United States and across the world in 2019. The trend of increasing broiler consumption is expected to continue due to affordability, health benefits, and production efficiency. To meet the growing demand of broilers, a substantial number of birds need to be produced and processed while minimizing bacteria contamination, water consumption and wastewater generation.

In this study, the microbial safety (mesophilic aerobic bacteria, coliforms, and Escherichia coli) of broiler carcasses and post-chill water (red water) was assessed, using innovative processing techniques and red water recycling. A total of 144 broilers …

Independent And Combined Effects Of Early-Life Iron Deficiency And Antibiotic Exposure On Growth And Hematological Outcomes In A Piglet Model, Ginger M. Fitzpatrick

Master's Theses

Iron deficiency (ID) affects over 2 billion individuals globally. Children under 5 are at increased risk of ID due to rapid growth and are especially vulnerable to its negative consequences because of iron’s essential role in cognitive development and immune maturation. ID is the leading cause of iron deficiency anemia (IDA), with IDA affecting approximately 40% of children in this age group. Antibiotic (abx) exposure is also prevalent during early life and may disrupt growth and through gut dysbiosis, with increasing use posing additional risk in younger populations. Geographically, there is overlap in regions with high anemia prevalence and those …

Evaluation Of Ultraviolet-C Light For Control Of Mites And Western Tarnished Plant Bug In Strawberry & Interactive Lethal Effects Of Common Strawberry Fungicides And Adjuvants On Phytoseiulus Persimilis, Colin T. Koubek

Master's Theses

California strawberry production relies heavily on chemical pesticides to manage arthropod pests and diseases, but pesticide resistance, regulatory pressure, and the need to conserve biological control agents have increased interest in alternative pest management tools. This thesis evaluated ultraviolet-C (UV-C) light as a nonchemical management tool for key strawberry arthropod pests and assessed the compatibility of common strawberry fungicides and adjuvants with the predatory mite Phytoseiulus persimilis Athias-Henriot. The first objective was to determine the ovicidal and lethal effects of UV-C light on Lygus hesperus Knight eggs and nymphs. Laboratory and field ovicide assays were conducted using UV-C doses relevant …

Object Detection And Classification For Man-Made Structures To Aid In Search And Rescue (Sar), Mio A. Nakagawa

Master's Theses

This project explores the use of various object detection and classification models to identify permanent man-made structures, specifically cell towers, water towers, watch towers as well as its corresponding shadows (attributes), from aerial imagery. The goal is to evaluate those models and test the feasibility of current models to detect man-made structures in aerial images, in an effort to support search and rescue operations as well as update network infrastructure databases. Multiple object detection models, as well as classification models, including YOLOv8 and VGG19 are implemented and trained on annotated aerial images to determine the presence or absence of man-made …

Empirical Comparsion Of Traveling Salesperson Approximation Algorithms, Shayan Daijavad

Master's Theses

The traveling salesperson problem deals with optimizing the route a traveling sales- person might take to visit a set of places exactly once and return back to their starting point. The problem is NP-hard, and it is hard to approximate in general, but special cases have many approximation algorithms, which come with tradeoffs. In this thesis we compare the runtime, approximation ratio, and overall implementation complexity of two approximation algorithms for the Euclidean version of the problem, a classical 2-approximation algorithm and the multifragment heuristic. We run both algorithms on randomly generated point sets and real world data from TSPLIB. …

Effects Of Irrigation And Nitrogen Management On Yield And Leaching Risk In Organic And Conventional Broccoli Fields, Shane Egerstrom

Master's Theses

Under regulatory pressures to reduce groundwater contamination by nitrate from fertilizer, such as those posed by the Central Coast Regional Water Quality Control Board’s Agricultural Order 4.0, a need exists to better understand interactions between irrigation and nitrogen (N) management. To increase N use efficiency (NUE), growers are encouraged to account for additional sources of N in their management plans, such as irrigation water N and preplant soil N. The availability of these N sources for plant uptake and how it is affected by other management conditions is not yet well documented. We conducted 6 field trials, 3 organic and …

Assessing Nitrogen Leaching Risk In Organic Vegetable Production, Megan Widle

Master's Theses

Nitrogen (N) leaching is the primary driver of groundwater contamination in agricultural regions. On California’s Central Coast, Agricultural Order 4.0 regulates this risk by constraining field-level N balances (N applied minus N removed). However, the assumption that unrecovered N is lost via leaching may not hold in organic and regenerative systems that promote soil organic matter accumulation. This study evaluated whether measured N leaching aligns with estimates derived from partial N budgets in organic systems, and whether management practices (intercrops, cover crops, and reduced tillage) can mitigate leaching risk. Four field trials were conducted to investigate N dynamics in organic …

