Digital Commons Network^™

Evaluating Large Language Model Performance To Support The Diagnosis And Management Of Patients With Primary Immune Disorders, Nicholas L Rider, Yingya Li, Aaron T Chin, Daniel V Digiacomo, Cullen Dutmer, Jocelyn R Farmer, Kirk Roberts, Guergana Savova, Mei-Sing Ong

Faculty, Staff and Student Publications

Background: Generative artificial intelligence (GAI) is transforming health care in a variety of ways; however, the present utility of GAI for supporting clinicians who treat rare disease such as primary immune disorders (PIs) is not well studied. We evaluated the ability of 6 state-of-the-art large language models (LLMs) for providing clinical guidance about PIs.

Objective: To quantitatively and qualitatively measure the utility of current, open-source LLMs for diagnosing and providing helpful clinical decision support about PIs.

Methods: Five expert clinical immunologists each provided 5 real-world, anonymized PI case vignettes via multi-turn prompting to 6 LLMs (OpenAI GPT-4o, Llama-3.1-8B-Instruct, Llama-3.1-70B-Instruct, Mistral-7B-Instruct-v0.3, …

Scientific Note: Garden Loosestrife (Lysimachia Vulgaris, Primulaceae), An Emerging Invasive Plant Species Of Riparian Corridors In The Mid-Atlantic Region, Christopher T. Martine, Amy L. Jewitt, Claire M. Ciafre, Kaitlin G. Henry, Elizabeth H. Williams, Pj Newhart, Melody P. Sain

Faculty Journal Articles

Lysimachia vulgaris (garden loosestrife, Primulaceae) is an herbaceous perennial native to Europe that has been identified as an aggressive invasive species in parts of North America. The status of the species in the Mid-Atlantic region of the US, however, is poorly determined. Using recent field observations (from iNaturalist, iMapInvasives, and EDDMapS records) we here report localized incursions of L. vulgaris in the Susquehanna River Valley of central Pennsylvania, along with notes on its ecology, threats to native plant communities, and broader distribution in the state.

The Landscape Of Malignant Transition: Unraveling Cancer Cell-Of-Origin And Heterogeneous Tissue Microenvironment, Ruihan Luo, Jiajia Liu, Tiangang Wang, Weiling Zhao, Yanfei Wang, Jianguo Wen, Hongyu Wang, Shanli Ding, Xiaobo Zhou

Faculty, Staff and Student Publications

Understanding disease progression and sophisticated tumor ecosystems is imperative for investigating tumorigenesis mechanisms and developing novel prevention strategies. Here, we dissected heterogeneous microenvironments during malignant transitions by leveraging data from 1396 samples spanning 13 major tissues. Within transitional stem-like subpopulations highly enriched in precancers and cancers, we identified 30 recurring cellular states strongly linked to malignancy, including hypoxia and epithelial senescence, revealing a high degree of plasticity in epithelial stem cells. By characterizing dynamics in stem-cell crosstalk with the microenvironment along the pseudotime axis, we found differential roles of ANXA1 at different stages of tumor development. In precancerous stages, reduced …

The Effect Of Individual Variation On Epidemiological Dynamics: From Super-Spreaders To Landscapes Of Risk, Alexis Shannon Beagle

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

Individuals that make up a population always display some level of variation between members. At the smallest scale, individuals always maintain genetic variation, but variation continues to arise at other scales of biological organization from physiological or immunological variation within individuals to variation in behavior between individuals that can be both genetically and environmentally mediated. The role of individual variation is particularly important in the context of infectious diseases because there is strong evidence that infections are highly heterogenous, indicating that patterns of individual variation drive a significant portion of the epidemiological patterns we observe. Individual variation leads to heterogeneity …

Use Of High-Throughput Phenomics With And Without Fungicide As A Wheat Breeding Tool, Gerardo Ivan Rivera Collazo

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

Wheat (Triticum aestivum) is an important food staple for many countries around the world and current consumption and production data demonstrate a production deficit. Breeders are challenged to help close this gap in production by selecting better cultivars with improved yields. Several methods aim to accelerate the breeding process to reduce the time required for releasing an elite variety. One of the main breeding bottlenecks is the lack of fast and reliable phenotypic data acquisition that could dissect physiological and morphological plant data. High-throughput remote sensing could have the potential to reduce this bottleneck by streamlining data acquisition, …

A Study Of Ice And Fire: Environmental Change Impacts On Lakes Of The Nebraska Sandhills, Daniel Gschwentner

