Digital Commons Network^™

Spatio-Temporal Variability Of San Francisco Bay Plume From Space, Piero L. F. Mazzini, Cassia Pianca, L. Fernando Pareja-Roman, Kelly L. Cole, Ryan K. Walter, Renato M. Castelao, Elias J. Hunter, Robert J. Chant

Physics

As brackish turbid waters exit San Francisco Bay, one of the largest estuaries in the U.S. West Coast, they form the San Francisco Bay Plume (SFBP), which spreads offshore and influences the Gulf of the Farallones (GoF), an ecologically significant region in the California Current System that is also home to three National Marine Sanctuaries. This paper provides the first observationally based investigation of the spatio-temporal variability of the SFBP, using a plume tracking algorithm applied to more than two decades (2002-2023) of ocean color data from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor onboard satellites Aqua and Terra. The …

Determining The Toxic Threshold And Other Use Characteristics For Industrial Hemp Seed Oil Used For Wood Product Protection, Daylan M. Barnes

Theses and Dissertations

Plant-based wood treatments have been utilized for many years, with varying success. Oils such as those extracted from linseed (flax), tung, and hemp plants have been used for thousands of years as finishes on wood. These are all drying oils, which dry to a film when exposed to air. Hemp seed oil has a high fatty acid content and can take a long time to dry on wood products but is valued in woodworking for being easy to use, food-safe, and having little to no odor. In this study, cold-pressed hemp seed oil, blended with a soybean carrier oil, is …

Soil Ethics In Practice: Harvesting Conservation Choices Among Puerto Rican Coffee Farmers, Patricia Marie Cordero-Irizarry

Theses and Dissertations

Coffee farming in Puerto Rico has declined over recent decades, partly due to deteriorating soil quality. However, the decision-making process behind farmers’ adoption of soil conservation practices remains unclear, particularly the overlooked role of soil ethics, which emphasizes the moral principles guiding human relationships with the soil. This mixed-methods study examined coffee farmers’ adoption of soil conservation practices by integrating the Values-Beliefs-Norms (VBN) theory and a newly developed Soil Ethics Survey (SES) instrument for the quantitative component, while using Decision-Making Theory and Social Cognitive Theory to qualitatively explore how farmers’ experiences and reflections shape their soil ethics. Quantitative findings revealed …

Unboxing The Black Box: Graph-Based Interpretability In Transformer Models, Ramak Nassiri

Theses and Dissertations

This thesis introduces a novel interpretability framework for transformer encoder models by hypothesizing that their internal embedding updates define a state transition system. We propose that transformers implicitly learn token-to-token influence dynamics, which can be analyzed using graph-theoretic methods. To validate this, we construct transition graphs from embedding changes and rank token importance using the PageRank algorithm. We develop two transformer models from scratch: a self-supervised model that incorporates serotype tokens to learn contextualized embeddings, and a supervised model initialized with these embeddings. Cosine similarity analysis of their token influence patterns reveals strong structural alignment, with values exceeding 93%. This …

Unraveling Quantum Properties Of Novel Two-Dimensional Systems Using A First-Principles Approach, Binod Regmi

Theses and Dissertations

We used first-principles density functional theory (DFT) to investigate the structural, electronic, and magnetic properties of an oxygen crystal in a copper slab, a ferrimagnetic electride with highly tunable magnetic anisotropy energy (MAE), and the Fermi surface analysis of different kagome metal phases. The Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional was used in the Vienna ab initio simulation package (VASP) for all these calculations. Because of dimensionality reduction, the electronic properties of copper change significantly at the two-dimensional (2D) scale due to whichwe observe more reconstruction in the geometry of the Fermi surface. Dimensionality reduction also influences charge transport. Moreover, we present …

An Enzyme-Coupled Isotope Dilution Mass Spectrometry Assay For Non-Adjacent Dna Photoproducts As Intrinsic Probes For G-Quadruplexes In Vitro, Savannah Sharee Scruggs

Arts & Sciences Graduate Student Theses and Dissertations

G-quadruplexes are noncanonical secondary structures that form in guanine-rich nucleic acid sequences and are thought to be involved in the control of gene expression.1 Unfortunately, it has been difficult to prove that these structures exist in vivo because of their dynamic nature. Rather than try to develop G-quadruplex specific binders as others have done,2 our idea is to photochemically trap certain types of G-quadruplexes by irreversible photoproduct formation3–5 and then detect the stable G-quadruplex-specific photoproducts by Isotopic Dilution Mass Spectrometry (IDMS).6 This IDMS method could then be used to unambiguously confirm the presence of specific types of G-quadruplexes in vivo …

