Digital Commons Network^™

Soundscapes Of Alaska's Arctic Coastal Plain: Implications For Wildlife, Maxwell Plichta

Biological Sciences

Passive acoustic monitoring is an effective tool for collecting baseline acoustic data in remote locations and for advancing our understanding of soundscapes, the sound that emanates from a landscape. Terrestrial Arctic soundscapes remain understudied. The Arctic Coastal Plain (ACP) of northern Alaska is an ecologically, culturally, and economically significant region, containing a mix of land-uses and management practices. This study leverages a spatially large (~8,000 km2), multi-year dataset of acoustic recordings and paired images collected across the ACP to investigate how natural and anthropogenic factors influence the soundscape (Chapter 2), and how acoustic metrics influence the behavior of caribou (Rangifer …

Orthogonal Comparison Of Nuclear And Mitochondrial Clonal Architectures In Hematologic Malignancies, Nehali Shah

Dissertations and Theses (Open Access)

Acute myeloid leukemia (AML) is a hematologic malignancy characterized by accumulation of mutations that disrupt hematopoietic differentiation and promote clonal expansion. Understanding how these mutations arise and evolve is essential for improving diagnosis, prognosis, and treatment stratification. Current methods are limited by either restricted genomic coverage (targeted panels) or low throughput and high cost (in single-cell whole genome sequencing, scWGS). An emerging alternative is the use of mitochondrial DNA (mtDNA) mutations as clonal markers.

This study aims to determine whether mitochondrial-derived clonal architectures correlate with nuclear-derived clonal architectures in AML, thereby evaluating mtDNA as a scalable orthogonal tool for lineage …

A Mixed Methods Study Of The Weather And Climate Science Curriculum Pilot In South Carolina K-12 Schools, 4-H, And Agricultural Education Programs, Emily B. Hood

All Dissertations

Weather and climate science topics in K-12 education are more important now than ever due to extreme weather and climate events happening worldwide. Most U.S. science teachers included climate science in their courses, but they may not have a sufficient background in the topic which can hinder their efforts, or there is no explicit curriculum for the teacher to utilize. Research indicates that there is a need for innovation in the curriculum to help prepare children to become the next generation of leaders and address complex problems, such as issues related to weather and climate science. There are a few …

Comparative Assessment Of Lower Limb Neuromusculoskeletal Activation And Joint Kinematics In Normal And Impaired Gait, Jack Ryan Schule

Theses and Dissertations

This thesis evaluates whether accessible and affordable technologies can provide clinically significant, quantifiable gait analysis comparable to traditional marker-based motion capture systems. Modern high-end systems offer excellent accuracy but remain financially and logistically inaccessible to many clinicians and researchers. To address this gap, a framework was developed using markerless pose estimation using the model, MediaPipe, inertial measurement units (IMUs) processed through an Extended Kalman Filter (EKF), and surface electromyography (sEMG) to measure joint kinematics and neuromuscular activity during gait. An experiment was performed where data was collected from participants with both normal gait and pathologies including: Osgood–Schlatter disease, Plica Band …

Taxonomy Of Endophytic Fungi Associated With Vallisneria Neotropicalis, Md. Arafat Rashid

Graduate Theses and Dissertations (2019 - present)

This study presents the first comprehensive taxonomic and ecological investigation of endophytic fungi (EF) associated with the submerged aquatic macrophyte Vallisneria neotropicalis in the southern United States. Over a 12 month period, from April 2023 to March 2024, leaf samples were collected from two distinct sites in Mobile Bay, Alabama a disturbed, brackish Causeway location and a cleaner, less impacted site at Meaher State Park. Using culture dependent methods, a total of 257 fungal endophytes were isolated from 1,200 leaf segments. All isolates belonged to the phylum Ascomycota, distributed across 3 classes, 6 orders, 10 families, and 19 taxa. The …

Twim #222: Biosensors In Bacteria, Madison Hayes, Alexis Austin, Dillon Nguyen, Angela Wilson, Rebecca Seipelt-Thiemann

School of Medical Diagnostics & Translational Sciences Publications

Podcast annotation TWiM #222: Biosensors in Bacteria from the weekly podcast series "This Week in Microbiology" (TWiM), a podcast where experts in microbiology discuss academic papers in their field in an informal way.

Twim #243: Beef And Bacillus, Sakiem Winston, Madison Wolford, Rebecca Seipelt-Thiemann, Angela Wilson

School of Medical Diagnostics & Translational Sciences Publications

Podcast annotation TWiM #243: Beef and Bacillus from the weekly podcast series "This Week in Microbiology" (TWiM), a podcast where experts in microbiology discuss academic papers in their field in an informal way.

