Physical Sciences and Mathematics Commons^™

Rapid Evolution Of A(H5n1) Influenza Viruses After Intercontinental Spread To North America, Ahmed Kandeil, Christopher Patton, Jeremy C. Jones, Trushar Jeevan, Walter N. Harrington, Sanja Trifkovic, Jon P. Seiler, Thomas Fabrizio, Karlie Woodard, Jasmine C. Turner, Jeri Carol Crumpton, Lance Miller, Adam Rubrum, Jennifer Debeauchamp, Charles J. Russell, Elena A. Govorkova, Peter Vogel, Mia Kim-Torchetti, Yohannes Berhane, David Stallknecht, Rebecca Poulson, Lisa Kercher, Richard J. Webby

United States Department of Agriculture Wildlife Services: Staff Publications

Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b underwent an explosive geographic expansion in 2021 among wild birds and domestic poultry across Asia, Europe, and Africa. By the end of 2021, 2.3.4.4b viruses were detected in North America, signifying further intercontinental spread. Here we show that the western movement of clade 2.3.4.4b was quickly followed by reassortment with viruses circulating in wild birds in North America, resulting in the acquisition of different combinations of ribonucleoprotein genes. These reassortant A(H5N1) viruses are genotypically and phenotypically diverse, with many causing severe disease with dramatic neurologic involvement in mammals. The proclivity of …

Enhancing Urban Water Quality Through Biological-Chemical Treatment: Aquatic Macroinvertebrate Community And Temporal Chlorophyll-A Response, Matthew Chaffee

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

With a growing human population, urbanization is impeding a plethora of natural waterways. Of these, urban ponds play a vital role in nutrient sequestration, flood prevention, and habitat sanctuaries. However, nutrient loading can reduce habitat effectiveness and promote harmful algae blooms. To reduce internal nutrient loads, a biological-chemical treatment strategy consisting of floating treatment wetlands (FTWs) and lanthanum were applied to two urban retention ponds, Densmore and Wilderness Ridge Ponds. To measure effectiveness, chlorophyll-a samples were collected and correlated with Sentinel-2. A novel band algorithm termed 3BR1 produced a strong correlation (R² = 0.72) to physical chlorophyll-a …

The Evaluation Of Feed Additives On Reducing Enteric Methane Production From Cattle, Reba L. Colin

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

Environmental sustainability can be positively impacted by the inclusion of feed additives to reduce enteric methane production from cattle. Methane production can be affected by feed additives that either alter the rumen environment or act as methanogenesis inhibitors. A reduction in methane from cattle can contribute to meeting carbon neutrality.

A metabolism study was conducted to evaluate Alga 1.0, a product containing bromoform, fed to cattle to evaluate the effects on gas emissions. Treatments were (0, 69, or 103 g/d Alga 1.0) fed in a corn-based diet. Headbox-style indirect calorimeters were used to measure gas emissions. Feeding Alga 1.0 linearly …

Experimental Analysis Of Nonlinear Wave Propagation In Bistable Mechanical Metamaterials With A Defect, Samuel R. Harre

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Mechanical metamaterials built up of compliant units can support the propagation of linear and nonlinear waves. A popular architecture consists of a one-dimensional chain of bistable elements connected by linear springs. This type of chain can support nonlinear transition waves that switch each element from one stable state to the other as they propagate along the chain. One way to manipulate the propagation of such waves is via introduction of a local inhomogeneity, i.e., a defect in the otherwise periodic chain. Recent analytical and numerical work has shown that based on its initial velocity, a transition wave may be reflected, …

On Dyadic Parity Check Codes And Their Generalizations, Meraiah Martinez

Department of Mathematics: Dissertations, Theses, and Student Research

In order to communicate information over a noisy channel, error-correcting codes can be used to ensure that small errors don’t prevent the transmission of a message. One family of codes that has been found to have good properties is low-density parity check (LDPC) codes. These are represented by sparse bipartite graphs and have low complexity graph-based decoding algorithms. Various graphical properties, such as the girth and stopping sets, influence when these algorithms might fail. Additionally, codes based on algebraically structured parity check matrices are desirable in applications due to their compact representations, practical implementation advantages, and tractable decoder performance analysis. …

