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Understanding The Variability Of Circulation And Water Quality At Experimental Oyster Leases In The Mississippi Sound Using A High-Resolution Nested Modeling Approach, Shihab Hossain Saran

Master's Theses

Four 50-acre experimental oyster leases; two near Saint Louis Bay (StLB) and two near Pascagoula Bay (PB) were recommended to provide science-based guidance for oyster reef restoration efforts in response to continued limited productivity of oysters in the Mississippi Sound (MSS). Two-way nested simulations using ROMS within COAWST modeling framework have been run with improved forcings to analyze circulation, salinity and temperature variability within and around the lease areas under the extreme freshwater inflow from Bonnet Carré Spillway (BCS) openings and local rivers in 2019. High-resolution atmospheric forcing data is crucial because diurnal sea-land breeze affects salinity variability by increasing …

Projected Range Shift Of The Atlantic Surfclam, Spisula Solidissima, And The Ocean Quahog, Arctica Islandica, Under Climate-Induced Benthic Warming: Forecasting Fishery Influence In The Mid-Atlantic Bight Throughout The 21st Century, Molly Mae Spencer

Master's Theses

The Atlantic surfclam, Spisula solidissima, and ocean quahog, Arctica islandica, are biomass dominant bivalve species on the eastern North American continental shelf, both supporting lucrative commercial fisheries in the Mid-Atlantic with a combined value of $53.6 million in ex-vessel revenue per year. Rapid climate change is expected to modify the geographic range of these bivalve populations across the Mid-Atlantic Bight (MAB), suggesting transformative consequences for the surfclam fishery. This study forecasted future distributions of the two species from years 2016 – 2095, based on projected bottom water temperatures and a temperature-dependent population dynamics model, to project subsequent fishery-based indicators …

Exploring Overbank Sediment Deposition Variation In Heavily Modified Floodplains Of The Lower Mississippi River: A Sedimentological And Geophysical Analysis, Seth Fradella

Master's Theses

Since the 1930s, the Lower Mississippi River (LMR) has experienced large-scale modifications to the channel profile and surrounding floodplains through dams, dikes, revetments, dredging, and channel cutoffs. Although these changes have improved navigation and reduced flood risk, unanticipated changes to the major flood return period, individual flood severity and duration, and sediment regime have become increasingly apparent and sometimes problematic, such as the 2011 and 2018-2020 floods. Flood control levees along the LMR have reduced the natural floodplain area by 70-90%, resulting in heavily restricted overbank storage capacity of water and sediment. For the same flood events in recent history, …

Differential Behavior Of Conformational Dynamics In Active And Inactive States Of Cannabinoid Receptor 1, Ugochi H. Isu, Adithya Polasa, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Cannabinoid receptor 1 (CB1) is a G protein-coupled receptor that regulates critical physiological processes including pain, appetite, and cognition. Understanding the conformational dynamics of CB1 associated with transitions between inactive and active signaling states is imperative for developing targeted modulators. Using microsecond-level all-atom molecular dynamics simulations, we identified marked differences in the conformational ensembles of inactive and active CB1 in apo. The inactive state exhibited substantially increased structural heterogeneity and plasticity compared to the more rigidified active state in the absence of stabilizing ligands. Transmembrane helices TM3 and TM7 were identified as distinguishing factors modulating the state-dependent dynamics. TM7 …

Reinforcement Nash Equilibrium Solver, Xinrun Wang, Chang Yang, Shuxin Li, Pengdeng Li, Xiao Huang, Hau Chan, Bo An

Research Collection School Of Computing and Information Systems

Nash Equilibrium (NE) is the canonical solution concept of game theory, which provides an elegant tool to understand the rationalities. Though mixed strategy NE exists in any game with finite players and actions, computing NE in two- or multi-player general-sum games is PPAD-Complete. Various alternative solutions, e.g., Correlated Equilibrium (CE), and learning methods, e.g., fictitious play (FP), are proposed to approximate NE. For convenience, we call these methods as "inexact solvers", or "solvers" for short. However, the alternative solutions differ from NE and the learning methods generally fail to converge to NE. Therefore, in this work, we propose REinforcement Nash …

