Physical Sciences and Mathematics Commons^™

Machine Learning And Rna Bioinformatics, Jason Rafe Miller

Graduate Theses, Dissertations, and Problem Reports (ETD)

The applied science of bioinformatics encompasses computational analysis of molecular biology data. Advances in genomics and DNA sequencing technology have enabled computational analysis of ribonucleic acids (RNAs), which play diverse and critical roles in most cells. To assist the study of human RNA, we trained machine learning models on RNA nucleotide sequences, devoid of domain knowledge. We built models that distinguish long non-coding lncRNA from protein-coding mRNA, and models that predict the cytoplasmic vs. nuclear preferences of lncRNAs. In a review of published lncRNA subcellular localization classifiers, we show that the commonly used validation protocol generates optimistic performance measures, and …

Exploring Crystal Polymorphism In Additive-Assisted Chemical Vapor-Deposited Transition Metal Chalcogenides And Oxides, Lawrence Kirimi Mubwika

Graduate Theses, Dissertations, and Problem Reports (ETD)

Crystal polymorphism is a phenomenon in which compounds with the same chemical formula can be crystallized into different crystal structures. This phenomenon can be observed in elemental materials, such as diamond and graphite, as well as in compounds, such as the trigonal (1H) or octahedral (1T) prismatic MoS₂. Crystals can also exhibit polytypism by stacking different polymorphs in a certain order, with the stacking sequence determining the variation between polytypes. Although all polymorphs and polytypes have the same chemical composition, each polymorph and polytype possesses unique electronic and physical properties.

This study explores the additive-assisted chemical vapor deposition …

A Multi-Wavelength Determination Of The Total Luminosity And Star Formation Rate Of The Milky Way, Joshua L. Mascoop

Graduate Theses, Dissertations, and Problem Reports (ETD)

The star formation rate (SFR) of the Milky Way is poorly understood in comparison to the SFR of other galaxies. In order to better find the Galaxy's place in the universe, it is imperative to understand the star formation activity occurring within it. We characterize the Galactic \hii\ region luminosity function (LF) at multiple infrared and radio wavelengths using a sample of 797 first Galactic quadrant \hii regions compiled from the WISE Catalog of Galactic \hii Regions. This sample is statistically complete for all regions powered by single stars of type O9.5V and earlier.

We find that neither a single …

Advances In Machine Learning Aided Seismic Interpretation And Inversion For Subsurface Characterization, Tobi Micheal Ore

Graduate Theses, Dissertations, and Problem Reports (ETD)

Geophysical data are used to “remotely sense” the subsurface to illuminate structures, stratigraphy, and features that are of interest in the exploration for energy, suitable storage for carbon dioxide, geothermal development, and environmental considerations. The interpretations of these data typically are regarded as partially an art, as it depends on the experience of the interpreter. This is further exacerbated with the big data era as this data is large and takes several days, even longer, to manually interpret. To bridge this gap of speed and subjective bias, machine learning has been successfully applied to automate the geophysical interpretation process. This …

Estimating Home Range Size And Density Of White-Tailed Deer (Odocoileus Virginianus) In West Virginia, Sarah M. Pesi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Big game hunting is an important source of revenue and recreation in the United States. Of big game species, white-tailed deer (Odocileus virginianus) are the most heavily pursued. White-tailed deer are a widespread generalist species, capable of existing at high densities. Hunting is often used as the primary method of managing deer populations, particularly in the eastern United States, where there is a lack of large predators. When populations reach high densities, there can be negative effects on the environment and conflicts with humans. Managers must consider both creating adequate hunting opportunities and reducing negative impacts when managing …

A Hyperbolic Relaxation Solver For Numerical Relativity, Thiago Assumpcao

Graduate Theses, Dissertations, and Problem Reports (ETD)

Numerical relativity (NR) simulations are essential for self-consistently modeling compact binary mergers, whose observations form the heart of gravitational-wave science. Stable NR simulations are the result of mathematical and computational breakthroughs spanning several decades: early attempts to numerically solve the two-body problem in General Relativity (GR) date back to the 1960s, while the first successful black-hole binary merger simulations were performed in 2005 with the generalized harmonic coordinates, and in 2006 using the moving-puncture gauge.

