Digital Commons Network^™

Observations On Late Cretaceous Micrampulla (Corethrales, Bacillariophyceae) From The Campbell Plateau (Zealandia), Southwest Pacific Ocean, Kenta Abe, David M. Harwood, Richard W. Jordan

Department of Earth and Atmospheric Sciences: Faculty Publications

Late Cretaceous (late Campanian) diatom assemblages from the Campbell Plateau (Zealandia), southwest Pacific Ocean, obtained from Deep Sea Drilling Project (DSDP) Leg 29 Site 275, contain well-preserved specimens of two enigmatic diatom species currently assigned to the genus Ktenodiscus; Micrampulla parvula originally described from the Maastrichtian-age Moreno Shale, California, and Pterotheca cretacea from DSDP Site 275. In general, the two species share a number of common features with modern Corethron (domed valves, probable heterovalvate frustules, T-shaped serrated articulated spines, marginal sockets), but differ in the location of the sockets (i.e. vertically at the base of the valve dome and …

Alfalfa Water Productivity And Yield Gaps In The U.S. Central Great Plains, Kaylin P. Fink, Patricio Grassini, Alexandre Rocateli, Leonardo M. Bastos, Jude Kastens, Luke P. Ryan, Xiaomao Lin, Andres Patrignani, Romulo P. Lollato

Department of Agronomy and Horticulture: Faculty Publications

Context: Yield gap (Yg) analyses using farmer-reported yield and management data have been performed for a number of annual grain crops, but it lacks for perennial forages. The U.S. accounts for 21 % of the global alfalfa production with a large rainfed area located in the central Great Plains, serving as an interesting case-study for Yg in perennial forages. Most existing alfalfa Yg analyses quantified the magnitude of the Yg but failed to identify associated management practices to reduce it. Challenging this analysis, a systematic benchmark for alfalfa water productivity [WP, kg dry matter per mm evapotranspiration (ETc)] that …

Measurements Of The Associated Production Of A W Boson And A Charm Quark In Proton–Proton Collisions At √S = 8tev, A. Tumasyan

Department of Physics and Astronomy: Faculty Publications

Measurements of the associated production of a W boson and a charm (c) quark in proton–proton collisions at a centre-of-mass energy of 8 TeV are reported. The analysis uses a data sample corresponding to a total integrated luminosity of 19.7 fb⁻¹ collected by the CMS detector at the LHC. The W bosons are identified through their leptonic decays to an electron or a muon, and a neutrino. Charm quark jets are selected using distinctive signatures of charm hadron decays. The product of the cross section and branching fraction σ(pp → W + c + X)β(W → ℓν), where ℓ …

Measurements Of The Higgs Boson Production Cross Section And Couplings In The W Boson Pair Decay Channel In Proton-Proton Collisions At √S = 13tev, A. Tumasyan

Department of Physics and Astronomy: Faculty Publications

Production cross sections of the standard model Higgs boson decaying to a pair of W bosons are measured in proton-proton collisions at a center-of-mass energy of 13 TeV. The analysis targets Higgs bosons produced via gluon fusion, vector boson fusion, and in association with a W or Z boson. Candidate events are required to have at least two charged leptons and moderate missing transverse momentum, targeting events with at least one leptonically decaying W boson originating from the Higgs boson. Results are presented in the form of inclusive and differential cross sections in the simplified template cross section framework, as …

Agronomic And Quality Impact Of A Shortened Translocation For Wheat Streak Mosaic Virus Resistance, Mary J. Guttieri, Robert L. Bowden, Guorong Zhang, Scott Haley, Katherine Anna Frels, Gary L. Hein, Katherine W. Jordan

Department of Agronomy and Horticulture: Faculty Publications

Wheat streak mosaic virus (WSMV) is a mite-vectored virus with substantial economic impact on wheat production. One of the effective sources of resistance to WSMV, Wsm1, is carried on a translocation from Thinopyrum intermedium. The original whole arm form of this translocation (T4DL·4JsS) was highly effective against WSMV but carried a substantial yield penalty in the absence of the virus. Shorter recombinants of the Th. intermedium translocation are now available. This study characterized the agronomic performance of near-isogenic sib-pair families in 10 yield trials using one of these shortened T4DL·4DS-4J^sS translocations, named “rec213,” in the absence …