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

The Nebraska Sandhills contain thousands of shallow, groundwater-fed lakes. These lakes are extremely sensitive to environmental and climatic changes due to their isolated hydrological setting and small volume. Building on previous work on the hydrology, geochemistry and long-term climate response of Sandhill lakes, my research considers how ecosystem processes such as primary production, nutrient limitation and water quality respond to short-term environmental and climatic change. In my first data chapter, I highlight that Sandhill lakes are nitrogen (N) but not phosphorus (P) limited and that N:P ratios are poor predictors of nutrient limitation status in Sandhill lakes. In my second …

Catching A Fever: A Comparison Of Vachellia Xanthophloea Populations In The Limpopo And Luvuvhu River Floodplains Of The Makuleke Contractual Park, Kianie B. David

School of Natural Resources: Dissertations, Theses, and Student Research

This study investigates patterns of stand structure regeneration, growth characteristics, and coarse woody debris (CWD) patterns in Vachellia xanthophloea (fever tree) stands within the Makuleke Contractual Park (MCP), a semi-arid savanna system in northern Kruger National Park (KNP), South Africa. Fieldwork was conducted across two stand types: a monospecific fever tree stand in Rietbok Vlei and a mixed-species stand in the Western Nhlangaluwe Floodplain where fever tree is established with Faidherbia albida (ana tree). Data were collected from 20 total 1/4-acre (1,011 m²) circular plots between both stands in 2024 and 2025, including seedling root collar diameter (RCD), …

Bioenergy Crop Production: Implications For Grassland Bird Communities In Southwestern Nebraska, Grace E. Schuster

School of Natural Resources: Dissertations, Theses, and Student Research

Biofuel and bioenergy systems are components of most climate stabilization pathways to reduce greenhouse gas emissions and limit global warming. Currently, corn (Zea mays) is the predominant feedstock used for bioenergy production in the United States. However, widespread production of this monoculture crop has resulted in many negative environmental impacts. The most notorious impact has been the loss of grassland habitat due to agriculture expansion which has had detrimental effects on wildlife that depend on grassland habitat. One such group, grassland birds, has faced steeper, more consistent, and more widespread declines than any other avian guild. Therefore, strategies …

Arcadia Magazine, 2025-07

Alumni Magazine

No abstract provided.

Identification Of Novel Components Of The Retinal Determination Gene Network In Drosophila Cell Lines, Robert Drewell, Jacqueline Dresch

Biology

The retinal determination genetic network controls the development of the visual system in all seeing animals through the molecular regulation of cells to adopt an eye tissue fate. The compound eye of the fruit fly, Drosophila melanogaster, is an excellent model system to study the complex mechanisms within the network that regulate specification of cellular identity during embryogenesis. In Drosophila, the two Pax6 paralogues, eyeless and twin of eyeless, sit at the very pinnacle of the network and their expression early in development activates critical downstream components of the retinal determination pathway. In this study, we investigate the expression of …

Electronic Resources Updates - 2025 Q2, Brigitte Galauner, Gregg Harris

Electronic Resources Quarterly Updates

No abstract provided.

Electrochemistry Behind Pfas: Mechanistic And Analytical Approach For Sensing And Degradation Strategies, Jonathan Josue Calvillo Solis

Open Access Theses & Dissertations

Understanding the fundamental electrochemistry of perfluoroalkyl substances (PFAS) is key to developing effective water remediation and sensing strategies. This work explores the thermodynamics and kinetics of perfluorooctanoic acid (PFOA) electroreduction, focusing on C-F bond cleavage. These insights were applied to design a highly sensitive electrochemical sensor for detecting trace levels of PFOA in water. This dissertation focuses on the electrochemical investigation of the reduction reaction of PFOA in aqueous and organic media employing different electrode materials. This exploration allows to understand the defluorination reaction of PFAS to further propose potential strategies for water treatment and PFOA electrosensing. Through electrochemical, spectroscopical …

Drone Delivery Of Bioweapons: Responsibilities For Force Readiness, James Giordano, Diane Dieuliis

Strategic Forums

This Strategic Forum by Dr. James Giordano and Dr. Diane DiEuliis explores the convergence of drone technology and emerging biotechnologies. This includes synthetic biology, gene editing, and nanoscale biomaterials, and their implications for military readiness and national security. It examines how these dual-use technologies could enable novel delivery methods for biological agents, expanding the threat landscape and lowering technical barriers. The analysis emphasizes the need for proactive defense planning, enhanced detection and countermeasures, and integrated strategies to mitigate risks, ensuring force readiness in the face of evolving biological threats.

