Digital Commons Network^™

Mycelial Modeling: Teaching Biology Students Statistical Modeling With Mushrooms, Colette Wolf

University Honors Theses

This paper summarizes and describes the development of a set of learning materials that were created to educate students and professionals from other fields in statistical modeling techniques. These materials are primarily aimed at biology students, but are still intended to be useful for anyone who is interested in incorporating decision trees and random forest models into their personal research in the future. By directing the reader towards the JMP software, these materials navigate around the statistical knowledge base and coding implementation practices that otherwise would serve as a barrier to learning statistical modeling techniques, and instead focus on the …

Effects Of Changing Fire Regimes On Black Huckleberry Habitat Suitability, Emily Labarge

University Honors Theses

Black huckleberries are a significant cultural, ecological, and economic species in the Pacific Northwest. Historically, black huckleberries were tended with cultural fire by Indigenous peoples, and now also hold importance as a resource in the non-timber forest product economy. Research has begun on the impacts of climate change on suitable black huckleberry habitat and on changing fire regimes, but not in relation to each other. To address this gap, I examined the area of overlap between suitable black huckleberry habitat and fire burn probability into mid-century climate projections. I determined the current ownership entities with management jurisdiction in areas with …

Assessing Spatial Distribution Of Plausible Earthquake-Triggered Landslides Relative To Ca. 1000 Ybp Earthquake On The Gales Creek Fault, Jacqueline Rheingans

University Honors Theses

Modern coseismic landslides cluster near the surface trace of the fault that ruptured, suggesting that clustering of paleolandslides may record information about paleoearthquakes. This study documents the pattern of prehistoric landslides near the Gales Creek Fault (GCF), northwest Oregon, to assess whether it reflects an independently known paleoearthquake. The GCF is located northwest of Portland through the Cascadia fore-arc basin where landslides are often triggered by intense rainfall during the wet season or potentially by seismic shaking on the megathrust or on crustal faults. In order to understand how a seismic event on the GCF will impact landslide distribution I …

The Role Of Urban Forests In Mitigating Flooding Effects: A Case Study In Savannah, Georgia, Gillian Bush

Undergraduate Theses, Capstones, and Recitals

Flooding in coastal communities is shaped by the interaction between natural systems and urban development. Chatham County, a low-elevation region in the Savannah, Georgia metropolitan area along the eastern coast of the United States, is prone to coastal storms and frequently affected by flooding. It serves as a useful case study to better understand the factors behind flooding and the areas that are most at risk. This study uses GIS-based analysis to examine the overlap between flood risk, urban forest cover, and impervious surfaces. The results indicate elevated vulnerability along major transportation corridors and barrier islands, where high-risk flood zones …

Digital Bodily Autonomy: Consent Issues, Labor Displacement, And Legal Understandings Of Ai Generated Deepfake Pornography, Mariah Barrett

Undergraduate Theses, Capstones, and Recitals

In the United States, nonconsensual pornographic deepfakes are becoming an increasingly prevalent problem as AI deepfake creation software improves and becomes widely available. Despite this, patchwork legislation across the country is inconsistent and conflicting regarding this issue. In this paper, I explore the background of pornography and obscenity laws and demonstrate how these frameworks are not properly constructed to apply to the digital sphere. Then, I address major themes within deepfake literature such as consent issues, bodily autonomy, labor displacement, and verifiable identity as a commodity through the case study of OnlyFans. I explore current and proposed legislation within the …

Rapid-Prototyping Nanofabrication: Lcd-Based Projection Lithography And Physical Vapor Deposition, Sabeel Saleem Mohammmed

University Honors Theses

The semiconductor industry's continued growth, driven in large part by demand for artificial intelligence hardware, has highlighted the need for greater workforce development in regions adjacent to major fabrication centers like Oregon's Silicon Forest. This capstone project lays the groundwork for a small scale and student led semiconductor fabrication lab at Portland State University by demonstrating two of the core steps in chip manufacturing: photolithography and thin film deposition. Rather than relying on conventional fixed reticles, this work explores a unique, low cost approach to patterning that uses an ultraviolet-compatible liquid crystal display (LCD) as a programmable reticle, allowing arbitrary …

