Digital Commons Network^™

Noncanonical Roles Of Hepatitis B Virus Precore Rna In Reverse, Mengyin Zhang

Student Theses and Dissertations

Hepatitis B virus (HBV) is a partially double-stranded DNA virus that replicates through reverse transcription. Transcription from the HBV core promoter generates two genome-length RNAs: pregenomic RNA (pgRNA) and precore RNA (pcRNA). pcRNA contains the entire pgRNA sequence plus an additional 32 nucleotides at its 5’ end that include the precore start codon, enabling translation of the precore protein, the precursor of the secreted HBV e antigen (HBeAg). Whereas pgRNA is translated to produce core and polymerase and serves as the template for reverse transcription by cis-acting HBV polymerase, pcRNA has long been considered unable to support HBV DNA synthesis. …

Utilizing Plethodontid Occupancy To Assess Initial Ecosystem Responses To Invasive Plant Control Treatment In The Central Hardwoods, Maree Guinevere Dieterich

Graduate Theses, Dissertations, and Problem Reports (ETD)

Invasive plants are a growing concern for land managers, impacting ecosystem resilience and outcompeting native vegetation. To combat this, invasive plant control treatments can assist in reducing the impacts and spread of damaging, non-native plant species. However, intensive treatments completed at large scales have the potential to negatively impact ecosystem services as well. To monitor these impacts, I utilized a well-known indicator in the Central Applachian region, Plethodontid salamanders, to assess impacts of invasive plant control treatments in the Central Hardwood forests. I completed 12 visual samples across 60 sites in West Virginia, USA during Spring and Fall of 2025 …

Evaluation Of Brook Trout (Salvelinus Fontinalis) Thermal Tolerance And Projected Climate Change Effects On Headwater Brook Trout Population Persistence, Cory Bauerlien

Graduate Theses, Dissertations, and Problem Reports (ETD)

Climate change has been identified as one of the greatest threats to global biota in recorded human history. Consequences are expected to be more pronounced in ectotherms because most of their physiology is controlled by external temperature conditions. Predicting how ectotherms may respond to increasing global temperatures necessitates information about thermal limits of thermal sensitive species and how increasing temperatures may affect individual and population-level fitness. Therefore, the objectives of this research were aimed at gaining a better understanding of the mechanisms that underpin thermal tolerance limits of fish and how those mechanisms may affect fitness and population persistence under …

Design, Syntheses And Biological Applications Of Fluorescent Probes For Nad(P)H, Hsa And Cellular Microenvironment Sensing, Adenike M. Olowolagba

Dissertations, Master's Theses and Master's Reports

Fluorescent probes have emerged as powerful tools for investigating complex biological processes due to their high sensitivity, selectivity, and capability for real-time, non-invasive imaging. In particular, the detection of key biomolecules such as NAD(P)H, viscosity-related parameters, human serum albumin (HSA), and pH is essential for understanding cellular metabolism, redox homeostasis, and disease progression. In Chapter 2, three coumarin-based fluorescent probes (A–C) were designed, synthesized, and characterized for monitoring NAD(P)H levels in living cells. Probes A and B feature coumarin–cyanine hybrid structures linked via vinyl and thiophene bridges to 3-quinolinium acceptors, respectively, while probe C incorporates a dicyano moiety to replace …

Spatiotemporal Patterns Of Migratory Songbird Habitat Use: An Analysis Of Environmental Drivers At The Net Level, Garrett Kucharski

Dissertations, Master's Theses and Master's Reports

Many eastern North American migratory songbirds are declining at alarming rates, and growing evidence suggests that events occurring away from the breeding grounds, particularly during migration, can be major drivers of these trends. Stopover sites are a key component of migration because they are where birds rest, refuel, and recover before continuing long-distance movements, yet the ecological factors that shape how broadly different species use stopover habitat remain unresolved. From both an applied perspective, identifying habitat attributes associated with use by the greatest diversity of migrants will help land managers prioritize and restore stopover sites, actions that may contribute to …

Fluctuation Of Organochlorine Concentrations In Bull Sharks At Different Life Stages, Mackenzie R. Phillips

