Digital Commons Network^™

An Association Test For Ordinal Outcomes In Clustered Data With Informative Cluster Size, Hasika K. Wickrama Senevirathne, Sandipan Dutta

Mathematics & Statistics Faculty Publications

In cluster-correlated data, the number of observations in a cluster can be associated with the outcome from that cluster. This phenomenon is known as informative cluster size which can occur in cluster-randomized clinical trial data. Several studies have found that ignoring the issue of informative cluster size can produce biased results in the analysis of clustered data. Most of the existing methods for addressing informative cluster size are suited to continuous outcomes. However, ordinal outcomes and covariates are often encountered in clustered data obtained from large clinical studies. The existing methods for ordinal association testing in clustered data can produce …

Logistic-T Multinomial Mixture Model For Clustering For Microbiome Data, Wenshu Dai, Yuan Fang, Sanjeena Subedi

Mathematics & Statistics Faculty Publications

The logistic-normal multinomial distribution has been used for modelling microbiome data obtained from high-throughput sequencing technologies, which are compositional in nature. A logistic-normal multinomial distribution is a hierarchical multinomial distribution that assumes the latent variable which are the additive log-ratio (ALR) transformed proportions in a multinomial distribution follows a Gaussian distribution. Model-based clustering algorithms have also been developed for clustering microbiome data based on the logistic-normal models. However, the Gaussian assumption may violated when the ALR transformed variable exhibit heavy-tailed distributions or has outliers. Our study introduces a novel mixture of logistic-t multinomial models that effectively address these challenges. Utilizing …

Real-World Anti-Amyloid Therapy Beyond Traditional Symptomatic Populations: A Longitudinal Case Series, Jayoung Han, Yuan Fang, Darlingtina Esiaka, Olufunmilola Abraham

Mathematics & Statistics Faculty Publications

Introduction: Anti-amyloid monoclonal antibodies are approved as disease-modifying therapies for early Alzheimer’s disease (AD), but real-world evidence remains limited, particularly among individuals treated during preclinical or minimally symptomatic stages. This study characterized clinical and biomarker trajectories among anti-amyloid therapy recipients across disease stages.

Method: We conducted a longitudinal retrospective case series of three biomarker-positive individuals from the Alzheimer’s Disease Neuroimaging Initiative who received lecanemab or donanemab. Clinical, cognitive, cerebrospinal fluid, plasma biomarker, and amyloid PET data were examined.

Results: In all three cases, most of the observation period preceded anti-amyloid therapy initiation. Clinical trajectories varied by biomarker profile and treatment …

Determining The Electric Field In A 10 Ns Pulsed Plasma In Fuel-Air Mixtures Using Efish, Md Ziaur Rahman, Christopher J. Kliewer, Brian D. Patterson, Chunqi Jiang

Bioelectrics Publications

Transient plasma ignition (TPI) utilizes non-equilibrium plasmas, produced by nanosecond high-voltage pulses, to improve lean-fuel combustion performance and reduce emission. It is known that the relatively high reduced electric field (E/N) in TPI plays an important role in generating energetic electrons and facilitating energy-efficient radical productions, resulting in reliable ignition for lean combustion. Determining the reduced electric field in the discharge is hence important for the understanding of the TPI process and ultimately allowing for the control of the plasma chemistry. This study reports spatiotemporally resolved measurements of the electric field (E) in a 10 ns pulsed plasma that is …

Ammonia Synthesis By Nanosecond Pulsed Atmospheric Pressure Plasma Jets Impinging On Water, Zach Caudell, Lynnet Rich, Olga Pakhomova, Chunqi Jiang

Bioelectrics Publications

Developing energy-efficient technologies for carbon-neutral ammonia (NH₃) synthesis is critical for decentralized fertilizer production and global decarbonization. This study investigates generating NH₃ from water using a nanosecond pulsed atmospheric pressure plasma jet (ns‑APPJ) operating in either N₂ or dry air. The plasma jet reactor employed approximately 250 ns, up-to-22 kV pulses at 500 Hz to sustain a nonequilibrium discharge impinging directly on static liquid water. The kinetics, energy efficiency, and product selectivity of NH3 formation were quantified as functions of the pulse voltage, repetition frequency (PRF), and gas flow rate. NH₃ production increased linearly with treatment time and scaled strongly …

Identifying Transcriptomic Signatures That Mediate The Causal Effect Of Genotype On Alzheimer's Disease., Simran Kaur, Anna L. Tyler, Giovanna L Durante, Gregory Cary, Gregory W. Carter, J Matthew Mahoney

