Digital Commons Network^™

Genomic Variation, Adaptive Evolution, And Invasive And Evolutionary History Of Microstegium Vimineum, Cameron William Corbett

Graduate Theses, Dissertations, and Problem Reports (ETD)

Invasive species can cause environmental and economic damage, but can offer unique opportunities to study rapid evolution and adaptation in novel environments. Microstegium vimineum (stiltgrass) is a prolific invasive grass in the eastern United States. Historical herbaria collections were used to identify patterns of invasion history and population dynamics over a spatial and temporal scale. Analyses of plastid genomes reveal a complex invasion history, including a single introduction in the southern United States linked to Japan and multiple repeated introductions in the northern United States from various source populations. Spread of introduced populations provide evidence of admixture among previously geographically …

The Effect Of Sars-Cov-2 On Bacterial Diversity And Abundance In Community Wastewater, Joshua Lambert

Graduate Theses, Dissertations, and Problem Reports (ETD)

Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) enters human respiratory cells through binding of its spike (S) protein to the ACE-2 receptor, which is highly expressed in lung cells, but is also found in over 150 other cell types encompassing major organs including GI enterocytes. SARS-CoV-2 causes gut dysbiosis in infected individuals and patients with COVID-19 and also coincides with lower alpha diversity of the individual’s gut microbiome. Certain gut microbiome-associated genera are lower in abundance in COVID-19 patients including Lachnospira, Prevetolla, Roseburia, Bifidobacterium, and Faecalibacterium while genera such as Bacteroides, Enterococcus and Proteobacteria are increased during a SARS-CoV-2 …

Machine Learning And Uass For Managing Autumn Olive (Elaeagnus Umbellata) On Reclaimed Surface Mines, Sean Michael Keane

Graduate Theses, Dissertations, and Problem Reports (ETD)

This research introduces an innovative approach for managing autumn olive (Elaeagnus umbellata) on reclaimed surface mines through the integration of machine learning algorithms and unmanned aerial systems. The proliferation of autumn olive presents significant ecological challenges on disturbed landscapes, necessitating more efficient detection and control methods. This study evaluated Random Forest classification and deep learning approaches using the U-Net architecture for identifying autumn olive across four phenological stages using high-resolution imagery. The RGB U-Net model achieved F1-scores of 0.927, 0.912, and 0.871 for autumn olive detection during peak, late, and senescence stages respectively, outperforming both multispectral and vegetation …

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

Graduate Theses, Dissertations, and Problem Reports (ETD)

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

A Multiscale Ai Framework For Forest And Agriculture Health Monitoring: Drone-Based Object Recognition And Segmentation For Automated Ecological Assessment, Sruthi Keerthi Valicharla

Graduate Theses, Dissertations, and Problem Reports (ETD)

Forest and agricultural ecosystems are increasingly at risk due to invasive species, pests, and diseases, necessitating scalable, automated, and intelligent monitoring solutions. Traditional field based forest and agriculture health assessments are limited by cost, time, and spatial coverage. This dissertation presents a multiscale deep learning framework that automates forest and agriculture health monitoring using drone imagery and computer vision techniques. The system operates across three spatial levels: forest level, tree level, and leaf level, combining object detection, segmentation, and classification models to support large scale ecological assessment.

At the forest level, high-altitude drone imagery is processed using object detection and …

Microbial And Plant Biodiversity In Appalachian Agroecosystems And Their Implications For Soil Health, Kinsey Reed Close

Graduate Theses, Dissertations, and Problem Reports (ETD)

The sustainability of agricultural landscapes depends on understanding the complex interactions between plants, soil, and microbes. In Appalachia, a region shaped by complex terrain and long histories of human and ecological interaction, small family farms produce hay, livestock, and row crops. These agroecosystems, though often treated as “artificial” by many ecologists, have the potential to support both food production and biodiversity conservation if managed with an understanding of ecological complexity. This dissertation examines how plant and microbial diversity interact with soil and management to influence nutrient cycling, soil health, and long-term resilience in Appalachian agricultural systems. A literature review revealed …

Effects Of Environmental And Anthropogenic Gradients On Fish Beta Diversity In Central Appalachian Streams, Alanna Kaylee Lowther Smith

Graduate Theses, Dissertations, and Problem Reports (ETD)

