Physical Sciences and Mathematics Commons^™

Comprehensive Analysis And Forensic Investigation Of Cyanide, Thiocyanate, And 2-Amino-2-Thiazoline-4-Carboxylic Acid In-Ante- And Postmortem Blood Utilizing Advanced Analytical Techniques, Abdullah Hamad Alluhayb

Electronic Theses and Dissertations

Cyanide (CN), present as cyanide anion (CN-) or hydrogen cyanide (HCN), is a deadly poison. The main mechanism of CN toxicity is blocking terminal electron transfer, leading to cellular hypoxia, cytotoxic anoxia, and potential death. Determining blood CN concen-trations along with its major metabolite, thiocyanate (SCN-), is crucial. A sensitive method for concurrent detection of CN and SCN- from human ante- and post-mortem blood via liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis was devel-oped. The method involved active microdiffusion with chemical modification using naph-thalene-2,3-dicarboxaldehyde (NDA) and taurine, while monobromobimane (MBB) mod-ification was used for SCN-. The method showed good sensitivity for …

Understanding The Role Of Hba/Hbd Variations On Deep Eutectic Solvent Properties And Activity Using Acetylsalicylic Acid As A Model Drug, Michael Frimpong

Electronic Theses and Dissertations

Deep eutectic solvents (DES) are emerging as a versatile class of solvents, attracting considerable attention for their unique solvent properties and potential applications. This study examines the effects of variations in combinations as well as molar ratios of hydrogen-bond acceptor (HBA) and hydrogen-bond donor (HBD) on the structure of DES. It further explores the structure-activity relationship, measured using the rate of acetylsalicylic acid (ASA) degradation in the solvent. The project is based on the model that variations in HBA/HBD combinations and their relative molar ratios impact the solvent structure (hydrogen bonding), observable in physicochemical measurements, infrared (IR), and nuclear magnetic …

Effects Of Agricultural Chemicals On Native Plants Of The Northern Great Plains, Gabrielle Bolwerk

Electronic Theses and Dissertations

Agricultural chemicals are ubiquitous on the Northern Great Plains landscape and have negative impacts on non-target plant communities, even at small doses. Northern Great Plains grassland plant communities may experience herbicide drift from agricultural fields or be subject to livestock pharmaceuticals in grazing lands. My research objective was to evaluate if and how native plants are affected by agricultural chemical presence at different concentrations. In Chapter 2, I studied the effect of different concentrations of three common agricultural herbicides (2,4-D, atrazine, and trifluralin) on the germination, emergence, and growth of native plant species of the Northern Great Plains. I performed …

Comparative Analysis Of Membership Inference Attacks In Federated Learning, Saroj Dayal

Electronic Theses and Dissertations

Given a federated learning model and a record, a membership inference attack can determine whether this record is part of the model’s training dataset. Federated learning is a machine learning technique that enables different parties to train a model without the need to centralize or share their local data. Membership inference attack risks the private datasets if those datasets are used to train the federated learning model and access to the generated model is available. There is a need to study the membership inference attack in the federated learning setting. In this thesis, we empirically investigated and compared various membership …

Striving For Appropriate Antibiotic Use: A Biomarker Initiative, And Outcomes Associated With Azithromycin Exposure, Amanda Gusovsky

Theses and Dissertations--Pharmacy

The introduction of antibiotics into clinical practice is considered the greatest medical breakthrough of the 20^thcentury. However, the use of antibiotics can contribute to the development of resistance. In the United States (U.S.), approximately 2.8 million people are infected with antibiotic-resistant bacteria each year, and more than 35,000 people die as a result. Moreover, some antibiotics are known to cause cardiac side effects including QT prolongation, hypotension, and ventricular arrythmias. The U.S. Centers for Disease Control and Prevention (CDC) defines appropriate antibiotic use as the effort to use “the right antibiotic, at the right dose, for the right …

Statistical Intervals For Neural Network And Its Relationship With Generalized Linear Model, Sheng Yuan

Theses and Dissertations--Statistics

Neural networks have experienced widespread adoption and have become integral in cutting-edge domains like computer vision, natural language processing, and various contemporary fields. However, addressing the statistical aspects of neural networks has been a persistent challenge, with limited satisfactory results. In my research, I focused on exploring statistical intervals applied to neural networks, specifically confidence intervals and tolerance intervals. I employed variance estimation methods, such as direct estimation and resampling, to assess neural networks and their performance under outlier scenarios. Remarkably, when outliers were present, the resampling method with infinitesimal jackknife estimation yielded confidence intervals that closely aligned with nominal …