Evaluating The Commercial Aquaculture Potential Of The Native Pacific Littleneck Clam (Leukoma Staminea) As A Climate Resilient Alternative To The Non-Native Manila Littleneck Clam (Ruditapes Philippinarum)., Skylar M. Wuelfing

Master's Theses

The California shellfish industry’s near-exclusive reliance on the non-native Manila littleneck clam (Ruditapes philippinarum) creates an economic vulnerability to climate-driven disturbances, which can cause mortality events that eradicate up to 80% of stocks. This singular reliance on an introduced species highlights a need for the evaluation of native alternatives like the Pacific littleneck clam (Leukoma staminea). Our goal was to assess the feasibility of using the native Pacific littleneck in commercial aquaculture by comparing their performance to the non-native Manila littlenecks across the following conditions: 1) a five-month field outplant trial at high and low intertidal …

Large Scale Kmer-Based Proteomic Analysis: An Application Towards Evolutionary Constraint Discovery, Matthew Chak

Master's Theses

Large protein databases now make it possible to study short peptides across natural protein sequence space at unprecedented scale, but exhaustively counting k-mers across billions of protein sequences remains computationally difficult. This thesis develops an exact amino-acid k-mer counting method based on direct addressing, in which fixed-length amino-acid strings are encoded as base-20 integers and updated with a sliding-window recurrence. By avoiding key storage and collision resolution, this approach removes overhead inherent to hash-map-based methods when the k-mer space is sufficiently dense. A memory analysis shows when direct addressing is preferable to open-addressing hash tables, and expected-saturation calculations motivate its …

Structured Dynamic Factor Analysis Of Environmental Time Series With Application To Morro Bay Estuary, Jose Garcia

Master's Theses

This thesis develops a structured dynamic factor analysis (sDFA) framework for decomposing multivariate environmental time series into latent biological and physical components. The methodology is applied to five years of high-resolution passive monitoring data collected from two sites in Morro Bay, California from 2020 through 2024. Relative contribution indices are developed based on the structured DFA that measure how much each latent process contributes to each observed variable at any given time. Structured DFA models fit to the application data suggest site-specific patterns in how biological and physical processes affect water quality variables. At the bay mouth location, physical processes …

Synthesis And Characterization Of A Graphene Oxide-Zif-8 Composite For Enhanced Post-Combustion Carbon Capture, Sydney Cooper

Master's Theses

Carbon dioxide (CO₂) emissions from fossil fuel combustion are a major contributor to climate change and its associated environmental impacts. The current standard technology for post-combustion carbon capture, aqueous amine scrubbing, is effective but requires significant regeneration energy and has high operational costs. As a result, solid sorbents have been investigated as lower-energy alternatives. Metal-organic frameworks (MOFs) are a promising class of porous nanomaterials due to their high surface area, tunable pore structures, and adjustable surface chemistry. Among them, zeolitic imidazolate framework-8 (ZIF-8) has high thermal and chemical stability, hydrophobicity, and favorable adsorption properties. However, conventional synthesis methods often rely …

Neuron Notes, Araceli Franco, Ethan Diec, Max Blennemann, Shibo Cong

Computer Science and Engineering Senior Theses

Mainstream digital note-taking tools such as Notion, Microsoft OneNote, and Evernote organize knowledge around linear documents and rigid folder hierarchies, a structure that strays from the associative, graph-like nature of human semantic memory. Mind-mapping and linked-note systems such as XMind, Obsidian, Roam Research, and Logseq move closer to that associative model but still constrain users to short labels, automatic layouts, or page-centric workflows that underutilize spatial and visual recall. This thesis presents Neuron Notes, a spatial, graph-based note-taking system designed to align digital organization with how people actually form and retrieve ideas. The system is implemented as a three-tier web …

Open Secrets, Robin Feldman Distinguished Professor Of Law, Vaughn Goehrig -- Center For Innovation

Vanderbilt Journal of Entertainment & Technology Law

Patents and trade secrets were never intended to meet, but in the world of biologic drugs, they’ve become as thick as thieves. Patent law’s disclosure requirement has demanded far too little of biologics manufacturers—allowing them to keep vital manufacturing details under trade secret lock and key. This intellectual property patchwork has been devastating for drug affordability: Because the most critical manufacturing information remains hidden, makers of follow-on biologics (called biosimilars) are often stuck reinventing the wheel, even after the original patents have expired. This Article makes two principal contributions to illuminating this problem. First, it presents, for the first time …

Essays On The Economics Of Aging: Structural And Machine Learning Approaches, Alexander S. Kwon

