Physical Sciences and Mathematics Commons^™

A Data-Driven Discovery System For Studying Extracellular Microrna Sorting And Rna-Protein Interactions, Sasan Azizian

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

Interactions between microRNAs (miRNAs) and RNA-binding proteins (RBPs) are pivotal in miRNA-mediated sorting, yet the molecular mechanisms underlying these interactions remain largely understudied. Few miRNA-binding proteins have been verified, typically requiring extensive laboratory work. This study introduces DeepMiRBP, a novel hybrid deep learning model designed to predict microRNA-binding proteins. The model integrates Bidirectional Long Short-Term Memory (Bi-LSTM) networks with attention mechanisms, transfer learning, and cosine similarity to offer a robust computational approach for inferring miRNA-protein interactions.

DeepMiRBP is implemented through two distinct architectures. The first architecture employs a Y-shaped model that uses Bi-LSTM networks and transfer learning to extract contextual …

On Neumann Boundary Conditions For Nonlocal Models With Finite Horizon, Scott Alex Hootman-Ng

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

Nonlocal models are have recently seen an explosive interest and development in the context of fracture mechanics, diffusion, image processing, population dynamics due to their ability to approximate differential-like operators with integral operators for inherently discontinuous solutions. Much of the work in the field focuses on how concepts from partial differential equations (PDEs) can be extended to the nonlocal domain. Boundary conditions for PDEs are crucial components for applications to physical problems, prescribing data on the domain boundary to capture the behavior of physical phenomena accurately with the underlying model. In this thesis we specifically examine a Neumann-type boundary condition …

Applications Of Artificial Intelligence On Drought Impact Monitoring And Assessment, Beichen Zhang

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

Drought, a prevalent and consequential natural disaster, poses widespread, indirect challenges across environmental and societal dimensions. Despite considerable focus on monitoring meteorological and hydrological drought and studying their characteristics, there is a gap in assessing its multifaceted impacts, especially on societal sectors. The dissertation comprises three research essays utilizing artificial intelligence to quantitatively study multi-dimensional drought impacts. The first essay leveraged deep learning and natural language processing to predict multi-dimensional drought impacts from textual datasets, including social media, news media, and citizen scientist reports. The findings demonstrate superior performance over traditional methods and unveil the spatial and temporal heterogeneity of …

Search For Physics Beyond The Standard Model In Top Quark Production With Additional Leptons In The Context Of Effective Field Theory, Furong Yan

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

The dissertation presents a search for new physics impacting top quark productions within the framework of effective field theory (EFT). Potential new physics effects are parameterized in terms of 26 dimension-six EFT operators into the event yields of six distinct top production processes in the detector level. The analysis targets multilepton final states consisting of two leptons of the same charge, three leptons and four leptons. The events are further categorized and binned in terms of kinematic distributions in order to gain sensitivity to the new physics effects. A likelihood function is formulated based on the predicted distribution in each …

Semigroup Well-Posedness And Finite Element Analysis Of A Biot-Stokes Interactive System, Sara Mcknight

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

The coupling of a porous medium modeled by the Biot equations and a fluid has many biological applications. There are numerous ways by which to model the fluid and to couple the porous medium with the fluid. This particular model couples the Biot equations to Stokes flow along the boundary, through the Beavers-Joseph-Saffman conditions. We address semigroup well-posedness of the system via an inf-sup approach, which along the way requires consideration of a related but uncoupled static Biot system. We also present the results of finite element analysis on both the uncoupled Biot system and the coupled system.

Advisor: Sara …

Perturbations Of Representations Of Cartan Inclusions, Catherine Zimmitti

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

A free semigroup algebra is the unital, weak operator topology closed algebra generated by a collection of Cuntz-Toeplitz isometries in B(H). Ken Davidson and David Pitts asked in [9] if a self-adjoint free semigroup algebra exists; Charles Read answered this question in [28] by constructing such an example, which Ken Davidson later simplified in [8]. The construction takes a standard representation of O₂ and multiplies it by a unitary operator in the diagonal MASA of the representation. This results in a new "perturbed" representation of O₂ generating a self-adjoint free semigroup algebra.