Today, NR continues to drive progress in gravity research, with ongoing efforts focused on increasing physical realism in simulations containing matter, exploring alternative theories of …

X-Ray Absorption And Related Studies In Superconducting Devices And Magnetic Thin Films, Ghadendra Bahadur Bhandari

Graduate Theses, Dissertations, and Problem Reports (ETD)

Superconducting and magnetic thin films are commonly used in sensors for analytical detectors, especially those that operate at very low temperatures, often below 1 Kelvin. These highly sensitive detectors, capable of functioning across a broad range of wavelengths, have garnered significant interest in scientific research. The focus of this thesis is to address a material challenge associated with an emerging technology known as microwave kinetic inductance detectors (MKIDs). The research involves the study of Al/Si and Al-Mn/Si-based thin films, as well as an investigation into the magnetic properties of LaMnO₃ thin films. LaMnO₃, a perovskite thin film that plays a …

Conformational Investigation Of Biopolymers Through Molecular Dynamics (Md) Simulations And In-Droplet Hdx-Ms Utilizing Cvssi, Samira Hajian Foroushani

Graduate Theses, Dissertations, and Problem Reports (ETD)

Over the last two decades, mass spectrometry (MS) has received significant interest in biological study platforms, especially in the areas of proteomics and metabolomics. With the development of soft ionization methods like electrospray ionization (ESI), mass spectrometry has emerged as a potent method for directly characterizing proteins in their native state. The recent invention of capillary vibrating sharp-edge spray ionization has opened new avenues for the study of biopolymer native structure including the usage of droplet charge tuning and in-droplet hydrogen-deuterium exchange (HDX) labeling. With this new technique comes the opportunity to study biopolymer ion structure preservation with molecular dynamics …

A Floquet Solver For Time Periodic Open Quantum Systems, Fenton Ross Clawson

Graduate Theses, Dissertations, and Problem Reports (ETD)

Computational physics has been a backbone of experimental and theoretical physics since the 1940’s, when the first nuclear bomb and ballistic simulations were per- formed at Los Alamos Laboratory. Nowadays, however, simulation of open quan- tum systems has been formalized into coding packages and user-friendly functions, such as QuTiP or Qiskit, which allow users to simulate these systems without hav- ing the in-depth knowledge required to build the computational backbone from the ground-up. With the shift in modern quantum physics towards the realization of quantum computation, a strong computational background is still necessary to lend validity to theoretical results and …

Α-Hydroxy C–H Functionalization Of Alcohols Via Boronic Acid, Hat, Photoredox Triad Catalytic System, Seth Christopher Cowan

Graduate Theses, Dissertations, and Problem Reports (ETD)

This dissertation explores the research that I have conducted in my time at West Virginia University. Most of my work has focused on the development of methods and studies to further understand the α-OH C–H functionalization of alcohols. This work involves a system of catalysts including photocatalysts, HAT catalysts, and boronic acid catalysts. Chapter 1 highlights a background for each of these areas. Photoredox catalysis has been an increasing area of chemistry over the past two decades as this technique can be used to design conditions to form new bonds in a selective manner through the utilization of light energy. …

Characterizing Prescribed Fire With Terrestrial Lidar In The New Jersey Pine Barrens, Samuel Rhule Stockton

Graduate Theses, Dissertations, and Problem Reports (ETD)

Prescribed burning has become a commonly used tool in the mitigation of wildfire, though monitoring the way it changes ecosystems has historically been a time-intensive process. Rapid change across ecosystems has necessitated advancements in remote sensing technologies to quantify the changes taking place. Single-scan terrestrial LiDAR scanning is one such method of monitoring these changes through the quantification of ecosystem structural characteristics. Acute disturbance events such as fire can transform the structure of an ecosystem, and by extension, change the way that ecosystem functions. The purpose of this study is to analyze the changes in vegetation density and distribution following …