Dissertations, Theses, and Capstone Projects

Population aging has made the study of older workers’ economic behavior increasingly important for understanding labor markets, retirement systems, and public policy. In many advanced economies, rising old-age dependency ratios have increased the need to understand labor-supply, retirement, and savings decisions later in life (OECD, 2025). In the United States, these issues are especially important because Social Security faces long-run financing pressure, with the Old-Age and Survivors Insurance Trust Fund projected to be depleted around 2033 (U.S. Social Security Administration, Office of the Chief Actuary, 2025). Longer life expectancy increases the expected length of retirement and raises the fiscal importance …

Weaning Stress Induced Alterations To The Hypothalamic-Pituitary-Thyroid And -Adrenal Axes In Swine, Isabel B. Walpole, Alyssa A. Smith, Kaylyn G. Rudy, Dayeon Jeon, J. Scott Radcliffe, J. Alex Pasternak

Animal and Food Sciences Faculty Publications

Combined modulation of the hypothalamic–pituitary–thyroid (HPT) and hypothalamic–pituitary–adrenal (HPA) axes is known to play a critical role in maintaining physiological stability in response to stress. In this study, stress induced modulation of these axes was examined using 20 pigs/treatment either weaned (WN), weaned with feed/water restriction 9 h (FR), transported 9 h (TRANS), or remaining with sow (SOS) and euthanized at 32 or 56 h post-weaning. Serum cortisol, thyroxine (T4), and triiodothyronine (T3) were measured before weaning and after 24, 32, and 56 h with no difference in cortisol concentrations among treatments at any timepoint. However, both T3 and T4 …

Assessing Aflatoxin Knowledge, Perceptions, And Related Practices, In A Rural Coastal Community: A Population-Based Cross-Sectional Survey, Rosebella Iseme, Joseph Abuodha, Anthony Ngugi, Innocent Abayo, Mansoor Saleh

Population Health, East Africa

Background

Aflatoxin contamination is a significant yet under-addressed food safety challenge in low-resource settings, driven by a complex interplay of environmental, agricultural, and socio-economic factors. Limited access to agricultural inputs, inadequate post-harvest handling and storage, and weak regulatory enforcement alongside food scarcity and climate change heighten the risk of contamination and exposure. Human exposure is associated with serious health consequences, including hepatocellular carcinoma, immune suppression, and childhood stunting. Although aflatoxin is increasingly recognized as a global food safety concern, little is known about community-level knowledge, risk perceptions, and preventive practices. This study examined household heads’ awareness, perceptions, and behaviours related …

Nlrp3 Inflammasome: A Link Between Systemic Infection And Alzheimer’S Disease, Tatiana Barichello, Felipe Dal-Pizzol

Faculty, Staff and Student Publications

No abstract provided.

Full-Body Ai Agent: A Perspective On Multi-Scale Collaborative Ai For Systemic Biology And Precision Medicine., Aoqi Wang, Jiajia Liu, Jianguo Wen, Yangyang Luo, Zhiwei Fan, Liren Yang, Xi Hu, Ruihan Luo, Yankai Yu, Sophia Li, Weiling Zhao, Xiaobo Zhou

Faculty, Staff and Student Publications

Artificial intelligence (AI) is increasingly applied to biomedical research, but most current systems remain limited to specific tasks, data types, or biological scales. This makes it difficult to connect molecular alterations, organelle dysfunction, cellular behavior, tissue remodeling, organ physiology, systemic regulation, and whole-body phenotypes into coherent biological reasoning. In this Perspective, we propose the Full-Body AI Agent as a hypothetical multi-agent framework and conceptual blueprint for future systemic biology and precision medicine, rather than a fully implemented software platform. This framework envisions a supervisory Full-Body AI Agent coordinating seven biological-level agents, namely Molecule, Organelle, Cell, Tissue, Organ, Organ System, and …

Ldm-Morph: Latent Diffusion Model Guided Deformable Image Registration, Jiong Wu, Tinsu Pan, Kuang Gong

Faculty, Staff and Student Publications

Deformable image registration plays an essential role in various medical image tasks. Existing deep learning-based deformable registration frameworks primarily utilize convolutional neural networks (CNNs) or Transformers to learn features to predict the deformations. However, the lack of semantic information in the learned features limits the registration performance. Furthermore, the similarity metric of the loss function is often evaluated only in the pixel space, which ignores the matching of high-level anatomical features and can lead to deformation folding. To address these issues, in this work, we proposed LDM-Morph, an unsupervised deformable registration algorithm for medical image registration. LDM-Morph integrated features extracted …