Understanding the environmental and spatial drivers of community composition is essential for conserving freshwater biodiversity. We examined how environmental gradients, land cover, and spatial structure influence fish beta diversity in wadeable streams across West Virginia, USA. We quantified total beta diversity and partitioned it into species replacement and richness difference components and used local contributions to beta diversity (LCBD) to identify compositionally unique sites. Community–environment relationships were evaluated with distance-based redundancy analysis (dbRDA), and a beta regression GLMM was used to test how elevation, slope, land cover, and stream order (factor) predicted LCBD while accounting for spatial structure (dbMEMs) and …

Examining The Role Of Microbial Communities In Soil Carbon Cycling Across Levels Of Complexity, Chansotheary Dang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Microorganisms provide the foundation for many ecosystem processes and are important drivers of carbon and nutrient cycling. The advancement of next generation sequencing has allowed researchers to lift open the lid on the ‘black box’ in microbial ecology. While previously unculturable microbes can now be characterized with the 16S rRNA gene, answering ‘who’s there?’ is only part of the challenge. Hidden inside the ‘black box’ remains the question, ‘who’s doing what?’. Recent development in trait-based methods like quantitative stable isotope probing (qSIP) equipped microbial ecologists with the tool to connect taxon-specific traits to ecosystem processes. Despite the growing body of …

Measures Of Feed Efficiency In Beef Cattle: Biological Basis And Effect On Response To Dietary Supplementation, Modoluwamu Idowu

Graduate Theses, Dissertations, and Problem Reports (ETD)

During the feedlot receiving period, newly weaned beef cattle face various stressors, including weaning, transportation, vaccination, and exposure to pathogens. Additionally, changes in diet and low dry matter intake contribute to nutrient deficiencies, heightening susceptibility to disease and performance declines. Therefore, we examined the effects of dietary supplementation with a multicomponent blend of prebiotics and probiotics on the health, immune status, metabolism, and performance of newly weaned beef steers during a 35-day receiving period. Our results showed that compared to the control group, the supplemental additive (SYNB) increased average daily gain (ADG), dry matter intake, and meal events during the …

Development And Implementation Of Occupational Therapy Group Protocols For Individuals In Recovery For Substance Use Disorder: Considering Social Determinants Of Health And Occupational Areas Of Need, Samantha Jane Windisch

Graduate Theses, Dissertations, and Problem Reports (ETD)

Substance use disorders (SUDs) are becoming a more widespread issue globally. According to the National Survey on Drug Use and Health, 19.7 million adults in the U.S. suffered from an SUD in 2017. (SAMSHA, 2018). Recurrent alcohol and/or drug use that results in significant disability, including health issues, and/or a failure to prioritize obligations like employment, school, or family life are characteristics of SUD (SAMHSA, 2022). Research suggests that healthcare providers must integrate cutting-edge and successful treatments for this population to lower the risk of overdose and relapse rates, given the swift global spread of addictive disorders. In the past, …

Long-Term Prescription Opioid Use, Cancer Stage, And Economic Burden Among Older Cancer Survivors With Non-Cancer Chronic Pain Conditions, Rudi Safarudin

Graduate Theses, Dissertations, and Problem Reports (ETD)

Opioids are commonly prescribed to treat pain conditions, which are highly prevalent among older adults (≥65 years). Recent evidence shows that opioids may have carcinogenic effects through immunosuppression and free-radical pathways, which could promote cancer growth. Two population-based studies have reported an association of opioid use with incident cancer. Many individuals with non-cancer chronic pain conditions (NCPCs) may use opioids for a long term. However, the association of long-term prescription opioid (LPO) use with cancer stage at diagnosis is still unknown. Furthermore, evidence suggests that individuals with cancer and pre-existing NCPCs may persistently use opioids, even in the absence of …

Exploring The Usage Of Acid Mine Drainage Sludge As A Soil Amendment For Reclaimed Mine Lands, Brady Watters

Graduate Theses, Dissertations, and Problem Reports (ETD)

Acid mine drainage (AMD) is a form of water pollution generated when water and oxygen come into contact with sulfide minerals, forming metal ions, sulfuric acid, and sulphates in solution. AMD is characterized by its toxic metals content and low pH, both of which are an environmental concern. The treatment of AMD separates the contaminants into a high-water content sludge. This sludge is a pure waste product under current evaluation for alternative uses as well as improvements to storage and treatment processes. This thesis focused on analyzing the potential for AMD sludge to be used in recently reclaimed lands as …