Experimental Verification And Time-Resolved Bispectral Analysis Of Nonlinear Coupling In The Toroidicity-Induced Alfv´En Eigenmode Spectrum, Gregory Allen Riggs

Graduate Theses, Dissertations, and Problem Reports (ETD)

In magnetically-confined fusion devices, the toroidicity-induced Alfv´en eigenmode (TAE) is a well-studied, weakly stable solution of the linearized ideal magnetohydrodynamic (MHD) equations. Due to intrinsic coupling of poloidal harmonics of the shear Alfv´en wave (SAW) in toroidal geometry, the rotational transform of magnetic field lines modulates the effective index of refraction, ensuring gaps in the so-called “Alfv´en continuum.” Experimental verification of theoretical predictions for various parameters of interest (i.e., frequency, mode structure, instability threshold, etc.) is established in the literature.

We present the first systematic study of TAE-TAE phase coherence in an experimental device, using the DIII-D tokamak. Crucially, nonlinear …

Synthesis, Characterization, And Reactivity Studies Of Pyridine Dipyrrolide Iron-Carbene Complexes With Electronically Distinct Carbene Moieties, Jose G. Rodriguez

Graduate Theses, Dissertations, and Problem Reports (ETD)

First, three (^MesPDP^Ph) iron carbene complexes with electronically distinct carbene moieties were synthesized. These transitional iron carbene complexes were first characterized by ¹H nuclear magnetic resonance (NMR) spectroscopy as their spectra showed paramagnetically shifted resonances. Additionally, their respected solid state structures were collected via X-ray diffraction. The two donor/acceptor iron carbene complexes [(^MesPDP^Ph)Fe(C(CO₂Me)(4-FPh) and (^MesPDP^Ph)Fe(C(CO₂Me)(4-MeOPh)] demonstrated a weak Fe-O interaction between the iron center and ester function group while the (^MesPDP^Ph)Fe(IMe) displayed a C_2v symmetric structure in the …

The Search, The Localization, And The Characterization: Fast Radio Transients, Reshma Anna Thomas

Graduate Theses, Dissertations, and Problem Reports (ETD)

Fast radio transients are energetic bursts in centimeter or meter wave-lengths, lasting only milliseconds, and originating from both Galactic and extra-Galactic sources. In our Galaxy, these transients primarily originate from pulsars, which are rotating neutron stars. The more energetic extra-galactic transients, known as fast radio bursts (FRBs), have unknown origins. This thesis explores various techniques, including single dish and interferometric observations, to detect and accurately localize fast radio transients. It also investigates how the propagation effects of radio waves can reveal characteristics of the local environment and potential FRB sources. Furthermore, it demonstrates how FRBs can be used to study …

A Self-Supervised Knowledge Distillation Approach To Anomaly Detection In X-Ray Imagery, Kaden Quinn Mceldowney

Graduate Theses, Dissertations, and Problem Reports (ETD)

Many cargo containers enter the United States every day by truck, rail, and sea. As a result of the large number of cargo containers entering the United States, not all of them can be thoroughly inspected. Most of these containers contain properly documented and legal cargo, but some people take advantage of this situation by hiding illicit items in the cargo containers such as drugs. To more efficiently and thoroughly inspect cargo containers, Customs and Border Protection (CBP) uses X-ray imaging machines to obtain images that reveal the interior of cargo containers. These X-ray images must be inspected to ensure …

Geochemical Phase Associations Of Rare Earth Elements And Lithium In Black Shales Of The Usa: A Study In The Appalachian And Haynesville Basins, Shailee Bhattacharya

Graduate Theses, Dissertations, and Problem Reports (ETD)

Critical elements are an indispensable part of the clean energy transition. In the race for alternative energy technologies, lithium and rare earth elements have a proven record of being few of the most sought-after minerals. Limited availability of conventional mineral ores warrants a need to explore, understand and exploit unconventional sources of these elements. To that end, several studies have attempted to understand the rock and mineral assemblages of diverse geological systems. This doctoral thesis focuses on understanding the geochemistry of REE and Li in sedimentary environments, particularly black shale basins in the US. A suite of samples from natural …