Bias, Structure, And Inference In Applied Network Analysis, Anna Vasenina

Dartmouth College Ph.D Dissertations

This dissertation develops mathematical and statistical methods for extracting reliable information from network data across biological applications, with an emphasis on understanding what observed network structure can and cannot resolve. The first study leverages protein–protein interaction network topology in the c-di-GMP signaling system of Pseudomonas fluorescens, showing that node centrality measures accurately classify protein domain types and that physical interaction structure contributes statistically significant predictive power for biofilm formation phenotypes across nearly 200 environments, while gene expression does not. The second study examines sampling bias in lemur-plant trophic interaction networks in Madagascar, demonstrating that differential detection of diurnal versus …

Fluvial-Tidal Controls On Dune Morphology And The Effects Of Nature-Based Morphology In Mitigating Storm Impacts, Abiola A. Adebiyi

Electronic Theses and Dissertations

Nature-based morphological features in coastal areas, such as dunes, coral reefs, and seagrass, play dual roles as both receivers of threats from increasing human activity and climate change and defenders that mitigate potential impacts. Therefore, it is imperative to improve our understanding of how these features may affect hydrodynamic processes under various conditions. To address this need, the objectives of this research are two-fold: 1) to enhance our knowledge of changes of bedform morphology in response to different fluvial-tidal controls in the Lower Columbia River (LCR), and 2) to investigate how natural-based features may mitigate tropical storm impacts using a …

A Novel, Embedding-Based Approach To Longitudinal Survey Data Imputation, Julia Rezvani

University Honors Theses

Longitudinal surveys are ubiquitous in the social sciences as a means of tracking changes in behavior and opinions with time and identifying potential causal mechanisms. These surveys are frequently plagued by missing data and semantic drift, both of which limit their effectiveness and scientific utility. Imputation algorithms allow researchers to fill gaps in collected survey datasets, imperfectly reconstructing lost data. Although deep learning algorithms have been used in imputation to great success, approaches which simultaneously leverage the semantic and temporal structure of longitudinal surveys have not yet been developed. We propose a novel imputation architecture which is capable of leveraging …

Refining A Flow Injection Analysis Method For Trace Concentrations Of Iron In Seawater, Brooke I. Stafford, Liam W. Hodgson, Noah S. Schuhmann, Elijah J. Vestal, Claire P. Till

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Iron is an essential micronutrient required for the growth of phytoplankton, the base of the oceanic food chain. Iron exists in the ocean in extremely low concentrations, limiting primary productivity in ~⅓ of the surface ocean, and can be affected by physical processes such as upwelling of water masses, and by biological and chemical processes within the water. In order to further our understanding of iron availability in the ocean, here we refine and improve our understanding of an analytical method to measure nanomolar iron in seawater. The method used is an adaptation of Lohan et al. (2006), a flow …

Exploring The Relationship Between Tree Dbh And Lichen Cover On Coast Redwood, Grace M. Personeus, Sierra Gittleman, Alisa A. Zarattini

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

We investigated the relationship between Diameter at Breast Height (DBH) and lichen cover on coast redwood (Sequoia sempervirens) to see if larger trees had higher percentages of cover. We measured cover using 10 cover classes on the southeastern and southwestern sides of trees in a secondary growth forest. We found a significant relationship between DBH and cover, yet no significant difference between the two sides measured. We suggest that further research with a larger sample size and more varied age classes will provide further insight into the relationship.

