Digital Commons Network^™

The Lived Experience Of Fly Fishing And Its Significance For Cultivating A Communion Of Subjects, Eric Landon Mcduffie

Antioch University Dissertations & Theses

Inspired by the lived fly fishing experiences encountered with my grandfather and the spiritually ecological writings of Thomas Berry, I explored how the sacred art of fly fishing connects participants with the natural world from a universal perspective given to us by Thomas Berry in The New Story. Berry described three principles that make up the entire universe: Differentiation, Subjectivity and Communion. I wanted to understand how lived fly fishing experiences fit into Berry’s three universal principles and how an individual’s lived fly fishing experience(s) cultivate(s) a “Communion of subjects.”1 Answers to these two questions informed five initial approaches to …

Meteorology, Weather And War In South East Asia: Malaya C. 1940-1960, Fiona Williamson

Research Collection College of Integrative Studies

This article interrogates the positioning of British colonial meteorology in Malaysia and Singapore from the 1940s to 1960. This period spanned a global conflict and an internecine war, effecting profound sociopolitical changes from which neither Malaysia nor Singapore would emerge the same. The meteorological services were essential to Britain's armed conflicts, providing vital weather information to the army, navy and, especially, the air forces, as well as supporting the aviation and shipping industry often in difficult and dangerous circumstances. This article argues that British military policy in South East Asia and the specific concerns of the colonial government in Malaya …

Quantifying Links Between Phytoplankton Physiology And The Environment, Gabrielle M. Armin

Open Access Dissertations

Phytoplankton are microscopic, primary producers in aquatic ecosystems worldwide. They are key links in global biogeochemical cycles, converting inorganic compounds into bioavailable nutrients which fuel fisheries. Through photosynthesis, phytoplankton play an essential role in the carbon cycle and marine biological pump, drawing carbon from the atmosphere, which is eventually sequestered in the oceans, regulating our Earth’s climate. Due to their influential role in large scale processes, there have been many efforts to characterize and quantify phytoplankton impacts to ecosystem health and global nutrient cycles. Often, phytoplankton physiology has been highly simplified in global or ecosystem models, limiting their representation to …

Light, Symbiosis, And The Biology Of Corals, Taylor R. Lindsay

Open Access Dissertations

Light is critical for the survival of most shallow water scleractinian corals. Corals are mixotrophs, acquiring energy via both feeding on water column plankton and photosynthesis via a symbiotic relationship with dinoflagellates living within their tissues. Corals rely heavily on photosynthetically derived metabolites through this symbiotic relationship, intrinsically linking their biology to light availability. Corals are known to modulate their biology to maximize light capture. However, there is a limited understanding of the interaction between morphology, physiology, and energetic strategy, as well as how light may affect these relationships. In Chapter 1, we quantified the morphology, physiology and energetic …

Development Of A Scituate Reservoir Mitigation Model For Assessing Flood Control During Extreme Scenarios, Supria Paul

Open Access Dissertations

Effective reservoir management is essential for mitigating downstream flooding, especially with the increasing frequency and intensity of extreme weather events impacting major drinking water reservoirs such as the Scituate Reservoir in Rhode Island. These reservoirs provide water for large populations but can be overwhelmed by intense precipitation, flooding and land cover changes. Climate change is expected to increase precipitation in the study area located in New England, highlighting the need for improved reservoir systems, especially given the aging dams and higher risk of failures. Additionally, land cover changes, like the widespread defoliation caused by the Gypsy Moth infestations, affect water …

Development And Characterization Of Polysaccharide-Based Controlled Drug Delivery Platforms, Amanda Pepler

Open Access Dissertations

Drug delivery research focuses on overcoming challenges in patient treatment. Most therapeutics are delivered systemically through oral or intravenous routes. However, these administration methods are often inefficient due to therapeutic hydrophobicity, poor bioavailability, and liver metabolic clearance, necessitating frequent dosing. When treatment plans require frequent dosing, patients experience significant fluctuations in therapeutic concentration in the bloodstream, which can increase adverse side effects. These factors contribute to low patient compliance. Therefore, the core focus of drug delivery research is to develop new administration routes for therapeutics. Drug delivery systems (DDS) that can target therapeutics to a localized region offer advantages over …