Twim #286: Integrons And Invasion, Andrea Ayala-Lopez, Brittney Heist,, Thomas Salazar, Rebecca Seipelt-Thiemann, Mel Melendrez-Vallard, Angela Wilson

School of Medical Diagnostics & Translational Sciences Publications

Podcast annotation TWiM #286: Integrons and Invasion from the weekly podcast series "This Week in Microbiology" (TWiM), a podcast where experts in microbiology discuss academic papers in their field in an informal way.

Impact Of Polystyrene Nanoplastics On Oncogenic Signaling Pathways In Prostate Cells, Luis Alfonso Adel-Alvarez

Open Access Theses & Dissertations

Prostate cancer (PC) remains the most prevalent malignant disease among the male population worldwide, with a dramatic increase observed in the European Union from the 1980s to the 2000s. The etiology of PC is attributed to both hereditary factors and environmental pollutants. Among these, endocrine disruptors and polystyrene nanoparticles (PSNPs) interact with the prostate gland via the circulatory system, inducing intense oxidative stress. This study aims to characterize, for the first time, the pathobiological effects of PSNPs in both non-malignant (RWPE1) and malignant (22RV1) prostate cell lines. The objective was to elucidate the mechanisms by which environmental pollutants, such as …

Gpu-Based Electromagnetic Microwave Tomography For Brain Imaging And Stroke Detection, Pablo Sotelo Torres

Open Access Theses & Dissertations

Each year, an estimated 795,000 people in the U.S. suffer a stroke, with approximately 610,000 being first-time cases. Of these, 87% are ischemic strokes, while the remaining 13% are hemorrhagic. Current imaging methods, such as Computed Tomography (CT), Positron Emission Tomography (PET), and Magnetic Resonance Imaging (MRI), provide useful information into brain tissue properties; while each technique has its advantages, they remain expensive, non-portable, and often too slow for emergency bedside or in-ambulance use. Electromagnetic Microwave Tomography (EMT) offers a promising alternative: an affordable, portable, rapid, and safe method for stroke detection. By contrasting dielectric properties between healthy and affected …

The Transition Zone Hypothesis On Biodiversity Of The Indian River Lagoon System, Florida, Richard L. Turner

Ocean Engineering and Marine Sciences Faculty Publications

The Indian River Lagoon System (IRL) is regarded as having a high level of biodiversity. The level of biodiversity is often attributed in part to the 2-degree latitudinal span (251 km) of the IRL and to its position in a transitional zone between tropical and temperate biotic provinces. This hypothesis was tested for submerged aquatic vegetation (SAV) based on a recent treatise (Littler, Littler, and Hanisak, 2008). Five of seven species of seagrass are tropical, and two have either a broad or very narrow latitudinal distribution; the transition-zone hypothesis does not hold for seagrasses. Most macroalgae (131 spp.) are tropical/subtropical; …

Integrating Innovative Sensing And Ground Measurements For Forage Mass Estimation In Rye Pasture, Pedro Henrique Jota Fernandes

Department of Animal Science: Dissertations, Theses, and Student Research

The United States beef industry relies on forages to provide up to 80% of total lifetime dry matter intake, making accurate forage mass estimation essential for determining stocking rates, improving grazing efficiency, and supporting economic sustainability. Traditional methods to quantify forage mass, however, are time-consuming and labor-intensive. This thesis presents research efforts to achieve accurate forage mass estimation in cereal rye pasture by integrating novel sensing technologies.

Chapter 1 reviews the importance and evolution of forage mass estimation methods, from destructive clipping to indirect approaches based on canopy measurements. It then introduces remote sensing, from proximal tools to drone- and …

Investigation Of Changes In Exotic Bird Serum Vitamin D Levels Between Indoor And Outdoor Housing, Alexander J. Marley

Department of Animal Science: Dissertations, Theses, and Student Research

Vitamin D is a fat-soluble vitamin that is directly related to sunlight and is involved in multiple physiological processes including calcium metabolism, feather quality, and chick development. Most vertebrate species are capable of both absorption of exogenous vitamin D and internal synthesis of vitamin D, with vitamin D3 (cholecalciferol), being more accessible and bioactive in bird species. In exotic bird species, dietary requirements for vitamin D3 are largely unknown, and the ability to maintain adequate serum concentrations of vitamin D3 metabolites without direct sunlight exposure also requires evaluation. Concerns arise in situations where individuals may be housed indoors for extended …