Enhanced Privacy-Enabled Face Recognition Using Κ-Identity Optimization, Ryan Karl

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

Facial recognition is becoming more and more prevalent in the daily lives of the common person. Law enforcement utilizes facial recognition to find and track suspects. The newest smartphones have the ability to unlock using the user's face. Some door locks utilize facial recognition to allow correct users to enter restricted spaces. The list of applications that use facial recognition will only increase as hardware becomes more cost-effective and more computationally powerful. As this technology becomes more prevalent in our lives, it is important to understand and protect the data provided to these companies. Any data transmitted should be encrypted …

Capturing The Generation And Structural Transformations Of Molecular Ions, Jun Heo, Doeyeong Kim, Alekos Segalina, Hosung Ki, Doo-Sik Ahn, Seonggon Lee, Jungmin Kim, Yongjun Cha, Kyung Won Lee, Jie Yang, J. Pedro F. Nunes, Xijie Wang, Hyotcherl Ihee

Department of Physics and Astronomy: Faculty Publications

Molecular ions are ubiquitous and play pivotal roles^1–3 in many reactions, particularly in the context of atmospheric and interstellar chemistry^4–6. However, their structures and conformational transitions^7,8, particularly in the gas phase, are less explored than those of neutral molecules owing to experimental difficulties. A case in point is the halonium ions^9–11, whose highly reactive nature and ring strain make them short-lived intermediates that are readily attacked even by weak nucleophiles and thus challenging to isolate or capture before they undergo further reaction. Here we show that megaelectronvolt ultrafast electron diffraction (MeV-UED)^12–14, …

Prediction Of Giant Tunneling Magnetoresistance In Ruo2/Tio2/Ruo2 (110) Antiferromagnetic Tunnel Junctions, Yuan-Yuan Jiang, Zi-An Wang, Kartik Samanta, Shu-Hui Zhang, Rui-Chun Xiao, W. J. Lu, Y. P. Sun, Evgeny Y. Tsymbal, Ding-Fu Shao

Department of Physics and Astronomy: Faculty Publications

Using first-principles quantum-transport calculations, we investigate spin-dependent electronic and transport properties of antiferromagnetic tunnel junctions (AFMTJs) that consist of (110)-oriented antiferromagnetic (AFM) metal RuO₂ electrodes and an insulating TiO₂ tunneling barrier. We predict the emergence of a giant tunneling magnetoresistance (TMR) effect in a wide energy window, a series of barrier layer thicknesses, and different interface terminations, indicating the robustness of this effect. We show that the predicted TMR cannot be explained in terms of the global transport spin-polarization of RuO₂ (110) but is well understood based on matching the momentum-dependent spin-polarized conduction channels of the two …

Differentiating By Prime Numbers, Jack Jeffries

Department of Mathematics: Faculty Publications

It is likely a fair assumption that you, the reader, are not only familiar with but even quite adept at differentiating by x. What about differentiating by 13? That certainly didn’t come up in my calculus class! From a calculus perspective, this is ridiculous: are we supposed to take a limit as 13 changes? One notion of differentiating by 13, or any other prime number, is the notion of p-derivation discovered independently by Joyal [Joy85] and Buium [Bui96]. p-derivations have been put to use in a range of applications in algebra, number theory, and arithmetic geometry. Despite the wide range …

3dgaunet: 3d Generative Adversarial Networks With A 3d U-Net Based Generator To Achieve The Accurate And Effective Synthesis Of Clinical Tumor Image Data For Pancreatic Cancer, Yu Shi, Hannah Tang, Michael J. Baine, Michael A. Hollingsworth, Huijing Du, Dandan Zheng, Chi Zhang, Hongfeng Yu

