Physical Sciences and Mathematics Commons^™

Efficient Two-Stage Analysis For Complex Trait Association With Arbitrary Depth Sequencing Data, Zheng Xu, Song Yan, Shuai Yuan, Cong Wu, Sixia Chen, Zifang Guo

School of Computing: Faculty Publications

Sequencing-based genetic association analysis is typically performed by first generating genotype calls from sequence data and then performing association tests on the called genotypes. Standard approaches require accurate genotype calling (GC), which can be achieved either with high sequencing depth (typically available in a small number of individuals) or via computationally intensive multi-sample linkage disequilibrium (LD)-aware methods. We propose a computationally efficient two-stage combination approach for association analysis, in which single-nucleotide polymorphisms (SNPs) are screened in the first stage via a rapid maximum likelihood (ML)-based method on sequence data directly (without first calling genotypes), and then the selected SNPs are …

How Do Land Use And Land Cover Changes After Farmland Abandonment Affect Soil Properties And Soil Nutrients In Mediterranean Mountain Agroecosystems?, Estela Nadal-Romero, Makki Khorchani, Leticia Gaspar, José Arnáez, Erik Cammeraat, Ana Navas, Teodoro Lasanta

School of Natural Resources: Faculty Publications

Mediterranean mountains are sensitive agroecosystems that have suffered intense land use and land cover changes (LULCC) during the last century. From the middle of the twentieth century, most of the cultivated lands in Mediterranean mountains were abandoned, allowing the recovery of vegetation (through natural revegetation and afforestation programmes). To examine the effects of farmland abandonment, secondary succession (natural revegetation) and afforestation, an intensive soil sampling was carried out in the Aragu´as catchment (Central Spanish Pyrenees) including sparsely vegetated areas (badlands), grasslands, shrublands and afforested sites. LULCC were mapped, and soil physico-chemical properties were analysed in reference sites (unaltered areas during …

Formal Conjugacy Growth In Graph Products I, Laura Ciobanu,, Susan Hermiller, Valentin Mercier

Department of Mathematics: Faculty Publications

In this paper we give a recursive formula for the conjugacy growth series of a graph product in terms of the conjugacy growth and standard growth series of subgraph products. We also show that the conjugacy and standard growth rates in a graph product are equal provided that this property holds for each vertex group. All results are obtained for the standard generating set consisting of the union of generating sets of the vertex groups.

The Concentration Of Heavy Metals In Lincoln Nebraska's Tap Water, Evan Neuhaus

Honors Theses

Heavy metals are commonplace in nature, and are typically found in scarce quantities in all drinking sources. However, in high enough concentrations, they can have a myriad of negative health effects. This study seeks to find the concentrations of such metals in the Lincoln water supply utilizing the resources of the Water Center at the University of Nebraska at Lincoln. To test for discrete concentrations of trace elements, a method of using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) was implemented. ICP-MS uses plasma to ionize and atomize a sample which is then filtered into a series of cones into a …

Drought Affects Sex Ratio And Growth Of Painted Turtles In A Long-Term Study In Nebraska, Larkin A. Powell, Ellen P. Dolph, Charrissa R. Neil

School of Natural Resources: Faculty Publications

Climate forecasts suggest the Great Plains of North America have increased risk of droughts during global warming. Environmental factors have potential to influence turtle populations in aquatic habitats through temperature-dependent sex determination and influences on food availability. Long-term studies are critical to evaluate the influence of climatic variation on turtles. We used a 12-year set of mark-recapture data collected from painted turtles (Chrysemys picta, n = 162) in a pond in Keith County, Nebraska during 2005–2016 to assess variation in sex ratio and growth dynamics. Southwest Nebraska experienced two periods of drought during our study (Palmer Hydrologic Drought …

The Influence Of Complex Coastlines On The Sea Breeze And Convection Initiation In Coastal North Carolina, Logan Howard, Adam L. Houston

