Digital Commons Network^™

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 …

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

Complex Biosystems Program: Dissertations and Student Research

The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …

Continuous Time Recurrent Network For Human Activity Detection, Abdallah Al Zubi

Durham School of Architectural Engineering and Construction: Dissertations, Theses, and Student Research

Human activity detection is crucial to personalize the control of the building environment. For example, understanding certain human activities (e.g., walking, sitting, etc.) for an occupant in a building helps provide the proper thermal comfort control. However, these applications require large-scale neural networks that are challenging to implement and train.

In this thesis, we implemented a continuous-time recurrent neural network implementation (CTRNN) network that can solve real-time human activity detection with a smaller-size network. The CTRNN uses differential equations with a time constant to describe the neuron equations. It was implemented and trained for the first time using TensorFlow. Specifically, …

K-12 Teachers' Perspectives On Mobile Technology Integration: A Qualitative Study, Steven Justin Bingham

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

The purpose of this qualitative case study was to develop an understanding of mobile technology integration in K–12 classrooms from the perspective of classroom teachers during the 2022-2023 school year. The increase in mobile technologies being utilized in schools made it imperative to understand how mobile devices are being integrated into the classroom from the teacher’s perspective. The central research question was, how do teachers at K–12 schools in the Midwest describe their perception and usage of mobile technology integration in teaching and learning? The data collection consisted of semi-structured interviews with fourteen participants from one school district in the …

Nebraska Elementary School Teachers’ Desired Principal Leadership Qualities And Teachers’ Interest Of Becoming A Principal, Gene James Russel

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

The purpose of this study is to examine Nebraska elementary teachers’ desired leadership qualities and teachers’ interest of becoming a principal. Part of this study is a replication of William A. Schernikau’s dissertation completed at the University of Nebraska-Lincoln in 1991. Part of William A. Schernikau’s study was designed to replicate a study that was conducted in 1964 by Ward Campbell at the University of Southern California.

In Schernikau’s (1991) study, there are seven categories of principal leadership qualities that was examined based on elementary teachers’ perceptions: (a) management skills, (b) staff relations, (c) community relations, (d) personal characteristics, (e) …

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 …

Uv Dynamics Of Different Ring Molecules Studied By Ultrafast Electron Diffraction, Sajib Kumar Saha

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

Understanding natural light-induced phenomena requires a direct viewing of atomic motion during structural evolution, which, in turn, facilitates controlling and manipulating these light-induced processes. Ultrafast Electron Diffraction (UED) is a structure-sensitive technique that can probe electronic and nuclear dynamics at sub-angstrom spatial and femtosecond time scales. UED has become a vital tool for studying photo-induced molecular dynamics and underlying science. Organic ring systems are prevalent in biology, materials, and pharmaceuticals. Their synthesis and transformation are fundamental in synthetic chemistry, influencing various fields. We used UV photons to photo-excite different cyclic molecules and investigated their photo-dynamics using gas phase UED. The …

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 …

Modeling Overdraft-Driven Nitrate Transport In Shallow Wells For Mitigation And Scenario Planning, Jonathan Cronk

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

In Nebraska, average nitrate concentrations in groundwater have doubled since 1974, making water quality management more important than ever. As droughts, heat waves, and floods become more common climate events, understanding their impacts will be necessary to make informed management decisions. Emerging literature describes that drought correlates to an increase in the concentration of nitrate-N at domestic and irrigation wells, however the relative contributions of the mechanisms thought to be responsible is currently unknown.

This research assessed the impact of recharge and pumping rate changes as two mechanisms affecting nitrate-N concentration during drought, assessed the relationship between well depth and …

Meta-Analysis Of Insulated Concrete Wall Panel Design Methods For Shear And Flexure Behavior, Maryam Al-Bayati

Durham School of Architectural Engineering and Construction: Dissertations, Theses, and Student Research

Insulated Concrete wall panels have been designed and constructed since the early 1950s with various shear ties, dimensions, and methods; nonetheless, thermal bridging and rational design are still a concern. Many companies have recently developed plastic connectors that have gradually replaced solid concrete sections and steel connectors due to their superior thermal efficiency and strength. However, there is no generally accepted method for predicting the behavior of sandwich wall panels in structural engineering practice or codes, but many methods have been used since the early 1920. This study aims to evaluate the accuracy of current methods for predicting the flexural …

Gene Variants In Bola-Dmb, Decr1, Fasn And Srebf1 Associated With Conceptus Death On Day 16 Of Pregnancy In Holstein Cows [Abstract], Carolina L. Gonzalez-Berrios, Courtney Bowden, Pablo J. Pinedo, Jeanette V. Bishop, Hana Van Campen, Thomas R. R. Hansen, Milton G. Thomas

United States Department of Agriculture Wildlife Services: Staff Publications

Investigating the influences of single nucleotide polymorphisms (SNP) associated with conceptus death (CD) on day 16 of pregnancy could distinguish cows who have inferior value for fertility traits. We hypothesized that CD is associated with SNP genotypes that disrupt maternal recognition and lead to early pregnancy loss. RNA sequences from Holstein cow pregnancies (n = 15) with normal conceptuses (Norm) or CD were subjected to SNP discovery via Qiagen CLC Genomics Workbench. Selected SNP were based on previous fertility studies, differentially expressed genes within pregnancy development analyses and proximity to SNP associated with fertility traits in the Cattle QTL …

Report To The U. S. Congress On Financing Mechanisms For Open Access Publishing Of Federally Funded Research, White House Office Of Science And Technology Policy

Copyright, Fair Use, Scholarly Communication, etc.