School of Computing: Faculty Publications

Pancreatic ductal adenocarcinoma (PDAC) presents a critical global health challenge, and early detection is crucial for improving the 5-year survival rate. Recent medical imaging and computational algorithm advances offer potential solutions for early diagnosis. Deep learning, particularly in the form of convolutional neural networks (CNNs), has demonstrated success in medical image analysis tasks, including classification and segmentation. However, the limited availability of clinical data for training purposes continues to represent a significant obstacle. Data augmentation, generative adversarial networks (GANs), and cross-validation are potential techniques to address this limitation and improve model performance, but effective solutions are still rare for 3D …

The Influence Of Grazing Systems On Bird Species Richness And Density In The Nebraska Sandhills, Silka L.F. Kempema, Walter H. Schacht, Larkin A. Powell

School of Natural Resources: Faculty Publications

Grazing is the de facto method of habitat management used in much of the Nebraska Sandhills. Ranchers use a variety of grazing systems, and our goal was to evaluate the effects of systems on grassland birds. We estimated the species richness and density of grassland birds for three grazing systems used on private ranches: long, medium, and short duration grazing systems. We observed sixty species, and the grazing system with pastures utilizing long duration grazing periods had the highest estimates of species richness as well as the most heterogeneous habitat structure. Differences in species richness among systems were most pronounced …

Drought In The Breadbasket Of America And The Influence Of Oceanic Teleconnections, Olivia G. Campbell, Gregory B. Goodrich

School of Natural Resources: Faculty Publications

From 1980 to 2020, drought events accounted for only 11.4% of the billion-dollar disasters in the United States (U.S.), yet caused the second-highest total amount in damages, at USD 236.6 billion. With the average cost of a drought being upwards of USD 9.5 billion, these natural disasters can create serious problems in agriculture. Drought is defined as a period of below-average precipitation that causes damage to agriculture and water supplies. Previous research has linked drought events in the U.S. Great Plains to oceanic teleconnections in the Pacific and Atlantic basins, indicating the influence of El Niño—Southern Oscillation (ENSO), the Pacific …

Pathogenicity In Chickens And Turkeys Of A 2021 United States H5n1 Highly Pathogenic Avian Influenza Clade 2.3.4.4b Wild Bird Virus Compared To Two Previous H5n8 Clade 2.3.4.4 Viruses, Mary J. Pantin-Jackwood, Erica Spackman, Christina Leyson, Sungsu Youk, Scott A. Lee, Linda M. Moon, Mia K. Torchetti, Mary L. Killian, Julianna B. Lenoch, Darrell R. Kapczynski, David E. Swayne, David L. Suarez

United States Department of Agriculture Wildlife Services: Staff Publications

Highly pathogenic avian influenza viruses (HPAIVs) of subtype H5 of the Gs/GD/96 lineage remain a major threat to poultry due to endemicity in wild birds. H5N1 HPAIVs from this lineage were detected in 2021 in the United States (US) and since then have infected many wild and domestic birds. We evaluated the pathobiology of an early US H5N1 HPAIV (clade 2.3.4.4b, 2021) and two H5N8 HPAIVs from previous outbreaks in the US (clade 2.3.4.4c, 2014) and Europe (clade 2.3.4.4b, 2016) in chickens and turkeys. Differences in clinical signs, mean death times (MDTs), and virus transmissibility were found between chickens and …

Raccoon Spatial Ecology In The Rural Southeastern United States, Jacob E. Hill, Madison L. Miller, James L. Helton, Richard B. Chipman, Amy T. Gilbert, James C. Beasley, Guha Dharmarajan, Olin E. Rhodes Jr.