Using Extended Two-Step Floating Catchment Area To Map Children’S Level Of Access To Physical Books In West Virginia, Heather A. Maxey

Graduate Theses, Dissertations, and Problem Reports (ETD)

The state of West Virginia lacked a comprehensive, in-depth analysis of the availability of physical books across the state. Access to reading material is vital to a child’s educational development as well as lifelong learning beyond childhood. To guide policy decisions and planning for outreach which addresses reading levels and beyond, I mapped levels of access stemming from socioeconomic barriers, spatial barriers, and an integrated index of both types of barriers. To map spatial access, I utilized a modified Extended Two-Step Floating Catchment Area model, deriving techniques from Hong et al’s 2023 article addressing access for health care in WV. …

Driving After Marijuana Use Among Us College Students During The Covid-19 Pandemic, Yuni Tang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Introduction: Adolescents and college-aged adults account for a large proportion of the United States population and are susceptible to drugs, including marijuana. Since the late 1960s in the United States, numerous states have legalized marijuana for medical and recreational purposes. These recent policy changes may alter people’s attitudes and behaviors about marijuana use, particularly young adults. The expansion of state-level marijuana legalization may also increase accessibility in younger populations and increase reckless driving behavior associated with marijuana use, including driving after marijuana use. During the COVID-19 pandemic, adolescents and young adults experienced heightened stress and anxiety, which have significantly contributed …

Application Of Computational Biophysics Techniques To Characterize Cell Membrane-Associated Events, Kyle Billings

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell membranes are crowded environments which can modulate protein structure-function relationships through interaction with lipids, other proteins, carbohydrate structures and so on. This work focuses the impact of the membrane environment on two varieties of peptides: Microbial rhodopsin proteins, and cyclic peptides.

Life on Earth is dependent on the ability of plants and microbes to harness sunlight for energy production. Their ability to transform light into carbohydrates requires tailor-made machinery, and for a wealth of microorganisms, microbial rhodopsin proteins (MR) are critical for maintaining the concentration gradients used to produce the energy molecule Adenosine triphosphate (ATP). The central retinal molecule …

Understanding Visitor Use At Florida Keys National Marine Sanctuary, Melissa Maria Hurtado Alvarez

Graduate Theses, Dissertations, and Problem Reports (ETD)

Effective management and monitoring of visitor recreational use is fundamental in marine protected areas. It is common to hear that tourism and outdoor recreation are often qualified as double-edged activities, making valuable socioeconomic contributions but also causing degradation of the environment. The convergence of social and natural resource research and practices can help managers to create better policies that will maximize human benefits from, and minimize human pressures on, ocean and coastal environments. For this study online surveys were sent via Qualtrics to email addresses obtained from the state of Florida during the summer of 2020. The first paper assessed …

Environmental Controls On The Terrestrial Water Cycle In Forested Mountain Ecosystems., Luis Andrés Guillén

Graduate Theses, Dissertations, and Problem Reports (ETD)

Water is a key resource to natural ecosystems and human societies alike, and the water cycle is fundamentally linked to the climate and the characteristics of catchments. However, the challenges posed by environmental change makes it imperative to understand how the water cycle is affected by biotic and abiotic factors, in particular, in areas that are crucial sources of water like forested headwater catchments. Therefore, this doctoral dissertation aims to advance the knowledge on the dynamics between climate, vegetation and landscape that determine the water balance of forested mountain ecosystems. This document presents five chapters, an introductory chapter, three standalone …

Increased Dementia Mortality In West Virginia Counties With Mountaintop Removal Mining?, A. K. Salm, Michael J. Benson

Faculty & Staff Scholarship

(MTM), a practice that has been ongoing in some counties of West Virginia (WV) USA since the 1970s. PM inhalation has been linked to central nervous system pathophysiology, including cognitive decline and dementia. Here we compared county dementia mortality statistics in MTM vs. non-MTM WV counties over a period spanning 2001–2015. We found significantly elevated age-adjusted vascular or unspecified dementia mortality/100,000 population in WV MTM counties where, after adjusting for socioeconomic variables, dementia mortality was 15.60 (±3.14 Standard Error of the Mean (S.E.M.)) times higher than that of non-MTM counties. Further analyses with satellite imaging data revealed a highly significant …

