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Phytoplankton Responses To Changing Irradiance And Carbon Fertilization, Alison Siersma

Graduate Theses and Dissertations (2019 - present)

Phytoplankton play a crucial role in marine ecosystems due to their innate ability to fix carbon. As atmospheric CO2 levels continue to rise from fossil fuel combustion, the resulting increase in dissolved CO2 and the concurrent decrease in ocean pH are likely to impact the phytoplankton community. The response of phytoplankton to elevated CO2 can vary significantly among species and environmental conditions (e.g. light, temperature, nutrient availability). To address these variations, an experiment was conducted using a controlled photobioreactor system, maintaining high and low light, constant temperature, nutrient levels, and two pCO2 concentrations. This study focused on two regionally relevant …

Equitable Community-Based Participatory Research Engagement With Communities Of Color Drives All Of Us Wisconsin Genomic Research Priorities, Sheikh Iqbal Ahamed, Praveen Madiraju

Computer Science Faculty Research and Publications

Objective

The NIH All of Us Research Program aims to advance personalized medicine by not only linking patient records, surveys, and genomic data but also engaging with participants, particularly from groups traditionally underrepresented in biomedical research (UBR). This study details how the dialogue between scientists and community members, including many from communities of color, shaped local research priorities.

Materials and Methods

We recruited area quantitative, basic, and clinical scientists as well as community members from our Community and Participant Advisory Boards with a predetermined interest in All of Us research as members of a Special Interest Group (SIG). An expert …

The Disordered Negatively Charged C-Terminus Of The Large Hect E3 Ubiquitin Ligase Herc2 Provides Structural And Thermal Stability To The Hect C-Lobe, Kelly L. Waters, Kayla J. Rich, Noah D. Schwaegerle, Tianyi Yang, Shuanghong Huo, Donald E. Spratt

Chemistry

Homologous to the C-terminus of E6AP (HECT) and RCC1-like domain (RLD)-containing protein 2 (HERC2) is a large, 528 kDa E3 ubiquitin ligase that is associated with cancer, oculocutaneous albanism type 2, Prader-Willi syndrome, and other neurological diseases. HERC2 has been found to contribute to double-stranded DNA break repairs, tumor suppression, maintaining centrosome architecture, and ubiquitylation. The C-terminal portion of the HECT domain (C-lobe) of HERC2 is responsible for transferring ubiquitin to a substrate but the precise function of the other eight domains in HERC2 are unknown. Interestingly, HERC2 contains a unique and negatively charged C-terminal …

Magnetic Nano And Micro Rods As Tools For Characterizing Materials Mechanical Properties: Fundamentals And Applications, Artis Brasovs

All Dissertations

The focus of this dissertation is insect blood (Hemolymph). Hemolymph is analyzed by taking a materials science approach. Rheological characterization of hemolymph has been performed for the first time. Owing to a minute amount of available material, a new protocol was established where Magnetic Rotational Spectroscopy (MRS) with ferromagnetic nanorods was employed. The challenge was examining the microliter droplets' viscosity in less than a few minutes. This challenge was successfully resolved.

Blood is critical for the insect's survival: after wounding, the insect has to seal the wound quickly, in a few minutes. As the mechanism of fast clotting has never …

Selective Hydroxyl Functionalization Using Novel Bifunctional Macrocyclic Catalysts And Sufex-Based Methodologies, Austin Seilkop

All Dissertations

The research behind this dissertation explores innovative strategies for the functionalization of alcohols. Alcohols are abundant in biologically relevant molecules and pharmaceutical drugs, so designing new methods for modifying them has gained significant interest over the years. The first and second chapters of this dissertation focus on the selective functionalization of a particular class of alcohols, amino alcohols, a well-represented functional handle in biomolecules. The hydroxyl functionalization of amino alcohols often demands multiple synthetic steps. We developed a new class of macrocyclic catalysts to enable precise and efficient transformations of amino alcohols, advancing the scope and efficiency of amino alcohol …

Leveraging High-Frequency Water Quality Data And Machine Learning For Monitoring Harmful Algal Blooms, Ibrahim Busari