Investigation Of Early Complex Formation Of Huntingtin Protein With And Without Lipids, Alyssa R. Stonebraker

Graduate Theses, Dissertations, and Problem Reports

Huntington’s disease (HD) is a fatal neurodegenerative disease caused by the expansion of the polyglutamine (polyQ) domain of the huntingtin protein (htt). The expansion of the polyQ domain beyond a threshold of approximately 35 repeats triggers complex toxic aggregation mechanisms and results in altered interactions between htt and lipid membranes. Many factors modulate these processes. One such modulator includes sequences flanking the polyQ domain, most notably the first 17 amino acids at the N-terminus of the protein (Nt17), and environmental factors including the presence of membranous structures. Nt17 has the propensity to form an amphipathic a-helix in the presence of …

Electrical And Optical Characteristics Of Wide Pressure-Range Capacitive Coupled Rf Discharge, Diaa Ibrahim, Abdou Garamoon, Farouk Elakshar, Ashraf Alsharif

Al-Azhar Bulletin of Science

A homemade RF capacitive coupled discharge system operating in wide range of pressures (from low pressure up to atmospheric pressure) was constructed. Electrical and optical characteristics of the constructed system were measured for argon discharge operated at wide range of pressure (from low pressure up to atmospheric pressure) and RF power up to 150 Watt. The discharge was operated using two bare metallic copper electrodes with separation distance of 5 mm and it was kept constant in all discharge conditions. Discharge current and discharge voltage were measured for various power and argon gas pressure conditions. The electrical characteristics of the …

Investigating The Environmental And Molecular Dependence Of Single-Molecule Blinking-Based Multiplexing, Grace Desalvo

Dissertations, Theses, and Masters Projects

Visualizing nanoscale biological systems allows us to uncover their detailed structure and functions, which have major implications in the biomedical field. Super-resolution microscopy is a powerful tool for fluorescence imaging because, by overcoming the diffraction limit of light, it accesses structural detail with unprecedented spatial resolution. Although multicolor super-resolution imaging has been successfully implemented in many experiments, its efficiency is limited by reliance on spectral measurement for emitter identification, which limits the combinations of compatible probes to be used together. Blinking-based multiplexing (BBM) is a novel approach that circumvents the need for spectrally-distinct emitters by instead exploiting the intrinsic differences …

A Comprehensive Study Of Bills Of Materials For Software Systems, Trevor Stalnaker

Dissertations, Theses, and Masters Projects

Software Bills of Materials (SBOMs) have emerged as tools to facilitate the management of software dependencies, vulnerabilities, licenses, and the supply chain. Significant effort has been devoted to increasing SBOM awareness and developing SBOM formats and tools. Despite this effort, recent studies have shown that SBOMs are still an early technology not adequately adopted in practice yet, mainly due to limited SBOM tooling and lack of industry consensus on SBOM content, tool usage, and practical benefits. Expanding on previous research, this paper reports a comprehensive study that first investigates the current challenges stakeholders encounter when creating and using SBOMs. The …

From Field To Shore: Policy Improvements To Better Protect Ecosystem And Human Health From Poultry Wastes In Virginia, Rachael A. King

Dissertations, Theses, and Masters Projects

Commercial poultry production is a large industry with economic importance in Virginia. However, mismanagement of manures and wastes generated from the poultry industry can be a serious threat to ecosystem and human health. Primarily, there is a concern about nutrient pollution related to runoff and infiltration of poultry wastes. High nutrient loading can cause groundwater contamination, eutrophication, and harmful algal blooms (HABs). Additional concerns include metals, antibiotics, and pesticides that can be found in poultry wastes. To determine existing threats to ecosystem and human health from the poultry industry, Virginia policies regulating the industry are reviewed and their strengths and …

Ecosystem Transitions And State Changes Rapidly Alter The Coastal Carbon Landscape: Evidence From The Chesapeake Bay Region, Alexander Jason Smith

Dissertations, Theses, and Masters Projects

The coastal landscape is a naturally shifting mosaic of distinct ecosystems that are rapidly migrating with climate change. While directional changes in climate, such as warming and sea level rise, are fundamentally reorganizing the coastal landscape, ecosystem function, especially carbon storage, is affected to an unknown degree. This dissertation presents four chapters that examine the role of ecosystem transitions in coastal carbon dynamics across a range of spatial scales – within individual ecosystems, between two ecosystems, and at the landscape between an array of ecosystems. Ghost forests, or the marsh-forest ecotone, serves as an ideal example of a migratory ecotone. …