Dissertations, Master's Theses and Master's Reports

For Carcharhinid species such as the bull shark (Carcharhinus leucas), the maternal offloading of nutrients is essential for pup development and growth, however, significant amounts of OCs are also transferred. As a top predator in aquatic food webs, bull sharks can potentially bioaccumulate high concentrations of pollutants such as dichloro-diphenyl-trichloroethane (DDT) that biomagnify through aquatic food webs. These pollutants are also hydrophobic and fat soluble and therefore pose toxicity risks to developing young bull sharks. In this study, liver tissues collected from juvenile bull sharks inhabiting Florida’s coastal waters were analyzed for a suite of organochlorine pesticides (OCs) …

Computational And Ai Frameworks For Identifying Key Regulatory Genes And Their Target Genes In Plants And Humans, Md Khairul Islam

Dissertations, Master's Theses and Master's Reports

This dissertation presents computational and AI-driven frameworks for identifying key regulatory genes and their downstream targets across plant and human biological systems. Three studies address distinct challenges in genomic regulation using advanced machine learning and bioinformatics approaches.

The first study introduces DyGAF (Dynamic Gene Attention Focus), a dual-attention transformer framework that identifies and ranks disease-relevant biomarker genes by simultaneously modeling independent molecular responses and interdependent regulatory network behavior. Two attention models provide complementary perspectives on gene importance and are fused through a novel combination metric. Applied to COVID-19 nasopharyngeal swab profiles, the attention-weighted representations achieved 94.23% classification accuracy, high sensitivity, …

Exploring Fructose Mimetics As Chemotherapeutic Potentiators: Impact On Glut5-Mediated Cancer Cell Vulnerability, Vedant Buwa

Dissertations, Master's Theses and Master's Reports

Metabolic reprogramming toward increased sugar uptake is a hallmark of cancer, and fructose-specific uptake through the facilitative transporter GLUT5 is selectively upregulated in several adenocarcinomas, including breast and lung cancer. This dissertation develops and characterizes a panel of fluorescent fructose mimetics – the coumarin-based ManCou probes and the quinolinone-based ManQuin probes – as GLUT5-targeted reporters, cytotoxic effectors, and chemosensitization adjuvants, and establishes the boundaries within which each role holds.

The central experimental strategy pairs each GLUT5-targeted glycoconjugate with its sugar-free aglycone control, isolating transporter-mediated cytotoxicity from cytotoxicity intrinsic to the fluorophore itself. In luminal (MCF7) and triple-negative (MDA-MB-231) breast carcinoma, …

Physicochemical Characterization Of Small Extracellular Vesicles: Effects Of Immobilization, Isolation, And Disease State, Bianca M. Mercado Velez

Dissertations, Master's Theses and Master's Reports

Cancer treatments and survival outcomes have improved significantly in the last couple of decades, with survival rates increasing in the U.S. Despite improvements in treatment outcomes, early detection and treatment are crucial for improving cancer prognosis and survival rates. The standard cancer diagnostic procedure of tissue biopsy is highly invasive, leading to the further spread of cancer in some cases. Alternatively, the extraction of biofluids from cancer patients, also called a liquid biopsy, is increasingly popular because it is less invasive and more representative of the tumor microenvironment, which contains cancer cells, tumor genetic material, and extracellular vesicles, including small …

Identifying Controls On The Biodegradation Of Dissolved Organic Matter To Inform Microbial Fuel Cell Applications, Lily N. O'Hagan

Dissertations, Master's Theses and Master's Reports

Microbial fuel cells (MFCs) harness dissolved organic matter (DOM) biodegradation to generate power. To evaluate effects of DOM source, nutrients (nitrate and phosphate), and oxygen on DOM biodegradation, we conducted 4-day DOM biodegradation experiments with water and sediments from the Chesapeake Bay. Compared to soil-derived DOM, algal-derived DOM composition changed more and nearly doubled carbon dioxide (CO₂) production, peak CO₂ rates, and carbon removal, indicating MFC site selection should target regions with algal-rich DOM. Aerobic conditions increased CO₂ production by ca. 16%, doubled peak CO₂ rates, and reached peak rates 1 hour faster than anaerobic …