Time-Activity Budgets Of Stiff-Tailed Ducks In Puerto Rico, Nickolas S. Goodman, Jack C. Eitniear, James T. Anderson

Faculty & Staff Scholarship

Habitat loss and degradation have contributed to declining populations of stiff-tailed ducks including the migratory northern ruddy duck (Oxyura jamaicensis rubida), and non-migratory masked duck (Nomonyx dominicus) and West Indian ruddy duck (Oxyura j. jamaicensis). Studies collecting time-activity budgets on waterfowl can provide important insight into habitat use, behavior, and niche partitioning. Even though the northern ruddy duck and West Indian ruddy duck are recognized as the same species, we treated them separately to appraise possible ecological differences. We recorded 24-h time-activity budgets for masked ducks (n = 142), northern ruddy ducks ( …

Contextual Factors Associated With County-Level Suicide Rates In The United States, 1999 To 2016, Danielle L. Steelsmith, Cynthia A. Fontanella, John V. Campo, Jefferey A. Bridge, Keith L. Warren, Elisabeth D. Root

Faculty & Staff Scholarship

Importance Understanding geographic and community-level factors associated with suicide can inform targeted suicide prevention efforts.

Objectives To estimate suicide rates and trajectories, assess associated county-level contextual factors, and explore variation across the rural-urban continuum.

Design, Setting, and Participants This cross-sectional study included all individuals aged 25 to 64 years who died by suicide from January 1, 1999, to December 31, 2016, in the United States. Spatial analysis was used to map excess risk of suicide, and longitudinal random-effects models using negative binomial regression tested associations of contextual variables with suicide rates as well as interactions among county-level contextual variables. Data …

Soil And Tree Nutrient Status Of High Elevation Mixed Red Spruce (Picea Rubens Sarg.) And Broadleaf Deciduous Forests, Phillip M. Crim, Louis M. Mcdonald, Jonathan R. Cumming

Faculty & Staff Scholarship

Abstract: Anthropogenic and industrial emissions have resulted in historically high levels of acidic deposition into central Appalachian forests. Despite the reduction in acidic inputs due to legislation curbing industrial emissions in the United States, continued N deposition may impact forest ecosystems. Soil and foliar samples were collected from four high elevation red spruce sites along a modeled gradient of historic N deposition. The three most abundant tree species at all sites, Acer rubrum L., Betula alleghaniensis Britt., and Picea rubens Sarg., were sampled. Bulk soil beneath the canopies of individual trees were collected from the top 15-cm and separated into …

Compound-Specific Isotope Analysis Of Amino Acids In Biological Tissues: Applications In Forensic Entomology, Food Authentication And Soft-Biometrics In Humans, Mayara Patricia Viana De Matos

Graduate Theses, Dissertations, and Problem Reports (ETD)

In this work we demonstrate the power of compound-specific isotope analysis (CSIA) to analyze proteinaceous biological materials in three distinct forensic applications, including: 1) linking necrophagous blow flies in different life stages to their primary carrion diet; 2) identifying the harvesting area of oysters for food authentication purposes; and 3) the ability to predict biometric traits about humans from their hair.

In the first application, we measured the amino-acid-level fractionation that occurs at each major life stage of Calliphora vicina (Robineau-Desvoidy) (Diptera: Calliphoridae) blow flies. Adult blow flies oviposited on raw pork muscle, beef muscle, or chicken liver. Larvae, pupae …

Comparing Stakeholder Attitudes Toward White-Tailed Deer And Rare Plant Management In Canaan Valley, West Virginia, Kelley L. Flaherty, Philip J. Turk, James T. Anderson

Faculty & Staff Scholarship

Canaan Valley, West Virginia, USA provides habitat for many plants considered rare in West Virginia. The local white-tailed deer (Odocoileus virginianus Zimm.) are a popular attraction for visitors as well as resident and nonresident hunters. However, concerns exist over the impact of white-tailed deer herbivory on rare plant communities in the wetlands. We evaluated stakeholder attitudes regarding white-tailed deer management and rare plant conservation by mailing surveys to property owners in Canaan Valley and Tucker County, WV, and providing surveys to visitors at Canaan Valley State Park and National Wildlife Refuge. Individuals that had incurred crop damage were …

Historic Log Buildings As Archives Of Past Forest Ecology, Kristen K. De Graauw

Graduate Theses, Dissertations, and Problem Reports (ETD)