Faculty Research 2026

The combined effects of thousands of genetic polymorphisms account for Alzheimer's disease (AD) genetic risk. Most AD polymorphisms affect gene expression. Thus, the transcriptome, the set of all gene expression levels for every gene in the genome, is a major mediator between the genotype to phenotype. This study uses genotypes, transcriptomes, and clinical phenotypes to identify the transcriptomic signature that mediates the causal effect of genotype on AD. By utilizing a causal inference method known as high dimensional mediation analysis (HDMA) on the Religious Orders Study/Memory and Aging Project (ROSMAP) longitudinal cohort, the genotype, transcriptome, and phenotype data were reduced …

Nourishing Roots: Supporting Indigenous Food Education In School Gardens, Tatiana Marina Patino Madriaga

Cal Poly Humboldt theses and projects

This project asked: How can a school garden at Hoopa Valley Elementary support Indigenous food education, student well-being, and relational learning? To explore this question, I designed and implemented a garden classroom and facilitated hands-on garden and culinary workshops with students.

The garden was planned in September, built in October, and had plants in the ground by November. Over the course of the project, I facilitated four workshops, one Earth Day community event, and weekly garden classes. Approximately 350 students participated in the garden in some capacity, reflecting broad, school-wide engagement.

Methods included participant observation, documentation of student engagement, and …

Bacterial Community Function In Pitcher Plant Leaves As An Experimental And Mathematical Model Of Functional Dynamics, Amelia Jackson

Cal Poly Humboldt theses and projects

This work looks at two different sites with differing abiotic factors in measures of altitude, temperature and precipitation. The site with higher altitude, larger temperature range, and lower precipitation, located in Plumas National Forest (Quincy, CA), had a flat BEF trend that suggests functional redundancy The site with lower altitude, more moderate temperatures, and higher precipitation located in Six Rivers National Forest (Gasquet, CA), also had a flat BEF trend. These abiotic factors could correlate to the significantly different bacterial compositions between sites. The second portion of this work is modeling the host antagonist relationship between Eyxra moths and their …

"What Power Do We Have?" Community Capacity And Justice In Samoa, California’S Floating Offshore Wind Terminal Development, Lauren Mccall Hart

Cal Poly Humboldt theses and projects

Floating offshore wind (OSW) is a relatively novel technology in the United States, which is positioned to play an integral role in California’s decarbonization strategy. Two federal OSW lease areas have been established off the coast of Northern California, and plans are underway to develop supporting port infrastructure, including the Humboldt Bay Offshore Wind Heavy Lift Marine Terminal (HLMT). The proposed HLMT site is adjacent to communities on the Samoa Peninsula of Humboldt Bay, which currently face socio-environmental vulnerabilities and critical infrastructure gaps. The social implications of OSW port development remain poorly understood, particularly in rural and underserved communities. This …

Depth And Soil Physical Context Govern Soil Organic Carbon, While Woody Cover Moderates Native Vegetation Relationships In California Rangelands, Dabid Zuniga Garcia

Cal Poly Humboldt theses and projects

Soil organic carbon (SOC) is central to soil function and an important component of climate mitigation in rangeland ecosystems, but the controls on SOC across California’s working rangelands remain understudied. Using data from Point Blue Conservation Science’s Rangeland Monitoring Network, this study evaluated how soil properties, vegetation structure, and recent climate relate to SOC concentration at depths of 0–10 cm and 10–40 cm across 145 ranches spanning four California regions. Linear mixed-effects models showed that SOC was consistently higher in topsoil than subsoil and highest in coastal sites relative to interior valleys. Bulk density was the strongest negative predictor of …

Ai Deployment Authorisation: A Global Standard For Machine-Readable Governance Of High-Risk Artificial Intelligence, Daniel Djan Saparning

Student Publications

Modern artificial intelligence (AI) governance lacks a formal, enforceable mechanism for determining whether a given AI system is legally permitted to operate in a specific domain and jurisdiction. Existing approaches-such as model cards, audits, and benchmark evaluations provide descriptive information about model behaviour and training data but do not produce binding deployment decisions with legal or financial force. This paper introduces the AI Deployment Authorisation Score (ADAS). This machine-readable, regulator-grade framework evaluates AI systems across five legally and economically grounded dimensions: Risk, Alignment, Externality, Control, and Auditability, derived from safety engineering, alignment theory, algorithmic accountability, and liability economics. ADAS produces …