Role Of Bifidobacterium Pseudocatenulatum In Degradation And Consumption Of Xylan-Derived Carbohydrates, Elizabeth Drey, Car Reen Kok, Robert Hutkins

Department of Food Science and Technology: Faculty Publications

Xylans, a family of xylose-based polysaccharides, are dietary fibers resistant to digestion. They therefore reach the large intestine intact; there, they are utilized by members of the gut microbiota. They are initially broken down by primary degraders that utilize extracellular xylanases to cleave xylan into smaller oligomers. The resulting xylooligosaccharides (XOS) can either be further metabolized directly by primary degraders or cross-feed secondary consumers, including Bifidobacterium. While several Bifidobacterium species have metabolic systems for XOS, most grow poorly on longer- chain XOS and xylan substrates. In this study, we isolated strains of Bifidobacterium pseudocatenulatum and observed that some, including …

The Genomic And Bulked Segregant Analysis Of Curcuma Alismatifolia Revealed Its Diverse Bract Pigmentation, Xuezhu Liao, Yuanjun Ye, Xiaoni Zhang, Dan Peng, Mengmeng Hou, Gaofei Fu, Jianjun Tan, Jianli Zhao, Rihong Jiang, Yechun Xu, Jinmei Liu, Jinliang Yang, Wusheng Liu, Luke R. Tembrock, Genfa Zhu, Zhiqiang Wu

Department of Agronomy and Horticulture: Faculty Publications

Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy ‘‘flowers’’ through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. Curcuma alismatifolia, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of C. alismatifolia ‘‘Chiang Mai Pink’’ and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed C. alismatifolia contains a …

Migratory Connectivity Of North American Waterfowl Across Administrative Flyways, Anthony Roberts, Amy L. Scarpignato, Allison Huysman, Jeffrey A. Hostetler, Emily B. Cohen

United States Fish and Wildlife Service: Publications

Management of waterfowl that migrate seasonally across North America occurs within four flyways that were delineated in the early 1900s to include the annual movements of populations. Movements may have changed over the past century since the administrative flyways were established, and may do so while management plans are in use, so information about transitions among flyways through time can illustrate how management assumptions may change. Today there are more than 12 million records from 60 years of migratory waterfowl band recoveries to assess adaptive management approaches that will be most effective when they account for movements within and between …

Math Club, Lily Rippeteau, Sarah Cunningham

Honors Program: Expanded Learning Clubs

No abstract provided.

Tutoring Club, Ryan Hruby, Ally Jay

Honors Program: Expanded Learning Clubs

Tutoring Club connects high-school students with club leaders who are able to assist them with understanding and completing their class concepts, assignments, and projects.

Reflections On Pedagogical Practice And Development Through Multidisciplinary Triadic Peer Mentorship, Nicole Charles, Nathalie Moon, Andrew P. Dicks

To Improve the Academy: A Journal of Educational Development

This article presents a critical reflection on the experiences of three university instructors (two teaching stream and one tenure stream) within a 6-month peer-to-peer mentoring for teaching community of practice (P2P CoP). As part of the P2P CoP, the authors (who were previously unknown to one another) formed a “teaching triad” at a tri-campus, research-intensive Canadian university. They regularly met in person for 1 hour on a weekly basis throughout the Winter 2019 semester to discuss teaching-related matters, undertook classroom visits to observe one another teach, and participated in pedagogical workshops with other P2P CoP members. In this article, the …

How Search Committees Assess Teaching: Lessons For Ctls, Katharine Phelps Walsh, Laura Ochs Pottmeyer, Deborah Meizlish, Chad Hershock

To Improve the Academy: A Journal of Educational Development

This study updates and expands upon past work on how tenure-track hiring committees evaluate teaching effectiveness to provide centers for teaching and learning (CTLs) current data as they support graduate students and postdocs navigating the academic hiring process. In this study, 166 hiring committee chairs from nine academic disciplines and a variety of institution types (e.g., Baccalaureate, Master’s, and Doctoral) responded to survey questions addressing how they evaluate teaching effectiveness for tenure-track positions. Results indicate that hiring chairs across institution types and disciplines value a candidate’s teaching effectiveness. Hiring committees use a variety of documents to gather information about an …

Landscape Change, Scale, And Human Response To Change In The Great Plains, Kate Bird

