Digital Commons Network^™

The Development Of Tools For The Production Of Fusarium Oxysporum Race 4 Resistant Cotton Varieties, Thomas Rylands

All Theses

Fusarium oxysporum race 4 (FOV4) is a fungal pathogen that infects cotton (Gossypium spp.) plants, resulting in fusarium wilt (FW) disease that causes significant wilting, yield loss, and eventually death. Since cotton is such an important crop globally, with tens of millions of bales of fiber produced and sold worldwide each year, it is critical to develop effective strategies to combat this pathogen. This research aims to achieve that goal through two projects: (i) develop an efficient co-culture system to test fungal treatments in vitro, and (ii) develop a computer vision pipeline to more accurately assess plant resistance …

Evaluation Of Ocean Lidar Enhancement Through Miniaturization And Gated Pmt-Based Range Extension, Chandler Austin Slater

OES Theses and Dissertations

Oceanographic lidar systems remotely characterize the vertical structure of the upper ocean by recording the light backscattered from a laser pulse as it propagates through the water column. Historically these systems have been constrained by limited detection ranges, often capturing only a portion of the illuminated water column, typically fading to noise around the 10% isolume. A primary constraint has been the limited dynamic range of digitizers, which inhibits the ability to resolve both intense near-field and faint far-field backscatter signals within a single acquisition. To address this, we developed a novel optical lidar system incorporating gated photomultiplier tubes (PMTs) …

Evaluating Fall And Spring Planted Cover Crops For Integrated Management Of Herbicide Resistant Palmer Amaranth And Effect On Soil Health, Vipin Kumar

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

Herbicide-resistant Palmer amaranth (Amaranthus palmeri S. Watson) pose a severe threat to agronomic crop productivity in the United States, including corn and soybean production in Nebraska. Therefore, there is an urgent need for diversified and sustainable management approaches. Integrating cover crops (CCs) with herbicide programs represents a promising strategy to achieve Palmer amaranth suppression, sustain crop yields, and contribute to long-term soil health in irrigated corn–soybean production systems in Nebraska.

A meta-analysis of 41 studies and 595 paired observations demonstrated that CCs reduced Amaranthus spp. density and biomass by 37–59% depending on the growing season, with grasses and mixtures …

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. …

Post-Fire Soil Health Assessment Of The Grasslands And Woodlands In The Semi-Arid Nebraska Sandhills, Stephanie M. Lugo

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Grasslands in the Nebraska Sandhills are shaped by natural wildfires, which help maintain the structure and function of native grasslands. In recent decades, afforestation with ponderosa pine and eastern redcedar has introduced new woodlands that altered the region’s fire dynamics and raised important questions about the effects of wildfire on different vegetation types. As wildfires become more frequent, understanding their impacts on soil health in grasslands and woodlands becomes increasingly important. This study examines the short-term effects of the 2022 Bovee Fire on physical, chemical, and biological soil properties in native grasslands and ponderosa pine and eastern redcedar afforested woodlands. …

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 …

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 …

Impacts Of Halophila Stipulacea Invasion On Organic Matter Dynamics In Thalassia Testudinum Dominated Seagrass Meadows, Puerto Rico, Jonathan D. Herald

Master's Theses

Halophila stipulacea (Forsskål & Niebuhr) is a tropical seagrass native to the Red Sea, Persian Gulf, and Indian Ocean. In 2002, invasive populations of H. stipulacea were identified in the Caribbean Sea where it now forms large meadows, displaces native seagrasses, alters invertebrate and fish communities, and potentially affects organic matter dynamics in invaded meadows. This study investigated differences in organic matter dynamics between meadows of H. stipulacea and native Thalassia testudinum within the Jobos Bay National Estuarine Research Reserve (JBNERR) on the southern coast of Puerto Rico. From March 2023-March 2024, sampling was conducted across four sites to investigate …

Effects Of Urbanization On The Population Genetics And Morphology Of The White-Footed Mouse (Peromyscus Leucopus) Across An Urban–Rural Gradient, Sydney A. Morton