Reversible Fluorescence Quenching And Recovery In Pvp-Supported Copper Nanoparticles, Sara Rayan

Senior Honors Theses and Projects

Copper nanoclusters stabilized by polyvinylpyrrolidone (PVP) exhibit unique fluorescence properties that are highly sensitive to changes in their chemical environment, making them promising candidates for sensing applications. This study investigates the reversible fluorescence quenching and recovery behavior of PVP-supported copper nanoparticles in response to iron(III) ions and evaluates the selectivity of this response across different chemical conditions. Fluorescence quenching was examined using Fe³⁺ introduced as FeCl₃, followed by recovery experiments using ascorbic acid to assess reversibility through redox-driven interactions. To determine whether the observed response is specific to iron, potassium ferricyanide was used as an alternative Fe³⁺ source. Additional comparisons …

Investigating The Effects Of Atg3 On Autophagosome Size And Number, Keeran R. Senthil Kumar

Senior Honors Theses and Projects

Macroautophagy, or autophagy, is a highly conserved catabolic process in all eukaryotes which allows for the degradation of large cytosolic contents. It occurs in two forms: bulk autophagy, which is induced by nutrient deprivation and targets nonspecific cargo, and selective autophagy, which is induced by cellular stress and sequesters specific substrates. The process of autophagosome formation is carried out by a group of Atg (autophagy-related) proteins, one of which is Atg3. Atg3 functions as an E2-like enzyme by conjugating Atg8 — a ubiquitin-like protein — to phosphatidylethanolamine (PE), a step required for autophagosome membrane formation. This lipidation process is catalyzed …

Oligarchy And Democratic Decline: A Platonic Framework For Analyzing The Contemporary American Political System, Jonah Huskey-Wright

Senior Honors Theses and Projects

This paper explores the idea that there is a meaningful philosophical connection between Plato’s account of oligarchy and the development of the modern American political order. Rather than approaching American politics only through constitutional design, electoral procedures, or institutional mechanics, the paper argues that political systems must also be understood as reflections of the values and motivations of the people who inhabit them. Drawing on Plato’s framework that links the ordering of the human soul to the ordering of political regimes, the project examines how the priorities a society places on certain goods—particularly wealth, economic achievement, and material success—can shape …

Efficient Organic Molecular Crystal Structure Prediction Using The Density Functional Tight-Binding Method, Maureen M. Kitheka, Yan Jing, Yan Yao, Puja Goyal

Faculty Publications – Chemistry

Over the years, computational crystal structure prediction (CSP) for organic molecules has thrived as an area of research, spanning various scientific disciplines and having significant applications in industries such as pharmaceuticals and agrochemicals. Within the field of batteries, redox-active organic materials (ROMs) such as quinones have received increased attention as promising electrode materials for rechargeable batteries. However, experimental determination of the crystal structure of intermediate species formed during the discharge/charge cycle can often be challenging. Incomplete X-ray diffraction patterns can also lead to difficulties in crystal structure determination for ROMs used in batteries. Use of a semiempirical electronic structure method …

Detecting And Repairing Conflicting Constraints In Co-Trained Physics-Informed Neural Networks For Composite Curing Processes, Cooper J. Evans

Dissertations, Master's Theses and Master's Reports

Composite materials have become a critical component of modern manufacturing, especially in the automotive and aerospace industries. The curing process for these composites has been modeled using a variety of partial differential equations representing the heat transfer and composite curing kinetics. Optimizing the applied temperature profile is critical for maximizing the efficiency and capacity of composite part manufacturers. Constraints must be placed on the inputs and outputs of the model, including but not limited to, the applied temperature profile, part temperature, and final degree of cure. Conflicting sets of constraints are easy to unknowingly impose due to the highly coupled …

Impact Of Powdered Tart Cherry Supplementation On Performance Recovery Following Repeated Sprint Exercise, Anthony M. Hagele, Kyle S. Levers, Kevin F. Holley, Alex C. Schrautemeier, Joesi M. Krieger, Joshua M. Iannotti, Connor J. Gaige, Ralf Jäger, Chad Kerksick

Faculty Scholarship

Background: Due to its high polyphenol content and purported capability to mitigate post-exercise muscle soreness and promote recovery, tart cherry (TC) supplementation has been proposed to enhance recovery and athletic performance. This study examined the effects of powdered TC supplementation on various recovery and performance metrics following a repeated sprint exercise protocol in physically active young adults.