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

Great Plains landscapes are undergoing changes at multiple spatial and temporal scales due to processes ranging from woody encroachment to climate change. These changes may fundamentally alter the agroecosystems of the Great Plains such that the provisioning of ecosystem services including biodiversity and livestock production is affected. Improving our understanding of the effects of landscape change at multiple scales and how humans perceive and respond to these changes is important for facilitating research and management that enhances the resilience of these agroecosystems. As such, I first applied discontinuity theory and graph theory to evaluate the functional connectivity of the Central …

The Freedom Collection 2017–2021: Part 2, Uncl Members’ Subject Usage Preferences And Profiles, David C. Tyler

University of Nebraska-Lincoln Libraries: White Papers

With data supplied by a colleague, the author looked into the by-subject downloading activities of the members of the University of Nebraska Consortium of Libraries (UNCL): University of Nebraska at Kearney, University of Nebraska-Lincoln, University of Nebraska Medical Center, and University of Nebraska Omaha.

The Freedom Collection 2017–2021: Part 1, The Composition Of The Freedom Collection And Uncl’S Downloads By Member And Subject, David C. Tyler

University of Nebraska-Lincoln Libraries: White Papers

With data provided by a colleague, the author looked at the University of Nebraska Consortium of Libraries (UNCL) downloading activity of Elsevier's Freedom Collection for the 2017-2021 interval. Members include the University of Nebraska at Kearney, University of Nebraska-Lincoln, University of Nebraska Medical Center, and University of Nebraska Omaha.

The author looked at activity by member and by subject at the level of journals' Library of Congress Classifications.

This report was submitted in the fall of 2022 to the UNL Libraries Collections Strategies Committee (CSC) and to the members of the Collections Strategies and Open Scholarship (CSOS) department.

Getting Ahead Of Flash Drought: From Early Warning To Early Action, Jason A. Otkin, Molly Woloszyn, Hailan Wang, Mark D. Svoboda, Marina Skumanich, Roger Pulwarty, Joel Lisonbee, Andrew Hoell, Mike Hobbins, Tonya Haigh, Amanda E. Cravens

National Drought Mitigation Center: Faculty Publications

Flash droughts, characterized by their unusually rapid intensification, have garnered increasing attention within the weather, climate, agriculture, and ecological communities in recent years due to their large environmental and socioeconomic impacts. Because flash droughts intensify quickly, they require different early warning capabilities and management approaches than are typically used for slower-developing “conventional” droughts. In this essay, we describe an integrated research-and-applications agenda that emphasizes the need to reconceptualize our understanding of flash drought within existing drought early warning systems by focusing on opportunities to improve monitoring and prediction. We illustrate the need for engagement among physical scientists, social scientists, operational …

Executive Functioning In Language Learning Disabilities: Defining Executive Functioning, Executive Functioning Deficits, And Clinical Intervention Strategies To Support Children, Kaylie Trumble

Honors Program: Senior Projects (Public)

This thesis aims to select a working definition of executive functioning (EF) to identify possible EF deficits and clinical interventions strategies to support children. Included are EF deficits, ways of assessing EF components, and intervention strategies for executive dysfunction in LLD. Scenarios are provided to demonstrate both matching strategies to a child and strength/deficit in EF, along with a sample intervention script.

The Emerging Digital Infrastructure For Research In The Humanities, Donald J. Waters

Copyright, Fair Use, Scholarly Communication, etc.

This article advances the thesis that three decades of investments by national and international funders, combined with those of scholars, technologists, librarians, archivists, and their institutions, have resulted in a digital infrastructure in the humanities that is now capable of supporting end-to-end research workflows. The article refers to key developments in the epigraphy and paleography of the premodern period. It draws primarily on work in classical studies but also highlights related work in the adjacent disciplines of Egyptology, ancient Near East studies, and medieval studies. The argument makes a case that much has been achieved but it does not declare …

Engaging Children With Animals Increases Their Awareness Of Their Footprint On Earth, Brett Foster

Honors Program: Senior Projects (Public)

Teachers should reserve time in their classrooms to connect curriculum to animals and environmental topics. Connecting core subjects like writing, reading, or even math to animals builds student investment in learning as they can connect the topics of animals to their lives. Animals are all around us and are a topic that students naturally spend a lot of time with and can easily identify in the world around them. There are several benefits of incorporating animals into the curriculum, including an increased sense of empathy, an awareness of their environmental impact, and an investment in their community.