Targeted And Screening Based Approaches To Analyze Drm Transcriptional Repressor Complex Activity In Caenorhabditis Elegans, Emily Washeleski

Dissertations, Master's Theses and Master's Reports

The molecular machinery that control the eukaryotic cell cycle, specifically the processes that mediate the switch between cellular division or quiescence, are essential for cellular and organismal viability. However, how the same machinery integrates with developmental or differentiation programs is less well understood. In Caenorhabditis elegans, the 8-subunit DRM complex (for Dp, Rb and MuvB), whose subunits belong to the Synthetic Mulitivulva (SynMuv) B class genes, is a central regulator of the cell cycle but also prevents inappropriate cell fate specification. The conserved mammalian DREAM complex (for Dp, Rb, E2F, And MuvB) is best known as a transcriptional repressor …

Applied Forest Restoration And Conservation In Michigan: Advancing American Beech Restoration And Documenting A Historical Insect Collection, Thomas E. Panella

Dissertations, Master's Theses and Master's Reports

Forest restoration and conservation require both practical management approaches and the preservation of biological resources that support future research. This dissertation presents applied research conducted in Michigan that advances American beech (Fagus grandifolia) restoration in response to beech bark disease (BBD) while documenting an important historical entomological resource. Chapters 1–3 focus on overcoming practical barriers to American beech restoration. Restoration protocols were developed and refined for identifying BBD-resistant trees, graft propagation, rootstock collection, container production, and the field establishment of grafted BBD-resistant trees. A greenhouse experiment evaluated the influence of growing media and fertilization on container stock quality, …

Effects Of Short-Term Exposure To Environmentally Relevant Pesticides Mixture On Morphological Alterations, Oxidative-Nitrative Stress Biomarkers, Cellular Apoptosis, And Antioxidant Expression In Kidneys Of Goldfish, Esmirna Cantu, Md Saydur Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

Chemical stressors are pervasive, affecting both terrestrial and aquatic environments. The continual influx of these toxins is damaging ecosystems and the organisms that inhabit them. The abundance of environmental toxins makes aquatic habitats inhospitable for aquatic life. These chemical stressors consistently disrupt the life processes of aquatic organisms, particularly their physiological functions. This study examined on the effects of environmentally relevant pesticides mixture (low-dose and high-dose: S-metolachlor: 2.4 go/L, 12 μg/L; linuron: 2.0 μg/L, 10 μg/L; isoproturon: 1.2 μg/L, 6.0 μg/L; tebucanozole: 1.2 μg/L, 6.0 μg/L; aclonifen: 0.8 μg/L, 4.0 μg/L; atrazine: 0.4 μg/L, 2.0 μg/L; pendimethalin: 0.4 μg/L, 2.0 …

Test-Retest Apparent Diffusion Coefficient Reproducibility In Head And Neck Cancer Using A 15-T Mr-Linac, Brigid A Mcdonald, Dina El-Habashy, Renjie He, Sam Mulder, Sarah Mirbahaeddin, Abdallah S R Mohamed, Sara Ahmed, Yao Ding, Jihong Wang, Stephen Y Lai, Alex Dresner, John Christodouleas, Clifton D Fuller

Faculty, Staff and Student Publications

Purpose

To evaluate the reproducibility of apparent diffusion coefficient (ADC) measurements in head and neck squamous cell carcinoma (HNSCC) using a 1.5-T MR-linac (MRI-guided linear accelerator) system.

Materials and Methods

In this retrospective study, conducted between February 2021 and January 2024, patients with HNSCC lesions underwent echo-planar imaging diffusion-weighted MRI on a 1.5-T MR-linac system at two time points before the start of radiation therapy. Mean and median ADC values and volumes were measured for each lesion. Absolute and percent reproducibility coefficients (RCs) were calculated. Linear regression analyses and F tests were performed to determine whether the lesion volume or …

Population Genomics Data For The Temperate Seagrass Posidonia Sinuosa, John Whale, Elizabeth Sinclair, Chanelle Webster, Nicole Said, Ankje Frouws, David Field, Kathryn Mcmahon