Honors Theses

The sea breeze is a common phenomenon in coastal regions around the world. Their development and propagation can be treated as a density current. It is well known that many factors influence density current propagation, including wind. Depending on the orientation, the wind speed and shear can enhance or inhibit the development of the sea breeze. In places like eastern North Carolina, complex coastal geography can create river and sound breezes that, upon collision, have the potential to initiate thunderstorms. Using Cloud Model 1, simulations were conducted to model the behavior of the sea breezes in eastern North Carolina and …

Chatgpt As Metamorphosis Designer For The Future Of Artificial Intelligence (Ai): A Conceptual Investigation, Amarjit Kumar Singh (Library Assistant), Dr. Pankaj Mathur (Deputy Librarian)

Library Philosophy and Practice (e-journal)

Abstract

Purpose: The purpose of this research paper is to explore ChatGPT’s potential as an innovative designer tool for the future development of artificial intelligence. Specifically, this conceptual investigation aims to analyze ChatGPT’s capabilities as a tool for designing and developing near about human intelligent systems for futuristic used and developed in the field of Artificial Intelligence (AI). Also with the helps of this paper, researchers are analyzed the strengths and weaknesses of ChatGPT as a tool, and identify possible areas for improvement in its development and implementation. This investigation focused on the various features and functions of ChatGPT that …

Using Game Theory To Model Tripolar Deterrence And Escalation Dynamics, Grace Farson

Honors Theses

The study investigated how game theory can been utilized to model multipolar escalation dynamics between Russia, China, and the United States. In addition, the study focused on analyzing various parameters that affected potential conflict outcomes to further new deterrence thought in a tripolar environment.

A preliminary game theoretic model was created to model and analyze escalation dynamics. The model was built upon framework presented by Zagare and Kilgour in their work ‘Perfect Deterrence’. The model is based on assumptions and rules set prior to game play. The model was then analyzed based upon these assumptions using a form of mathematical …

The Earliest Dipodomyine Heteromyid In North America And The Phylogenetic Relationships Of Geomorph Rodents, Joshua X. Samuels, Jonathan J.-M. Calede, Robert M. Hunt Jr.

Department of Earth and Atmospheric Sciences: Faculty Publications

Dipodomyine heteromyids (kangaroo rats and mice) are a diverse group of aridadapted ricochetal rodents of North America. Here, a new genus and species of a large dipodomyine is reported from early Miocene-aged deposits of the John Day Formation in Oregon that represents the earliest record of the subfamily. The taxon is known from a single specimen consisting of a nearly complete skull, dentary, partial pes, and caudal vertebra. The specimen is characterized by a mosaic of ancestral and highly derived cranial features of heteromyids. Specifically, the dental morphology and some cranial characteristics are similar to early heteromyids, but other aspects …

Planning For The Lake Izabal Basin Research Endeavor (Libre) Continental Scientific Drilling Project In Eastern Guatemala, Jonathan Obrist-Farner, Andreas Eckert, Peter M. J. Douglas, Liseth Perez, Alex Correa-Metrio, Bronwen L. Konecky, Thorsten Bauersachs, Susan Zimmerman, Stephanie Scheidt, Mark Brenner, Steffen Kutterolf, Jeremy Maurer, Omar Flores, Caroline M. Burberry, Anders Noren, Amy Myrbo, Matthew Lachniet, Nigel Wattrus, Derek Gibson, The Libre Scientific Team

Department of Earth and Atmospheric Sciences: Faculty Publications

As Earth’s atmospheric temperatures and human populations increase, more people are becoming vulnerable to natural and human-induced disasters. This is particularly true in Central America, where the growing human population is experiencing climate extremes (droughts and floods), and the region is susceptible to geological hazards, such as earthquakes and volcanic eruptions, and environmental deterioration in many forms (soil erosion, lake eutrophication, heavy metal contamination, etc.). Instrumental and historical data from the region are insufficient to understand and document past hazards, a necessary first step for mitigating future risks. Long, continuous, well-resolved geological records can, however, provide a window into past …