I have focused …

Icebar: Feedback-Driven Iterative Repair Of Alloy Specifications, Simón Gutiérrez Brida, Germán Regis, Guolong Zheng, Hamid Bagheri, Thanhvu Nguyen, Nazareno Aguirre, Marcelo Frias

School of Computing: Faculty Publications

Automated program repair (APR) techniques have shown great success in automatically finding fixes for programs in programming languages such as C or Java. In this work, we focus on repairing formal specifications, in particular for the Alloy specification language. As opposed to most APR tools, our approach to repair Alloy specifications, named ICEBAR, does not use test-based oracles for patch assessment. Instead, ICEBAR relies on the use of property-based oracles, commonly found in Alloy specifications as predicates and assertions. These property-based oracles define stronger conditions for patch assessment, thus reducing the notorious overfitting issue caused by using test-based oracles, …

The Road Not Taken: Exploring Alias Analysis Based Optimizations Missed By The Compiler, Khushboo Chitre, Piyus Kedia, Rahul Purandare

School of Computing: Faculty Publications

Context-sensitive inter-procedural alias analyses are more precise than intra-procedural alias analyses. However, context-sensitive inter-procedural alias analyses are not scalable. As a consequence, most of the production compilers sacrifice precision for scalability and implement intra-procedural alias analysis. The alias analysis is used by many compiler optimizations, including loop transformations. Due to the imprecision of alias analysis, the program’s performance may suffer, especially in the presence of loops.

Previous work proposed a general approach based on code-versioning with dynamic checks to disambiguate pointers at runtime. However, the overhead of dynamic checks in this approach is 𝑂(𝑙𝑜𝑔 𝑛), which is substantially high to …

Reproducibility Of Protein X-Ray Diffuse Scattering And Potential Utility For Modeling Atomic Displacement Parameters, Zhen Su, Medhanjali Dasgupta, Frédéric Poitevin, Irimpan I. Mathews, Henry Van Den Bedem, Michael E. Wall, Chun Hong Yoon, Mark A. Wilson

Department of Biochemistry: Faculty Publications

Protein structure and dynamics can be probed using x-ray crystallography. Whereas the Bragg peaks are only sensitive to the average unit-cell electron density, the signal between the Bragg peaks—diffuse scattering—is sensitive to spatial correlations in electron-density variations. Although diffuse scattering contains valuable information about protein dynamics, the diffuse signal is more difficult to isolate from the background compared to the Bragg signal, and the reproducibility of diffuse signal is not yet well understood. We present a systematic study of the reproducibility of diffuse scattering from isocyanide hydratase in three different protein forms. Both replicate diffuse datasets and datasets obtained from …

3d Pore Structure Characterization Of Stored Grain Bed, Charles Nwaizu, Qiang Zhang, Christiana Iluno

Department of Food Science and Technology: Faculty Publications

An image analysis technique for reconstruction of the complex 3D pore structure within bulk grain from 2D section images was presented. The technique relies on aligning successive 2D images of cut-sections obtained from colored-wax solidified soybean grain beds, which were then subjected to image processing using ImageJ software developed by the National Institute of Health (NIH, Bethesda, Md.) for the reconstruction and visualization of different airflow paths within the bulk grain. Porosity and tortuosity values were quantified from the 3D image volume and 3D reconstructed inter-connected airflow paths to develop empirical mathematical models for predicting porosity and tortuosity as a …

Machine Learning-Based Peripheral Artery Disease Identification Using Laboratory-Based Gait Data, Ali Al-Ramini, Mahdi Hassan, Farahnaz Fallahtafti, Mohammad Ali Takallou, Basheer Qolomany, Iraklis I. Pipinos, Fadi Alsaleem, Sara A. Myers

Department of Mechanical and Materials Engineering: Faculty Publications

Peripheral artery disease (PAD) manifests from atherosclerosis, which limits blood flow to the legs and causes changes in muscle structure and function, and in gait performance. PAD is underdiagnosed, which delays treatment and worsens clinical outcomes. To overcome this challenge, the purpose of this study is to develop machine learning (ML) models that distinguish individuals with and without PAD. This is the first step to using ML to identify those with PAD risk early. We built ML models based on previously acquired overground walking biomechanics data from patients with PAD and healthy controls. Gait signatures were characterized using ankle, knee, …