Impacts Of Multiple Coastal Stressors Across Life-History Stages In The Eastern Oyster, Amaelia Zyck

Open Access Dissertations

Urbanized estuaries are characterized as a complex of biotic and abiotic stressors, which currently challenge marine life and are expected to intensify and become increasingly unpredictable under the ongoing impacts of climate change. The persistence of coastal species that inhabit these stressful environments will ultimately depend on their ability to adapt. Many of these species have complex life cycles, featuring distinct morphological and physiological developmental stages that can exhibit unique responses to environmental pressures. However, since all stages share the same genome, selective pressures acting on one stage can have cascading effects throughout the life cycle. The larval stage, being …

Novel Methodology And Proof-Of-Concept For Proton Ct Using Spot Profile Rather Than Bragg Peak Location, Brett Albert Ruben

Open Access Dissertations

Proton radiation therapy offers a highly precise method for cancer treatment, theoretically providing superior dose deposition characteristics compared to conventional X-ray radiation therapy. Its steep and finite dose fall-off region allows for superior tumor coverage while reducing, though not eliminating, dose to surrounding healthy tissue. However, its full potential is limited by range uncertainties, particularly those arising from the reliance on X-ray-based imaging methods called computed tomography (CT) for proton-based treatment. CT image Hounsfield Units (HU) must be converted to stopping power ratios (SPR) as these ratios are the clinically relevant value for accurately planning particle interactions during proton therapy. …

Confronting The Seaport Resilience Gap: Incentives, Frameworks, And Case Studies For Enhancing Resilience To Natural Hazards In Port Planning And Policy, Rosemarie Fusco

Open Access Dissertations

This dissertation investigates the critical issue of seaport resilience, focusing on the gaps in resilience planning and the role of incentives in motivating resilience investment. The research arc addresses the question: What incentivizes seaports to increase natural hazard resilience (NHR)? It is organized into three interconnected manuscripts, each examining distinct aspects of the problem.

The first manuscript critically examines the resilience planning approaches of Small Island Developing States (SIDS) as outlined in their National Adaptation Plans (NAPs), highlighting the limited consideration of seaports despite their critical role in economic and social connectivity. SIDS offer critical insight into seaport resilience due …

Textual Sediments: Genre And The Planetary Novel, William Bowden

Open Access Dissertations

This dissertation investigates how twenty-first-century prose fiction navigates the ecological and temporal dimensions of planetary crisis. In response to accelerating pressures - climate change, ecological collapse, and the intensification of capitalist modernity - literary studies has turned increasingly to the planetary as a conceptual frame. Yet this shift has often outpaced the development of adequate critical vocabularies and narrative methodologies. By drawing on ecocriticism, narrative theory, phenomenology, and related fields, Textual Sediments proposes a new framework for reading what it terms the planetary novel: a sedimentary genre characterized by temporal layering, formal hybridity, and a recursive engagement with scale. Through …

Quantifying Mixotrophy Potential As A Function Of Environmental And Biological Drivers In Coastal And Estuarine Plankton Communities, Erica Ewton