Executive Summary The White House Office of Science and Technology Policy (OSTP) submits this report to the Appropriations Committees of the Senate and the House in fulfillment of the requirement in the Committee Report accompanying the Consolidated Appropriations Act, 2023 (P.L. 117-328) for financing mechanisms for open access publishing of federally funded research.1 According to that Report, “The Committee recognizes the considerable progress made by OSTP” and “encourages OSTP to continue its efforts to coordinate the implementation of public access policies across Federal departments and agencies and to identify additional opportunities to enhance access to the results of Federally funded …

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 …

A Study Of The Behavior Of Light And Matter Using Computer Simulations And Experimental Techniques, Bret Alan Gergely

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

This thesis comprises four individual chapters, each showcasing unique research and findings. The first chapter details the simulation of an experiment that was performed by Shahriar S. Afshar. He claimed in 2007 that his modified version of the double-slit experiment violated complementarity. A priniciple developed by Niels Bohr. The experiment is simulated using the path integral formulation of quantum mechanics and agreement is found with the wave-particle duality relation given by Englert, Greenberg and Yasin (EGY). It is concluded that the use of Afshar’s experiment to provide a testbed for quantum mechanical interpretations is limited. The second chapter presents an …

A Generalized Machine Learning-Based Classifier Considering Cost-Effective Features For Automated Fault Detection And Diagnosis (Afdd) Of Packaged Rooftop Units, Md Rasel Uddin

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

Packaged rooftop units (RTUs) are widely used for space conditioning in commercial buildings and manufacturing facilities. The typical soft faults related to RTUs degrade the system's performance in terms of cooling capacity, power consumption, and Coefficient of Performance (COP), detrimentally affecting both the equipment and energy consumption and the environment. Previous research in soft fault detection for rooftop units lacked classifier validation using lab and field data, developing a generalizable algorithm, and analyzing its performance across varying fault intensities.

Using a simulated data library for multiple rooftop units, this study proposes a machine-learning classifier with a reduced set of 9 …

An Analysis Of Plant Response To Herbivory, Lawrence Gustavo Seminario-Romero

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

Herbivory is often believed to always negatively affect the growth of plants, but there are plant species that can actually benefit from being consumed by herbivores. These plants have a phenotypic trait known as “compensatory growth.” A plant that exhibits compensatory growth is able to increase its intrinsic growth rate as a response to taking damage caused by herbivory, and as a result, produce more biomass. Very few mathematical models used to describe plant-herbivore interactions have accounted for plant compensatory growth. Moreover, these models tend to assume that herbivores follow a Holling type II functional response, which may not necessarily …

Why Domain-Specific Science Knowledge Matters In Teacher Certification: Focusing On Evidence For Effective Science Teaching (Revised Version), Elizabeth B. Lewis, Lyrica L. Lucas, Amy Tankersley, Elizabeth Hasseler

Department of Teaching, Learning, and Teacher Education: Faculty Publications

The landscape of teacher preparation is complex. From a research perspective, how to prepare teachers presents as a multilevel, multivariable puzzle. For decades, federal and state policymakers, educational researchers, and administrators, along with teacher education institutions, school districts, and other stakeholders have tried to determine and measure the key malleable factors that result in effective teaching (NRC, 2010).

Periodically, state departments of education review secondary science teaching endorsement policy guidelines. As revisions occur, teacher educators in higher education and district administrators need to engage in a multidisciplinary discussion about:

1. the ways in which strong domain-specific science content knowledge contributes …

Skin Lipids Alone Enable Conspecific Tracking In An Invasive Reptile, The Argentine Black And White Tegu Lizard (Salvator Merianae), M. Rockwell Parker, Eric A. Tillman, Lauren A. Nazarian, Megan L. Barlowe, Julianna M. Lincoln, Bryan M. Kluever

United States Department of Agriculture Wildlife Services: Staff Publications

Locating potential mates in non-native habitats is one of the most important challenges faced by invasive vertebrate species. The Argentine black and white tegu lizard (Salvator merianae) is a major invasive reptile species in the contiguous United States and is rapidly expanding its range across Florida and the Southeast, in part due to inadequate management strategies and tools. Because a wide array of reptiles, especially squamates (snakes and lizards), have been well-studied for their reliance on chemical cues to locate conspecifics, our project aimed to isolate chemical cues from tegus and assess the ability of adult males and …