Contrastive General Graph Matching With Adaptive Augmentation Sampling, Jianyuan Bo, Yuan Fang

Research Collection School Of Computing and Information Systems

Graph matching has important applications in pattern recognition and beyond. Current approaches predominantly adopt supervised learning, demanding extensive labeled data which can be limited or costly. Meanwhile, self-supervised learning methods for graph matching often require additional side information such as extra categorical information and input features, limiting their application to the general case. Moreover, designing the optimal graph augmentations for self-supervised graph matching presents another challenge to ensure robustness and effcacy. To address these issues, we introduce a novel Graph-centric Contrastive framework for Graph Matching (GCGM), capitalizing on a vast pool of graph augmentations for contrastive learning, yet without needing …

Frameworks For The Techno-Economic Assessment Of Membrane-Based Bioprocessing Platforms, Juan Jose Romero Conde

All Dissertations

This dissertation describes developing and implementing computational frameworks for simulating and optimizing purification processes in the biopharmaceutical industry. The framework performs techno-economic analyses to establish value propositions for new process alternatives, especially membrane technologies. Initially, the focus is developing a framework capable of simulating monoclonal antibody (mAb) capture using membrane and resin media in multi-column chromatography (MCC) platforms for continuous manufacturing. Subsequently, the impact of capture MCC is compared against other intensification strategies in established mAb manufacturing facilities. Finally, the framework application expands to simulate the purification of adeno-associated virus (AAV) vectors for gene therapy.

Chapter 2 details the framework …

Assessment Of Tce And Chiral Pcb Dechlorination Rate, Congener Diversity, And Enantioselectivity In Town Creek, Sc, Usa Sediment Microcosms, Catherine P. Sumner

All Dissertations

Polychlorinated biphenyls (PCBs) and trichloroethene (TCE) are ubiquitous contaminants and are recognized as persistent organic pollutants due to their extreme chemical stability. PCBs were manufactured by chlorinating biphenyls that created 209 congeners with various structures, of which 19 are chiral and can exist as a pair of stable atropisomers. PCBs have been known to cause developmental and neurological toxicity in humans and wildlife; they can act as endocrine disrupters, carcinogens, and teratogens. Sangamo Weston Inc. was an industrial plant located near Town Creek in Pickens Country, South Carolina, that manufactured capacitors and used Aroclors 1016 and 1254 as dialectic fluids …

Genomic Data Science Approaches For Understanding Human Diseases, Snehal Shah

All Dissertations

The intricate interplay of genetic predisposition, environmental influences, and lifestyle acts as the multifactorial landscape of diseases. Understanding this complexity presents a significant challenge. Molecular insights into disease mechanisms, particularly the interactions of DNA, RNA, and proteins with environmental and lifestyle factors, have revolutionized disease diagnosis, prognosis, and treatment. High-throughput technologies, such as next-generation sequencing, generate large amounts of molecular data, holding a wealth of knowledge. These datasets unveil the roles of genes and their interactions with various factors through analysis, shedding light on previously unknown molecular mechanisms underlying disease pathogenesis. Furthermore, they facilitate the discovery of biomarkers crucial for …

Gan With Skip Patch Discriminator For Biological Electron Microscopy Image Generation, Nishith Ranjon Roy

Graduate Theses and Dissertations

GAN models have been successfully used for image generation in various sections such as real-life objects like human faces, cars, animal faces, landscapes, etc. This work focuses on biological electron microscopy (EM) image generation. Unlike other real-life objects, biological EM images are obtained through electron microscopy techniques to study biological specimens. Electron microscopy offers high resolution and magnification capabilities, making it a powerful tool for visualizing biological structures at the nanoscale. However, using GAN models for biological EM image generation poses challenges due to the complex and unique arrangements of biological structures and the sparse and asymmetrical patterns in EM …