Open Access Dissertations

The discovery of mixotrophic plankton has bridged gaps in nutrient cycling budgets and altered the understanding of food webs and energy transfer. Mixotrophic plankton are capable of simultaneous or sequential photosynthesis and heterotrophy, providing multiple avenues of nutrition and thus reducing limitations that affect specialists. These energy dense cells provide increased biomass for higher trophic levels, which may increase organism sizes throughout the food web. Additionally, they may be physically denser, which alters biogeochemical cycling including carbon sequestration. The work presented here uses LysoTracker Green, an acidotropic stain that attaches to phagocytic vacuoles within potentially phagotrophic small (< 20 µm diameter) phytoplankton communities (‘mixoplankton’), to better understand their abundance, relative abundance, and growth rates in relation to the matrix of natural conditions they inhabit. Understanding the prevalence and drivers of mixoplankton is vital to better parameterize biogeochemical cycling and energy transfer in the ocean and for models that predict the fate of future oceans.In the first study, I compared the abundance of mixoplankton in the Northeast U.S. Shelf (NES) and Coastal California Current System (CCS) during two cruises in the NES in summer 2021 and one cruise in the CCS in summer 2022. These two contrasting coastal systems span the breadth of environmental conditions observed in temperate marine ecosystems and thus provided an opportunity to examine indicators of mixoplankton across temperate coastal regions. I discovered higher mixoplankton abundance in the NES than CCS yet similar population sizes of nanoeukaryotic photosynthesizers, resulting in higher relative abundance of mixoplankton in the NES than CCS. Across both systems, I found increased mixoplankton abundance associated with decreasing temperature and combined nitrate + nitrite concentrations (N+N), and increasing light intensity and Synechococcus abundance …

Investigating The Photophysical Dynamics Of Anthracene And Acridine Derivatives Using Time-Resolved Spectroscopy, Sophia Tiano

Open Access Dissertations

Anthracenes and acridines are among the simplest visible light absorbing heterocyclic and polycyclic aromatic hydrocarbons and as such are extensively used in a variety of applications including photosensitizers and fluorescent sensors. Although the photophysics of some derivatives have been studied in the past, there is still a lot of unknown fundamental information that is vital in order to optimize these molecules for particular applications. Transient absorption spectroscopy was used to study the photophysics of the 9-substituted methyl, hydroxymethyl and formyl derivatives of acridine and anthracene. The growth and decay of the triplet-triplet absorption peak were quantified for each dye in …

Stability And Global Dynamics Of Autonomous And Nonautonomous Discrete Population Models With Stocking, Harvesting, And Cooperation, Sam Habach

Open Access Dissertations

This dissertation investigates the local and global behavior of several classes of discrete population models involving stocking, harvesting, and cooperation. The study is divided into three major manuscripts, each offering new theoretical in sights, bifurcation results, and applications to real-world data.

In Manuscript 1, we study the Beverton-Holt population models with constant and proportional stocking and harvesting, as well as sigmoid Beverton-Holt models under constant stocking and harvesting, both in autonomous and non-autonomous settings. We analyze stability and explore global dynamics using established local and global dynamics theorems, bifurcation theory, and explicit solutions when available. Special attention is given to …

A Socio-Ecological Investigation Of Ulithian Spearfishing, Joshua Pi

Open Access Dissertations

Coral reef socio-ecological systems (SESs) characterize the interconnected relationships between coral reef ecosystems and reef-dependent communities. One such SES exists in Ulithi Atoll, Federated States of Micronesia, where Ulithians fish, steward, and govern their reefs through customary marine tenure, traditional ecological knowledge, and cultural taboos. In recent decades, rapid modernization in Ulithi has introduced new fishing technologies, transformed fishing practices, and ultimately reshaped the functioning of Ulithi’s traditional SES. One significant change was the introduction of spearfishing during the mid-20^th century, which is more selective and individualistic compared to other community-centric fishing methods that have existed for generations. This …

Ultra-Rapid Electrophilic Cysteine Arylation Using Pyridinium Salts, Bradley M. Lipka

Open Access Dissertations

Small molecule-based bioconjugation enables in vitro and in vivo functionalization of proteins and peptides, significantly expanding the chemical space of biomacromolecules. Among these transformations, nucleophilic aromatic substitution (S_NAr) of cysteine residues is a widely employed strategy for protein bioconjugation.