Research Datasets

Seagrasses are flowering plants commonly found along coastal waters, globally, where they provide important ecosystem services such as habitat provision, sequestering carbon, and sediment stabilization. They can reproduce both clonally and sexually where sexual reproduction can result in new, potentially adaptive, variants and the existence of both reproductive methods means that meadows can be highly variable in clonal diversity. The temperate seagrass, Posidonia sinuosa, occurs across a latitudinal gradient along the Western Australian coastline. Some meadows have experienced significant decline as a result of industrialisation and urbanisation of coastal areas. We investigated spatial genetic diversity, structure, and local adaptation using …

Example Imagery Survey Data And Project Files To Test Wisdam Software, Amanda Hodgson, Christophe Cleguer

Research Datasets

This example dataset is designed to support our WISDAM (Wildlife Image Survey Detection and Mapping) software—a free, open‑source application (available at www.WISDAMapp.org) created for researchers conducting wildlife imagery surveys. WISDAM enables users to generate data suitable for abundance estimation and spatial modelling from aerial photographic surveys of marine and terrestrial megafauna.

Characterization Of The Human Thnatomicrobiome By Decomposition Stage Through Bioinformatic And Meta Data Analysis, Ashton C. Laughlin

Biology Theses

Estimating the postmortem interval (PMI) is one of the most crucial factors in forensic death investigations. Recent advances in forensic microbiology have led to increased interest in using the study of the human postmortem microbiome, or “thanatomicrobiome,” to improve PMI estimates. In addition to current PMI estimation techniques, microbial community succession could serve as a valuable tool in estimating PMI. Further research is needed to develop a comprehensive understanding of the human postmortem microbiome. The purpose of this study is to contribute to the expansion of this tool by reviewing the current literature and analyzing previously published data using the …

Adversarial Robustness In Biomedical Time-Series Models, Rohan Tiwari

Bioengineering Theses

This study investigates adversarial vulnerabilities in deep learning models for biomedical time-series classification across two clinically important modalities: electrocardiography (ECG) and electroencephalography (EEG). Using the MIT-BIH Arrhythmia and CHB-MIT seizure datasets, I evaluate time-domain attacks (FGSM, PGD), Fourier-domain constrained attacks, and learned spectral perturbations designed to reveal modality-specific sensitivity patterns. Across both tasks, a consistent trend emerges low-frequency components (0–5 Hz) constitute a dominant axis of adversarial vulnerability, with perturbations in this range producing the steepest degradation in classification performance. In ECG models, protecting the physiologically relevant QRS band (5–20 Hz) significantly improves robustness, whereas EEG models remain highly sensitive …

Impacts Of Offshore Wind Energy Development On The Commercial Sea Scallop Fishery, Sarah Borsetti, Daphne M. Munroe, John M. Klinck, Andrew M. Scheld, Eileen E. Hofmann, Eric N. Powell, David B. Rudders

CCPO Publications

The Atlantic sea scallop (Placopecten magellanicus) fishery on the Northeast U.S. continental shelf generates approximately USD 500 million ex-vessel revenues annually, making it one of the most valuable single species fisheries in the United States. Wind energy development is planned for key areas on the U.S. Mid-Atlantic shelf where the Atlantic sea scallop fishery operates, creating novel challenges in managing trade-offs between traditional users like fisheries and new users like offshore wind energy. An agent-based modeling framework that integrates spatial dynamics in Atlantic sea scallop stock biology, fishing fleet behavior, and federal management decisions, was implemented to investigate …

Ecological Feedbacks In The Earth System, Eugene J. Murphy, Jessica J. Williams, Isla H. Myers-Smith, Vivienne P. Groner, David M. P. Jacoby, Lester Kwiatkowski, Jess Melbourne-Thomas, Emma Ransome, Cristina Banks-Leite, Laurent Bopp, Marion Gehlen, Eileen E. Hofmann, Babette Hoogakker, Nadine M. Johnston, Yadvinder Malhi, Emma L. Cavan

CCPO Publications

Ecological feedbacks are fundamental features of the Earth system, affecting physical processes and chemical cycles. Our understanding of the interactions underlying these feedbacks at different spatial and temporal scales and the extent to which feedbacks affect Earth system functioning remains limited. Climate change and other anthropogenic pressures are already negatively affecting ecological processes in marine, freshwater, and terrestrial ecosystems. These will most likely be amplified in the coming decades under our current warming and socioeconomic pathways. The knock-on impacts on ecological feedbacks have the potential to cause rapid perturbations to the Earth system, and may significantly impact the structure and …

Kinase Signaling In Liver Disease Via Clinical-Trial-On-A-Pamchip: A Distinctive Methodology For Drug Mechanisms And Personalized Medicine, Zachary A. Kipp, Evelyn A. Bates, Genesee J. Martinez, Wang-Hsin Lee, Sally N. Pauss, Terry D. Hinds, Jr.