Gas-Phase Proton Affinities Of Proline- And Pipecolic Acid-Containing Dipeptides, Trinh Ton

Dissertations, Theses, and Masters Projects

Mass spectrometry (MS) is one of the most used techniques in proteomics because it allows for both high-throughput and quantitative analyses. Bottom-up MS-based proteomics involves breaking down proteins into smaller chains of amino acids called peptides, ionizing and fragmenting the peptides, and identifying the fragments using sequencing databases. These databases depend on the random fragmentation at the backbone peptide bond of the peptides, as predicted by the mobile proton model. Research has shown that peptides containing proline or pipecolic acid have selective fragmentations that could lead to incorrect identification in the sequencing algorithms. These selective cleavages are called “the proline …

Chesapeake Bay Carbonate Cycle: Past, Present, And Future, Fei Da

Dissertations, Theses, and Masters Projects

Multiple natural and anthropogenic drivers are expanding the variability of the estuarine carbonate system (CO2 system). These changes in the CO2 system are threatening the health of ecologically and economically important bivalve species. This dissertation investigates the Chesapeake Bay CO2 system by using numerical models and historical water quality data, focusing on the past three decades, the contemporary period, and the late 2060s. In Chapter 2, sensitivity experiments are conducted with a 3-D Chesapeake Bay hydrodynamic-biogeochemical model and reveal that the magnitude of decadal trends in the CO2 system over the past 30 years is much greater than that observed …

Domain-Specific Optimization For Machine Learning System, Yu Chen

Dissertations, Theses, and Masters Projects

The machine learning (ML) system has been an indispensable part of the ML ecosystem in recent years. The rapid growth of ML brings new system challenges such as the need of handling more large-scale data and computation, the requirements for higher execution performance, and lower resource usage, stimulating the demand for improving ML system. General-purpose system optimization is widely used but brings limited benefits because ML applications vary in execution behaviors based on their algorithms, input data, and configurations. It's difficult to perform comprehensive ML system optimizations without application specific information. Therefore, domain-specific optimization, a method that optimizes particular types …

Spontaneous Symmetry Breaking And Goldstone Theorem, Emilia Szymańska

2023 REYES Proceedings

We discuss the concept of spontaneous symmetry breaking and illustrate it with a general example. We consider Wigner-Weyl and Nambu-Goldstone realisations of symmetry in the quantum theory. Next, we state Goldstone’s theorem and sketch its proof. We discuss why quantum chromodynamics is not realised in the Wigner-Weyl mode. We also consider different order parameters of spontaneous chiral symmetry breaking.

Unttangling Irregular Actin Cytoskeleton Architectures In Tomograms Of The Cell With Struwwel Tracer, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating …

Copula-Based Models For Bivariate And Multivariate Zero-Inflated Count Time Series Data, Dimuthu Fernando, Norou Diawara

College of Sciences Posters

Count time series data have multiple applications. The applications can be found in areas of finance, climate, public health and crime data analyses. In some scenarios, count time series come as multivariate vectors that exhibit not only serial dependence within each time series but also with cross correlation among the series. When considering these observed counts, analysis presents crucial challenges when a value, say zero, occurs more often than usual. There is presence of zero-inflation in the data.

In this presentation, we mainly focus on modeling bivariate zero-inflated count time series model based on a joint distribution of the two …

Ml-Based Surrogates And Emulators, Tareq Alghamdi, Yaohang Li, Nobuo Sato

College of Sciences Posters

No abstract provided.

A Novel Parking Management In Smart City Vehicular Datacenters, Syed Rizvi, Susan Zehra, Steven Olariu

College of Sciences Posters

Researchers have shown that most vehicles spend the majority of their time parked in parking garages, lots, or driveways. During this time, their computing resources are unused and untapped. This has led to substantial interest in Vehicular Cloud, an area of research in which each vehicle acts as a computation node. The main difference between traditional cloud computing and vehicular cloud computing is the availability of nodes. In traditional clouds, nodes are available 24/7, while in vehicular clouds, nodes (vehicles) are only available while parked in parking lots. This creates a dynamic environment as vehicles enter and exit parking garages …

Robustembed: Robust Sentence Embeddings Using Self-Supervised Contrastive Pre-Training, Javad Asl, Eduardo Blanco, Daniel Takabi