Master's Theses

Urbanization alters landscapes in ways that can reshape wildlife populations by changing habitat connectivity, resource availability, and selective pressures. To investigate how urbanization influences both genetic differentiation and morphology in small mammals, I examined Peromyscus leucopus (PELE) across an urban–rural gradient in northern Georgia. Using RADseq SNP data from PELE individuals across 13 sites, I quantified pairwise genetic differentiation (F_ST) and tested how various environmental variables, including impervious surface cover, human population density, and tree canopy cover, predict genetic differentiation after accounting for geographic distance. Genetic differentiation increased with geographic distance and, after controlling for isolation by …

Mountain Communities During A Time Of War: A Case Study Of The Hutsul Region In The Carpathian Mountains Of Ukraine, Pavlo Rybaruk

Electronic Theses and Dissertations

This thesis investigates the ethno-ecological technologies employed by the Hutsul people within the highland agrarian economy of the Carpathian Mountains. Over centuries, the Hutsuls have developed ethno-ecological technologies that maintain ecological integrity while supporting community livelihoods.

The study addresses three primary research questions: What are the most important ethno-ecological technologies of the Hutsul highland economy? How might these traditional ethno-ecological practices be applied to economic, agricultural, and tourism development in the Hutsul region? How might these traditional ethno-ecological practices be combined with contemporary approaches to encourage sustainable development in the region?

The research explores the devastating impact of the Russian …

Solar Powered Conservation: The Effects Of Solar Photovoltaic Facilities On Avian Community Composition, Michael Christopher Ferrara

Graduate Theses and Dissertations

The expansion of solar photovoltaic energy infrastructure is transforming landscapes worldwide. Increasingly, facilities are planted with native vegetation, yet how vegetation characteristics and landscape variables shape wildlife communities in solar facilities remains poorly understood. Because avian populations have been in decline and are sensitive to habitat changes, understanding how solar facilities influence avian communities is important. In Chapter 1, we used autonomous recording units, local vegetation measurements, and land use and land cover data to quantify how avian community occupancy is influenced by solar cover in solar facilities and comparable reference sites. We used a Bayesian multi-species occupancy model to …

Predictive Modeling Of Listeria Monocytogenes Growth In Ready-To-Eat Meat Products, Manjari Singh

Graduate Theses and Dissertations

Listeria monocytogenes remains a significant food safety concern in ready-to-eat (RTE) meat and poultry products due to its persistence under refrigerated and stressed conditions. Predictive models play a vital role in risk assessment and food safety management; broth models are highly conservation & results in overprocessing. This thesis focuses on developing and validating meat-specific predictive models for Listeria monocytogenes growth and lag for RTE beef, pork, and poultry products. Matrix-specific secondary models were built to predict the maximum specific growth rate (μmax) of Listeria monocytogenes under varying environmental conditions, including temperature, pH, water activity, salt, organic acids, and nitrites. Growth …

Multiple Aspects Of Environmental Temperature Have Complex Interactions With Avian Parental Behavior To Influence Offspring Outcomes, William H. Kirkpatrick

Graduate Theses and Dissertations

Anthropogenic climate change is projected to shift not only average temperatures across the globe, but also the amount of thermal variation experienced in the natural environment. Exposure to shifts in averages and a wider range of thermal experiences will cause shifts in wildlife behavior. In avian species, behaviors exhibited during reproduction have implications for the well-being of their offspring. Here, I explore specific incubation behaviors in four species: Scaled Quail (Callipepla squamata), Northern Bobwhite Quail (Colinus virginianus), Tree Swallows (Tachycineta bicolor), and Eastern Bluebirds (Sialia sialis). I examined constancy, or the percentage of time on the nest, and off-bout duration, …

Broiler Responsiveness To Dietary Amino Acid Density In A Commercial Setting, Virginia Slick

Graduate Theses and Dissertations

The majority of research assessing the amino acid responsiveness in broilers has been conducted in experimental designs utilizing pens that contain 12 to 25 birds with high replication. While this trial design is beneficial as a way to perform high replications with multiple treatments in a way that is both economically and spatially feasible, it may not accurately translate to a rearing environment more similar to that of commercial open floor housing. This research was conducted to determine if the effects of lysine driven amino acid density diets that have been found in the traditional floor pen setting correlate to …