Although many reagents facilitate cysteine arylation, they are disadvantageous in two crucial aspects - limited synthetic modularity and undesired hydrophobicity. First, conventional cysteine arylating reagents are frequently activated by multiple electron-withdrawing groups (EWGs) on a single aromatic ring, leaving few synthetic handles to derivatize the reagents for advanced applications. Second, these labeling reagents are generally hydrophobic in nature and …

Free Energy Approaches To Understanding The Mechanism Of Membrane-Active Peptides, Hannah R. Scott

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cancer is a leading cause of death in the world today. Current methods of treatment fail to distinguish the difference between cancer cells and cells of healthy tissue, leading to off-target effects, often with terminal outcomes. A potential solution to this challenge is to target the cancer cells’ microenvironment. One universal characteristic across all cancer cells is the acidic extracellular environment. The pH-Low Insertion Peptide (pHLIP) is a membrane-active peptide with acid-sensitive function, undergoing folding and insertion into a transmembrane alpha-helix. pHLIP is a promising candidate to be used to deliver anti-cancer agents exclusively to cancer cells. Although the mechanism …

Neural And Computational Approach To Understanding Environmental Modulation Of Behavioral Identity In Zebrafish, John W. Hageter

Graduate Theses, Dissertations, and Problem Reports (ETD)

Organisms rely on behavior for survival. Animals engage in behaviors that allow for feeding, mating, exploring and navigating their environment among others. Necessary for these behaviors to develop are the environmental factors and underlying circuitry which make behavior possible. Specifically, how the environment guides underlying neural circuitry to develop unique facets or phenotypes of a larger behavior are key to understanding why unique behaviors exist. In this thesis, I build foundational evidence for determining these mechanisms through the use of the zebrafish local search behavior. This is a behavior that zebrafish employ following the loss of environmental illumination where they …

Investigation Of Protein-Ligand Binding Interactions Through The Computational Methods Of Molecular Dynamics And Graph Neural Networks, Alexander Benjamin Wroe

Graduate Theses, Dissertations, and Problem Reports (ETD)

Studies in protein ligand binding are a significant focus in the field of medicinal chemistry

and biochemistry, facilitating a greater understanding of the structure-function relationship

of the protein and controlling function via drug development. In this research, we identify

new binding sites for lipids on the microbial membrane protein, proteorhodopsin, and apply

machine learning approaches to accelerate the generation of binding affinity-like data for the

use in the identification of potential small molecule drugs. The platelet activating factor

receptor. Cardiolipin, a lipid in membranes, and proteorhodopsin, a microbial proton pump,

are both commonly found in microbial membranes, but little is …

Mathematical Contributions To The Study Of Chemotaxis And Cell Signaling, Hajr Zam

Graduate Theses, Dissertations, and Problem Reports (ETD)

This dissertation presents results from two mathematical projects concerned with the biology of cells. Chapter 1 provides biological background and places the two mathematical problems in the context of cell signaling. The larger project, with Prof. H. Hattori on a chemotaxis model is presented in Chapters 3 and 4. Work with Prof. \'{A}. Hal\'{a}sz on a chemical reaction network system with linear multimers and two types of labels is presented in Chapter 2. The chemotaxis system describes the one-dimensional dynamics of a species of cells with two chemical species, a chemo-attractant and chemo-repellent. The goal is to analyze the behavior …

Late Ordovician Evolution Of Sea Scorpions: Eurypterids Of The Big Hill Lagerstätte, Joseph Donaldson Bingham Jr.