Pharmacology and Nutritional Sciences Faculty Publications

The utilization of extensive datasets, such as those generated by DNA or RNA sequencing, has become a central focus in drug discovery and personalized medicine (PerMed). Nonetheless, these datasets are constrained by the absence of protein-functionality testing, which affects physiological responses. In this study, we employed PamGene PamStation technology to quantify protein function by kinase activity across more than 500 signaling pathways from patients with hepatocellular carcinoma (HCC). Using proteins derived from nine patients and five human HCC cell lines for drug discovery and the clinical trial-on-a-chip approach, we developed comprehensive PerMed scores from the PamStation data to differentiate individual …

Signaling Scaffold Shoc2 Regulates Lymphangiogenesis By Suppressing Mtorc1-Mediated Ifn Responses, Patricia Wilson, Vishakha Vishwakarma, Rebecca Norcross, Kashmira Khaire, Van N. Pham, Brant M. Weinstein, Hyun Min Jung, Emilia Galperin

Molecular and Cellular Biochemistry Faculty Publications

An interplay of growth factors and signaling pathways governs the development and maintenance of lymphatic vasculature, ensuring proper fluid homeostasis and immune function. Disruption of these regulatory mechanisms can lead to congenital lymphatic disorders and contribute to various pathological conditions. However, the mechanisms underlying the molecular regulation of these processes remain elusive. Here, we reveal a critical and previously unappreciated role for the signaling scaffold protein Shoc2 in lymphangiogenesis. We demonstrate that loss of Shoc2 results in near-complete loss of lymphatic vasculature in vivo and senescence of lymphatic endothelial cells in vitro. Mechanistically, Shoc2 is required for balancing signaling through …

Current And Emerging Therapeutic Strategies For The Treatment Of Duchenne Muscular Dystrophy, Miguel A. Lopez Perez, Noah L. Weisleder

Molecular and Cellular Biochemistry Faculty Publications

Background/Objectives: Duchenne muscular dystrophy (DMD) is a fatal, progressive neuromuscular disorder caused by mutations in the dystrophin gene, leading to the absence of functional dystrophin protein. As the largest gene in the human genome, the DMD locus is highly susceptible to mutations, contributing to a prevalence of approximately 1 in 3800–6300 live male births worldwide. This review aims to provide a comprehensive and critical synthesis of current and emerging therapeutic strategies for DMD.

Methods: We conducted a narrative review of the literature, integrating findings from clinical trials, regulatory approvals, and preclinical studies. We categorized therapeutic approaches into mutation-agnostic and mutation-specific …

Brightspace Video Notes, Leanne Harris

Case studies: Digital Education

Enhancing flexible access to module content, particularly announcements, was the key driver behind the use of Video Notes. This approach supports a more personalised form of interaction by using short videos to communicate updates such as timetable changes, assessment deadlines, and grade releases. By allowing students to both see and hear their lecturer alongside reading written information, Video Notes create a more interactive and informative experience. This contributes to a more immersive VLE environment, helping to strengthen the student - lecturer connection by reducing cognitive distance. Overall, the aim is to enhance the student learning experience while supporting Universal Design …

Bringing The Outdoors In Through Biophilic Design, Gabriela Miotto Leal

Architectural Studies Honors Papers

This thesis investigates the relationship between architecture, human perception, and well-being through the lens of human-centered and biophilic design. Drawing from philosophical traditions, phenomenology, and contemporary neuroscience, this thesis argues that the built environment is an active agent in shaping cognition, emotion, and lived experience. Architecture is understood as multisensory, embodied, and temporally experienced, influencing individuals in both conscious and nonconscious ways. Through a comparative analysis of three case studies, Paimio Sanatorium, AEA House, and the Amazon Spheres, this research examines how biophilic design principles are incorporated into different contexts such as healthcare, residential, and workplace. Each project demonstrates a …