Isolation Of The 2019 Bonnet Carré Spillway Effects On The Habitat Suitability Of Brown Shrimp (Farfantepenaeus Aztecus) And Blue Crab (Callinectes Sapidus) Using A Modeling Approach, Mallory Dyson

Master's Theses

In 2019, an unprecedented flood year, the Bonnet Carré Spillway (BCS) was opened on two separate occasions (February 27^th to April 11^th, and May 10^th through July 27^th) diverting a volume 6 times the volume of Lake Pontchartrain into the surrounding coastal waters of Louisiana, Mississippi, and Alabama. The goal of this research was to determine the spatio-temporal influence of these freshwater releases on two economically and ecologically important species (Farfantepenaeus aztecus and Callinectes sapidus) with variable responses to salinity and temperature depending on the age class. The Habitat Suitability Index (HSI) …

Benchmarking Dna Foundation Models For Genomic And Genetic Tasks, Haonan Feng, Lang Wu, Bingxin Zhao, Chad Huff, Jianjun Zhang, Jia Wu, Lifeng Lin, Peng Wei, Chong Wu

School of Medicine Faculty Publications

The rapid evolution of DNA foundation models promises to revolutionize genomics, yet comprehensive evaluations are lacking. Here, we present a comprehensive, unbiased benchmark of five models (DNABERT-2, Nucleotide Transformer V2, HyenaDNA, Caduceus-Ph, and GROVER) across diverse genomic and genetic tasks including sequence classification, gene expression prediction, variant effect quantification, and topologically associating domain (TAD) region recognition, using zero-shot embeddings. Our analysis reveals that mean token embedding consistently and significantly improves sequence classification performance, outperforming other pooling strategies. Model performance varies among tasks and datasets; while general purpose DNA foundation models showed competitive performance in pathogenic variant identification, they were less …

Transdisciplinary Perspectives On Ai: The Fourth Annual Conference Of The European Culture And Technology Laboratory, Connell Vaughan, Ioana Madalina Moldovan, Silivan Moldovan, Noel Fitzpatrick

Books/Book Chapters

The fourth annual conference of the ECT Lab+ was hosted by Technical University of Cluj-Napoca over two days in October 2024 at the Cluj Innovation Park. The conference brought together experts from the Arts, Humanities, Social Sciences, Technology, and other fields to discuss and reflect on the advent of Artificial Intelligence and how the associated technologies are transforming how we live, work and study. Under the title Transdisciplinary perspectives on AI: Alternative Histories, Current Practices and Possible Futures the conference moved beyond simplistic technophila and technophobia to consider whether we can co-evolve with these new technologies which combine machine learning …

Tannin Supplementation Alters Foraging Behavior And Spatial Distribution In Beef Cattle, Bashiri Iddy Muzzo, R. Douglas Ramsey, Kelvyn Bladen, Juan J. Villalba

Wildland Resources Student Research

Beef production on chemically uniform grass monocultures can limit nutrient synchrony and contribute to uneven pasture use. We evaluated whether supplementing tannins with bioactive plant secondary compounds improves foraging dynamics and landscape use by beef cattle grazing a meadow bromegrass monoculture in ways aligned with rangeland sustainability. Twenty-four Angus cow–calf pairs were allocated to six 3.6-ha paddocks (four pairs/paddock), randomly assigned to Control (Ctrl; n = 3) or Tannin treatment (TT; n = 3). Animals received 1 kg/cow/day of DDGs, with TT receiving an added 0.4% tannins (2:1 condensed:hydrolyzable). Grazing occurred during four 15-day periods (July– September) across two years. …

Predicting The Response Of Triple Negative Breast Cancer To Neoadjuvant Systemic Therapy Via Biology-Based Modeling And Habitat Analysis, Casey E Stowers, Chengyue Wu, Clinton Yam, Jingfei Ma, Gaiane M Rauch, Thomas E Yankeelov