Graduate Theses, Dissertations, and Problem Reports (ETD)

Eurypterids are a group of diverse chelicerates that first appeared during the Middle Ordovician (467.3 Ma) and went extinct at the end of the Permian (251.9 Ma). The fossil record of eurypterids during the Ordovician is relatively sparce, comprising only 12 species representing the Megalograptidae, a ‘waeringopterid’ clade, Rhenopteridae, Onychopterellidae, Adelophthalmoidea, and Eurypteroidea clades. This study describes early eurypterids from the Katian aged (~452 Ma) Big Hill Lagerstätte of Michigan. The described material represents two new species, herein named Machipterus margaritae sp. nov. (based on 21 specimens preserving the ventral prosoma and prosomal appendages, and opisthosoma) and Dikranopterus lysinae sp. …

Do Dung Beetles Sink Or Swim: Exploring Dung Beetle Response To Precipitation, Lauren T. Cheshire

Graduate Theses, Dissertations, and Problem Reports (ETD)

Global climate change constitutes a major threat to biodiversity and ecosystem services of many taxa. The Mid-Atlantic region of the US is expecting to see an increase in extreme precipitation events and flooding. Dung beetles (Scarabaeinae) can tunnel below the soil surface allowing for water to dissipate into the soil rather than sit on the surface and add to flooding conditions. They also can decrease methane emission by burying dung and reduce outbreaks of pests that prefer the moist environment of dung. They contribute roughly $380 million in ecosystem services annually in the United States, yet their services may be …

Computational Approaches For Diagnosing Neurological Impairments And Restoring Functional Movement, Serhii Bahdasariants

Graduate Theses, Dissertations, and Problem Reports (ETD)

Movement is the primary means by which the nervous system converts intention into interaction with the environment. Voluntary limb motion enables standing, walking, reaching, and grasping—actions that underpin self‑care, communication, and economic participation. When diseases or injuries disrupt the pathways that couple neural commands to muscle forces—whether through cortical stroke, spinal cord injury, or peripheral nerve damage—mechanical outcomes such as weakness, loss of coordination, and ultimately reduced mobility emerge. These impairments cascade into secondary complications, increased dependence on caregivers, and diminished quality of life. Quantifying how the lesion alters the mechanics of movement is therefore essential for designing targeted interventions …

Functionalized Carbon Nanohoops: Synthesis, Structural Insights, And Pathways To Carbon Nanobelts, Liu Li

Graduate Theses, Dissertations, and Problem Reports (ETD)

The development of structurally defined carbon nanostructures has gained significant attention due to their unique electronic, optical, and mechanical properties. Cycloparaphenylenes (CPPs), also known as carbon nanohoops, and carbon nanobelts (CNBs) represent key molecular segments of carbon nanotubes (CNTs), offering a bottom-up approach to precise nanotube construction. This dissertation focuses on the synthesis, structural characterization, and functionalization of CPPs, as well as the development of novel synthetic pathways for CNBs. A series of functionalized CPPs, including [9]-, [12]-, [15]-, and [18]CPPs, were synthesized using a modular approach involving a Diels-Alder adduct formation followed by a Ni(cod)2/bpymediated macrocyclization reaction. The influence …

Individual And Collective Properties Of Tunable Photochemical Belousov-Zhabotinsky Micro-Reactors, Kudakwashe Benedict Shumba

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell-like model chemical systems are powerful tools that can be used to explore the role of intercellular coupling on population level behaviors in communities of biological cells. Firstly, we present a new method for fabricating such micro-reactors using the photosensitive Belousov–Zhabotinsky (BZ) reaction system employed in silica microparticles. These BZ micro-reactors have a tunable response to photochemical coupling, varying from a fully excitatory response to a fully inhibitory response. Their response can be tuned through variations in either the reactive mixture or, on an individual micro-reactor level, by changes in the synthesis temperature used during the fabrication of the silica …

Introduction Of Polar Functional Groups To Pyridinedipyrrolide Zirconium Photosensitizers Through Post-Synthetic Modifications, Marisa Nicole Tordella

Graduate Theses, Dissertations, and Problem Reports (ETD)

Photosensitizers are vital components to applications such as photoredox catalysis, photodynamic therapy, and various avenues of solar energy production. The abilities of transition metal photosensitizers containing precious metals have been well studied over the years. However, because of the growing scarcity of these metals, there has been a shift in finding more earth abundant alternatives. To help fill this gap in the literature, the Milsmann group has developed and studied the photophysical properties of Zr(IV) complexes with various ligand systems. Due to the electron deficient metal center, these complexes exhibit ligand-to-metal charge transfer (LMCT), unlike the metal-to-ligand charge transfer commonly …