School of Cybersecurity Faculty Publications

Pre-trained language models (PLMs) have demonstrated their exceptional performance across a wide range of natural language processing tasks. The utilization of PLM-based sentence embeddings enables the generation of contextual representations that capture rich semantic information. However, despite their success with unseen samples, current PLM-based representations suffer from poor robustness in adversarial scenarios. In this paper, we propose RobustEmbed, a self-supervised sentence embedding framework that enhances both generalization and robustness in various text representation tasks and against diverse adversarial attacks. By generating high-risk adversarial perturbations to promote higher invariance in the embedding space and leveraging the perturbation within a novel contrastive …

A Global Comparison Of Marine Chlorophyll Variability Observed In Eulerian And Lagrangian Perspectives, Angela M. Kuhn, Matthew Mazloff, Stephanie Dutkiewicz, Oliver Jahn, Sophie Clayton, Tatiana Rynearson, Andrew D. Barton

OES Faculty Publications

The California Current System is a diatom‐dominated region characterized by seasonal coastal upwelling and additional elevated mesoscale activity. Cyclonic mesoscale eddies in the region trap productive coastal waters with their planktonic communities and transport them offshore with limited interaction with surrounding waters, effectively acting as natural mesocosms, where phytoplankton populations undergo ecological succession as eddies age. This study examines diatom community composition within two mesoscale cyclonic eddies that formed in the same region of the California Current System 2 months apart and in the California Current waters surrounding them. The diatom communities were analyzed in the context of shifting environmental …

Levels Of Autotrophy And Heterotrophy In Mesophotic Corals Near The End Photic Zone, Amy Carmignani, Veronica Z. Radice, Kathryn M. Mcmahon, Alex I. Holman, Karen Miller, Kliti Grice, Zoe Richards

Biological Sciences Faculty Publications

Mesophotic corals live at ~30-150 m depth and can sustain metabolic processes under light-limited conditions by enhancing autotrophy through specialized photoadaptations or increasing heterotrophic nutrient acquisition. These acclimatory processes are often species-specific, however mesophotic ecosystems are largely unexplored and acclimation limits for most species are unknown. This study examined mesophotic coral ecosystems using a remotely operated vehicle (Ashmore Reef, Western Australia at 40–75m depth) to investigate the trophic ecology of five species of scleractinian coral (from genera Leptoseris, Pachyseris, and Craterastrea) using stable isotope analyses (δ¹³C and δ¹⁵N) of host and symbiont tissues …

Disparate Population And Holobiont Structure Of Pocilloporid Corals Across The Red Sea Gradient Demonstrate Species-Specific Evolutionary Trajectories, Carol Buitrago-López, Anny Cárdenas, Benjamin C.C. Hume, Thierry Gosselin, Fabian Staubach, Manuel Aranda, Daniel J. Barshis, Yvonne Sawall, Christian R. Voolstra

Biological Sciences Faculty Publications

Global habitat degradation heightens the need to better understand patterns of genetic connectivity and diversity of marine biota across geographical ranges to guide conservation efforts. Corals across the Red Sea are subject to pronounced environmental differences, but studies so far suggest that animal populations are largely connected, excepting evidence for a genetic break between the northern-central and southern regions. Here, we investigated population structure and holobiont assemblage of two common pocilloporid corals, Pocillopora verrucosa and Stylophora pistillata, across the Red Sea. We found little evidence for population differentiation in P. verrucosa, except for the southernmost site. Conversely, S. …

A Multi-Taxon Analysis Of European Red Lists Reveal Major Threats To Biodiversity, Axel Hochkirch, Melanie Bilz, Catarina C. Ferreira, Anja Danielczak, David Allen, Ana Nieto, Carlo Rondinini, Kate Harding, Craig Hilton-Taylor, Caroline M. Pollock, Mary Seddon, Jean-Christophe Vié, Keith N. A. Alexander, Emily Beech, Manuel Biscoito, Yoan Braud, Ian J. Burfield, Filippo Maria Buzzetti, Marta Cálix, Kent E. Carpenter, Ning Labbish Chao, Dragan Chobanov, Maarten J. M. Christenhusz, Bruce B. Collette, Mia T. Comeros-Raynal, Neil Cox, Matthew Craig, Annabelle Cuttelod, William R. T. Darwall, Benoit Dodelin, Nicholas K. Dulvy, Eve Englefield, Michael F. Fay, Nicholas Fettes, Jörg Freyhof, Silvia García, Mariana García Criado, Michael Harvey, Nick Hodgetts, Christina Ieronymidou, Vincent J. Kalkman, Shelagh P. Kell, James Kemp, Sonia Khela, Richard V. Lansdown, Julia M. Lawson, Danna J. Leaman, Joana Magos Brehm, Nigel Maxted, Rebecca M. Miller, Eike Neubert, Baudewijn Odé, David Pollard, Riley Pollom, Rob Pople, Juan José Presa Asensio, Gina M. Ralph, Hassan Rankou, Malin Rivers, Stuart P. M. Roberts, Barry Russell, Alexander Sennikov, Fabien Soldati, Anna Staneva, Emilie Stump, Andy Symes, Dmitry Telnov, Helen Temple, Andrew Terry, Anastasiya Timoshyna, Chris Van Swaay, Henry Väre, Rachel H. L. Walls, Luc Willemse, Brett Wilson, Jemma Window, Emma G. E. Wright, Thomas Zuna-Kratky