Allosteric And Uncompetitive Inhibition Of Yeast Alcohol Dehydrogenase Identified By Enzyme Kinetics, Dylan Jeremy Harrison, Jenny A. Cappuccio

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Enzyme kinetics is a powerful technique used to quantify the rate at which an enzyme converts a substrate into a product and to identify potential inhibitors. In this study, kinetic analysis was employed to assess the activity of yeast alcohol dehydrogenase (YADH) in the presence and absence of sweeteners commonly found in alcoholic beverages. YADH catalyzes the oxidation of ethanol to acetaldehyde using NAD⁺ as a cofactor; the reduction to NADH can be monitored spectrophotometrically at 340 nm. Based on structural similarities to the ribose moiety of NAD⁺, it was hypothesized that sucrose and sucralose could directly interact with the …

A Professional Development Course On Data-Driven Dynamical Systems At A Primarily Undergraduate Institution: Part A - Scientific Content, Alessandro M. Selvitella, Jeffrey R. Anderson

CODEE Journal

In the age of data-driven decision making, ordinary differential equations (ODEs) remain a powerful and interpretable framework for modeling dynamic processes, especially when integrated with modern tools from statistical learning and data-driven dynamical systems. Yet, general undergraduate and graduate curricula do not typically address key opportunities in data-driven dynamical systems.

This first paper in a series focuses on the mathematical and methodological core of a professional development course first developed in the academic year 2025-2026 at a Primarily Undergraduate Institution, Purdue University Fort Wayne. The curriculum developed in this course emphasized how regression, regularization, and sparse identification can be used …

Phase-Resolved Measurement And Arbitrary Mode Conversion Of Structured Light, Somayeh Ghazanfarpour

Electronic Theses and Dissertations

This dissertation presents a single-shot phase and amplitude retrieval technique based on spatial light modulator (SLM)-based digital holography. The proposed method enables accurate reconstruction of complex optical fields from a single interferogram, reducing sensitivity to environmental fluctuations and improving experimental stability compared to conventional multi-shot approaches. In addition, a programmable arbitrary mode converter is developed using SLM-based wavefront shaping. By introducing controlled astigmatism and engineering the differential Gouy phase between orthogonal components, the system enables flexible transformation between structured light modes, including Hermite–Gaussian and Laguerre–Gaussian beams. Numerical results demonstrate reliable phase recovery and efficient mode conversion, validating the performance of …

Re: Approval Letter For The Quarterly Operations And Maintenance Report Grove Gulch Sedimentation Bay For Fourth Quarter 2025 Silver Bow Creek/Bute Area Npl Site – Butte Priority Soils Operable Unit Consent Decree-Civil Action No. Cv 89-039-Bu-She (Dated May 15, 2026)., Emma Rott

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Quantifying Terrain Controls On Satellite-Based Snow Water Equivalent Estimation: A Spatially Explicit Machine Learning Approach, Brant Giovannetti

Geography and the Environment: Graduate Student Capstones

Terrain variables are widely incorporated into machine learning Snow Water Equivalent (SWE) models but are rarely evaluated for their independent contribution relative to spectral predictors. Using a four-tier stepwise Random Forest framework with Harmonized Landsat Sentinel-2 imagery and Airborne Snow Observatory LiDAR ground truth, this study isolates the contribution of elevation, slope, northness, and eastness across Peak and Ablation snowpack regimes in the East Taylor River Watershed, Colorado. During peak snowpack, adding terrain improved R² by 0.214, with elevation alone accounting for 42.8% of model importance. During ablation, full-dataset terrain gains were modest, increasing R² by only 0.036. However, when …

Geospatial Governance Failures In The Department Of Defense: Contractor Noncompliance, Ai Adoption, And The Parallel Treatment Of Gis And Cybersecurity, Lyndsey Olmstead

Geography and the Environment: Graduate Student Capstones

The Department of Defense's treatment of geographic information systems and cybersecurity as parallel rather than integrated policy domains produces geographically predictable vulnerability patterns across its global military installation footprint. This capstone investigates that conclusion through original spatial analysis, constructing a five-variable composite geospatial vulnerability index across the six U.S. Combatant Command regions using publicly available unclassified data. EUCOM ranked highest overall, driven by GPS/PNT spoofing density, commercial satellite coverage, and cyber incident frequency; CENTCOM ranked second, driven by OSINT exposure incidents and governance risk. The null hypothesis of random geographic distribution is rejected. Findings confirm the structural governance gap documented …