Pan-Arctic Soil Moisture Control On Tundra Carbon Sequestration And Plant Productivity, Donatella Zona, Peter M. Lafleur, Koen Hufkens, Beniamino Gioli, Barbara Bailey, George Burba, Eugénie S. Euskirchen, Jennifer D. Watts, Kyle A. Arndt, Mary Farina, John S. Kimball, Martin Heimann, Mathias Göckede, Martijn Pallandt, Torben R. Christensen, Mikhail Mastepanov, Efrén López-Blanco, Albertus J. Dolman, Roisin Commane, Charles E. Miller, Josh Hashemi, Lars Kutzbach, David Holl, Julia Boike, Christian Wille, Torsten Sachs, Aram Kalhori, Elyn R. Humphreys, Oliver Sonnentag, Gesa Meyer, Gabriel H. Gosselin, Philip Marsh, Walter C. Oechel

Daugherty Water for Food Global Institute: Faculty Publications

Long-term atmospheric CO₂ concentration records have suggested a reduction in the positive effect of warming on high-latitude carbon uptake since the 1990s. A variety of mechanisms have been proposed to explain the reduced net carbon sink of northern ecosystems with increased air temperature, including water stress on vegetation and increased respiration over recent decades. However, the lack of consistent long-term carbon flux and in situ soil moisture data has severely limited our ability to identify the mechanisms responsible for the recent reduced carbon sink strength. In this study, we used a record of nearly 100 site-years of eddy covariance …

Socioeconomic Factors In The Diagnosis And Treatment Of Malignant Melanoma In Hispanic Vs. Non-Hispanic Patients: A National Cancer Database (Ncdb) Study, Julia Griffin, Sarah J. Aurit, Timothy Malouff, Peter Silberstein

Department of Statistics: Faculty Publications

Background: The incidence of melanoma is rapidly increasing in the United States. There is a paucity of research of how melanoma affects the Hispanic population, the quickest growing population.

Objective: To identify and understand how socioeconomic factors affect a Hispanic patients health outcome and treatment of malignant melanoma with comparisons to white, non-Hispanic (WNH) patients.

Methods: A retrospective study utilizing the National Cancer Database (NCDB) was completed investigating Hispanic patients (n=2282) and WNH patients (n=190,469) with Stage I-IV malignant melanoma. Outcome and socioeconomic variables were identified and compared across groups. Data was analyzed with SPSS and SAS …

Estimating The Prevalence Of Two Or More Diseases Using Outcomes From Multiplex Group Testing, Md S. Warasi, Joshua M. Tebbs, Christopher S. Mcmahan, Christopher R. Bilder

Department of Statistics: Faculty Publications

When screening a population for infectious diseases, pooling individual specimens (e.g., blood, swabs, urine, etc.) can provide enormous cost savings when compared to testing specimens individually. In the biostatistics literature, testing pools of specimens is commonly known as group testing or pooled testing. Although estimating a population-level prevalence with group testing data has received a large amount of attention, most of this work has focused on applications involving a single disease, such as human immunodeficiency virus. Modern methods of screening now involve testing pools and individuals for multiple diseases simultaneously through the use of multiplex assays. Hou et al. (2017, …

Penguins Go Parallel: A Grammar Of Graphics Framework For Generalized Parallel Coordinate Plots, Susan Vanderplas, Yawei Ge, Antony Unwin, Heike Hofmann

Department of Statistics: Faculty Publications

Parallel Coordinate Plots (PCP) are a valuable tool for exploratory data analysis of high-dimensional numerical data. The use of PCPs is limited when working with categorical variables or a mix of categorical and continuous variables. In this article, we propose Generalized Parallel Coordinate Plots (GPCP) to extend the ability of PCPs from just numeric variables to dealing seamlessly with a mix of categorical and numeric variables in a single plot. In this process we find that existing solutions for categorical values only, such as hammock plots or parsets become edge cases in the new framework. By focusing on individual observations …

Remembering Paul Johnsgard, Linda R, Brown, Josef Kren

Zea E-Books Collection

Paul A. Johnsgard (1931–2021) was a friend of many, an artist, prolific author, teacher, and humble admirer of all living creatures. It was impossible to find someone at Nebraska Audubon Society or Nebraska Ornithologists’ Union meetings who did not know Paul Johnsgard. His more than 100 published books made him known not just in a community of ornithologists, birdwatchers, and bird lovers in the United States but also abroad. He was a world-renowned ornithologist and naturalist who remained deeply embedded in his local culture and its prairie environment.