Methods: 40 (18 M, 22 F) healthy, active participants (24.6 ± 5.5 yrs, 171.5 ± 11 cm, 71.7 ± 14.5 kg, 24.2 ± 3.1 kg·m−2) participated in this randomized, double-blind, placebo-controlled, parallel study design. Placebo (PLA) or powdered TC supplementation (500 …

Labor Market Impacts Of Immigration Enforcement: Evidence From The Second Trump Administration, Rachel Letts

Economics Honors Papers

The onset of the second Trump Administration saw a stark immigration policy shock in the U.S. with record numbers of Immigration Customs Enforcement (ICE) detentions. This paper seeks to understand the labor market impacts of this immigration enforcement that have disproportionately affected the risk of being detained for non-white individuals. To estimate the effect of this policy shock, a triple difference model is used comparing non-white individuals to white individuals living in Metropolitan Statistical Areas (MSAs) with above or below average concentrations of immigration detentions before and after this immigration shock. The regression analysis finds that since the beginning of …

Hear & Now: Culturally Responsive Music Education Through Digital Audio Workstations & Musique Concrète, Benjamin T. Connolly

Pitzer Senior Theses

Hear & Now: Culturally Responsive Music Education Through Digital Audio Workstations & Musique Concrète is a two-part ethnomusicological study of how the capacities and affordability of modern electronic instruments could be utilized within school curricula as an affordable alternative to traditional music classes. I explore the musique concrète movement from mid-20th century France, aiming my examination towards the movement’s emphasis on the materiality of sound production and utilization of modern technology during the composition process. From there, the paper transitions into a study on the affordances of contemporary music technologies through a series of interviews with electronic composers, tracing the …

Learning Without Training, Ryan O'Dowd

CGU Theses & Dissertations

We live in an era of big data. Whether it be algorithms designed to help corporations efficiently allocate the use of their resources, systems to block or intercept transmissions in times of war, or the helpful pocket companion known as ChatGPT, machine learning is at the heart of managing the real-world problems associated with massive data. With the success of neural networks on such large-scale problems, more research in machine learning is being conducted now than ever before. This dissertation focuses on three different projects rooted in mathematical theory for machine learning applications. Common themes throughout involve the synthesis of …

On The Influence Of Faraday Waves On Transport In Resonant Acoustic Mixing, Preston David Silverstein

CGU Theses & Dissertations

Resonant acoustic mixing (RAM) uses low frequency high acceleration oscillatory forcing to combine fluids, particles, and powders. Although progress has been in adjacent RAM fields, there are still gaps in understanding how Faraday surface instabilities affect momentum transport to the bulk fluid and particles therein. This work investigates the energy pathways that an oscillatory mixer has and connects surface deformation to bulk rotational flow and particle forcing. This study is conducted in three phases. In phase 1, a thermodynamic first- and second-law analysis couples the surface features with the scale of subsurface rotational features. Experimental surface measurements showed that for …

The Epistemic Limits Of Evolutionary Debunking: An Evaluation Of Evolutionary Arguments Against Moral Realism, José Ernesto Guzmán

CGU Theses & Dissertations

Evolutionary debunking arguments contend that the evolutionary origins of moral belief undermine the epistemic standing of moral realism. Sharon Street's Darwinian Dilemma and Richard Joyce's genealogical undercutting argument represent the two most influential formulations of this challenge. This project subjects both to sustained internal critique and finds them wanting. The central contribution is a bridge-requirement framework identifying four principles (BR₁ through BR₄) that any evolutionary debunking argument must supply to move validly from genealogical premises to epistemic conclusions. BR₁ connects genealogy to justification. BR₂ connects population-level evolutionary explanations to individual-level epistemic consequences. BR₃ connects semantic features of moral discourse to …

Middle School Girls' Math Self-Concepts In Japan And The United States: A Socio-Ecological Approach, Kimberly A. Megyesi-Brem

CGU Theses & Dissertations

In Japan and the United States, women’s underrepresentation in STEM fields in tertiary education limits opportunities for social mobility and economic stability. Efforts to address this issue need to consider the role played by the intractable girls’ inferiority in math (GIM) myth that contributes to girls’ lower engagement in math through lower math self-concepts. Prior research shows that perceived teacher support through is one area where the GIM myth relates to girls’ math self-concepts through teacher bias about girls’ math competence. However, research has predominantly been focused at the individual level, including studies that conclude that girls’ lower math self-concepts …