Use Of Computational Methods To Determine The Relative Thermodynamic Stability Of Myricetin, Quercetin And 4-Methylesculetin For Use As Spin Traps, Cole Walker

Electronic Theses and Dissertations

The research conducted focused on the oxidative intermediates of antioxidants known as Myricetin, Quercetin, and 4-Methylesutin by calculating the reaction mechanism. During this research, computational quantum chemistry on selected parts for the 3 antioxidants previously mentioned were performed to find the most stable intermediate to act as a spin trap. The hypothesis is that the intermediates found can act as spin traps which will allow longer preservation of a free radical to be identified using Electron Paramagnetic Resonance (EPR) spectroscopy. This may be because the buildup of excess free radicals in a system leads them to cause damage down to …

Medical Image Analysis Based On Graph Machine Learning And Variational Methods, Sina Mohammadi

Computational and Data Sciences (PhD) Dissertations

This study explores advanced methodologies for enhancing brain tumor segmentation, addressing the complexity and diversity of tumor sub-regions in medical imaging. We introduce a novel approach utilizing Graph Neural Networks (GNNs) that incorporate both spectral and spatial insights for segmentation. By leveraging various supervoxel creation methods such as VCCS, SLIC, Watershed, Meanshift, and Felzenszwalb-Huttenlocher, we structured 3D MRI images into a graph format. This format enabled the implementation of Spectral and Spatial GNNs to capture comprehensive local and global tumor characteristics effectively. Our Spectral-Spatial GNN model, integrating the Laplacian matrix, demonstrated significant improvements in segmenting distinct tumor sub-regions of Necrosis, …

Assessing The Reactivity Of Amino Acids To Chlorination Using Capillary Electrophoresis, Pedro De Allende

Electronic Theses, Projects, and Dissertations

Amino acids (AA) are ubiquitous in wastewater systems. One of the most popular wastewater treatments is chlorination which is effective at eradicating bacteria and overall treating the wastewater, but it can also produce disinfection by-products (DBPs). Certain DBPs have been classified as Class B Carcinogens to humans and are therefore highly regulated and monitored. Past studies have shown that natural organic matter (NOM), specifically amino acids, can be precursors to DBPs if chlorinated to the correct dose. This thesis project explored AA chlorination's mechanism(s) to understand further which products arise. In particular, the investigation detailed which steps of the mechanism …

Tales In The Teeth: Using Isotopic Analysis To Understand The Paleoecology And Social Behavior Of Brontotheres Of The Intermountain Basins During The Middle Eocene, John Michael Michalski

All Graduate Reports and Creative Projects, Fall 2023 to Present

Isotopic analysis has been a common practice used in paleontology to study ancient ecosystems, and the lives of animals therein. Oxygen isotopic analysis is of particular importance not only because of its use in studying paleoecology, diet, and migration, but also its use in studying mountain elevation, and its impact on ancient ecosystems. I use stable oxygen isotopic analysis to study the habits and ecology of brontotheres from intermountain basins surrounding the Uinta Mountains of Utah and Wyoming, USA. I studied the oxygen isotopes from 16 fossil specimens of teeth, most of which belonged to brontotheres, including the genera Palaeosyops …

Invasion Potential Of Nonnative Fishes Through A Large Western Dam Into A Prized And Vulnerable Ecosystem, Barrett T. Friesen

All Graduate Theses and Dissertations, Fall 2023 to Present

Native river fish face threats from habitat fragmentation, water overallocation, invasive species establishment, and powerful synergies amongst these factors. In the Colorado River Basin, USA, these threats coalesce at Glen Canyon Dam (GCD), which impounds the Colorado River to create Lake Powell, a reservoir inhabited by nonnative fish species. There is widespread concern low water level in Lake Powell may allow nonnative fish to escape through the dam, adversely affecting native fish species downstream in the Grand Canyon. In this study we characterized the seasonal distribution of nonnative fishes in the vicinity of GCD and identified environmental conditions that may …

Interactions Between Nano/Micro-Sized Particles And Microbes For Agricultural And Environmental Applications, Li-Ting Yen

All Graduate Theses and Dissertations, Fall 2023 to Present

Among the challenges posed by a growing global population, diminishing arable land and water resources affected by climate change are critical for enhancing crop yields, ensuring food security, and maintaining water quality and environmental health.