Benthic Infaunal Responses To Shoreline Restoration, Jessica Lauren Cline

Theses and Dissertations

In the age of increasing urban coastal sprawl, natural shorelines are being replaced by hard armoring structures, which result in the loss of valuable ecosystem services. Hybrid living shorelines, areas that include limited and less intensive armoring strategies paired with the integration of plants and other natural materials, present an opportunity to marry the need for more aggressive stabilization with the continued preservation of ecosystem functions and biological communities. This project uses benthic infauna to evaluate the success of a living shoreline installation in Palm Bay, Florida. The deployment features experimental treatments of breakwaters and red mangroves to explore how …

Establishing Procedures For Primary Human Myoblast Cell Culture, Erica Duffy

Biomedical Engineering

Peripheral Artery Disease (PAD) affects an estimated 200 million people worldwide and is the leading cause of amputation in the United States. PAD is characterized by atherosclerotic narrowing of arteries, resulting in ischemia from reduced blood flow to distal tissues. Although surgical and percutaneous interventions can restore perfusion, fewer than 50% of patients experience sustained benefit, highlighting the need for alternative therapeutic strategies. One promising approach is promoting arteriogenesis, the growth and outward remodeling of pre-existing collateral vessels that improve blood flow around the occluded arteries. Arteriogenesis is regulated by regenerative, M2-polarized macrophages, making macrophage polarization a key therapeutic target. …

Hyperspectral Indicators And Characterization Of Glyphosate-Induced Stress In Common Lambsquarters (Chenopodium Album L.), Mario Andrés Soto Valencia

Graduate Theses and Dissertations

Hyperspectral sensing enables detection of herbicide stress in weeds, but practical use requires strategies for redundancy control, rating variability management, and evaluator bias mitigation. This thesis evaluates common lambsquarters (Chenopodium album) under glyphosate exposure, aiming to identify key wavelengths, construct vegetation indices, and improve injury modeling. Greenhouse experiments used dimensionality reduction methods (principal component analysis, Relief F, Bayesian discriminant analysis) to isolate 34 unique wavelengths from about 3,200 bands. Calibration data were collected 14 days after treatment (DAT) to support wavelength selection and model development, while data from 27 DAT were used for independent validation. Class comparisons across six statistically …

Biomedical Data Repositories Require Governance For Artificial Intelligence/Machine Learning Applications At Every Step, Yael Bensoussan, You Chen, Benjamin X Collins, Ashley Cordes, Barbara J Evans, Kadija S Ferryman, Samantha Hurst, Xiaoqian Jiang, Aaron Y Lee, Shannon Mcweeney, Jillian Parker, Jean-Christophe Bélisle-Pipon, Eric Rosenthal, Zhijun Yin, Joseph Yracheta, Bradley Adam Malin

Faculty, Staff and Student Publications

Objectives: The NIH's Bridge2AI Program has funded 4 "new flagship biomedical and behavioral datasets that are properly documented and ready for use with AI [artificial intelligence] or ML [machine learning] technologies" to promote the adoption of AI. This article discusses the challenges and lessons learned in data collection and governance to ensure their responsible use.

Materials and methods: We outline major steps involved in creating and using these datasets in ethically acceptable ways, including (1) data selection-what data are being selected and why, (2) increasing attention to public concerns, (3) the role of participant consent depending on data source, (4) …

Microinjection, Gene Knockdown, And Crispr-Mediated Gene Knock-In In The Hard Coral, Astrangia Poculata, Jacob F. Warner, Ryan Besemer, Alicia Schickle, Erin Borbee, Isabella V. Changsut, Koty H. Sharp, Leslie S. Babonis

Arts & Sciences Faculty Publications

Cnidarians have become valuable models for understanding many aspects of developmental biology including the evolution of body plan diversity, novel cell type specification, and regeneration. Most of our understanding of gene function during early development in cnidarians comes from a small number of experimental systems including Hydra and the sea anemone, Nematostella vectensis. Few molecular tools have been developed for use in hard corals, limiting our understanding of this diverse and ecologically important clade. Here, we report the development of a suite of tools for manipulating and analyzing gene expression during early development in the northern star coral, Astrangia poculata. …

Tracing The Journey Of Dissolved Organic Matter: From Leaf Litter Photodegradation To Microbial Processing In Tropical Streams, Samantha Nicole Sullivan