United States Department of Agriculture Wildlife Services: Staff Publications

The movement ecology of raccoons varies widely across habitats with important implications for the management of zoonotic diseases such as rabies. However, the spatial ecology of raccoons remains poorly understood in many regions of the United States, particularly in the southeast. To better understand the spatial ecology of raccoons in the southeastern US, we investigated the role of sex, season, and habitat on monthly raccoon home range and core area sizes in three common rural habitats (bottomland hardwood, upland pine, and riparian forest) in South Carolina, USA. From 2018–2022, we obtained 264 monthly home ranges from 46 raccoons. Mean monthly …

Raccoon Spatial Ecology In The Rural Southeastern United States, Jacob E. Hill, Madison L. Miller, James L. Helton, Richard B. Chipman, Amy Gilbert, University Of Georgia, Guha Dharmarajan, Olin E. Rhodes Jr.

United States Department of Agriculture Wildlife Services: Staff Publications

The movement ecology of raccoons varies widely across habitats with important implications for the management of zoonotic diseases such as rabies. However, the spatial ecology of raccoons remains poorly understood in many regions of the United States, particularly in the southeast. To better understand the spatial ecology of raccoons in the southeastern United States, we investigated the role of sex, season, and habitat on monthly raccoon home range and core area sizes in three common rural habitats (bottomland hardwood, upland pine, and riparian forest) in South Carolina, USA. From 2018–2022, we obtained 264 monthly home ranges from 46 raccoons. Mean …

Relativistic Ultrafast Electron Diffraction At High Repetition Rates, K. M. Siddiqui, D. B. Durham, F. Cropp, F. Ji, S. Paiagua, C. Ophus, N. C. Andresen, L. Jin, J. Wu, S. Wang, X. Zhang, W. You, M. Murnane, Martin Centurion, X. Wang, D. S. Slaughter, R. A. Kaindl, P. Musumeci, A. M. Minor, D. Filippetto

Martin Centurion Publications

The ability to resolve the dynamics of matter on its native temporal and spatial scales constitutes a key challenge and convergent theme across chemistry, biology, and materials science. The last couple of decades have witnessed ultrafast electron diffraction (UED) emerge as one of the forefront techniques with the sensitivity to resolve atomic motions. Increasingly sophisticated UED instruments are being developed that are aimed at increasing the beam brightness in order to observe structural signatures, but so far they have been limited to low average current beams. Here, we present the technical design and capabilities of the HiRES (High Repetition-rate Electron …

Bridging Domain Gaps For Cross-Spectrum And Long-Range Face Recognition Using Domain Adaptive Machine Learning, Cedric Armel Nimpa Fondje

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

Face recognition technology has witnessed significant advancements in recent decades, enabling its widespread adoption in various applications such as security, surveillance, and biometrics applications. However, one of the primary challenges faced by existing face recognition systems is their limited performance when presented with images from different modalities or domains( such as infrared to visible, long range to close range, nighttime to daytime, profile to f rontal, etc.) Additionally, advancements in camera sensors, analytics beyond the visible spectrum, and the increasing size of cross-modal datasets have led to a particular interest in cross-modal learning for face recognition in the biometrics and …

Probing The Electroweak Phase Transition With Exotic Higgs Decays, Marcela Carena, Jonathan Kozaczuk, Zhen Liu, Tong Ou, Michael J. Ramsey-Musolf, Jessie Shelton, Yikun Wang, Ke-Pan Xie

Department of Physics and Astronomy: Faculty Publications

An essential goal of the Higgs physics program at the LHC and beyond is to explore the nature of the Higgs potential and shed light on the mechanism of electroweak symmetry breaking. An important class of models alter the thermal history of electroweak symmetry breaking from the predictions of the Standard Model (SM). This paper reviews the existence of a region of parameter space where a strong first-order electroweak phase transition is compatible with exotic decays of the SM-like Higgs boson. A dedicated search for exotic Higgs decays can actively explore this framework at the Large Hadron Collider (LHC), while …

Formal Concept Analysis For Image Classification And Machine Learning Models For Anti-Crispr Protein Discovery In Bioinformatics, Minal Khatri