We invited about 75 people to write a short memory of Paul. …

Simulation Of Monthly Mean And Monthly Base Flow Of Streamflow Using Random Forests For The Mississippi River Alluvial Plain, 1901 To 2018, Benjamin J. Dietsch, William H. Asquith, Brian K. Breaker, Stephen M. Westenbroek, Wade H. Kress

United States Geological Survey: Water Reports and Publications

Improved simulations of streamflow and base flow for selected sites within and adjacent to the Mississippi River Alluvial Plain area are important for modeling groundwater flow because surface-water flows have a substantial effect on groundwater levels. One method for simulating streamflow and base flow, random forest (RF) models, was developed from the data at gaged sites and, in turn, was used to make monthly mean streamflow and base-flow predictions at 162 ungaged sites in the study area. Daily streamflow observations and computed base flow from 247 streamgages were used as the basis for the development of these RF models. RF …

Assessing Functional Biodiversity For The Future Of Plants, Planet, And People, Ali Loker

Doctor of Plant Health Program: Dissertations and Student Research

Biodiversity plays a critical role in supporting life in global ecosystems and its links to ecosystem services and sustainability are recognized by scientific and non-scientific communities. Growing awareness of the importance of biodiversity is accelerated by discussions of its loss, and how to design interventions to conserve and mitigate a biodiversity crisis. Stakeholders are funding and implementing assessment strategies at various scales to help direct conservation efforts. There is also growing interest in measuring and communicating biodiversity outcomes.

Functional biodiversity characterizes the multiplicity of life forms into groups based on their diverse contributions to natural and agro-ecosystems. Assessing functional biodiversity …

Nebraska Statewide Groundwater-Level Monitoring Report 2022, Aaron R. Young, Mark E. Burbach, Sue Olafsen Lackey, Robert Matthew Joeckel, Jeffrey Westrop

Conservation and Survey Division

No abstract provided.

Global Three-Dimensional Water Vapor Feature-Tracking For Horizontal Winds Using Hyperspectral Infrared Sounder Data From Overlapped Tracks Of Two Satellites, Amir Ouyed, Nadia Smith, Xubin Zeng, Thomas Galarneau Jr., Hui Su, Ross D. Dixon

Department of Earth and Atmospheric Sciences: Faculty Publications

The lack of measurements of three-dimensional (3D) distribution of horizontal wind vectors is a major challenge in atmospheric science. Here, we develop an algorithm to retrieve winds for nine pressure levels at 1° grid spacing from 70°N to 70°S. The retrieval is done by tracking water vapor from the hyperspectral Cross-track Infrared Sounder aboard two polar satellites (NOAA-20 and Suomi-NPP) that have overlapped tracks separated by 50 min. We impose a gross error check by flagging retrievals that are too different from ERA-5 reanalysis. Testing the algorithm for the first week of January and July 2020 indicates that our algorithm …

Viscoelastic Properties Of Human Facial Skin And Comparisons With Facial Prosthetic Elastomers, Mark W. Beatty, Alvin G. Wee, D. B. Marx, Lauren Ridgway, Bobby Simetich, Thiago Carvalho De Sousa, Kevin Vakilzadian, Joel Schulte

Department of Statistics: Faculty Publications

Prosthesis discomfort and a lack of skin-like quality is a source of patient dissatisfaction with facial prostheses. To engineer skin-like replacements, knowledge of the differences between facial skin properties and those for prosthetic materials is essential. This project measured six viscoelastic properties (percent laxity, stiffness, elastic deformation, creep, absorbed energy, and percent elasticity) at six facial locations with a suction device in a human adult population equally stratified for age, sex, and race. The same properties were measured for eight facial prosthetic elastomers currently available for clinical usage. The results showed that the prosthetic materials were 1.8 to 6.4 times …