Iron (Fe), an essential micronutrient, is vital to plant growth. The partially oxidized form of vivianite, metavivianite (metaVT), is reported to be a promising alternative Fe fertilizer. Previous studies have shown the effectiveness of bulk metaVT on plants grown on calcareous soil for mitigating Fe efficiency and the extremely low solubility of bulk metaVT (Ksp=10^-36) in electrolyte solutions, such as CaCl₂. …

An Examination Of The Effects Of Prey Density, Mortality, Nutrients, And Foraging Tradeoffs On A System With Inducible Defenses: An Empirical And Theoretical Approach, Benjamin C. Ralston Daniel

All Graduate Theses and Dissertations, Fall 2023 to Present

To grasp the functioning and stability of ecosystems, it is important to understand species interactions. With many ecosystems becoming more imperiled from urbanization and anthropogenic influences it is important to understand ways in which species can adapt to rapid changes in their environment. Phenotypic plasticity is one such tool at nature’s disposal to initiate rapid change, where species with the same genetic makeup can have different expressed traits depending on their environment. Inducible defenses are one such form of phenotypic plasticity in which prey can express different levels and forms of defense depending on the threat of predation present in …

Soil Additives And Alternative Crops For Drought Defense In The Intermountain West, Tina M. Sullivan

All Graduate Theses and Dissertations, Fall 2023 to Present

The Western U.S. looks for water optimization and conservation as agriculture is the largest water diverter, and resources are pressured by urban growth, winter snowpack instability, and drought persistence. Agricultural producers have several potential options to optimize water use with different investments associated with them. Options with varying levels of risks and known management practices include alternative crops, soil wetting agents, and crop biologicals.

An alternative crop that grew incredibly fast in popularity was industrial hemp (Cannabis sativa) despite limited agronomic knowledge for best management practices. Field trials occurred (2020-2022) near Logan, UT to test a total of …

Metal Assisted O2-Dependent Carbon-Carbon Bond Cleavage Of Β-Diketones And Flavonols, Stephen N. Anderson

All Graduate Theses and Dissertations, Fall 2023 to Present

Almost everything we interact with on a daily basis has been synthesized by chemists ranging from plastics, food preservatives, and medications. The diversity of synthetic molecules are achieved by the formation of new bonds between existing molecules and/or through the cleaving of bonds found in a molecule. There are uncountable amount of conditions reported to facilitate chemical reactions which all depend on the nature of molecules being used and the environment it is used in.

In recent years, more attention has been paid to identify chemical reactions that can use more environmentally favorable conditions and reduce the use of limited …

Shedding Light On Past Ice-Free Intervals In Northwest Greenland: Luminescence Dating Of The Base Of The Camp Century Ice Core, Hawke Woznick

All Graduate Theses and Dissertations, Fall 2023 to Present

The goal of this thesis is to provide greater resolution on the age and character of the subglacial sediment recovered from the base of the Camp Century ice core, northwestern Greenland. Geochemical analysis indicated that the upper sub-ice sediments were geochemically different and experienced greater weathering than the basal unit underlying a one-meter silty ice lens. Analysis of feldspars within the very fine sand fraction indicates they are dominated by potassium feldspar. Sediment was dated using luminescence, which provides an age for the last time sediment was exposed to light. Luminescence analysis returned ages around 420 thousand years old, which …

Staying Fresh: Unconventional Approaches Towards Advancing Energy Sustainability, Water Resources, And Community Resiliency In The Southwestern United States, Judith Hoyt