In this thesis, …

Further Developing Drought Early Warning Information Systems Using Mixed-Methods And Multiple Streams Of Data, Caily Claire Schwartz

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

Drought is a complex phenomenon with varying degrees of impacts and monitoring methods. No drought is alike, creating a challenge for both water managers and communities. No area is immune to a drought. Due to the cyclical nature of drought events, clear information to those impacted is necessary to reduce risk and move towards proactive responses, as opposed to reactive responses. To better provide communication and mitigation tools, Drought Early Warning Information Systems (DEWIS) have been developed in various regions and contexts. To improve early warning, an understanding of the end user’s perceptions of risk, and the applicability of data …

Integrating Water And Nitrogen Management For Sustainable Agriculture: Optimizing Resource Use Efficiency And Maximizing Crop Productivity, Jiaming Duan

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

Advisors: Derek Heeren and Daran Rudnick Maize, accounting for over 95% of national grain production in the United States, is highly sensitive to water and nitrogen (N) inputs. Conventional agricultural practices often lead to excessive application, causing groundwater contamination through nitrate leaching. Therefore, there is a demand for integrating water and nitrogen management with innovative scheduling methods for sustainable agricultural development.

This dissertation first reviewed two decades of U.S.-based research, highlighting the optimal management of water and N to enhance yield, water use efficiency (WUE), and nitrogen use efficiency (NUE). Findings indicate that maintaining optimal levels of N and water …

Long Term Ultrasonic Monitoring And Machine Learning Investigation Of Micro-Crack Damaged Concrete, Yalei Tang

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

The thermal modulation method is a recently developed nonlinear ultrasonic technique for evaluating material damage. This method utilizes thermal strain changes resulting from temperature variations to excite the nonlinear behavior of materials and modulate high-frequency ultrasonic waves within them. Its working principle suggests significant potential for application in large-scale concrete structures and in-situ monitoring of real structures. Despite numerous laboratory demonstrations of its effectiveness, several gaps remain before it can be applied to in-service large concrete structures.

This study investigates the potential of the thermal modulation technique for evaluating concrete structures in ambient conditions, addressing key uncertainties for practical implementation. …

Development Of Feature Extraction Models To Improve Image Analysis Applications In Cancer, Yu Shi

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

Cancer poses a significant global health challenge. With an estimated 20 million new cases diagnosed worldwide in 2022 and 9.7 million fatalities attributable to the disease, the economic burden of cancer is immense. It impacts healthcare systems and imposes substantial costs for its care on patients and their families. Despite advancements in early detection, prevention, and treatment that have reduced overall cancer mortality rates, the growing prevalence of cancer, particularly among younger individuals, remains a pressing issue.

Recent advancements in medical imaging technology have progressed significantly with the help of emerging computer vision and artificial intelligence (AI) technology. Despite these …

Optimizing Scalability For Formal Analysis With Evolutionary Algorithm, Jianghao Wang

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

Predominantly employed to tackle hardware validation challenges in the early years, formal methods have since expanded to software engineering, introducing a significant level of rigor and precision to software analysis. Its use of mathematical notations and logical reasoning allows for abstract modeling of programs, enabling researchers and engineers to perform a multitude of analysis tasks to verify system dependability and rigorously prove the correctness of system properties. Despite the availability of many automated analysis tools including those considered lightweight, the practical adoption of formal methods in software development has been limited due to scalability concerns, especially when applied to large …

Virtual Unknotting Numbers For Families Of Virtual Torus Knots, Kaitlin R. Tademy

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

A virtual torus knot T(p,q,VC) sits in the intersection of the well-understood torus knot and the not-so-well-understood virtual knot, making it an intriguing object to study.

The unknotting number of a classical knot K is defined unambiguously. However, "the" unknotting number when K is a virtual knot is not as clear to define, since virtual knots have both classical and virtual crossings. We will define virtual unknotting number vu(K) as the minimum number of (classical) crossing changes required to unknot K. Under this definition of virtual unknotting, not all …

We're Swarming Again! Swarming, Collectivity, And Trope: The Case Of Extinction Rebellion, Tyler J. Behymer

Department of Communication Studies: Dissertations, Theses, and Student Research

This thesis explores the rhetoric of the eco-movement Extinction Rebellion, focusing on the use of swarming and nature tropes to mobilize collective action and revivify contemporary notions of collectivity. Drawing on rhetoric of social movement scholarship, cultural studies, and psychoanalysis, this essay theorizes swarming as a tropological economy that expands the conditions of propriety in the context of collectivity. Through an analysis of Extinction Rebellion’s discourse, this study demonstrates how the naturalization of swarming tropes works in various ways to rewild conventional political discourse, galvanize disruptive collective assembly, and challenge green neoliberalism.