Experimental Determination Of Diffusion Flame Extinction Boundaries Over A Pmma Sphere: The Effect Of Sub-Surface Solid Heating, James S. T'Ien, Chengyao Li

Faculty Scholarship

The SoFIE-GEL (Solid Fuel Ignition and Extinction-Growth and Extinction Limit) microgravity combustion experiment was recently conducted aboard the International Space Station (ISS). In these tests, diffusion flame extinction limits of 4-cm diameter PMMA (polymethacrylate) spheres were determined as a function of forced flows (0.2 to 80 cm/s), oxygen concentrations (13 % to 34 %) and pressure (0.15–1.1 atm). In particular, the effect of sample heat-up is investigated. The sample surface layer is preheated by the ignitor and the diffusion flame itself before the extinction procedure (e.g. flow velocity decrease or increase or oxygen decrease) is implemented. The degree of sample …

Primary Investigation Of Rice-Fish Co-Culture: Investigating The Feasibility Of Raising Fish In Flooded Rice Paddies In The Southern Usa, Yulin Jia, Aaron K. Jackson, Bartholomew Green, S. Adam Fuller, Heather Box, Laduska Sells, Candis Ray, Paxton Harper, Brennan Smith

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

With limited land and water resources available it has become critical to maximize output for agricultural products while maintaining sustainable farming practices. Ricefish co-culture can be used to maximize limited land and water resources for production of rice and fish concurrently and reduce the need of chemical inputs. While rice-fish co-culture has been practiced in Asia for centuries, very few studies have examined the feasibility and economic impact of rice fish co-culture in the U.S.A. Two studies were conducted in Stuttgart, Arkansas, U.S.A. from 2023-2024 to investigate the suitability of raising Koi carp in flooded rice paddies with a sushi …

Endothelium- And Fibroblast-Derived C-Type Natriuretic Peptide Prevents The Development And Progression Of Aortic Aneurysm, Aisah A. Aubdool, Amie J. Moyes, Cristina Perez-Ternero, Reshma S. Baliga, Jaspinder Singh Sanghera, M. Taaha Syed, Kareemah Jaigirdar, Anmolpreet K. Panesar, Janice C. Tsui, Yanming Li, Hernan G. Vasquez, Ying H. Shen, Scott A. Lemaire, Juliette Raffort, Ziad Mallat, Hong S. Lu, Alan Daugherty, Adrian J. Hobbs

Physiology Faculty Publications

BACKGROUND: Thoracic (TAA) and abdominal (AAA) aortic aneurysm are life-threatening diseases characterized by dilation, inflammation, and structural weakness; development of pharmacological therapies is desperately needed. CNP (C-type natriuretic peptide) plays a key role in vascular homeostasis, mediating vasodilator, anti-inflammatory, and antiatherogenic actions. Since such processes drive AA, we determined the role of endogenous CNP in offsetting pathogenesis. METHODS: Tissue from patients with AA was analyzed to determine the consequences on CNP signaling. Ascending and suprarenal aortic diameters were assessed at baseline and following Ang II (angiotensin II; 1.44 mg/kg per day) infusion in wild-type, endothelium-restricted (ecCNP^-/-), fibroblast-restricted (fbCNP …

At The Nexus Between Epigenetics And Senescence, Toby L. Chambers, Jaden Wells, Pieter Jan Koopmans, Francielly Morena, Zain B. Malik, Nicholas P. Greene, Antonio Filareto, Michael Franti, Patrizia Sini, Harald Weinstabl, Robert T. Brooke, Milda Milčiūtė, Juozas Gordevičius, Steve Horvath, Yuan Wen, Cory M. Dungan, Kevin A. Murach

Physiology Faculty Publications

Senescent cells emerge with aging and injury. The contribution of senescent cells to DNA methylation age (DNAmAGE) in vivo is uncertain. Furthermore, stem cell therapy can mediate “rejuvenation”, but how tissue regeneration controlled by resident stem cells affects whole tissue DNAmAGE is unclear. We assessed DNAmAGE with or without senolytics (BI01) in aged male mice (24–25 months) 35 days following muscle healing (BaCl₂-induced regeneration versus non-injured). Young injured mice (5–6 months) without senolytics were comparators. DNAmAGE was decelerated by up to 68% after injury in aged muscle. DNAmAGE was modestly but further significantly decelerated by injury recovery with …

Consumer Behavior Of Gen Z In Kosovo: Purchasing Preferences And Brand Engagement, Sara Dumani