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

This study investigates two critical areas in bioinformatics: enhancing transparency in medical image analysis and advancing the discovery of Anti-CRISPR (Acr) proteins, which have potential in developing more precise and controlled CRISPR-Cas gene editing tools. While CNN’s are increasingly applied in critical fields like medical diagnosis, understanding their decision-making process remains a challenge. Although visualization techniques like Saliency maps offer insights into CNN’s decision-making for individual images, they do not explicitly establish a relationship between the high-level features learned by CNN’s and the class labels across dataset. To bridge this gap, Formal Concept Analysis (FCA) framework is leveraged as a …

Soft Microreactors For The Deposition Of Microstructures And The Related Surface Chemistries Of Polymeric Materials, Jessica Wagner

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

The precise control over small volumes of liquids is of great interest to various fields such as biotechnology, drug development, and diagnostics. Working at small scales reduces cost, time, and waste, which is why microfluidic lab-on-chip technologies have become popular in a wide range of industries and applications. Additionally, there are differences in properties such as mass transport and heat dissipation at the micron scale compared to in bulk. Microfluidic devices contain several interfaces to consider when preparing to fabricate devices. The substrate/device, substrate/solution, and solution/device interfaces are all of importance and must carefully be tuned depending on the desired …

Hydroxyapatite-Based Coatings On Silicon Wafers And Printed Zirconia, Antoine Chauvin

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Dental surgery needs a naturally attract implant design that can ensure both osseointegration and soft tissue integration. Hydroxyapatite (HAp), the main mineral constituent of dentine and tooth enamel, is commonly used as a coating component, notably for overlaying titanium– or ceramics–based implants. This thesis aims to investigate the behavior of a HAp-based coating, specifically designed to be compatible with a porous substrate. Coating layers are made by sol–gel dip coating by immersion of porous substrates made by additive manufacturing into solutions of HAp, having been mixed with polyethyleneimine (PEI), to improve the adhesion of HAp on the substrate. First, the …

Motif-Cluster: A Spatial Clustering Package For Repetitive Motif Binding Patterns, Mengyuan Zhou

School of Computing: Dissertations, Theses, and Student Research

Previous efforts in using genome-wide analysis of transcription factor binding sites (TFBSs) have overlooked the importance of ranking potential significant regulatory regions, especially those with repetitive binding within a local region. Identifying these homogenous binding sites is critical because they have the potential to amplify the binding affinity and regulation activity of transcription factors, impacting gene expression and cellular functions. To address this issue, we developed an open-source tool Motif-Cluster that prioritizes and visualizes transcription factor regulatory regions by incorporating the idea of local motif clusters. Motif-Cluster can rank the significant transcription factor regulatory regions without the need for experimental …

A Climatology Of Mesoscale Airmasses With High Theta-E, Charles J. Kropiewnicki

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

A Mesoscale Airmass with High Theta-E (MAHTE) is a narrow region of larger theta-e located on the cool side of an airmass boundary. MAHTEs typically possesses higher CAPE than the warm side of the boundary, creating a more favorable environment for severe convection. MAHTEs can also be characterized by larger low-level shear and lower LCLs and may also have a propensity for supporting tornadogenesis. The majority of MAHTE research to date has been comprised of case studies, and the prevalence of MAHTEs is not well understood. This project fills that knowledge gap by creating a climatology of MAHTE occurrence. This …

Unexpectedness Stratified By Codimension, Frank Zimmitti

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

A recent series of papers, starting with the paper of Cook, Harbourne, Migliore and Nagel on the projective plane in 2018, studies a notion of unexpectedness for finite sets Z of points in N-dimensional projective space. Say the complete linear system L of forms of degree d vanishing on Z has dimension t yet for any general point P the linear system of forms vanishing on Z with multiplicity m at P is nonempty. If the dimension of L is more than the expected dimension of t−r, where r is N+m−1 choose N …