Faculty, Staff and Student Publications

Despite being the standard-of-care treatment, neoadjuvant therapy (NAT) attains a complete response only in approximately half of the patients with triple negative breast cancer. Thus, methods to predict and optimize patient response to NAT are needed. Previously, we employed patient-specific MRI data to calibrate a biology-based mathematical model that describes cell movement, proliferation, and death due to drug at the tumor level and cell proliferation at an image voxel level. We now extend our approach by using MRI data to group voxels into "habitats" whereby tumor cells of a habitat share the same proliferation. With this approach, we now calibrate …

Evolving Towards Efficient Technologies In Power Systems: The Paradigm Of Energy Internet Survey, Dina Emad, Omar Abdel-Rahim, Tanemasa Asano, Sobhy M. Abdelkader

Mansoura Engineering Journal

The Energy Internet represents a significant advancement in the modernization and automation of electricity systems, offering a framework for future smart grids where all electrical devices are interconnected through energy routers. This system integrates advanced power electronics, information technology, and smart control technologies, enabling the accommodation of diverse energy sources and storage devices. With its bidirectional energy flow and sharing capabilities, the Energy Internet holds great promise for the future. However, several challenges must be addressed to fully realize this potential. This review provides an overview of the Energy Internet framework and explores key challenges, particularly those related to energy …

Phylogenetics Of Cyrtodactylus In West Nusa Tenggara: A New Distribution Record Of Cyrtodactylus Jatnai From Lombok Island And A Cryptic Species From Sumbawa Island, Sandra Rafika Devi, Rury Eprilurahman, Tuty Arisuryanti, Yuliadi Zamroni, Imran Sadewo, Windi Edriyanti, Maulana Faiz Ilham Kholiq, Evelyn Elvira

Turkish Journal of Zoology

Cyrtodactylus is one of the most diverse vertebrates of the Gekkonidae family, first described by Gray in 1827 and widely distributed in Asia, Northern Australia, and the Pacific Islands including Wallacea. The biodiversity in West Nusa Tenggara—a region in Wallacea—has been underestimated despite high fauna endemicity. Conservation strategies are needed to maintain the stability of Cyrtodactylus populations in their habitat. Therefore, this study aims to enhance the understanding of cryptic species and potential new distribution records of the genus Cyrtodactylus in West Nusa Tenggara. Molecular character identification was carried out by isolating the ND2 gene in liver tissue using polymerase …

Intro To Ai Literacies Discussion, Miranda Rectenwald

Generative AI Teaching Activities

Students consider and dicuss key literacies when using generative AI tools.

The Effect Of Noise Pollution On The Diversity And Abundance Of Bird Species At Different Locations At Warner Parks, Nashville, Tn, Jeremy T. Little, Wyatt L. Fooks, Darlene Panvini, Jackson Whiteside

Science University Research Symposium (SURS)

Noise pollution is a significant abiotic factor that can alter bird biodiversity and abundance of birds in urbanized areas. A new road is proposed through a relatively untouched area of Warner Parks in Nashville, TN, which may affect the bird community. Acoustic Song Meters were used to monitor bird sounds and soundscapes in the proposed road site and two areas of the park with different levels of noise pollution (roadside=high noise; isolated=low noise) for three weeks. Recordings were analyzed to determine bird species and abundance at each site to predict how increasing noise pollution may affect bird diversity in the …

Antifungal Effects Of Fatty Acids On The Growth Of Ophidiomyces Ophiodiicola In A Simulated Snake Skin Environment, Krupa S. Patel, Lizbeth Delarosa, Jacey Cardenas, Thalia Rodriguez, John Niedzwiecki

Science University Research Symposium (SURS)

Emerging infectious diseases have increasingly threatened wildlife populations worldwide, with devastating impacts observed in frogs, bats, and more recently, snakes. Snake fungal disease (SFD), caused by the pathogenic fungus Ophidiomyces ophiodiicola (Oo), currently poses a serious threat to snake populations across multiple regions. Infected snakes exhibit disrupted skin shedding, rough or scaly patches, crusty sores, and ulcers that compromise their health and survival. Although the mechanisms underlying transmission and susceptibility to SFD remain unclear, the snake cutaneous microbiome is known to act as a defensive barrier, mediating interactions between the host and invading pathogens. The lipid layer is a key …