A Portable, Digital Nucleic Acid Amplification Test For Use At The Point Of Care, Bethany J. Fike

Graduate Theses, Dissertations, and Problem Reports (ETD)

Nucleic acid tests are key tools for the detection and diagnosis of many diseases. In many cases, the amplification of nucleic acids is required to reach a detectable level. Although nucleic acid tests have great success, there is a need to make nucleic acid amplification tests more accessible to a point-of-care (POC) setting for diagnosis, prognosis, and monitoring of infectious diseases. Traditionally, these tests are performed through bulk Polymerase Chain Reaction (PCR) and are monitored in real time with a change in fluorescence intensity. With these bulk testing methods, only a qualitative or semi-quantitative result is possible. For more exact …

Machine Learning Based Intrusion Detection Framework For Can Bus Vulnerabilities In Modern Vehicles, Obinna C. Agbo

Graduate Theses, Dissertations, and Problem Reports (ETD)

The Controller Area Network (CAN) bus is a crucial communication backbone in modern vehicles, connecting various Electronic Control Units (ECUs). However, inherent design weaknesses such as the lack of encryption and authentication make CAN networks vulnerable to cyber-attacks, including spoofing, Denial of Service (DoS), and fuzzing attacks. This thesis thoroughly evaluates these vulnerabilities and the limitations of existing security frameworks like Message Authentication Codes (MACs) and encryption, advocating for the adoption of Intrusion Detection Systems (IDS) as a more practical solution for CAN bus security. The proposed IDS leverages advanced machine learning techniques to accurately detect intrusions, even under complex …

On Cyclically 4-Connected Cubic Graphs, R. J. Kingan, S. R. Kingan

Publications and Research

A 3-connected cubic graph is cyclically 4-connected if it has at least n ≥ 8 vertices and when removal of a set of three edges results in a disconnected graph, only one component has cycles. By introducing the notion of cycle spread to quantify the distance between pairs of edges, we get a new characterization of cyclically 4-connected graphs. Let Q_n and V_n denote the ladder and Möbius ladder on n ≥ 8 vertices, respectively. We prove that a 3-connected cubic graph G is cyclically 4-connected if and only if G is either the Petersen graph, Q …

Photo-Induced Charge State Dynamics Of The Neutral And Negatively Charged Silicon Vacancy Centers In Room-Temperature Diamond, G. Garcia-Arellano, G. I. López-Morales, N. B. Manson, J. Flick, A. A. Wood, C. A. Meriles

Publications and Research

The silicon vacancy (SiV) center in diamond is drawing much attention due to its optical and spin properties, attractive for quantum information processing and sensing. Comparatively little is known, however, about the dynamics governing SiV charge state interconversion mainly due to challenges associated with generating, stabilizing, and characterizing all possible charge states, particularly at room temperature. Here, multi-color confocal microscopy and density functional theory are used to examine photo-induced SiV recombination — from neutral, to single-, to double-negatively charged — over a broad spectral window in chemical-vapor-deposition (CVD) diamond under ambient conditions. For the SiV⁰ to SiV^‒ transition, …

A Gis Tool For Optimal Forage Species Selection, David B. Hannaway, Christopher Daly, Michael D. Halbleib, Linda Brewer, Sophie Baur, Chelsea Clark, Emilie Krecklow, Scott Bassett

IGC Proceedings (1977-2023)

To determine appropriate forage species for US ecoregions, geographic information technologies (GIS) are being used to create climatic and soil factor maps. Excel spreadsheets and RStudio are used to create response functions of forage species to minimum and maximum temperature, annual precipitation, soil pH, soil salinity, and salinity. National forage data and expert opinion will evaluate quantitative tolerances, seasonal yield profiles, and pollinator suitability. These maps and agronomic and livestock use information will be shared with forage specialists and farmers to provide alternatives for improved perenniality, increased diversity, and system circularity. Future work will include development and evaluation of climate …

Seven Properties Of Highly Effective Problems, Thomas Ales, Kevin Peterson, Constantine Roussos

Journal of Mathematics and Science: Collaborative Explorations

In an effort to provide more critical thinking opportunities in their courses, instructors are embracing the power of problem- and project-based learning (PBL). In this paper we address the importance of problem quality when utilizing PBL. We list seven important properties that a high-quality problem should have. We conclude with an example of a problem that possesses all seven properties.