Theses

This capstone project examines the consumer behavior of Generation Z in Kosovo by analyzing their purchasing preferences and brand engagement. The Generation Z demographic, which includes individuals born between 1996 and 2010, is the focus of this study. This generation is characterized by digital savviness and a significant influence from social media platforms, shaping their purchasing decisions and brand engagement. Generation Z’s behavior is often marked by a preference for online shopping, collaborative marketing approaches, and sustainability, making it essential to understand these factors in the context of Kosovo. The data for analyzing Generation Z’s consumer behavior were collected through …

Development Of Nanopocket Membranes For The Isolation And Purification Of Extracellular Vesicles, Munther Alsudais

Theses

Extracellular vesicles (EVs) play a crucial role in intercellular communication and serve as significant biomarkers for various diseases. EVs carry biomolecules such as lipids, proteins, DNA, and RNA, which reflect the physiological state of their cells of origin, making them promising tools for non-invasive diagnostics and therapeutic applications. Effective isolation of EVs is essential for advancing scientific understanding of their biological roles and unlocking their clinical potential. Porous membranes have been widely used for the purification of various biological species from biological fluids. While membranes have prove highly effective for general size-based separation, recent innovations have focused on structurally refined …

Online And Offline Multi-Variate Time Series Forecasting With Neuroevolution Based Neural Architecture Search, Zimeng Lyu

Theses

Time series forecasting plays a crucial role in various fields, ranging from financial markets and predictive maintenance in industrial settings to healthcare analytics. Traditionally, statistical approaches were employed primarily for univariate forecasting tasks, but modern applications often require robust solutions capable of handling complex, multivariate, noisy, and non-stationary data. Current state-of-the-art solutions predominantly utilize transformer-based models, which demand significant computational resources, limiting their practicality, especially in resource-constrained environments. This dissertation introduces novel and efficient approaches to multivariate time series forecasting, leveraging NeuroEvolution-based Neural Architecture Search (NAS) methodologies. Specifically, two robust algorithms---Evolutionary eXploration of Augmenting Memory Models (EXAMM) for offline forecasting …

Network And Tree-Based Approaches To Data-Driven Modeling Of Complex Climate Systems, Adam M. Giammarese

Theses

The guiding thread throughout this thesis work is data-driven modeling of Earth's climate. We investigate a variety of settings within the field of complex climate systems, such as gridded, high-resolution reanalysis data, lower-resolution climate indices, and incomplete paleoclimate records with missing values. We begin with reanalysis data of high spatial and temporal resolution, and use climate network analysis to uncover hidden trends in the data in regards to the Amazon rainforest and its changing role in the global climate system. We introduce a novel formulation of k-nearest neighbors climate networks to study changing trends at a local level, and apply …

Investigating Focal Adhesion Kinase Activation In Arteriovenous Fistula Maturation, Sam Fulkerson, Fuji Anday, Thi Hong Phuong Nguyen, Tatyana Isayeva-Waldrop, Steve Lim, Kevin Ingle, Timmy Lee

Expo Student Presentations

2025 Summer Expo Poster Presentation

• Biological & Life Sciences

Decoding Emt Heterogeneity In Pancreatic Cancer, John David Slowikowski, Julienne L. Carstens

Expo Student Presentations

2025 Summer Expo Poster Presentation

• Biological & Life Sciences
• Works in Progress

Measures Of Muscle Strength, Rate Of Force Development, And Fatiguability Across The Menstrual Cycle, Cassidy Wisler

All NMU Master's Theses

BACKGROUND: Hormone fluctuations and inconsistencies across the menstrual cycle paired with a shortage of literature on female physiology in exercise have made understanding on female exercise performance troublesome. Performance-based research has fallen behind and the increase in women participation and current evidence does not warrant general guidance on modulating specific exercise across the menstrual cycle. PURPOSE: The purpose of this study was to determine the effects of estrogen and progesterone on muscle strength, rate of force development, and fatiguability. METHODS: Nineteen recreationally active and eumenorrheic females (25.3 ± 5.8 yrs, 73.4 ± 12.2 kgs) volunteered to participate in the study. …

Investigating The Role Of Msbdnf – Trkb Signaling In The Maintenance Of Mitochondrial Populations Through The Bnip3 Mitophagy Pathway, Jack A. Horton