Chemistry & Biochemistry Theses & Dissertations

Dissolved organic matter (DOM) is a major reservoir of organic carbon in aquatic ecosystems and plays a central role in global carbon cycling through its transformation and remineralization to carbon dioxide (CO₂). As DOM moves from terrestrial environments into streams and rivers, its chemical composition is altered by a combination of microbial and photochemical oxidation processes that regulate both its reactivity and its persistence during transport. However, the molecular mechanisms governing these oxidative transitions, particularly in tropical ecosystems characterized by strong hydrologic seasonality and substantial inputs of plant-derived material, remain insufficiently resolved. This dissertation integrates ultrahigh-resolution mass spectrometry, optical characterization, …

Fusarium Equiseti Pathogen Of Potato In Kenya And Its Potential In Vitro Biocontrol Using Fungal Endophytes, Marie Cecile Muhorakeye, Fathiya M. Khamis, Everlyne Samita Namikoye, Komivi S. Akutse

All Peer-Reviewed Publications

Accurate pathogen diagnosis is fundamental for effective crop disease management. In Kenya, a pathogen causing significant damage in potato farms was initially misidentified as Phytophthora infestans. This study aimed to correctly identify this pathogen and explore initial control measures using a polyphasic approach. The methodology integrated morphological observation, pathogenicity testing, and molecular analysis using ITS and EF1-α gene sequencing. The results confirmed the pathogen’s identity as Fusarium equiseti, with morphological features consistent with this species and molecular sequencing showing 99.6% identity to reference strains. This is the first official report of Fusarium equiseti as a potato pathogen in Kenya. Furthermore, …

Optimizing Endothelial Cell Specific Polymersome-Based Atheroprotective Therapies, Ally C. Brawner

All Theses

Atherosclerotic cardiovascular disease is the number one cause of death in the United States and the world. Every year, billions of dollars are spent in the US alone for direct treatments of this disease, especially on prescription medicines like statins. However, these medications have been unable to curtail global mortality rates, partially because they do not target the entirety of atherosclerotic pathophysiology. A key area of this pathophysiology is that atheroprone arteries typically include pro-inflammatory endothelial cells that exhibit decreased levels of apoAI-mediated cholesterol efflux and an increased release of adhesion molecules, such as VCAM-1. The objective of my project …

Effect Of Polymer Contaminants Sourced From Coated Paper On The Performance Of The Resulting Recycled Paper, Ezekiel J. Guevarra

All Theses

The growing demand for sustainable packaging has accelerated the use of paper-based materials as alternatives to plastics. To provide barrier and functional properties, these materials are often modified with polymer coatings. While beneficial during use, such coatings can persist as contaminants during recycling, potentially disrupting fiber bonding and reducing the quality of recycled paper. This study examined the impact of extrusion-coated low-density polyethylene (LDPE) films and two aqueous dispersions (Vapor/Water-Barrier, Acrylic Film (VWAF) and Oil & Grease Barrier (OGBF)) on contaminant distribution and mechanical performance of recycled handsheets. Kraft paper coated at varying levels was repulped and formed into handsheets, …

Molecular Pathway Dysregulation In Chronic Liver Disease: Metabolic And Mechanotransductive Drivers Of Hepatic Pathophysiology, Samantha Harvat

Department of Chemical and Biomolecular Engineering: Dissertations, Theses, and Student Research

Metabolic dysfunction–associated steatotic liver disease (MASLD) represents a rapidly growing cause of chronic liver injury, yet the molecular interactions linking metabolic stress, inflammation, fibrosis, and hepatocellular carcinoma (HCC) remain incompletely defined. This thesis integrates transcriptomic analyses across multiple GEO datasets to identify coordinated metabolic, inflammatory, and mechanotransductive pathways that collectively drive disease progression.

Analysis of human liver biopsy datasets (GSE126848 and GSE89632) revealed consistent suppression of glycolysis, β-oxidation, and oxidative phosphorylation across MASLD and MASH samples, accompanied by modest compensatory TCA cycle activation. These alterations reflect impaired metabolic flexibility, mitochondrial stress, and increased ROS susceptibility. Concurrently, cytokine-network enrichment demonstrated activation …

Detecting Prescribed Fire, Haying And Grazing Events Via Remote Sensing To Create Grassland Disturbance Landcovers For The Ring-Necked Pheasant (Phasianus Colchicus), Megan Amy Baldissara

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

This dissertation developed disturbance detection models to fulfill the need for remote sensing landcover products describing grassland structure. The use of landcover products derived from remote sensing is increasing over time in pheasant (Phasianus colchicus) research. Such landcover, however, does not provide relevant pheasant structural habitat information (Chapter 1). Pheasants require tall, high-density grassland for nesting, tall grassland with medium density for brood rearing, and tall grassland for wintering. Time since disturbance can serve as a proxy for structure, as it shapes vegetation by removing biomass and resetting succession. Disturbance is easier to detect than structure with current …