Biological Sciences Faculty Publications

Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species’ distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity …

Biodiversity Of Philippine Marine Fishes: A Dna Barcode Reference Library Based On Voucher Specimens, Katherine E. Bemis, Matthew G. Girard, Mudjekeewis D. Santos, Kent E. Carpenter, Jonathan R. Deeds, Diane E. Pitassy, Nicko Amor L. Flores, Elizabeth S. Hunter, Amy C. Driskell, Kenneth S. Macdonald Iii, Lee A. Weigt, Jeffrey T. Williams

Biological Sciences Faculty Publications

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased …

Marine Heatwaves Modulate The Genotypic And Physiological Responses Of Reef-Building Corals To Subsequent Heat Stress, Kristen T. Brown, Amatzia Genin, Matheus A. Mello-Athayde, Ellie Bergstrom, Adriana Campili, Aaron Chai, Sophie G. Dove, Maureen Ho, Devin Rowell, Eugenia M. Sampayo, Veronica Z. Radice

Biological Sciences Faculty Publications

Back-to-back marine heatwaves in 2016 and 2017 resulted in severe coral bleaching and mortality across the Great Barrier Reef (GBR). Encouragingly, some corals that survived these events exhibit increased bleaching resistance and may represent thermally tolerant populations that can better cope with ocean warming. Using the GBR as a natural laboratory, we investigated whether a history of minimal (Heron Island) or severe (Lizard Island) coral bleaching in 2016 and 2017 equates to stress tolerance in a successive heatwave (2020). We examined the genetic diversity, physiological performance, and trophic plasticity of juvenile (<10 cm) and adult (>25 cm) corals of two common genera ( …

Dataset For Gendered Language, Shweta Soundararajan

Datasets

Gendered language is the use of words that denote an individual’s gender. This can be explicit where the gender is evident in the actual word used, e.g. mother, she, man, but it can also be implicit where social roles or behaviours can signal an individual’s gender - for example, expectations that women display communal traits (e.g., affectionate, caring, gentle) and men display agentic traits (e.g., assertive, competitive, decisive). The use of gendered language in NLP systems can perpetuate gender stereotypes and bias. This paper proposes an approach to generating gendered language datasets using ChatGPT which will provide data for data-driven …

Bioanalytical Studies Of Disease Protein Profiles: Maldi-Tof Ms, Prajkta Satish Chivte

Graduate Research Theses & Dissertations

Coronavirus disease-2019 (COVID-19), which is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has ravaged the world for the past 3 years. Even today, there still exists a need for rapid, accurate, economical and non-invasive diagnostic testing platforms that yield high specificity and sensitivity towards the constantly mutating SARS-CoV-2. Research has consistently indicated saliva to be a more amenable specimen type for early detection of SARS-CoV-2, compared to the oral and nasopharyngeal swabs. Considering the limitations and high demand of the existing COVID-19 testing platforms, this dissertation work studies used MALDI-ToF MS (matrix-assisted laser desorption/ionization-time of …

Alignment And Range Verification In Proton Therapy Using Proton Radiography And Proton Ct, Joseph Piet

Graduate Research Theses & Dissertations

Protons are used in radiation therapy to lower doses to healthy tissues by utilizing their Bragg peak. Protons can be used both in imaging and treatment. One of the uses of protons in imaging we tested is its use to align patients using a single beam's eye proton radiograph (pRad). By using a beam's eye pRad, and comparing the water equivalent thickness (WET) to proton digitally reconstructed radiographs (pDRRs), we show that we can measure the best alignment on six axes, three translational and three rotational. This is done by defining a cost function, chi squared, which quantifies the misalignment …