Osc-Co2: Coattention And Cosegmentation Framework For Plant State Change With Multiple Features, Rubi Quiñones, Ashok Samal, Sruti Das Choudhury, Francisco Muñoz-Arriola

School of Computing: Faculty Publications

Cosegmentation and coattention are extensions of traditional segmentation methods aimed at detecting a common object (or objects) in a group of images. Current cosegmentation and coattention methods are ineffective for objects, such as plants, that change their morphological state while being captured in different modalities and views. The Object State Change using Coattention-Cosegmentation (OSC-CO²) is an end-to-end unsupervised deep-learning framework that enhances traditional segmentation techniques, processing, analyzing, selecting, and combining suitable segmentation results that may contain most of our target object’s pixels, and then displaying a final segmented image. The framework leverages coattention-based convolutional neural networks (CNNs) and …

Short History Of The Unl Digital Commons, Paul Royster

University of Nebraska-Lincoln Libraries: Presentations

From 2005 through 2023, the UNL Digital Commons grew to be a leading example of an institutional repository. This presentation reports on personnel, history, strategy, and outstanding examples of series or contributors.

Announcement about the session:

UNL Digital Commons began in 2005 and grew into America’s 3rd-largest and most-trafficked institutional repository. Approaching 100 million downloads and spreading UNL scholarship and branding across the globe, the UNL Digital Commons boasts works from a wide variety of affiliated faculty, researchers, and students. Their participation is opening the dissemination of scholarship in radical and fundamental ways. In this session, Paul Royster traces this …

Pleistocene Bats (Late Irvingtonian And Late Rancholabrean) From Nuckolls And Sherman Counties, Nebraska, Nicholas J. Czaplewski, Richard George Corner

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

We document rare finds of fossil bats from two localities representing the Pleistocene epoch in southern and central Nebraska, Albert Ahrens locality (No-104, late Irvingtonian age, Middle Pleistocene), Nuckolls County, and Litchfield (Sm-102, late Rancholabrean age, latest Pleistocene), Sherman County. The Albert Ahrens local fauna with strong boreal influence has produced two bats, Lasiurus cf. borealis and Cf. Myotis sp. The Litchfield local fauna, also showing a strong boreal influence, has yielded two bats, Eptesicus fuscus and Cf. Myotis, among a diverse Pleistocene fauna of small vertebrates and a pollen record indicating a boreal mixed conifer and deciduous woodland, …

Executive Order On The Safe, Secure, And Trustworthy Development And Use Of Artificial Intelligence, Joseph R. Biden

Copyright, Fair Use, Scholarly Communication, etc.

Section 1. Purpose. Artificial intelligence (AI) holds extraordinary potential for both promise and peril. Responsible AI use has the potential to help solve urgent challenges while making our world more prosperous, productive, innovative, and secure. At the same time, irresponsible use could exacerbate societal harms such as fraud, discrimination, bias, and disinformation; displace and disempower workers; stifle competition; and pose risks to national security. Harnessing AI for good and realizing its myriad benefits requires mitigating its substantial risks. This endeavor demands a society-wide effort that includes government, the private sector, academia, and civil society.

My Administration places the highest urgency …

Roadway Floods And Their Associated Weather-Related Conditions: New Insights Using Cars 511 Data For State And Federal Highways In Nebraska, Usa, Logan R. Bundy, Mark Anderson, Clinton M. Rowe, Rezaul Mamood

Department of Earth and Atmospheric Sciences: Faculty Publications

This study examined roadway flooding event data provided by the Nebraska Department of Transportation via the Condition Acquisition Reporting System (CARS) 511 archive (2016–2021). With these data, a novel analysis was completed to further the understanding of where, when, and why (meteorologically) roadway flooding occurs on Nebraska state and federal highways. In the study period, 298 roadway floods occurred, with an annual median of 16 per year. There was a greater risk for roadway floods to transpire more frequently in eastern Nebraska, which was attributed to the spatial climatology of heavy rainfall and the higher density of roadways and rivers. …

A Critical Review Of Risk Matrices Used In Water Safety Planning: Improving Risk Matrix Construction, Kaycie Lane, Steve E. Hrudey

Department of Civil and Environmental Engineering: Faculty Publications

Risk matrices are used in water safety planning to prioritize improvements to drinking water systems. While water safety plans (WSPs) are promoted globally, no study has evaluated whether risk matrices are comprehensively constructed to accurately assess risk. We used risk matrix criteria adapted from previous risk matrix research to evaluate risk matrices found in twelve templates across global jurisdictions. WSP templates were found using the WSPortal website and definitions of likelihood and impact were extracted from each template to assist in the evaluation of WSP risk matrices. Application of the criteria developed from a detailed mathematical analysis by revealed that …