Dynamic Mutational Profiling Of Binding Interactions And Allosteric Networks In Conformational Ensembles Of The Sars-Cov-2 Spike Protein Complexes With Classes Of Antibodies Targeting Cryptic Binding Sites: Confluence Of Binding And Allostery Determines Molecular Mechanisms And Hotspots Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The ongoing evolution of SARS-CoV-2 variants has underscored the need to understand not only the structural basis of antibody recognition but also the dynamic and allosteric mechanisms that could underlie complexity of broad and escape-resistant neutralization. In this study, we employed a multi-scale approach integrating structural analysis, hierarchical molecular simulations, mutational scanning and network-based allosteric modeling to dissect how Class 4 antibodies (represented by S2X35, 25F9, and SA55) and Class 5 antibodies (represented by S2H97, WRAIR-2063 and WRAIR-2134) can modulate conformational behavior, binding energetics, allosteric interactions and immune escape patterns of the SARS-CoV-2 spike protein. Using hierarchical simulations of the …

Developing Microelectrode Arrays As Multiplex Point-Of-Care Diagnostics, Yu-Chia Chang

Arts & Sciences Graduate Student Theses and Dissertations

Antibiotic resistance poses a significant global health challenge, particularly in urinary tract infections (UTIs), where 92% of cases exhibit resistance to at least one antibiotic, causing over 260,000 deaths annually. The emergence of antibiotic-resistant bacteria and growing awareness of the adverse effects of unnecessary antibiotic use highlight the urgent need for better UTI diagnostics. Current state-of-the-art methods are either expensive and time-consuming, or they lack specific details about the nature of the antibiotic and only determine inflammation. This hinders timely and effective treatment decisions regarding whether an antibiotic is actually necessary. Given this backdrop, there is a demand for a …

Antifungal Peptides From Casein Milk Of Etawa Crossbreed (Capra Hircus) As Biopreservation Agent For Bread And Molecular Docking Studies, Dian Riana Ningsih, Winarto Haryadi, Rachma Wikandari, Tri Joko Raharjo

Karbala International Journal of Modern Science

Bread without peptide fraction treatment started to grow mold on the fourth day with a total of 24x10⁷ fungi colonies/ml. Meanwhile, the addition of peptide fractions GMC5, GMC6, GMC7, and GMC8 effectively preserved bread for up to 4 days, indicated by no mold growth. The best treatment was the GMC6 peptide fraction on day 8 which grew the least amount of fungus at 7x10⁷ spores/ml. Peptide interaction with the CaATPase receptor Aspergillus sp. was carried out using HADDOCK 2.4. The 3D CaATPase structure prediction resulted in a model with good structural quality. This was supported by residues in …

Crop Yield Prediction At Multiple Spatial Scales With Statistical Machine Learning, Vaibhav Charan, Pratishtha Poudel

Discovery Undergraduate Interdisciplinary Research Internship

Understanding and accurately predicting crop yield is becoming increasingly important today in the face of global food security challenges, and thus, the availability of standardized data and scalable models is the need of the hour. To support this, researchers have developed CY-Bench (Crop Yield Benchmark), a comprehensive dataset that helps forecast maize and wheat yields on a global scale. This research project primarily involved working with the CY-Bench dataset aiming to improve crop yield prediction through machine learning. Initially, papers explaining the CY-Bench dataset and other papers for agriculture modeling were studied and analyzed in detail. The research then progressed …

Volumetric Imaging Of Cellular Dynamics Using Light-Sheet Microscopy: From Subcellular Structures To Whole Organisms, Md Nasful Huda Prince

Optical Science and Engineering ETDs

Advancing biomedical imaging requires platforms that combine high-resolution, speed, and stability across biological scales. This dissertation presents three innovations designed to address limitations of conventional light-sheet and oblique plane imaging. First, we introduce Reflected Inline Detection in Epi-Oblique Plane Microscopy (RIDE-OPM), a compact and drift-resistant system that eliminates a tertiary detection path while maintaining alignment flexibility, enabling robust long-term live imaging. Second, we present a high-speed Axially Swept Light-Sheet Microscopy (ASLM) platform for cleared tissues, using dual foci and synchronized sweeping to achieve isotropic sub-micron resolution at up to 40 frames-per-second, a fourfold improvement over standard ASLM. Integrated with a …

Breast Cancer Survival Rates And Determinants In Ethiopia: A Systematic Review And Meta-Analysis Of Longitudinal Studies, Abenezer M. Tafese, Meseker T. Fentie, Beminate L. Seifu, Angwach A. Asnake, Bikiltu D. Dirbaba, Abdisa G. Jara, Elsabeth Tizazu Asare, Brandon George

College of Population Health Faculty Papers

BACKGROUND: Breast cancer is the most common cancer and the leading cause of cancer mortality among women in Ethiopia, accounting for 32% of new cancer cases and 17.6% of cancer deaths. Despite its growing burden, comprehensive data on survival rates and contributing factors remain limited. This systematic review and meta-analysis aimed to synthesize existing data on breast cancer survival in Ethiopia and identify key determinants influencing outcomes.