Fungal Foes And Fatty Defenses: How Simulated Snake Skin Lipids Influence Ophidiomyces Ophiodiicola Growth, Thalia Rodriguez, Jacey Cardenas, Lizbeth Delarosa, Krupa Patel, John Niedzwiecki

Science University Research Symposium (SURS)

Emerging fungal diseases are a continuous threat to wildlife health as well as biodiversity. Fungal diseases, such as white nose syndrome in bats, can devastate populations by disrupting their ecosystems. Many other species around the world are affected by fungal diseases, such as amphibians, birds, and snakes. In more recent years, snake fungal disease (SFD) emerged due to the fungal pathogen Ophidiomyces ophiodiicola (O.o). Like Pseudogymnoascus destructans, the fungal pathogen responsible for white nose syndrome, O.o targets the skin which contains many fatty acids. Some studies have shown that fatty acids present in bat skin are able to inhibit fungal …

Surviving The Seasons: Climate And Time Effects On Native Songbirds, Essence Donaldson, Todd Hoskinson, John Niedzwiecki

Science University Research Symposium (SURS)

Bird populations across North America have declined sharply in recent decades due to habitat loss, climate change, and changes in food availability. As bird numbers fall, ecosystems lose essential pollinators, seed dispersers, and insect predators. Long-term monitoring of bird populations is vital for understanding how environmental changes influence their survival and abundance. This study examines capture data from a long-term bird banding station at Percy Warner Nature Center in Nashville, Tennessee, focusing on five native species: Northern Cardinal (NOCA), American Robin (AMRO), American Goldfinch (AMGO), Tufted Titmouse (TUTI), and Carolina Chickadee (CACH), from fall 1983 to fall 2023. We analyzed …

2025 - The Sixth Annual Fall Symposium Of Student Scholars

Symposium of Student Scholars Program Books

The full program book from the Fall 2025 Symposium of Student Scholars, held in November 2025. Includes abstracts from the presentations and posters.

Fish-Spec: Fast Identification System For Handheld Spectroscopy And Species Classification, Mitchell Sueker, Nicholas Mackinnon, Gregory Bearman, Amanda Tabb, Diane Kim, Rosalee S. Hellberg, Alireza Akhbardeh, Hamid Reza Marateb, Jianwei Qin, Moon Kim, Fartash Vasefi, Hossein Kashani Zadeh

Food Science Faculty Articles and Research

Accurate fish species identification is critical to prevent mislabeling and fraud in the seafood industry. We present a handheld multi-mode point spectroscopy system that combines fluorescence (365 and 395 nm excitation) and reflectance measurements in the visible to near-infrared (∼350–900 nm) and short-wave infrared (∼900–1700 nm) regions for rapid, non-destructive classification of fish fillets. Tissue spectra were acquired at 25 positions on 68 fillets from 11 species, in both frozen and thawed states. Feature-level fusion across all four modes enabled higher classification accuracy than any single mode alone. A global machine-learning model classified all species with 85 ± 2.8 %, …

Harnessing Hyperspectral Imaging And Deep Learning For Terrestrial Habitat Mapping In Arid Landscapes: A Case Study In Saudi Arabia, Ali Elgendy, Hesham Morgan, Brandon Tran, Rejoice Thomas, Tamer Ismail, Yehya Kh. Shehadeh, Ahmed Elgharib, Ahmed Abdullah Al-Dughairi, Ali El Muburak, Khaled Allam Harhash, Hesham El-Askary

Mathematics, Physics, and Computer Science Faculty Articles and Research

Arid ecosystems remain under-mapped at actionable scales despite their ecological importance. Decision makers lack reliable, high-resolution habitat maps in drylands to prioritize protection and target restoration. This research integrates spaceborne hyperspectral imaging from the Environmental Mapping and Analysis Program (EnMAP) with deep learning semantic segmentation models to produce an updated level of habitat classification based on the International Union for Conservation of Nature (IUCN) for part of the Imam Turki bin Abdullah Royal Reserve, Saudi Arabia. Using ground control points and the full EnMAP spectral cube without band selection, U-Net and DeepLabV3+ architectures were each implemented with VGG19 and ResNet-101 …