Introducing Flexible Assessment Into A Computer Networks Course: A Case Study, Joe Meehean

Journal of Mathematics and Science: Collaborative Explorations

With overall positive results and limited drawbacks, I have adapted modern pedagogical techniques to address a common difficulty encountered when teaching a computer networks course. Due to the tiered nature of the skills taught in the course, students often fail unnecessarily. Using mastery learning, competency-based education, and specifications grading as a foundation, I have developed a course that allows students with varied skills and abilities to pass. The heart of this approach is the flexible assessment of programming assignments which eliminates due dates and allows students to have their work graded and regraded without penalty. Flexible assessment also defines an …

Petrography Study Of The Recent Sediments In Hareer’S Region At Basrah Governorate - Southern Iraq, K J. Al-Sudani, B N. Albadran, A S Y Al-Hadadi, M H. Al-Jaberi, Jennifer R. Pournelle

Faculty Publications

Two sites of Hareer’s region is located in the southern part of Iraq, specifically in the northern Basrah Governorate. The sites are at a depth of 5 meters. The results of heavy mineral analysis showed that there are fifteen types include; Opaque grain (Iron Oxide), Chlorite, Muscovite mica, Biotite, Orthopyroxene, Clinopyroxene, Amphibole (Hornblende and Actinolite), Epidote, Garnet, Kyanite, Staurolite, Zircon, and Tourmaline. On the other hand the light minerals and the results of the mineral analyses revealed that they were primarily composed of rock fragments, with a variety of quartz minerals, feldspar minerals, evaporate minerals, clay-coated grains, and trace amounts …

Extended Conformations Of Bifurcating Electron Transfer Flavoprotein Constitute Up To Half The Population, Possibly Mediating Conformational Change, Sharique A. Khan, Alan Hicks, Wellington C. Leite, James Byrnes, Biswajit Gorai, Maria-Andrea Mroginski, Hugh O'Neill, Anne-Francis Miller

Markey Cancer Center Faculty Publications

Electron transfer bifurcation enables biological systems to drive unfavourable (endergonic) electron transfer by coupling it to favourable (exergonic) transfer of a second electron. In electron transfer flavoproteins (ETFs), a domain-scale conformational change is believed to sever the favourable pathway after a single electron has used it, thereby preventing the energy dissipation that would accompany exergonic transfer of the second electron. To understand the conformation change that participates in turnover, we have deployed small-angle neutron scattering (SANS) and computational techniques to characterize the bifurcating ETF from Acidaminococcus fermentans (AfeETF). SANS data reveal an overall radius of gyration (Rg) of 30.1 ± …

Machine-Learning-Assisted Design Of Deep Eutectic Solvents Based On Uncovered Hydrogen Bond Patterns, Usman Lame Abbas, Yuxuan Zhang, Joseph Tapia, Md Selim, Jin Chen, Jian Shi, Qing Shao

Markey Cancer Center Faculty Publications

Non-ionic deep eutectic solvents (DESs) are non-ionic designer solvents with various applications in catalysis, extraction, carbon capture, and pharmaceuticals. However, discovering new DES candidates is challenging due to a lack of efficient tools that accurately predict DES formation. The search for DES relies heavily on intuition or trial-and-error processes, leading to low success rates or missed opportuni- ties. Recognizing that hydrogen bonds (HBs) play a central role in DES formation, we aim to identify HB features that distinguish DES from non-DES systems and use them to develop machine learning (ML) models to discover new DES systems. We first analyze the …

Putting Biomonitors To Work: Native Moss As A Screening Tool For Solid Waste Incineration, Sarah Jovan, Eleonore Jacobson, Jason M. Unrine, Nasser Jalili‑Jahani, Bruce Mccune