Game-Theoretic Approaches To Optimal Resource Allocation And Defense Strategies In Herbaceous Plants, Molly R. Creagar

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

Empirical evidence suggests that the attractiveness of a plant to herbivores can be affected by the investment in defense by neighboring plants, as well as investment in defense by the focal plant. Thus, allocation to defense may not only be influenced by the frequency and intensity of herbivory but also by defense strategies employed by other plants in the environment. We incorporate a neighborhood defense effect by applying spatial evolutionary game theory to optimal resource allocation in plants where cooperators are plants investing in defense and defectors are plants that do not. We use a stochastic dynamic programming model, along …

The Development And Evolution Of The Soil Health Nutrient Tool (Aka Haney Test) After Ten Years Of Implementation In A Commercial Agricultural Laboratory, Lance Michael Gunderson

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

The growing focus on soil health and regenerative agriculture has brought about the need for new integrated approaches for the analysis of soil. Prior, commercial agricultural laboratories relied on methods to measure chemical properties of the soil, such as pH and nutrients. The Soil Health Nutrient Tool (aka Haney Test) developed by Dr. Rick Haney (United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Blackland Research and Extension Station, Temple, Texas) integrates chemical and biological properties to provide a more holistic understanding of soil fertility management. Following adoption by commercial laboratories in 2013, criticisms regarding variability in measurements and lack …

Precipitation And Greenness In Pastoral Lands Of East Turkana, Kenya, Paul Akpejeluh

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

Pastoralism has long supported livelihoods and provided essential ecosystem services in landscapes of East Africa. Vegetation productivity is central to the functioning of pastoral systems but may be affected by changes in climate and landuse. Vegetation monitoring is important for understanding the effects of global change in pastoral lands; however, it can be time and resource intensive. Remote sensing provides opportunities for efficient multi-scale monitoring of vegetation and climatic drivers. In this thesis, I explore the utility of satellite and UAV remote sensing for monitoring vegetation and precipitation trends and relationships in the East of Lake Turkana Region of northern …

Connecting The Nebraska Water Quality Index To The Aquatic Microbial Community Of The North Platte River Basin, Nebraska, Paula R. Guastello

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

The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been monitored in Nebraska for nearly 20 years. Water quality parameters including those used in the Nebraska Water Quality Index have been shown in previous studies to impact bacterial growth. As such, this index has the potential to correlate with the freshwater microbial community. Here, I relate the Nebraska Water Quality Index to microbial community composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. This index …

Comparison Of Ceneb And Cohyst Hydrologic Models Within A Common Domain In Central Nebraska, William R. Moak

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

The Nebraska Department of Natural Resources (NDNR) has developed several hydrologic models to help effectively manage water resources in the state. These models guide water managers to allocate surface and groundwater supplies to a range of uses (irrigation, environmental protection, interstate water agreements) and evaluate the impacts of changes to the surface water-groundwater system (e.g., new wells, evolving recharge patterns). Two such models, the Central Nebraska (CENEB) model and the Cooperative Hydrology Study (COHYST) model cover north central and south central Nebraska, respectively, but the model domains overlap along a west-east strip between the Platte and Loup Rivers, enabling direct …

An Empirical Examination Of The Environmental Variability That Impacted Supercell Evolution, Longevity, And Severe Weather Production On 22 May 2019 In Oklahoma, Kyle D. Pittman

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

Mesoscale environmental heterogeneity can have significant impacts on thunderstorm organization, evolution, longevity, and severe weather production. This study examines the 22 May 2019 thunderstorm event in Oklahoma, where a relatively broad area of strong instability and vertical wind shear existed along a synoptic boundary and in the open warm sector that would seem to support long-lived supercells and tornadoes. There were two particularly dangerous situation (PDS) tornado watches issued during the event, but few severe reports and no tornadoes formed in the watch that covered the southwestern portion of the state. Several tornadic supercells and many more severe reports occurred …