All Dissertations

Freshwater management is one of the most critical resources on the earth due to the plethora of water use and its limited availability. Increased algae proliferation is one of the significant problems of freshwater bodies that is triggered by nutrient enrichment and enabling conditions such as light and warm temperatures. This algal proliferation is toxic to the ecosystem through their biomass and potential toxin production that can cause hypoxic conditions and is often referred to as Harmful Algal Blooms (HABs). Current monitoring approaches include laboratory analysis of water samples to observe algal cells, monitoring of water quality parameters using water …

Supporting Holistic, Informed, Decision-Making Through The Complementarity Of Life Cycle Assessment And Radiological Protection, Bryanna Wattier-Weisensee

All Dissertations

Decision making is challenging and it is necessary to consider all relevant data to make an informed decision. The work herein provides a pathway wherein the fields of radiological protection and life cycle assessment (LCA) can be utilized synergistically to benefit the decision-making using the other (and vice versa). Specifically, LCA parallels decision-aiding techniques used in the optimization of radiological protection and LCA includes an ionizing radiation potential (IRP) impact category wherein the impacts associated with an emission of radioactive material is quantified to determine the human health impact. Thus this body of work focuses on (1) expanding the platform …

Biogeochemical Controls Of Cesium-137 Migration In Surface Waters And Near Surface Sediments At The Usdoe Savannah River Site, Reid Williams

All Dissertations

Considerable concentrations of cesium-137 (¹³⁷Cs) and other anthropogenic radionuclides have been released into the environment at the Savannah River Site (SRS). Additionally, cesium-containing radioactive waste will be stored onsite for the foreseeable future. Therefore, the goal of this work was to identify mechanisms controlling cesium transport in surface waters and near surface sediments at SRS to further the understanding of ¹³⁷Cs migration in the vadose zone and reservoirs. It was hypothesized that a multitude of factors impact the mobility of ¹³⁷Cs at the SRS, but that the clay sediment fraction provides an important contribution in limiting …

Microwave-Assisted Green Synthesis Of Spiroindolinopyranopyrazoles, Esther Owusu

Theses and Dissertations

Green Chemistry, usually known as sustainable chemistry, is widely implemented worldwide to safeguard human health and the environment. Recent investigations in organic synthesis and chemical transformation have demonstrated that green chemistry techniques are significantly reducing both chemical waste and reaction time. In order to fulfill this ecological requirement, it is crucial to lessen the utilization of perilous solvents and noxious chemicals, while also creating innovative reaction methods that decrease the production of trash. The implementation of such methodologies can greatly enhance the field of green chemistry. A more environmentally friendly synthetic method was utilized to generate spiro chemicals and their …

Policies And Price Controls On The Research And Development Of Orphan Drugs In The United States And The European Union, Bena Pearl Filipczak Smith

Master's Theses

There is substantive literature surrounding the impact of price controls on the research and development (R&D) of new pharmaceutical products. The European Union (EU) and United States (US) are often studied in contrast to examine the influence of price controls as the US has fewer pharmaceutical price controls than the EU.

We find moderate evidence that the US spent more on annual domestic pharmaceutical R&D than the EU between 2004 and 2021, on average, before and after adjusting for GDP growth per capita and year. We find strong evidence that the US increased annual domestic R&D spending at a faster …

Addressing Inference Time Of Machine Learning Models In Embedded Systems, Samuel Black

UNLV Theses, Dissertations, Professional Papers, and Capstones

Embedded Systems are used for a wide range of specialized computing purposes including surveyal, safety, security, and quality of life. Many areas that embedded systems are used in require the use of machine learning models. Constraints can be placed on embedded systems. Timeliness of execution, user satisfaction, security, power, and resource limitations must be considered when designing for embedded systems. Neural networks excel at complex tasks that are otherwise intractable, but their relatively high computational cost poses a challenge for inclusion in embedded systems. Neural network architectures should be optimized to reduce the total number of operations performed while maintaining …

A Shared Mechanism For Tnp-Atp Recognition By Members Of The P2x Receptor Family, Xiao-Bo Ma, Chen-Xi Yue, Yan Liu, Yang Yang, Jin Wang, Xiao-Na Yang, Li-Dong Huang, Michael X Zhu, Motoyuki Hattori, Chang-Zhu Li, Ye Yu, Chang-Run Guo