Advisor: Casey Ryan Kelly

Assessing Soil Properties & Suitability For Optimized Irrigation Development In Sudan, Northern Africa, Suhib O. Hamid

Department of Biological Systems Engineering: Masters Project Reports

In Chapter 1, soil properties essential for efficient irrigation are thoroughly assessed. Factors such as soil texture, infiltration rates, and nutrient content are analyzed to provide insights into the selection of modern irrigation systems. Utilizing data collected from 3,192 locations through GPS and laboratory analyses, alongside sophisticated ranking systems, the research determines the most suitable irrigation methods for specific soil series. Findings highlight the remarkable efficiency of drip irrigation across various soil types, contrasting with the consistently lower performance of surface irrigation. The chapter emphasizes the significance of considering soil variability, evapotranspiration, and investment factors in selecting irrigation methods for …

Remotely Sensed Early Warning Of Algal Blooms In An Eastern Nebraska Reservoir: A Comparison Of Temporal And Spatial Indicators, Mercy Kipenda

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

Cyanobacterial harmful algal blooms (CyanoHABs) detrimentally affect human, animal, and ecosystem health. Remotely sensed early warning systems for cyanoHABs in inland lakes could contribute to more proactive water quality monitoring and help mitigate negative impacts. Advances in freely available remote sensing imagery, with finer spatial, temporal, and spectral resolutions, present new opportunities for the development and comparative analysis of methods to detect sudden deterioration in lake water quality. In this thesis, I compared and tested for temporal and spatial early warning signals of cyanoHABs in field-based and remotely sensed datasets from 2019 to 2023 in Pawnee Lake in southeast Nebraska, …

Studies Of Exotic Electronic, Optical, And Electrochemical Properties In Nanoparticle Assembly And Graphene, Jay Min Lim

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

It is well known that exotic properties and phenomena emerge as structural dimensions shrink to nanoscales. We self-assembled one-dimensional chains of gold nanoparticles in solution and quantified the growth process by monitoring the redshift of localized surface plasmon resonance (LSPR). Curiously, the redshift stopped while the chains continued to rearrange as manifested by gradual reduction in the LSPR peak. Using electromagnetic simulations, we quantitatively explained the phenomena as a rapid “addition-polymerization” followed by a sharp transition to “condensation-process.” Next, recognizing the significant electric field enhancement in the interparticle gap, a photoluminescent-active Eu³⁺ ion was used to probe Surface-Enhanced Photoluminescence …

Smart Automatic Modal Hammer Predictor-Corrector Approach For Accurate Excitation Of Dynamical Systems, Mohammad Nasr

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

This research introduces an innovative solution that revolutionizes the study of linear and nonlinear dynamical systems—a smart automatic modal hammer. With its affordability and intelligent capabilities, this automatic modal hammer becomes an invaluable tool for research and industry, enabling repeatable strikes with precise force control. This system's significance becomes particularly evident when studying nonlinear systems, which heavily rely on the excitation level for their dynamics. By offering a cost-effective design this proposed system proves to be robust in accelerating research on nonlinear dynamics, providing researchers with an efficient and accessible means to delve deeper into these complex systems. The proposed …

The Growth Of Ethanol In Brazil: Sugarcane, Corn, And A Few Other Things, Fabio Mattos

Cornhusker Economics

Although we can expect more ethanol produced from corn in the coming years, it is unclear whether it will keep expanding at the same pace as in recent years or how much it will contribute to total ethanol production.

One point to keep an eye on is the typical dynamics of markets. If supply and demand conditions and price movements make corn-ethanol more profitable, ethanol plants in Brazil will keep increasing their production. If it makes more economic sense to produce corn-ethanol (as it happened recently), they will use more corn to produce ethanol.