Bernstein-Sato Theory For Singular Rings In Positive Characteristic, Jack Jack, Luis Núñez-Betancourt, Eamon Quinlan-Gallego

Department of Mathematics: Faculty Publications

The Bernstein-Sato polynomial is an important invariant of an element or an ideal in a polynomial ring or power series ring of characteristic zero, with interesting connections to various algebraic and topological aspects of the singularities of the vanishing locus. Work of Mustaţă, later extended by Bitoun and the third author, provides an analogous Bernstein-Sato theory for regular rings of positive characteristic.

In this paper, we extend this theory to singular ambient rings in positive characteristic. We establish finiteness and rationality results for Bernstein-Sato roots for large classes of singular rings, and relate these roots to other classes of numerical …

Azimuthal Correlations In Z +Jets Events In Proton–Proton Collisions At √S = 13tev, Cms Collaboration

Department of Physics and Astronomy: Faculty Publications

The production of Z bosons associated with jets is measured in pp collisions at √ s = 13 TeV with data recorded with the CMS experiment at the LHC corresponding to an integrated luminosity of 36.3 fb⁻¹. The multiplicity of jets with transverse momentum p_T > 30 GeV is measured for different regions of the Z boson’s p_T(Z ), from lower than 10 GeV to higher than 100 GeV. The azimuthal correlation Δφ between the Z boson and the leading jet, as well as the correlations between the two leading jets are measured in three regions …

Importance Of Snowmelt On Soil Nitrate Leaching To Groundwater – A Model Study, Sahila Beegum, Arindam Malakar, Chittaranjan Ray, Daniel D. Snow

Nebraska Water Center: Faculty Publications

The movement of nitrate to surface water bodies during snow accumulation and melting has been extensively studied, but there are only limited studies on the influence of snow processes on nitrate leaching to groundwater. The present study investigated the impact of snow processes on nitrate leaching to groundwater based on a simulation modeling approach using HYDRUS-1D. HYDRUS-1D model has a temperature threshold-based snow model in addition to water, solute, and heat simulation components. The snow component in HYDRUS-1D was previously not applied to snow simulation studies since the method does not consider a detailed physical and process-based representation of snow …

Gloria - A Globally Representative Hyperspectral In Situ Dataset For Optical Sensing Of Water Quality, Moritz K. Lehmann

School of Natural Resources: Faculty Publications

The development of algorithms for remote sensing of water quality (RSWQ) requires a large amount of in situ data to account for the bio-geo-optical diversity of inland and coastal waters. The GLObal Reflectance community dataset for Imaging and optical sensing of Aquatic environments (GLORIA) includes 7,572 curated hyperspectral remote sensing reflectance measurements at 1nm intervals within the 350 to 900nm wavelength range. In addition, at least one co-located water quality measurement of chlorophyll α, total suspended solids, absorption by dissolved substances, and Secchi depth, is provided. The data were contributed by researchers affiliated with 59 institutions worldwide and come from …

Tri-Plane Diagrams For Simple Surfaces In S4, Manuel Aragón, Zack Dooley, Alexander Goldman, Yucong Lei, Isaiah Martinez, Nicholas Meyer, Devon Peters, Scott Warrander, Ana Wright, Alex Zupan

Department of Mathematics: Faculty Publications

Meier and Zupan proved that an orientable surface K in S⁴ admits a tri-plane diagram with zero crossings if and only if K is unknotted, so that the crossing number of K is zero. We determine the minimal crossing numbers of nonorientable unknotted surfaces in S⁴, proving that c(P^n,m) = max{1, |n−m|}, where P^n,m denotes the connected sum of n unknotted projective planes with normal Euler number +2 and m unknotted projective planes with normal Euler number −2. In addition, we convert Yoshikawa’s table of knotted surface ch-diagrams to tri-plane …

Exhumed Fluvial Landforms Reveal Evolution Of Late Eocene– Pliocene Rivers On The Central And Northern Great Plains, Usa, Jesse T. Korus, Robert Matthew Joeckel