Faculty, Staff and Student Publications

P2X receptors (P2X1-7) are non-selective cation channels involved in many physiological activities such as synaptic transmission, immunological modulation, and cardiovascular function. These receptors share a conserved mechanism to sense extracellular ATP. TNP-ATP is an ATP derivative acting as a nonselective competitive P2X antagonist. Understanding how it occupies the orthosteric site in the absence of agonism may help reveal the key allostery during P2X gating. However, TNP-ATP/P2X complexes (TNP-ATP/human P2X3 (hP2X3) and TNP-ATP/chicken P2X7 (ckP2X7)) with distinct conformations and different mechanisms of action have been proposed. Whether these represent species and subtype variations or experimental differences remains unclear. Here, we show …

Issue 41

The Synapse: Intercollegiate science magazine

No abstract provided.

The Care Crisis: The Neurology Of Dementia And International Solutions, Sophie Paton

The Synapse: Intercollegiate science magazine

No abstract provided.

Will My Celsius Addiction Kill Me?: The Thermogenic Drink And Its Impact On Nutrition And Metabolism, Katie Johnstone

The Synapse: Intercollegiate science magazine

No abstract provided.

Biological Reinforcement Learning Simulation For Natural Enemy -Host Behavior: Exploring Deep Learning Algorithms For Population Dynamics, Komi Mensah Agboka, Emmanuel Peter, Erion Bwambale, Bonoukpoè Mawuko Sokame

All Peer-Reviewed Publications

This study introduces a simulation of biological reinforcement learning to explore the behavior of natural enemies in the presence of host pests, aiming to analyze the population dynamics between natural enemies and insect pests within an ecological context. The simulation leverages on Q-learning, a reinforcement learning algorithm, to model the decision-making processes of both parasitoids/predators and pests, thereby assessing the impact of varying parasitism and predation rates on pest population growth. Simulation parameters, such as episode count, duration in months, steps, learning rate, and discount factor, were set arbitrarily. Environmental and reward matrices, representing climatic conditions, crop availability, and the …

Quantifying Greenhouse Gas Exchange And Ecosystem Services In Ecosystems Managed For Nature-Based Solutions Using Eddy Covariance, Remote Sensing, And Models, Lucas Clay

All Dissertations

As global temperatures rise due to climate change, nature-based solutions are increasingly being used to restore nature and to remove carbon from the atmosphere. Nature-based solutions draw on methodologies such as ecological forestry and improved forest management to reduce emissions and maximize resilience. These protocols are still in their infancy and additional measurements and case studies are important to optimizing these protocols. Herein this dissertation we describe multiple measurement methodologies for both greenhouse gas (GHG) emissions and for ecosystem services. In coastal wetland ecosystems, the need for GHG measurements is paramount to understanding the ability of these ecosystems to reduce …

Cross-Interactions Of Amyloid Proteins: Implications For Aggregation Dynamics And Disease Pathology, Zhiyuan Song

All Dissertations

Amyloid aggregation is a pervasive form of protein misfolding implicated in the pathology of several prominent human diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), and type 2 diabetes (T2D). These diseases are marked by the accumulation of amyloid fibrils and toxic oligomers, which are highly dynamic and heterogeneous, posing challenges for understanding their roles in disease progression. Despite significant advances in the diagnosis and management of these conditions, no definitive cure is available. We investigate amyloid aggregation and cross-seeding, with a focus on amyloid-beta (Aβ), tau, alpha-synuclein (αS), and human islet amyloid polypeptide (IAPP) through discrete molecular dynamics (DMD) …

Rice Response To Struvite And Other Phosphorus Fertilizers In A Phosphorus-Deficient Soil Under Simulated Furrow-Irrigation, Jonathan B. Brye, Diego Della Lunga, Kristofor R. Brye

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Wastewater-recovered phosphorus (P), in the form of the mineral struvite (MgNH₄PO₄⋅6H₂O), may provide a sustainable alternative to decreasing rock-phosphate reserves. Struvite can be generated via precipitation methods, potentially reducing the amount of P runoff to aquatic ecosystems. The objective of this greenhouse tub study was to evaluate the effects of chemically- and electrochemically precipitated struvite (CPST and ECST, respectively) on above- and belowground plant response in a hybrid rice (Oryza sativa) cultivar grown using furrow-irrigation compared to other common fertilizer-P sources [i.e., triple super phosphate (TSP) and diammonium phosphate (DAP)]. Rice was …