The Dunning-Kruger Effect In Sixth Grade Adolescents: Improving Metacognition For Self-Regulated Learning, Julie H. Chen

Scripps Senior Theses

The Dunning-Kruger (DK) effect is a cognitive bias where low-performing individuals overestimate their own abilities, and top-performing individuals underestimate their own abilities relative to their peers. The purpose of this proposed study is to investigate the DK effect in sixth grade adolescents and to use metacognition as an intervention to improve self-assessment calibrations. This study will investigate adolescents in Piaget’s formal operational stage, aiming to improve metacognition levels. The study will occur over 12 weeks, and participants will be given a preparation handbook with or without metacognition activities for the purpose of preparing for the California Assessment of Student Performance …

Effects Of Teacher Training On Identifying Inattentive Type Adhd In Afab Students, Gabrielle A. Boles

Scripps Senior Theses

Teachers are more likely to detect hyperactive ADHD symptoms than inattentive ones, which often results in students, especially girls with inattentive symptoms, being under-referred (Willcut, 2012). This study evaluates whether a targeted, inattentive-focused, and gender responsive teacher training reduces gendered and symptom-based biases in referral decisions. K-5 teachers will be randomly assigned to receive either standard general ADHD identification training or an inattentive-focused, gender-responsive training, and will then be asked to review vignettes depicting children with hyperactive and inattentive symptoms, with varying student genders. Referral accuracy and knowledge of ADHD will be measured. Training condition, symptom presentation, and student gender …

Why We Can’T “Get Over It”: Offense And The Moral Limits Of Epistocracy, Yui Kurosawa

CMC Senior Theses

This thesis examines whether an epistocracy — rule of the knowledgeable — could ever be implemented as a morally permissible alternative to democracy. Building on Jason Brennan’s instrumental critique of democracy in Against Democracy, I lay out his argument that systematic voter ignorance undermines the epistemic capacity of “one person, one vote” to reliably generate just and well-informed political decisions. Brennan argues that epistocratic institutions, which allocate political power according to political competence rather than by equal distribution, are better positioned to achieve such decisions and therefore more legitimate than democracy.

Epistocracy, as an aspirational alternative, may indeed be promising; …

Associate Of Arts New Degree, Academic Affairs

Program Revisions/Additions

No abstract provided.

Formation-Based Ai Ethics: Ethical Formation, Responsibility, And Opportunity Cost In Ai Ecosystems, Maurice Emelu

2026 Faculty Bibliography

Recent efforts in AI ethics have been dominated by the proliferation of high-level principles intended to guide responsible development and deployment. Yet persistent implementation failures suggest that principlism and tool-based approaches alone do not cultivate the moral capacity required to govern sociotechnical systems. This article advances a formation based framework for AI ethics that situates moral agency throughout the developmental conditions of design, use, and the AI lifecycle. Drawing on Aristotelian-MacIntyrean virtue ethics applied to media ecology, and sociotechnical responsibility, the argument reframes AI as a formative environment that shapes patterns of attention, judgment, delegation, and accountability over time. Against …

Asymptotics Of Discrete Convolution Powers And Applications To Difference Schemes, Pedro Henrique Alves Silva Dos Santos

Honors Theses

In this thesis we provide Gaussian Estimates and Local Limit Theorems describing the asymptotic behavior of convolution powers of a class of complex-valued functions on $\mathbb{Z}^d$. Convolution powers arise naturally in the study of partial differential equations, as well as in random walks in probability theory. In particular, they are connected to the stability theory of difference schemes used to approximate solutions to partial differential equations. We take inspiration from the work of Vidar Thomée on stability theory to restrict our attention to convolution powers of functions whose Fourier Transforms satisfy certain local expansions. We then combine the Cauchy Integral …

Hegemonic Microtonality: Decolonizing The Soundscape Of Music Theory Pedagogy, Ash K. Wetty

Honors Theses

This thesis examines how Western music theory pedagogy—long organized around tonal and twelve-tone equal-temperament frameworks—structures both what is taught and how students are trained to listen. Through a literature review tracing the historical construction of tonal universality in undergraduate curricula, the project argues that dominant models of music theory reproduce broader epistemic hierarchies inherited from Western conservatory traditions. Situating these histories within my own experience as a student navigating institutional listening norms, the thesis combines critical self-reflection with ethnographic research conducted across five liberal arts institutions, including the CBB consortium and JanPlan research at Wesleyan University and Amherst College. Rather …