All NMU Master's Theses

Maintenance of mitochondrial transport and clearance at the pre- and post-synaptic terminal is an essential function of neuromuscular junctions to meet their high energy demands. Damaged or dysfunctional mitochondria can put stress on these synaptic junctions, ultimately leading to the degradation of the synapse and subsequent cell death. Dysfunctional mitochondria are also often present in neuromuscular diseases such as ALS. One possible mechanism by which neurons may eliminate dysfunctional mitochondria is through the muscle-synthesized BDNF (msBDNF) /TrkB-mediated Bcl-2 nineteen-kD interacting protein (BNIP3) mitophagy pathway, although the relationship is not well-defined. BNIP3 localizes to the mitochondria and triggers a loss of …

The Effect Of Skeletal Muscle-Synthesized Bdnf On Motor Neuron Soma Size And Bdnf Protein Abundance, Sydney Benson

All NMU Master's Theses

Brain derived neurotrophic factor (BDNF) is a neurotrophin essential to neuron health and maintenance in both the central nervous system and periphery. It acts as a positive feedback system for the body’s motor neurons and the muscles they innervate, strengthening the synapse between them. Skeletal muscle-synthesized BDNF transmission occurs across the neuromuscular junction, the site where motor neuron axons synapse with muscle fibers. BDNF transmission to tropomyosin receptor kinase B (TrkB) at the motor neuron axon terminal causes clathrin mediated endocytosis of the complex and an intracellular signaling cascade that recruits dynein motor proteins for retrograde transport of the BDNF/TrkB …

Elucidating The Role Of Mir-10a/B In The Wound Healing Process In Larval Zebrafish, Jacquelyn E. Jacobs

All NMU Master's Theses

This study explores the regulatory role of microRNA-10 (miR-10) in larval zebrafish caudal fin regeneration, a model with broad implications for the future of regenerative medicine. Building on prior research from the lab, which indicated that miR-10 knockdown impairs regeneration, we verified this finding through rescue experiments, assessed its influence on healing projections, and examined its role in the innate immune response during the wound healing process. To address these questions, we employed a multi-faceted approach, including timed matings, microinjections, immunohistochemistry, fixed sample microscopy, and live imaging. Our results show that the experimental introduction of exogenous miR-10 can rescue the …

Marigold Lodge: Family Home, Meeting Venue, And Community Landmark; Willard (Bill) Wichers: “Mr. Holland”, Sarah Lundy, Charlotte Ulloa

Archives and Special Collections Quarterly

Marigold Lodge: Family Home, Meeting Venue, and Community Landmark

Column: From the Director of Archives and Special Collections

Willard (Bill) Wichers: “Mr. Holland”

Characterization Of Lactobacilli-Containing Catheter Segments Developed By Using Selective Laser Sintered Mold., Caden Maners

Master of Engineering Theses

Catheter-associated urinary tract infections (CAUTIs) are a major healthcare burden with current prevention strategies offering limited success. This study presents a novel, self-coating biomaterial approach using a silicone-based bioink embedded with thermally sensitive probiotic strains (L. crispatus, L. rhamnosus, and L. reuteri). Catheter segments were fabricated via bio-injection molding using 3D-printed CAD molds. These Lactobacilli, selected for their probiotic and antimicrobial potential, serve as a non- antibiotic strategy to reduce infection risk. These segments were evaluated for mechanical strength (Shore A hardness), thermal stability (TGA/DSC), porosity and bacterial presence (SEM), biofilm formation (crystal-violet assay), as well as mass retention in …

Shared Genetic Architecture Of Posttraumatic Stress Disorder With Cardiovascular Imaging, Risk, And Diagnoses, Jie Shen, Wander Valentim, Eleni Friligkou, Cassie Overstreet, Karmel W. Choi, Dora Koller, Christopher J. O’Donnell, Murray B. Stein, Joel Gelernter, Haitao Lv, Ling Sun, Guido J. Falcone, Renato Polimanti, Gita A. Pathak, Edward Trapido, Ariane Rung, Et Al.

School of Public Health Faculty Publications

Patients with post-traumatic stress disorder face increased cardiovascular risk. This study examines shared genetic regions between post-traumatic stress disorder and 246 cardiovascular conditions across electronic health records, 82 cardiac imaging, and health behaviors defined by Life’s Essential 8. Post-traumatic stress disorder is genetically correlated with cardiovascular diagnoses in 33 regions, imaging traits in 4 regions, and health behaviors in 44 regions. Potentially shared causal variants between post-traumatic stress disorder and 17 cardiovascular conditions were observed in 11 regions. Subsequent observational analysis in AllofUS cohort showed post-traumatic stress disorder is associated with 13 diagnoses even after accounting for socioeconomic factors and …