Supply and demand conditions for ethanol, …

Multi-Case Study Of Left-Flank Boundaries Within Supercells, Peyton B. Stevenson

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

This study investigates the prevalence and significance of forward-flank convergence boundaries (FFCBs) and left-flank convergence boundaries (LFCBs) in shaping the structure and intensity of supercells, using observational data from various field projects. Unlike previous research focusing on individual cases, this study examines a diverse range of cases to provide comprehensive insights into the relationship between these boundaries and supercell characteristics such as intensity, longevity, and tornadogenesis. By analyzing high-resolution surface data, the research addresses the frequency, location, and intensity of these boundaries, and their impact on pseudo vertical vorticity, pseudo convergence, and density gradients. A total of 228 boundary identifications …

Biostratigraphic Revision Of Esthonyx (Tillidontia, Mammalia) In The Contect Of Climate Change In The Lower Eocene Of The Bighorn Basin, Wyoming, John Colter Johnson

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

Esthonyx is an early Eocene tillodont found in North America, Europe, and India. The genus was named by Edward Drinker (E. D.) Cope in 1874 based on specimens from the San Jose Formation in New Mexico. Since then, several species of Esthonyx have been described from North America alone. The best record of Esthonyx comes from the central Bighorn Basin (BHB) in Wyoming, where it appears in 220 localities in a 640 m-thick stratigraphic succession. Since the last summary of Esthonyx in the BHB, several hundred new specimens have been collected and curated at the Denver Museum of Nature and …

Phylogeny And Disparity Of Ammonoid Family Acanthoceratidae Over Ocean Anoxic Event 2, Lindsey Howard

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

The widespread use of genera as proxies for species in paleobiological studies might affect the results of these studies. Although most attention has been given to taxonomic diversity studies, this could also be true of disparity and phylogenetic studies. In particular, the assumption that particular character states truly diagnose all members of a genus might distort results. This study examines the disparity of Acanthoceratid ammonoids at both the generic and species level. 149 species from 42 genera were examined with 52 characters measured. Following the measurements, an inverse modeling simulation was run 100 times to generate a simulated phylogeny with …

Design And Evaluation Of An Esa-Based Method Of Ensemble Subsetting For A Wofs (Warn On Forecast-Like System), Daniel J. Butler

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

Forecasting severe thunderstorm environments in the southeastern United States can be challenging due to mesoscale heterogeneities such as shortwave troughs, pre-existing airmass boundaries, cold fronts aloft, low-level jets, dry air intrusions, and mesoscale lows. To combat these challenges, ensemble sensitivity analysis (ESA) may be applied to a Warn-on-Forecast (WOF)-like ensemble to improve forecasts of severe convection through ensemble weighting and subsetting. Ensemble-based weighting and subsetting uses ensemble members that most accurately represent the thunderstorm environment in areas of mesoscale heterogeneity. This study creates and evaluates the ensemble-based weighting and subsetting in four cases of severe thunderstorm occurrence. The open parameter …

Assessing Soil Properties For Optimized Irrigation Development In Sudan, Northern Africa, Suhib Hamid, Derek M. Heeren, Aaron R. Mittelstet, Saleh Taghvaeian, Randall S. Ritzema

Department of Biological Systems Engineering: Conference Presentations and White Papers

Sustainable irrigation methods maximize agricultural productivity in Northern African countries like Sudan. This project evaluates soil properties to develop optimized irrigation strategies for Sudan's arid and semi-arid climate. Assessing soil characteristics such as texture, infiltration rates, and nutrient content informs the selection of modern irrigation systems. Data from 3,192 locations, collected using GPS and ring infiltrometers for infiltration rates, alongside laboratory analyses for soil properties, were employed. A ranking system determined suitable irrigation systems for specific soil classes, considering factors like slope, wind, crop tolerance, available water capacity (AWC), drainage, germination, capital cost, labor cost, maintenance, and evapotranspiration (ET). The …

Hybridization Between The Rare Gray-Headed Chickadee And The Abundant Boreal Chickadee In The Midst Of Shifting Climate, Matthew R. Armstrong

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

As species respond to changing climate, distributions and abundances may shift and alter species interactions. Hybridization, a relatively widespread phenomenon becoming more common with climate change, can have beneficial and detrimental effects on population growth rates and genetic integrity. Beneficial effects due to the introduction of advantageous alleles and increased genetic diversity may result from hybridization. Species may also accrue fitness costs associated with changing climates if mismatches occur between environmental variables and phenotypes. The gray-headed chickadee, Poecile cinctus lathami, is an extremely rare songbird that has experienced marked declines in recent decades within its restricted distribution in Alaska …