Department of Earth and Atmospheric Sciences: Faculty Publications

Cenozoic strata on the Great Plains are the products of a long- lived, continental sediment routing system, and yet strikingly little is known about these ancient rivers. This article details the discovery of ~3100 fluvial ridges—erosionally inverted alluvial- fan, channel- fill, channel- belt, and valley- fill deposits—extending from the Rocky Mountain front to the eastern margin of the Great Plains. The direct detection of these channel bodies reveals new insights into late Eocene– Pliocene drainage evolution. Late Eocene– Oligocene streams were morphologically diverse. Alluvial fans adjacent to the Rocky Mountain front changed eastward to parallel or downstream- divergent, fixed, single- …

The Ecology Of Human-Caused Mortality For A Protected Large Carnivore, John F. Benson, Kyle D. Dougherty, Paul Beier, Walter M. Boyce, Bogdan Cristescu, Daniel J. Gammons, David K. Garcelon, J. Mark Higley, Quinton E. Martins, Anna C. Nisi, Seth P. D. Riley, Jeff A. Sikich, Thomas R. Stephenson, T. Winston Vickers, Greta M. Wengert, Christopher C. Wilmers, Heiko U. Wittmer, Justin A. Dellinger

School of Natural Resources: Faculty Publications

Mitigating human-caused mortality for large carnivores is a pressing global challenge for wildlife conservation. However, mortality is almost exclusively studied at local (within-population) scales creating a mismatch between our understanding of risk and the spatial extent most relevant to conservation and management of wide-ranging species. Here, we quantified mortality for 590 radio-collared mountain lions statewide across their distribution in California to identify drivers of human-caused mortality and investigate whether human-caused mortality is additive or compensatory. Human-caused mortality, primarily from conflict management and vehicles, exceeded natural mortality despite mountain lions being protected from hunting. Our data indicate that human-caused mortality is …

Search For The Higgs Boson Decay To A Pair Of Electrons In Proton-Proton Collisions At √S = 13 Tev, A. Tumasyan

Department of Physics and Astronomy: Faculty Publications

A search is presented for the Higgs boson decay to a pair of electrons (e⁺e⁻) in proton-proton collisions at √ s = 13 TeV. The data set was collected with the CMS experiment at the LHC between 2016 and 2018, corresponding to an integrated luminosity of 138 fb⁻¹. The analysis uses event categories targeting Higgs boson production via gluon fusion and vector boson fusion. The observed upper limit on the Higgs boson branching fraction to an electron pair is 3.0 × 10⁻⁴ (3.0 × 10⁻⁴ expected) at the 95% confidence level, which …

Erratum: Measurement Of Prompt And Nonprompt Charmonium Suppression In Pbpb Collisions At 5.02 Tev, A. Tumasyan

Department of Physics and Astronomy: Faculty Publications

In Fig. 3, the y axis titles were mistakenly written showing a single-differential cross section in either dimuon p_T or rapidity, when in fact the cross section is normalized by both the p_T and rapidity ranges used for a given measurement point. The corrected version is shown in the new Fig. 3 provided below.

Effects Of Intermixing And Oxygen Vacancies On A Two-Dimensional Electron Gas At The Polar (Tbsco3/Ktao) (001) Interface, Bhubnesh Lama, Evgeny Y. Tsymbal, Tula R. Paudel

Department of Physics and Astronomy: Faculty Publications

3d-5d perovskite oxides, ABO₃ (where A and B are 3d or 5d elements), form polar surfaces in the (001)- stacked thin films. As a result, the polar-polar (001) interface between two ABO₃ insulators could create polar discontinuity potentially producing a two-dimensional electron gas of higher density and stronger spatial localization compared to the widely studied polar-nonpolar oxide interfaces, such as (001) LaAlO₃/SrTiO₃. Here, as a model system, we explore the interface between polar (001) TbScO₃ and polar (001) KTaO₃ using first-principles density functional theory.We find that the …