This dissertation is composed of three separate but related manuscripts with the common theme of using historic log buildings from the central Appalachian Mountain region of eastern North America as ecological archives. In Chapter 1, I explore the biases, limitations, and ecological applications of tree-ring data from historic log buildings. European immigrants selected trees from a forested stand based on species, log sizes, and construction locations. Despite this selection bias, ecological information can be gleaned from historic log buildings, which offer a complementary record of past forest ecology and represent a site type that is not often associated with old-growth …

Estimating Taxon-Specific Population Dynamics In Diverse Microbial Communities, Benjamin J. Koch, Theresa A. Mchugh, Michaela Hayer, Egbert Schwartz, Steven J. Blazewicz, Paul Dijkstra, Natasja Van Gestel, Jane C. Marks, Rebecca L. Mau, Ember M. Morrissey, Jennifer Pett-Ridge, Bruce A. Hungate

Faculty & Staff Scholarship

Understanding how population-level dynamics contribute to ecosystem-level processes is a primary focus of ecological research and has led to important breakthroughs in the ecology of macroscopic organisms. However, the inability to measure population-specific rates, such as growth, for microbial taxa within natural assemblages has limited ecologists’ understanding of how microbial populations interact to regulate ecosystem processes. Here, we use isotope incorporation within DNA molecules to model taxon- specific population growth in the presence of 18O-labeled water. By applying this model to phylogenetic marker sequencing data collected from stable-isotope probing studies, we estimate rates of growth, mortal- ity, and turnover for …

Differentiating Human Populations Based On K-Mer Classification Of Hand Bacteria, Thrisha Doppala

Graduate Theses, Dissertations, and Problem Reports (ETD)

Bacterial communities found in and on the human body are not only used in studying human health conditions but are also effective in differentiating individuals due to their distinct profiles. Human palm regions harbor relatively more diverse bacterial communities and are indicative of population groups, life styles, geographic locations, age groups and health conditions. Sequences extracted from hypervariable region V3 of the 16S rRNA bacterial gene of hand bacterial samples from 9 different population groups were classified into Operational Taxonomic Units (OTU) with GreenGenes reference taxonomy using RDP (Ribosomal Database Project) classifier. Frequencies of identified OTUs were used to study …

Examination And Characterization Of Brook Trout Ecology Before And After A Broad Scale Disturbance Event In Headwater Streams Of West Virginia, Usa, Ross Gilbert Andrew

Graduate Theses, Dissertations, and Problem Reports (ETD)

No abstract provided.

Towards A Better Understanding Of Paleoindian Native American Settlement In Southern Ohio: A Multi-Scalar Approach, Matthew P Purtill

Graduate Theses, Dissertations, and Problem Reports (ETD)

No abstract provided.

Explanatory And Causality Analysis In Software Engineering, Yasser Ali Alshehri

Graduate Theses, Dissertations, and Problem Reports (ETD)

Software fault proneness and software development efforts are two key areas of software engineering. Improving them will significantly reduce the cost and promote good planning and practice in developing and managing software projects. Traditionally, studies of software fault proneness and software development efforts were focused on analysis and prediction, which can help to answer questions like `when’ and `where’. The focus of this dissertation is on explanatory and causality studies that address questions like `why’ and `how’.

First, we applied a case-control study to explain software fault proneness. We found that Bugfixes (Prerelease bugs), Developers, Code Churn, and Age of …

Quantitative Acoustic Differentiation Of Cryptic Species Illustrated With King And Clapper Rails, Lydia L. Stiffler, Katie M. Schroeder, James T. Anderson, Susan B. Mcrae, Todd E. Katzner

Faculty & Staff Scholarship

Reliable species identification is vital for survey and monitoring programs. Recently, the development of digital technology for recording and analyzing vocalizations has assisted in acoustic surveying for cryptic, rare, or elusive species. However, the quan- titative tools that exist for species differentiation are still being refined. Using vocali- zations recorded in the course of ecological studies of a King Rail (Rallus elegans) and a Clapper Rail (Rallus crepitans) population, we assessed the accuracy and effective- ness of three parametric (logistic regression, discriminant function analysis, quadratic discriminant function analysis) and six nonparametric (support vector machine, CART, Random Forest, k-nearest neighbor, weighted …