Data Governance Maturity, Ai Integration, And Equity In Colorado K-12 Public Schools, John R. Curtin

Electronic Theses and Dissertations

Colorado's 179 K-12 public school districts operate as autonomous governance units, each responsible for securing and managing student data assets that span health, financial, residential, and academic records. The accelerating integration of artificial intelligence (AI) and machine learning (ML) tools into administrative workflows, productivity software, and instructional platforms has fundamentally altered the risk landscape for student data, yet governance frameworks at the state, district, and school levels have not kept pace. This dissertation investigates whether Colorado's decentralized educational governance structure is institutionally capable of producing equitable, secure, and sustainable data governance outcomes in the AI era.

Drawing on Institutional Theory …

Some Results In Maximal Pattern Complexity, Casey Schlortt

Electronic Theses and Dissertations

For a finite alphabet 𝒜 and a sequence 𝑥 ∈ 𝒜^ℕ_⊬ , Kamae and Zamboni combined the ideas of block complexity and topological sequence entropy to define the maximal pattern complexity, 𝑝^∗_𝑛 (𝑥). They defined an aperiodic sequence 𝑥 over two letters as pattern Sturmian if it had the lowest possible maximal pattern complexity, 2𝑛. Later, Kamae and Rao extended their definition of pattern Sturmian sequences to be sequences over ℓ ≥ 2 letters which are not periodic by projection and have maximal pattern complexity ℓ𝑛.

This dissertation answers a question posed by Kamae and Zamboni …

Ka Here Tāngata:1 Mātauranga And Te Ao Māori In Biocultural Kākāpō (Strigops Habroptilus) Conservation Approaches, Sophie Perfetto

Electronic Theses and Dissertations

This master's thesis examines conservation as a form of living cultural heritage practice through the co-management of kākāpō (Strigops habroptilus), a critically endangered parrot and taonga species in Aotearoa New Zealand. Situated within ongoing histories of colonial dispossession and Western frameworks of land and species management, contemporary kākāpō conservation is shaped through the partnership between the Department of Conservation’s Kākāpō Recovery Programme and Ngāi Tahu. Drawing on semi-structured interviews collected during fieldwork from July to August 2025, this study examines how institutional partnerships structure decision-making, authority, and responsibility in contemporary conservation governance. Findings demonstrate that Māori knowledge systems …

Evaluation And Distillation Of Source Code Generation Tasks By Large Language Models, Danny Brahman

Electronic Theses and Dissertations

Large Language Models (LLMs) are predominantly assessed based on their common sense reasoning, language comprehension, and logical reasoning abilities. While models trained in specialized domains like mathematics or coding have demonstrated remarkable advancements in logical reasoning, there remains a significant gap in evaluating their code generation capabilities. Existing benchmark datasets fall short in pinpointing specific strengths and weaknesses, impeding targeted enhancements in models’ reasoning abilities to synthesize code.

To bridge this gap, this thesis introduces two novel contributions: CodeEval and CodeQual. CodeEval is an innovative, pedagogical benchmarking method that mirrors the evaluation processes encountered in academic programming courses. It comprises …

Beyond The Best Fit: Fitting Sir-Style Models To Data While Prioritizing Biological Meaning, Meredith L. Greer

CODEE Journal

Many students find comfort in mathematics because math classes have been a place where they can find the “right answer” to exercises. Modeling courses typically emphasize more nuance, teaching students to try modeling approaches, compare back with real-world mechanisms and data, and then refine their models, in an ongoing cycle. One topic, however, can cause students to quickly revert into “right answer” mode: fitting a model to data. Phrases such as best fit and minimize the distance suggest there is one optimal solution that can be determined by an algorithm, and these algorithms typically have no relationship to the biology …

Re: Approval Letter For The Quarterly Operations And Maintenance Report Grove Gulch Sedimentation Bay For First Quarter 2026 Silver Bow Creek/Bute Area Npl Site – Butte Priority Soils Operable Unit Consent Decree-Civil Action No. Cv 89-039-Bu-She (Dated May 15, 2026)., Emma Rott