Open Access Theses & Dissertations

This dissertation addresses critical challenges in urban heat management, sustainable energy resource utilization, and water quality communication through three studies. Study 1 investigates the impact of roof color on urban heat islands in Tucson, Arizona where approximately 70% of roofs display high albedo (i.e., light) colors. Energy consumption simulations conducted indicate that converting dark- to light-colored roofs could save Tucson approximately $1,400,000 annually in energy costs, highlighting the potential of cool roofs for energy savings and improved thermal comfort. Study 2 assesses the sources of lithium in subsurface waters in West Texas and South Central New Mexico. Water chemistry data …

Neural Networks For Decisions Under Uncertainty, Edwin Tomy George

Open Access Theses & Dissertations

Neural networks are used in many real-world applications, ranging from classification tasks to medical diagnostics. For each task, a neural network is typically able to make predictions due to its ability to extract meaningful patterns from processing large amounts of data. Thus, given the increases in available data in recent decades, the performance of neural networks in making accurate predictions has greatly increased. However, this data often comes with ingrained uncertainties due to measurement errors or the inherent variability of individual data points. Neural networks can learn despite the errors in the overall data, but what if we want them …

Experimental And Computational Investigation Of Green Laser Propagation Through Turbulent Medium In A Water Tank, Richard Owusu Adansi

Open Access Theses & Dissertations

Turbulence medium poses significant challenges to the propagation of laser beams, impacting applications such as free-space optical communication, remote sensing, and laser weapons systems. Therefore, comprehending and mitigating turbulence effects are vital for enhancing the performance of these systems. Analysis of a strong turbulence impact on electromagnetic wave propagation requires extensive knowledge of the Earth's atmospheric and Oceanic phenomena and Maxwell's electromagnetic theory of light as a propagating wave of electric and magnetic fields. Optical systems' propagation often encounters Strong Turbulence, causing interference and diffraction. Nonetheless, light propagation through randomly fluctuating media has been an exciting and active area of …

Identifying New Potential Breeding Pond Sites For The Dusky Gopher Frog In Southern Mississippi, Shelbie Kellum

Master's Theses

The main objective of this thesis was to identify potential new pond sites across southern Mississippi for the critically endangered dusky gopher frog (DGF). Ephemeral ponds are the preferred breeding habitat for the species, but they are quite rare in the region due to the diminishment of the longleaf pine ecosystem. This research addresses gaps in the current literature by providing a broad overview of dusky gopher frog breeding habitat identification. LiDAR derived datasets as well as tools within ArcGIS Pro were utilized in order to perform spatial analysis on sites of interest in south Mississippi. By using this methodology …

Experimental And Theoretical Investigation Of The Coordination Of 8-Hydroxquinoline Inhibitors To Biomimetic Zinc Complexes And Histone Deacetylase 8 (Hdac8), Anthony M. Baudino, Harris F. Ciaccio, Michael J. Turski, Xavier A. Akins, Phoebus Sun Cao, Elisa Morales, Roger D. Sommer, Adam R. Johnson, Donald J. Wink, Kyle A. Grice, Kari Stone

Chemistry Department Faculty Articles

Zinc is integral to diverse biological functions, acting catalytically, structurally, and supportively in essential enzyme cycles, despite its limited amounts in the body. Targeting zinc enzymes with potent drugs, such as Vorinostat, demonstrates the therapeutic efficacy of zinc-binding ligands, notably in cutaneous T-cell lymphoma treatments. Our study merges experimental and theoretical approaches to analyze the coordination of 8-hydroxylquinoline (8HQ) inhibitors with biomimetic zinc complexes and human histone deacetylase 8 (HDAC8), a monozinc hydrolase enzyme. Assessing 10 8HQ derivatives for structural and electronic characteristics against these models, we observe minimal inhibition efficacy, corroborated through protein–ligand docking analyses, highlighting the complexities of …

Robust Multivariate Estimation And Inference With The Minimum Density Power Divergence Estimator, Ebenezer Nkum