METHODS: A comprehensive systematic search was conducted in PubMed, Web of Science, Scopus, Embase, and CINAHL to identify studies on breast cancer survival in Ethiopia published between January 2014 and August 2024. Eligible …

Tides, Tourists, And Tails: Exploring Human-Wildlife Overlap On The Homer Spit, Alaska, Serena Seiler

Masters Theses & Specialist Projects

Coastal areas present unique challenges for human-wildlife coexistence due to their shared use by people and marine species. The Homer Spit in Homer, AK (59.6481° N, 151.5299° W) is a projection of land into Kachemak Bay on which lodging, restaurants, campgrounds, RV parks, fishing, and a variety of coastal activities exist or occur, especially during the summer months. Two of the most popular nearshore marine mammals that attract visitors are sea otters (Enhydra lutris) and harbor seals (Phoca vitulina). These two species spend time swimming, foraging, and resting around the Spit, potentially resulting in co occurrences with humans. Using a …

Rangelands Glossary, Department Of Primary Industries And Regional Development, Western Australia

Natural resources factsheets

An alphabetical list of common Rangelands terminology.

Fisheries Research Report No. 353: Ecological Risk Assessment For The North Coast Demersal Scalefish Resource, Kimberley A. Smith, Brett Crisafulli, Gabby E. Mitsopoulos, Fabian I. Trinnie, Taylor Grosse, T Thompson, Stephen J. Newman

Fisheries Research Reports

On the 26 March 2025, the Department of Primary Industries and Regional Development (DPIRD) convened an ecological risk assessment (ERA) of the fisheries that access the North Coast Demersal Scalefish Resource (Resource). This Resource comprises a large number of tropical demersal scalefish species that occur in waters of the North Coast Bioregion, including tropical snappers, emperors and cods.

This document contains the results of the ERA along with the background information used to support the risk scoring process. This includes an overview of the Western Australian commercial fisheries that access the Resource, namely the Pilbara Fish Trawl Interim Managed Fishery, …

Tree Rings And The Broader Ocean-Atmospheric Circulation In The Highland Himalayas, Sanjaya Bhandari

All-Inclusive List of Electronic Theses and Dissertations

Climate change has altered tree-growth patterns and resulted in higher sea-surface temperatures across the planet. The Himalayan biome is one of the most vulnerable areas in the world to climate change because it has caused changes in forests’ growth and glaciers’ retreat. Dendrochronology has been used to understand the impact of climate change on tree growth and for climate reconstruction. In this dissertation, I discuss the growth of trees in the highlands of the eastern, central, and western Himalayas for the last 500 years and relate these patterns to the present global warming scenario and broad-scale climate modes. I reconstructed …

Using Published Undergraduate Biomechanics Research On Hydra Mouth Opening To Train Undergraduates, Stephen Hackler, T. Goel, Jonah Pacis , '25, Eva-Maria S. Collins

Biology Faculty Works

Biophysics research is exciting because physical approaches to biology can provide novel insights, and it is challenging because it requires knowledge and skills from multiple disciplines. We have developed an undergraduate biophysics laboratory module that teaches fundamental skills such as time-lapse microscopy, image analysis, programming, critical reading of scientific literature, and basics of scientific writing and peer review. The module is accessible to students who are familiar with introductory statistics, cell biology, and differential calculus. We used published research on the biomechanics of Hydra mouth opening as a framework because it describes a stunning biological phenomenon: Hydra, a freshwater …

Fisheries Research Report No. 361: 2024 Assessment Of The Status Of The Elasmobranch Resource Of Western Australia, Matias Braccini, Alex Hesp

Fisheries Research Reports

This document provides the 2024 risk-based weight of evidence stock assessment for the elasmobranch (sharks and rays) resource of Western Australia (WA). Gummy (Mustelus antarcticus), dusky (Carcharhinus obscurus), whiskery (Furgaleus macki), and sandbar (C. plumbeus) sharks are the most commonly captured species (~80% of the elasmobranch catch) and have been selected as indicator species for the status of the temperate elasmobranch ‘suite’. However, over 100 elasmobranch species have been caught in commercial and/or recreational fisheries in WA and, with the increasing number of elasmobranch species being listed in national and international protection lists, species-specific scientific advice on stock status at …