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Re: Comment Letter For The Revised Draft Final Butte Priority Soils Operable Unit (Bpsou) Butte Treatment Lagoon (Btl) System Annual Report – 2025 (Dated May 11, 2026), Emma Rott

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Design Principle For Staple-Mediated Stabilization Of Peptides And Proteins, Samantha C. Hatfield

Theses and Dissertations

Macrocyclization, or stapling, has emerged as a powerful strategy to enhance the stability and function of peptides and proteins by constraining their conformational ensembles. Stapling can improve thermodynamic stability, increase resistance to proteolytic degradation, and enhance biomolecular recognition, making it particularly valuable for the development of peptide-based therapeutics. Despite these advantages, staple design remains largely empirical, relying on iterative screening of linker chemistries, lengths, and attachment sites. This trial-and-error approach limits scalability and hinders the rational design of stabilized peptide systems. In this work, we address this challenge by integrating large-scale experimental datasets with molecular dynamic simulations to develop predictive …

Projected Climate Change Impacts On Soil Greenhouse Gas Emissions From A Restored Freshwater Marsh, Annika Hendrickson

University Honors Theses

Wetlands provide valuable ecosystem services, one of which is a wetlands ability to sequester carbon. Climate change and human land use threaten a wetlands ability to do so. Globally, 21% of wetlands have been lost since the 1700s. As a result, restoration of wetlands has been increasing. However, wetlands in the process of restoration emit more methane than degraded ones, and as the climate continues to change, these fluxes could respond. Projected sea level rise is expected to cause salt water to infiltrate coastal freshwater systems, increasing the salinity. Past research has found that increased salinity has led to suppressed …

Medical Image Integrity Protection Through U-Net Based Roi Segmentation And Hybrid Integer Wavelet–Quadtree Embedding, Muna M. Jawad, Rasha F. Nadhim, Noor A. Yousif, Ashwaq T. Hashim

Journal of Intelligent Informatics, Networking, and Cybersecurity

For decades, secure techniques in medical images have focused on securing the sensitive information through limiting direct access to the images themselves. Nonetheless, these methods tend to cause distortion on the images that can affect the diagnostic value and cause loss of crucial information. There arises the fundamental problem of secure embedding of medical data in such a way that does not affect the diagnostic integrity of the image. To overcome this limitation, a secure yet hidden data-hiding mechanism is introduced that is exploited U-Net-based deep learning for accurate Region of Interest (ROI) segmentation. Therefore U-Net architecture is used for …

Structure Functions For The Inclusive Semileptonic B-Quark Decay At Nnlo: A Semi-Analytic Calculation, A. Broggio, B. Capdevila, A. Ferroglia, P. Gambino

Publications and Research

We present a study of the inclusive charmless semileptonic b decay, b → X_uℓv at next-to-next-to-leading order (NNLO) in perturbative QCD, with the primary aim of extracting the hadronic structure functions Wi at NNLO. The analysis is based on a numerical calculation of the relevant kinematic distributions using a phase-space slicing method to handle infrared-sensitive contributions from real gluon emissions. We use known results from Heavy Quark Effective Theory and Soft-Collinear Effective Theory to extract the singular terms and construct a model for the regular contributions to the structure functions at NNLO, then perform a fit to the …

2026 June 11 - Tennessee Weekly Drought Summary, Tennessee Climate Office, East Tennessee State University

Tennessee Climate Office Weekly Drought Summaries

No abstract provided.

Creating Sustainable School And Home Gardens: Managing Rainwater, Lawrence Krissek, Kathy Cabe Trundle

All Current Publications

Rainscaping can help solve drainage problems, reduce erosion, improve water quality, and conserve soil by effectively managing rainwater movement across the landscape. It can also provide environments with increased biodiversity while reducing the need for supplemental watering.  The details of rainscaping your garden are very site-specific, affected by the amount of space and money available, your garden’s physical and weather/climate characteristics, and your garden goals. This resource sheet addresses the use of natural methods to ensure efficient rainwater management.