Open Access Theses & Dissertations

The estimation of the location vector and scatter matrix plays a crucial role in many multivariate statistical methods. However, the classical likelihood-based estimation is greatly influenced by outliers, potentially leading to unreliable decisions. Hence, a fundamental challenge in multivariate statistics is to develop robust alternatives that can maintain performancein the presence of outliers and deviations from the assumed data distribution. Unfortunately, methods with good global robustness often substantially sacrifice efficiency. To address this, we propose the adoption of Minimum Density Power Divergence (MDPD) estimation, a well-established robust technique known for its efficiency and statistical robustness to outliers and model violations. …

Method Development For The Quantification Of Critically Valuable Elements In Permian Basin Produced Waters, Carley Oliver

Open Access Theses & Dissertations

Produced waters (PW) are a major byproduct of the oil and gas industrial hydraulic fracturing processes that create a major waste disposal issue with a need for disposal, treatment, and reuse method developments. The current primary disposal method is subsurface injection, which can lead to high pressures in the subsurface. PWs are often highly saline from mineral leaching due to long residence in subsurface reservoirs. According to the USGS National Minerals Information Center, bromine, calcium chloride, iodine, lithium, magnesium, and sodium chloride have been found in and extracted from these domestic subsurface brines, suggesting that there may be other economically …

Mitochondrial Function In Lungs Of Rats With Different Susceptibilities To Hyperoxia-Induced Acute Lung Injury, Pardis Taheri, Devanshi D. Dave, Ranjan K. Dash, Guru P. Sharma, Anne V. Clough, Elizabeth R. Jacobs, Said H. Audi

Biomedical Engineering Faculty Research and Publications

Adult rats exposed to hyperoxia (>95% O₂) die from respiratory failure in 60–72 h. However, rats preconditioned with >95% O₂ for 48 h followed by 24 h in room air acquire tolerance of hyperoxia (H-T), whereas rats preconditioned with 60% O₂ for 7 days become more susceptible (H-S). Our objective was to evaluate lung tissue mitochondrial bioenergetics in H-T and H-S rats. Bioenergetics was assessed in mitochondria isolated from lung tissue of H-T, H-S, and control rats. Expressions of complexes involved in oxidative phosphorylation (OxPhos) were measured in lung tissue homogenate. Pulmonary endothelial filtration coefficient …

Computational Models That Exploit Spatial, Temporal, And Voltage-Current Relationships In The Electrochemical Generation-Collection Of Redox-Active Molecules, Miguel Angel Abrego Tello

Graduate Theses and Dissertations

The numerical studies in this dissertation explore the application of redox cycling, an advanced electrochemical technique, for analyzing bioelectrochemical systems with a particular focus on small-volume samples and involves electrodes that can be activated to oxidize and reduce, separated by varying distances and featuring different geometries. The redox cycling approach facilitates the spatio-temporal interrogation of kinetics, mass transport, and the quantification and identification of chemical systems. We optimize a previously fabricated neural probe design on an SU-8 substrate, featuring coplanar arrays of nine microband electrodes suited for in vivo applications. Through comprehensive in situ and in silico redox cycling studies …

Investigating The Applications Of Peps To The Measurement Of The Stabilities Of Staphylococcal Nuclease (Stw) And Human Acidic Fibroblast Growth Factor (Hfgf1), Motolani Omolade Matthew

Graduate Theses and Dissertations

This dissertation presents a detailed investigation into the applications of Protein Equilibrium Population Snapshot H/D Exchange Electrospray Ionization Mass Spectrometry (PEPS-H/D exchange or PEPS) method. This method is based on protein equilibrium unfolding, and its fundamental capability is to capture a "snapshot" of the protein's state, allowing us to monitor the ratio of the unfolded to folded populations at different chemical denaturant concentrations. First, to increase the accuracy of PEPS data analysis for assessing protein stability, the traditional linear extrapolation method (LEM) was replaced. Instead of using LEM, which calculates free energy change based on the peak ratio of unfolded …