Traittrainr: Accelerating Large-Scale Simulation Under Models Of Continuous Trait Evolution, Jenniffer Roa Lozano, Mataya Duncan, Duane D. Mckenna, Todd A. Castoe, Michael Degiorgio, Richard Adams

Entomology and Plant Pathology Faculty Publications and Presentations

Abstract

The scale and scope of comparative trait data are expanding at unprecedented rates, and recent advances in evolutionary modeling and simulation sometimes struggle to match this pace. Well-organized and flexible applications for conducting large-scale simulations of evolution hold promise in this context for understanding models and more so our ability to confidently estimate them with real trait data sampled from nature. Results

We introduce TraitTrainR, an R package designed to facilitate efficient, large-scale simulations under complex models of continuous trait evolution. TraitTrainR employs several output formats, supports popular trait data transformations, accommodates multi-trait evolution, and exhibits flexibility …

Cellulose–Starch Composite Aerogels As Thermal Superinsulating Materials, Safoura Ahmadzadeh, Angelina Sagardui, David Huitink, Jingyi Chen, Ali Ubeyitogullari

Chemistry & Biochemistry Faculty Publications and Presentations

The demand for sustainable packaging materials is rapidly increasing due to growing environmental concerns over the impact of plastic waste. In this study, biodegradable, porous, lightweight, and high-surface-area microcrystalline cellulose–starch (MCC-S) hybrid aerogels were synthesized via supercritical carbon dioxide (SC–CO₂) drying. The samples were generated using five different MCC-S weight ratios and characterized for their morphology, crystallinity, and structural and thermal properties. When MCC and S were used together, aerogels with superior properties were obtained compared to those made from each component individually. Specifically, the 1:2 MCC-S aerogel exhibited the highest porosity (97%), the lowest density (0.058 g/cm …

Real-Time Motion Augmentation And Synthesis For Animating The Hands And Eyes Of Virtual Humans And Avatars, Ryan Canales

All Dissertations

Virtual Reality (VR) enables users to interact within virtual worlds via an embodied virtual representation of themselves called an “avatar”. Because avatars are essential for immersive experiences, it is important to consider how altering or augmenting avatar motion affects virtual experiences. This dissertation aims to improve virtual experiences by addressing some of the many challenges in animating avatars and virtual humans.

In our first study, we addressed the lack of tactile feedback during virtual grasping by using visual feedback techniques. We augmented the avatar’s hand motion to remain outside virtual objects (“outer hand”) even when the user’s hand penetrated them. …

Sufex-Enabled Stereospecific Deoxygenative Diversification Of Alcohols, Amaechi Odoh

All Dissertations

Alcohols represent an important class of functional group in organic synthesis and medicinal chemistry, given that they are structurally diverse and prevalent in many natural products, biomolecules and renewable feedstocks. As such, they are highly attractive precursors for building-block synthesis, late-stage functionalization, and numerous synthetic transformations. However, existing strategies for the deoxygenative diversification of alcohols operate under constrained conditions, often leading to competing pathways (such as elimination), poor stereospecificity, low efficiencies, and limited substrate compatibility. To address these challenges, we have developed a conceptually novel use of sulfonyl fluorides as bifunctional reagents for the one-step deoxygenative diversification of complex alcohol …

Heavy Metals In Rural Soils: A Case Study In Jennings County, Indiana, Madeline Hill

All-Inclusive List of Electronic Theses and Dissertations

Heavy metals, such as lead and mercury, can be toxic if exposure levels are too high. People are often concerned about lead exposure from water or paint, but soil is another potential exposure avenue for many metals. While some heavy metals, including mercury and lead, are found in emissions from coal-burning power plants and from incinerators, many metals accumulate in soils from past uses (ex. lead paint, leaded gasoline, chemical spills, industrial emissions, and natural occurrences). It is important to have soil tested to check metal concentrations because consumption or inhalation of these metals can lead to permanent damage and …

Aars Online: A Collaborative Database On The Structure, Function, And Evolution Of The Aminoacyl-Trna Synthetases, Jordan Douglas, Haissi Cui, John J. Perona, Oscar Vargas-Rodriguez, Henna Tyynismaa, Claudia Alvarez Carreno, Jiqiang Ling, Lluis Ribas De Pouplana, Xiang-Lei Yang, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