Population Demography, Occupancy, And Connectivity Of Invasive Bigheaded Carp In The Platte River, Nebraska And Its Tributaries, Blake W. Logan

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

Silver Carp Hypophthalmichthys molitrix and Bighead Carp H. nobilis, collectively referred to as bigheaded carp, are invasive species in the United States of America that have expanded their range throughout the Missouri River basin in the last three decades. It may be desirable to develop management plans directed at the monitoring, control, or removal of bigheaded carp within the Missouri River basin. However, a knowledge gap exists regarding bigheaded carp ecology in Missouri River tributaries, which may be important for the development of management plans. As such, this study characterized bigheaded carp population demographics, occupancy, and connectivity in …

Virtual Fencing In Livestock Management: Effects On Beef Cattle Stress And Enhancing Wildlife Conservation, Kaitlyn E. Dozler

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

I examined the effects of virtual fencing on beef cattle stress and how implementing the technology can aid wildlife habitat conservation at the University of Nebraska Gudmundsen Sandhills laboratory (GSL) near Whitman, NE. First, I examined how virtual fencing influences acute heart rate changes in beef cattle fitted with the virtual fencing collars. No significant difference in the average heart rate of a cow (P > 0.05) was observed between the 30 min control and virtual fenced periods for both trial dates. Second, I examined the influence of topography on wildlife species richness and presence at GSL using wildlife camera …

Spatial Ecology Of Mountain Lions Throughout Their Distribution In California, Kyle D. Dougherty

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

Mountain lions (Puma concolor) have been studied extensively throughout their wide geographic distribution in the Western Hemisphere, but most research has been conducted at relatively small spatial scales. We used GPS telemetry data contributed by researchers in 16 study areas throughout California to advance understanding of mountain lion spatial ecology. First, we investigated multi-scale resource selection of mountain lions relative to spatially varying risk of intentional human-caused mortality associated with livestock depredation management. We show that individuals that proactively avoided mortality risk when selecting home ranges were able to relax their avoidance of risk when making resource selection …

Enhancing Water Sustainability In North Africa: Literature Review And Synthesis Of Current Knowledge Gaps In Sudan, Osman M. A. Adam, Aaron R. Mittelstet, Derek M. Heeren, Troy E. Gilmore

Department of Biological Systems Engineering: Conference Presentations and White Papers

This study delves into the critical role of groundwater in addressing global water challenges, with a focus on the Nubian Sandstone Aquifer System (NSAS) in North Africa. Groundwater constitutes a source of potable water, irrigation, and industrial use, especially in arid regions where surface water is limited. We analyzed the status of water quantity, withdrawals, recharge, and geological characteristics in the NSAS, specifically in Sudan, Egypt, Libya, and Chad. Though the NSAS is largely an untapped resource, we evaluated various scenarios to determine the quantity of cropland that can be sustainably irrigated. The NSAS is located in an arid region, …

Heat Stress Changes The Bovine Methylome And Transcriptome And Investigation Of Two Novel Genetic Defects In Cattle, Rachel Renae Reith

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

Heat stress is a major concern for livestock producers due to its negative impact on animal health and productivity. Heat stress does so by altering expression of genes through different regulatory mechanisms such as DNA methylation. Understanding how heat stress alters gene expression will help elucidate the genetic basis of physiological changes as well as identify targets for possible heat stress mitigation. The purpose of the first study was to understand how heat stress alters the adipose and skeletal muscle transcriptomes in zilpaterol-fed Brahman, as zilpaterol improves muscle growth and may mitigate the effects of heat stress. Differential expression and …

Integrating Remote Sensing And Machine Learning To Determine Past, Current And Future Crop Water Use From The Nubian Sandstone Aquifer System, Moaz Ishag

Department of Biological Systems Engineering: Dissertations and Theses

The agriculture sector is a significant consumer of water, and sustainable water use begins with monitoring irrigated land. Delineating irrigated land supports decision-makers and promotes the sustainable use of this crucial resource. This study focuses on the Nubian Sandstone Aquifer System (NSAS), the largest aquifers in the world, which spans Egypt, Sudan, Libya, and Chad. The study aims to: 1) quantify the increase in irrigated hectares (both pivot and non-pivot) from 2000-2001 to 2023-2024; 2) identify major irrigated crop types and their water requirements; and 3) quantify groundwater crop water use from the NSAS using remote sensing via the Google …