Estimation Methods For Bayesian Exponential Random Graph Models Under The Horseshoe Prior., Pamela Linares

Electronic Theses and Dissertations

Networks are powerful tools for modeling the complexity of social interactions, biological systems, and information spread. A leading statistical frameworks for analyzing network data are Exponential Random Graph Models (ERGMs), which provide a principled approach to capturing structural dependencies. However, ERGMs remain challenging to estimate, especially in sparse or high-dimensional settings where models suffer from degeneracy and unstable parameter inference. This paper proposes a penalized Bayesian approach to ERGMs that utilizes the horseshoe prior, a sparsity-inducing global-local shrinkage prior. This prior offers robust regularization while preserving important signals, improving estimation by shrinking irrelevant parameters and reducing the impact of extreme …

Recent Studies On The Reactions And Synthesis Of Nitrogen And Sulfur - Containing Heterocyclic Pharmacophores., Bernard Louis Adjei

Electronic Theses and Dissertations

Nitrogen and sulfur-containing heterocycles remain significant classes of compounds in the field of medicinal and organic chemistry due to their unique structural features and diverse biological activities which make them of considerable interest for drug discovery and development. Notable examples of the nitrogen containing heterocycles include the phthalimide and glutarimide rings present in thalidomide. Thalidomide, a potent small-molecule therapeutic agent, precipitated a significant global drug crisis due to its teratogenicity, causing congenital malformations in phocomelia infants, which remains unrivaled over half a century ago. Currently, thalidomide derivatives are extensively utilized in the therapeutic management of various hematological malignancies. Recent investigations …

Synthetic And Pharmacological Diversity Of Nitrogen-Containing Heterocycles., Shramana Ghosh

Electronic Theses and Dissertations

Nitrogen-containing heterocycles are a foundational class of compounds in organic chemistry, playing critical roles in pharmaceuticals, agrochemicals, and natural products due to their structural diversity and biological relevance. Among them, isoindolinones are notable for their wide range of pharmacological activities. Structurally, isoindolinones possess a benzylic methylene group adjacent to the nitrogen atom, which allows for selective oxidative transformations to yield phthalimide derivatives, well-known intermediates in synthetic, pharmaceutical, and materials chemistry. Although phthalimide is traditionally employed as a protecting group for amines via the Gabriel synthesis, isoindolinone offers a valuable alternative. Through a modified Gabriel-like approach, isoindolinones can serve as more …

The Bandages Problem, James E. Marengo, Joseph G. Voelkel, David L. Farnsworth

Articles

A new probability problem, named the Bandages Problem, is described and solved. The problem involves repeatedly selecting and removing an item at random from a finite population that initially consists of a known configuration of single and paired items. For each selection, the probability that the chosen item is single is found. Generalizations are suggested.

Classification And Analysis Of Families Of Graphs With Focus On Nordhaus-Gaddum Bounds, Sibi Pranav Muthuprakash

Theses and Dissertations

Nordhaus-Gaddum type problems focus on bounding characteristics of graph and its complement. There are certain families of graphs which yield optimal upper bounds on various Nordhaus-Gaddum characteristics of graph. In this paper, we will talk about bounding combinatorial algebraic connectivity, normalized algebraic connectivity, the Cheeger constant, and the isoperimetric number of a graph and its complement. We will identify some optimal or near optimal families of graphs and conduct an analysis on these families that will help to bound these characteristics. We will also prove and conjecture some bounds that can help in formulating stronger bounds on these characteristics of …

Farm Management Practice For The Prevention Of Soil Erosion In The Carnarvon Horticultural Area, Kehinde O. Erinle

Horticulture research reports

The Carnarvon horticultural area has suffered considerable erosion damage following flooding of the Gascoyne River.

The purpose of this report is to describe the factors that contribute to soil erosion in the Carnarvon horticultural area (Section 1), provide guidelines for good soil management (Sections 2) and provide floodway hazard classes and associated soil management recommendations (Section 3).