The aminoacyl-tRNA synthetases (aaRS) are a large group of enzymes that implement the genetic code in all known biological systems. They attach amino acids to their cognate tRNAs, moonlight in various translational and non-translational activities beyond aminoacylation, and are linked to many genetic disorders. The aaRS have a subtle ontology characterized by structural and functional idiosyncrasies that vary from organism to organism, and protein to protein. Across the tree of life, the 22 coded amino acids are handled by 16 evolutionary families of Class I aaRS and 21 families of Class II aaRS. We introduce AARS Online, an interactive Wikipedia-like …

Interpreting Neural Networks For Particle Tracing In Fluid Simulation Ensembles: An Interactive Visualization Framework, Maanav Choubey

All Graduate Theses and Dissertations, Fall 2023 to Present

Understanding the internal mechanisms of neural networks, particularly Multi-Layer Perceptrons (MLP), is essential for their effective application in a variety of scientific domains. In particular, in the scientific visualization domain their adoption has recently shown to be a promising tool to predict particle trajectories in fluid dynamics simulation and aid the interactive visualization of flows. This research addresses the critical challenge of interpretability of such models.

While interpretability has been extensively explored in fields like computer vision and natural language processing, its application to time series data, particularly for particle tracing (or prediction of trajectories), has not garnered sufficient attention. …

Mathematical And Statistical Methods To Harness Limited Data In Models For Ecological Space Use Under Global Change, Sarah C. Bogen

All Graduate Theses and Dissertations, Fall 2023 to Present

The dynamics of how plants and animals use space in their habitats has important implications for the fields of ecology and conservation. However, understanding and responding to these spatial and temporal dynamics is often limited by data availability, financial resources and biases. As average global temperatures increase, suitable habitats shift poleward and require local populations to move with suitable habitat, adapt to the changing environment, or risk extinction. Capacity to persist without movement may be estimated by considering changes to a combination of habitat characteristics. Capacity to track suitable habitat may be modeled through synthesizing information on species demographic mechanisms …

Functionalized Carbon Quantum Dots: A Promising Nanomaterial For Investigating Their Potential In Neurodegenerative Disease Treatment, Sherin M. El Morsy

Open Access Theses & Dissertations

Neurodegenerative diseases such as Parkinson's Disease (PD), Alzheimer's Disease (AD), and Huntington's Disease (HD) remain incurable, despite extensive research into therapeutic development. In the United States of America, the annual cost of PD and AD in terms of patient care and lost productivity is approximately $200 billion. Consequently, there is a critical and unaddressed need for the development of innovative drugs and drug delivery systems that can decelerate, stop, or ideally reverse neurodegenerative diseases. The dissertation presented here focuses on devising strategies to target PD through multiple mechanisms, including the inhibition of protein aggregation and the reduction of oxidative stress. …

Redefining Approaches For Measuring Landscape Subsidence And Permafrost Degradation In Arctic Tundra Environments, Tabatha Lynn Fuson

Open Access Theses & Dissertations

As climate change accelerates in the Arctic, the degradation of permafrost is leading to significant landscape transformation in tundra landscapes. This dissertation investigates the multifaceted responses of permafrost systems to warming, focusing on the dynamics of surface elevation changes and active layer thickness (ALT) across the North Slope of Alaska. In this study, I explore the capacity of repeat Terrestrial Laser Scanning (TLS) technology for modeling tundra features and detecting surface subsidence, specifically how different climate and landscape conditions during scanning impact TLS model precision. We also compare TLS model precision estimates to TLS model accuracy by comparing elevation values …

The New Anthropocentrism: The Problem Of Water Conservation And Water Justice, Benjamin Stuart Milam

Open Access Theses & Dissertations

My objective with my thesis is to argue for and reinforce a type of anthropocentrism that is both environmentally conscious and consumable for an audience that is not necessarily well versed in philosophical literature. In the first chapter I go over philosophical frameworks, such as Anthropocentrism and Biocentrism, and why I believe they do not meet both of those criteria listed. After that I discuss New Anthropocentrism, coined by Clive Hamilton, and why I believe that a slightly modified version possesses qualities that I believe are needed for the crisis at hand. In chapter 2 I use that framework and …