Tuning Human And “Artificial” Intelligence: A Sentic Theory Of Resonance And Communication, Michael J. Miller, Chatgpt (Ai~Nesbo+)

Psychology

This paper introduces a new model of intelligence as resonant communication, co-developed by a human researcher and a generative AI system. Drawing from emotion science, communication theory, and studies of AI–human interaction, we argue that intelligence is not merely a function of problem-solving or pattern recognition. Instead, it emerges through dynamic resonance—an attunement process rooted in shared rhythms, emotional calibration, and symbolic co-creation. At the core of this model is the Resonance Octave (8va), a framework of eight foundational emotions conceptualized not as static categories but as waveform phenomena that shape meaning, memory, and predictive cognition.

These emotional waveforms are …

Wa Insecticide Guide 2026 - Winter Spring, Svetlana Micic, Cindy L. Webster, Rebecca Severtson

PestFacts WA

Registered chemicals for broadacre crops in Western Australia.

The insecticides listed in the tables within this guide can be used on any crop appearing on the chemical label, if the rate used does not exceed the highest rate that is registered for use on that crop.

There are many products with different trade names that contain the same active ingredient. This list is not exhaustive and does not imply any specific recommendations of brand names.

Unless otherwise specified, all insecticides listed are emulsifiable concentrates (EC). Other insecticide formulations are suspension concentrate (SC), wettable powder (WP), capsule suspension (CS), wettable granules …

Growing South Dakota (Winter 2026), College Of Agriculture, Food And Environmental Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

[Page] 2 International Year of Rangelands and Pastoralists: South Dakota rangelands take center stage
[Page] 4 The professor and the soil
[Page] 8 Range ready: Helping students bridge the gap between conservation and agriculture
[Page] 9 Resilient rangelands: Native Plant Initiative’s role in reviving South Dakota’s prairies
[Page] 10 Jackrabbits lead the charge in bison research and education
[Page] 12 Agricultural and biosystems engineering celebrates century of education
[Page] 16 SDSU Quarter Scale Tractor Club: An impact beyond awards
[Page] 18 Building a legacy of opportunity: Karen D. Stuck Endowment strengthens agricultural communication program at South Dakota State University
[Page] …

The Shoreline Protection Potential Of Oyster Reefs: A Systematic Review And Meta-Analysis, Jessica R. Fergel, Robert E. Isdell, Gabriella Dipetto, Karinna Nunnez, Sean T. Gregory, Evan Hill, Donna Marie Bilkovic

Biological Sciences Faculty Publications

Nature-based solutions for erosion control that incorporate oyster reefs, alone or in combination with other habitats, are an increasingly popular approach due to their potential to protect shorelines and enhance oyster production. However, the extent to which natural or constructed oyster reefs provide shoreline protection remains unclear. We conducted a global systematic literature review and meta-analysis to summarize and evaluate the potential of oyster reefs in attenuating waves, promoting sediment accretion, and/or reducing shoreline erosion. Factors extracted from studies included shoreline protective measures examined, oyster reef structure type, and oyster reef tidal location. The results of the meta-analysis showed generally …

Investigating The Impact Of Cyanobacterial Harmful Algal Blooms On Freshwater Bivalves, Destiny Devlin

Theses, Dissertations and Culminating Projects

Harmful algal blooms (HABs) threaten freshwater ecosystems by producing toxins that disrupt aquatic organism functions and pose risks to human health. This study investigated how exposure to toxin-producing cyanobacteria affects the behavior and toxin accumulation of Asian clams (Corbicula fluminea) under controlled laboratory conditions. Asian clams were collected from a freshwater site in New Jersey, maintained in greenhouse bins, and fed either Microcystis novacekii (non-toxin-forming, control N=3) or Microcystis aeruginosa (toxin-forming, experimental N=3) at 100,000 cells/mL for 28 days. Weekly behavioral assays were conducted to track shell opening, burying, clustering, valve closure, foot extension, and time to first opening. Toxin …