Development And Applications Of Capillary Vibrating Sharp-Edge Spray Ionization Coupled With Atmospheric Pressure Chemical Ionization (Cvssi-Apci), Madison Elizabeth Pursell

Graduate Theses, Dissertations, and Problem Reports (ETD)

Mass spectrometry (MS) is a technique that is used in fields in which both complex and non-complex mixtures are analyzed. The state-of-the-art ion sources that are utilized for MS are being demonstrated to be functional for direct infusion of samples as well as for use with online separations. However, ion sources, such as electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) can encounter problems such as ion suppression and an inability to ionize based on size and/or polarity, respectively. Further these sources are bulky and require gas flow, heat sources, and additional high voltage power supplies for optimal performance. …

Rational Design Of Small Molecules Targeting Mitochondrial Redox Proteins, Matheus Barbosa Belchior

Graduate Theses, Dissertations, and Problem Reports (ETD)

Reactive oxygen species play a crucial role in many cellular processes. Despite being a natural byproduct of cellular metabolism, overexpression of these species causes damage to the cell, leading to cell dysfunction. Central to the regulation of these highly reactive molecule is the mitochondria. Impairment in its function has been associated with oxidative stress within the cell. Herein, a ligand-based and structure-based approach to design new small molecules to inhibit mitochondrial redox proteins associated with oxidative stress and reactive oxygen species. In the first project two molecules were synthesized and characterized as potential monoamine oxidase B inhibitors. Results showed two …

Weakly Reversible Deficiency Zero Realizations Of Polynomial Dynamical Systems, Neal Ryan Buxton

Graduate Theses, Dissertations, and Problem Reports (ETD)

Weakly reversible, deficiency zero (WR0) systems form a large class of polynomial ODEs modeling chemical reaction networks. Their behavior is exceptionally stable: they have unique positive steady states, which are locally asymptotically stable (they are also conjectured to be globally asymptotically stable). This powerful result (the Deficiency Zero Theorem) applies to a large class of high dimensional, nonlinear polynomial dynamics, and is independent of the choice of parameters in the model. In this dissertation we present two algorithms that expands the scope of the Deficiency Zero Theorem to:

1. Networks with WR0 realizations, i.e. networks that are not necessarily WR0 …

Survival And Spatial Ecology Of North American River Otters (Lontra Canadensis) In West Virginia, Laurel Marie Glover

Graduate Theses, Dissertations, and Problem Reports (ETD)

Wildlife reintroductions function to regain wildlife populations in areas where they have been extirpated or greatly diminished. One such species that has been reintroduced to several states is the North American river otter (Lontra canadensis). The West Virginia Division of Natural Resources (WVDNR) conducted a river otter reintroduction effort between 1984-1997, releasing 245 individuals into the state. The reintroduction was deemed a success with the WVDNR opening a regulated trapping season for river otters in 2011, allowing trappers to take one river otter per season. As the population has reestablished in West Virginia, several management challenges have arisen …

Copula-Based Bayesian Model For Detecting Differential Gene Expression, Prasansha Liyanaarachchi, N. Rao Chaganty

Mathematics & Statistics Faculty Publications

Deoxyribonucleic acid, more commonly known as DNA, is a fundamental genetic material in all living organisms, containing thousands of genes, but only a subset exhibit differential expression and play a crucial role in diseases. Microarray technology has revolutionized the study of gene expression, with two primary types available for expression analysis: spotted cDNA arrays and oligonucleotide arrays. This research focuses on the statistical analysis of data from spotted cDNA microarrays. Numerous models have been developed to identify differentially expressed genes based on the red and green fluorescence intensities measured using these arrays. We propose a novel approach using a Gaussian …