Markey Cancer Center Faculty Publications

Solid waste incineration (SWI) can release numerous air pollutants although the geographic reach of emissions is not routinely monitored. While many studies use moss and lichens for biomonitoring trace elements, including around SWIs, few investigate the complex, multi-element footprint expected from SWI emissions. This study develops using native moss as a screening tool for SWI while also informing community concerns about an aging incinerator in rural Oregon, USA. Trained community volunteers helped collect 36 composite samples of epiphytic moss (Orthotrichum s.l.) along a 32-km transect from the SWI. We used ICP-MS to measure 40 elements in moss, including 14 rare …

Biliverdin Reductase-A Integrates Insulin Signaling With Mitochondrial Metabolism Through Phosphorylation Of Gsk3Β, Chiara Lanzillotta, Antonella Tramutola, Simona Lanzillotta, Viviana Greco, Sara Pagnotta, Caterina Sanchini, Silvia Di Angelantonio, Elena Forte, Serena Rinaldo, Alessio Paone, Francesca Cutruzzolà, Flavia Agata Cimini, Ilaria Barchetta, Maria Gisella Cavallo, Andrea Urbani, D. Allan Butterfield, Fabio Di Domenico, Bindu D. Paul, Marzia Perluigi, Joao M.N. Duarte

Markey Cancer Center Faculty Publications

Brain insulin resistance links the failure of energy metabolism with cognitive decline in both type 2 Diabetes Mellitus (T2D) and Alzheimer’s disease (AD), although the molecular changes preceding overt brain insulin resistance remain unexplored. Abnormal biliverdin reductase-A (BVR-A) levels were observed in both T2D and AD and were associated with insulin resistance. Here, we demonstrate that reduced BVR-A levels alter insulin signaling and mitochondrial bioenergetics in the brain. Loss of BVR-A leads to IRS1 hyper-activation but dys- regulates Akt-GSK3β complex in response to insulin, hindering the accumulation of pGSK3βS9 into the mito- chondria. This event impairs oxidative phosphorylation and fosters …

Perfluorooctanesulfonic Acid Exposure Leads To Downregulation Of 3-Hydroxy-3-Methylglutaryl-Coa Synthase 2 Expression And Upregulation Of Markers Associated With Intestinal Carcinogenesis In Mouse Intestinal Tissues, Josiane Weber Tessmann, Pan Deng, Jerika Durham, Chang Li, Moumita Banerjee, Qingding Wang, Ryan A. Goettl, Daheng He, Chi Wang, Eun Y. Lee, B. Mark Evers, Bernhard Hennig, Yekaterina Y. Zaytseva

Markey Cancer Center Faculty Publications

Perfluorooctanesulfonic acid (PFOS) is a widely recognized environment pollutant known for its high bio- accumulation potential and a long elimination half-life. Several studies have shown that PFOS can alter multiple biological pathways and negatively affect human health. Considering the direct exposure to the gastrointestinal (GI) tract to environmental pollutants, PFOS can potentially disrupt intestinal homeostasis. However, there is limited knowledge about the effect of PFOS exposure on normal intestinal tissues, and its contribution to GI- associated diseases remains to be determined. In this study, we examined the effect of PFOS exposure on the gene expression profile of intestinal tissues of …

Interactions Between Multiple Stressors, Nanomaterials And A Pathogen, In Caenorhabditis Elegans, Jarad Cochran

Theses and Dissertations--Plant and Soil Sciences

Metal and metal oxide nanoparticles (NP), which have received interest for use in agriculture, show in vitro and in vivo toxicity at relatively low concentrations. Silver nanoparticles (Ag NP) and zinc oxide nanoparticles (ZnO NP) cause adverse effects in model soil organisms under environmentally relevant conditions. In most toxicity assessments of nanomaterials, model organisms are exposed to a single stressor. Though single stressor experiments are essential to understanding the fate and effects of released NP, in nature, organisms are affected by multiple stressors, including pathogens, which might exacerbate or mitigate negative effects of NP exposure. There is limited research on …