This report:

• Provides detailed information on soil management for intensive irrigated cropping.
• Details cropping alternatives to better manage the soil erosion risk.
• Identifies appropriate plants for soil stabilisation in a range of situations.
• Promotes the concept of property management plans.
• Takes account of …

Comparative Nitrene-Transfer Chemistry To Olefins Mediated By First-Row Transition Metal Catalysts Supported By A Pyridinophane Macrocycle With N4 Ligation, Himanshu Bhatia, Lillian P. Adams, Ingrid Cordsiemon, Suraj Kumar Sahoo, Amitava Choudhury, Thomas R. Cundari, Pericles Stavropoulos

Chemistry Faculty Research & Creative Works

A 12-membered pyridinophane scaffold containing two pyridine and two tertiary amine residues is examined as a prototype ligand (^tBuN4) for supporting nitrene transfer to olefins. The known [(^tBuN4)M^II(MeCN)2]²⁺ (M = Mn, Fe, Co, and Ni) and [(^tBuN4)Cu^I(MeCN)]⁺ cations are synthesized with the hexafluorophosphate counteranion. The aziridination of para-substituted styrenes with PhI=NTs (Ts = tosyl) in various solvents proved to be high yielding for the Cu(I) and Cu(II) reagents, in contrast to the modest efficacy of all other metals. For α-substituted styrenes, aziridination is accompanied by products of aziridine …

Electrochemical And Electrocatalytic Properties Of Screen-Printable Carbon Inks Featuring Pyridinic Nitrogen-Containing Polymeric Binder, Albert Sam Junior

Electronic Theses and Dissertations

Screen-printable conductive inks have been widely applied to prepare electrodes for electrochemical sensing. These inks generally consist of conductive metal or carbon particles, solvents, and polymeric binders. Low-cost, carbon-based, screen-printable conductive inks are especially popular. However, screen-printed carbon electrodes (SPCEs) must often be modified after they are printed to impart the necessary characteristics (e.g., sensitivity, selectivity, stability) for the desired application. For example, nitrogen-doping of SPCEs, especially in ways that introduce pyridinic or pyrrolic nitrogen species, can impart electrocatalytic properties towards reduction of O₂, H₂O₂, and CO₂. While our previous work done …

The Effect Of The Markle Mill Dam Removal On The Habitat And Riverine Food Web Of Otter Creek, Jenna Blanton

All-Inclusive List of Electronic Theses and Dissertations

Across the United States, dam removals are increasing in frequency. Despite this, the effects of dam removal on freshwater food webs are under-studied. Most existing studies investigate the impacts on fish assemblages, and very few investigate the impact on diatom, crayfish, and turtle communities. Furthermore, low-head dams are more abundant than large hydropower dams, yet the impacts of their removal are less studied than their larger counterparts. I used a Before After Control Impact (BACI) study design to survey populations of benthic diatoms, riffle-dwelling crayfish, and aquatic turtles. Species richness, species evenness, and Shannon Diversity Index values were used to …

The Effect Of An Invasive Species (Lantana Camara) And A Fast-Growing Herb (Acanthus Pubescens) On The Plant And Animal Communities In Kibale National Park, Uganda, Kathleen Bufka

Theses and Dissertations

Fast-growing plant species, like Lantana camara and Acanthus pubescens, could threaten biodiversity in Kibale National Park, Uganda. I surveyed plants and wildlife in areas where these plants were frequently encountered compared to those areas where they are infrequent. I found mixed results based on plant traits and the animals considered. My findings support management efforts on these two species to prevent forest degradation.

Comparative Expression Of Cgmp-Dependent Protein Kinase G (Pkg) From Plasmodium And Toxoplasma, Tsopmo Asaah

Theses, Dissertations and Culminating Projects

Malaria and Toxoplasmosis are life threatening diseases to humans. The search for a cure and control of these diseases is still one of the major challenges of scientists worldwide. In this research we focused on two Malaria species; Plasmodium bergei² (Pb) and Plasmodium falciparum¹ (Pf) and also on Toxoplasma gondii. Part of the life cycle of these organisms is regulated by the enzyme cyclic GMP-dependent protein kinase G (PKG)⁴. This is our drug target in this research. We believe that inhibiting this enzyme will be a great step in fighting these diseases. In this research, we devised a comparative study …

Investigating The Influence Of Experimental Parameters On The Formation Of Gold Nanoparticles: A Green Synthesis And Design Of Experiments Approach, Isaac Opeyemi Subuloye

Master's Theses

This thesis examines the green synthesis of gold nanoparticles using catechin, a naturally occurring plant-derived compound, as both a reducing and capping agent. The synthesis process was guided by a structured Design of Experiments (DOE) methodology to ensure systematic investigation and optimization. A two-phase experimental approach was adopted. First, a full factorial screening design was used to evaluate the effects of catechin concentration, NaOH concentration, and pre-reaction time. This was followed by an optimization phase using a face-centered composite design to identify conditions that produce nanoparticles with ideal characteristics. The nanoparticles were analyzed using UV-visible spectroscopy and dynamic light scattering …