An Integrated Modeling Framework To Evaluate Circularity Of The Corn–Water–Ethanol–Beef Nexus, Heydi Han

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

This dissertation examines the transition from conventional linear agricultural and food bioenergy systems toward more circular, resilient, and resource-efficient configurations. Prior research indicates that spatial and temporal variability in soil, weather, animal biological responses, and management decisions strongly influences productivity, nutrient-use efficiency, and profitability. Studies have also shown that a diversified circular system can buffer these sources of variability, improving stability and adaptive capacity. Building on these insights, the central focus of this work is to develop an integrated modeling framework to evaluate circularity within the Corn-Water-Ethanol-Beef (CWEB) nexus and explore how climate variability and management choices shape system-wide performance. …

Avaren-Fc's Effects On Lymphoma Cells., Jacob Hahn

Electronic Theses and Dissertations

This thesis investigates the therapeutic potential of Avaren-Fc (AvFc), a novel lectin fusion protein that integrates the Fc region of human IgG1 with the engineered lectin Avaren, specifically targeting lymphoma. The study delineates the in vitro binding capabilities of Avaren-Fc with a human B-cell lymphoma cell line, a canine B-cell lymphoma cell line, healthy canine peripheral blood mononuclear cells (PBMCs), and healthy human PBMCs. AvFc was shown to exhibit significant binding to human lymphoma cells. Furthermore, the direct cytotoxicity of Avaren-Fc against canine lymphoma cells, canine lymphoma cells and healthy canine PBMCs was assessed. It was found that there is …

Identifying Correlates Of Protection Of A Pneumonic Plague Vaccine., Caleb Samuel Whitley

Electronic Theses and Dissertations

Pneumonic plague is caused by inhalation of the bacterial pathogen Yersinia pestis. The immune response during Pneumonic plague occurs in two phases; an initial asymptomatic phase followed by a highly inflammatory and destructive phase resulting in 100% mortality if left untreated. The rapid onset of severe disease following the asymptomatic phase makes it difficult to administer antibiotics in time to prevent lethal outcomes. Therefore, the development of an effective vaccine is likely needed to combat pneumonic plague in areas of the world where Y. pestis remains endemic. One candidate subunit vaccine is protective in mice, a natural host for …

Sensory And Motor Tectothalamic Circuits: Two Sides Of The Same Coin., Nazratan Naeem

Electronic Theses and Dissertations

Integration of sensorimotor information in the visual system has always been an intriguing topic to scientists, yet the subcortical sensory and motor circuits that are essential components of this process have remained elusive. In these studies, we used a blend of classical and contemporary techniques such as viral tracing, immunohistochemistry, optogenetics in-vitro whole cell electrophysiology, and electron microscopy in mice to characterize sensory and motor circuits of the superior colliculus (SC), a conserved visuomotor structure with connections with a wide variety of brain structures, including the thalamus. We focused on two SC cell types: visually responsive widefield vertical (WFV) cells …

Tumor Infiltrating Lymphocytes: From Discovery To Clinical Application., Lewis Clayton Chew

Electronic Theses and Dissertations

This thesis explores the evolution of TIL therapy from its discovery to clinical application, focusing on its use in treating metastatic cancer. Adoptive cell therapy (ACT), particularly TIL therapy, has emerged as a promising alternative to traditional treatments like chemotherapy. This review article traces the historical development of TILs, highlighting key experiments and clinical trials that have shaped its understanding and application as a therapeutic strategy for patients with metastatic and difficult to treat cancers including melanoma. Importantly, this article highlights recent advancements, including the FDA approval of Lifileucel, and explores emerging strategies to enhance therapeutic efficacy of TILs through …

Integrating Manager Perspectives Into The Evaluation Of Wetland Revegetation Strategies, Loren F. Taylor

All Graduate Theses and Dissertations, Fall 2023 to Present

Ecological restoration is the process of assisting the recovery of an ecosystem that has been degraded and is dependent on complex and context-specific decisions. The decision-making process influencing restoration is rarely examined alongside ecological processes. There is a need for research that incorporates the social, economic, institutional, and logistical considerations that shape real-world practices, as well as ecological processes. Decisions made by restoration practitioners and land managers (hereon “manager”) are challenged by the lack of information shared regarding the practical constraints (e.g., cost, labor, specialized equipment) they face. Revegetation, particularly in wetlands, poses challenges due to site conditions and degradation …