Machine Learning-Based Peripheral Artery Disease Identification Using Laboratory-Based Gait Data, Ali Al-Ramini, Mahdi Hassan, Farahnaz Fallahtafti, Mohammad Ali Takallou, Hafizur Rahman, Basheer Qolomany, Iraklis I. Pipinos, Fadi M. Alsaleem, Sara A. Myers

Department of Mechanical and Materials Engineering: Faculty Publications

Peripheral artery disease (PAD) manifests from atherosclerosis, which limits blood flow to the legs and causes changes in muscle structure and function, and in gait performance. PAD is underdiagnosed, which delays treatment and worsens clinical outcomes. To overcome this challenge, the purpose of this study is to develop machine learning (ML) models that distinguish individuals with and without PAD. This is the first step to using ML to identify those with PAD risk early. We built ML models based on previously acquired overground walking biomechanics data from patients with PAD and healthy controls. Gait signatures were characterized using ankle, knee, …

Cyclic Adp Ribose Isomers: Production, Chemical Structures, And Immune Signaling, Mohammad K. Manik, Yun Shi, Sulin Li, Mark A. Zaydman, Neha Damaraju, Samuel Eastman, Thomas G. Smith, Weixi Gu, Veronika Masic, Tamim Mosaiab, James S. Weagley, Steven J. Hancock, Eduardo Vasquez, Lauren Hartley-Tassell, Nestoras Kargios, Natsumi Maruta, Bryan Y.J. Lim, Hayden Burdett, Michael J. Landsberg, Mark A. Schembri, Ivan Prokes, Lijiang Song, Murray Grant, Aaron Diantonio, Jeffrey D. Nanson, Ming Guo, Jeffrey Milbrandt, Thomas Ve, Bostjan Kobe

Department of Agronomy and Horticulture: Faculty Publications

Cyclic adenosine diphosphate (ADP)–ribose (cADPR) isomers are signaling molecules produced by bacterial and plant Toll/interleukin-1 receptor (TIR) domains via nicotinamide adenine dinucleotide (oxidized form) (NAD+) hydrolysis. We show that v-cADPR (2′cADPR) and v2-cADPR (3′cADPR) isomers are cyclized by O-glycosidic bond formation between the ribose moieties in ADPR. Structures of 2′cADPR-producing TIR domains reveal conformational changes that lead to an active assembly that resembles those of Toll-like receptor adaptor TIR domains. Mutagenesis reveals a conserved tryptophan that is essential for cyclization. We show that 3′cADPR is an activator of ThsA effector proteins from the bacterial antiphage defense system termed Thoeris and …

Seasonal Habitat Selection By American White Pelicans, Frederick L. Cunningham, Guiming Wang, D. Tommy King

United States Department of Agriculture Wildlife Services: Staff Publications

Resource utilization strategies of avian migrants are a major concern for conservation and management. Understanding seasonal habitat selection by migratory birds helps us explain the ongoing continental declines of migratory bird populations. Our objective was to compare the secondorder and third-order habitat selection by the American White Pelican (Pelecanus erythrorhynchos; hereafter pelican) between the breeding and non-breeding grounds. We tested the Lack hypothesis that habitat selection by migratory birds is stronger on the breeding grounds than on the nonbreeding grounds. We used random-effect Dirichlet-multinomial models to estimate the second-order habitat selection between the seasons with the GPS locations …

Leveraging The Structure Of Dnaja1 To Discover Novel Potential Pancreatic Cancer Therapies, Heidi E. Roth, Aline De Lima Leite, Nicolas Y. Palermo, Robert Powers

Department of Chemistry: Faculty Publications

Pancreatic cancer remains one of the deadliest forms of cancer with a 5-year survival rate of only 11%. Difficult diagnosis and limited treatment options are the major causes of the poor outcome for pancreatic cancer. The human protein DNAJA1 has been proposed as a potential therapeutic target for pancreatic cancer, but its cellular and biological functions remain unclear. Previous studies have suggested that DNAJA10s cellular activity may be dependent upon its protein binding partners. To further investigate this assertion, the first 107 amino acid structures of DNAJA1 were solved by NMR, which includes the classical J-domain and its associated linker …

Measurement Of The Mass Dependence Of The Transverse Momentum Of Lepton Pairs In Drell–Yan Production In Proton–Proton Collisions At √S = 13tev, A. Tumasyan

Department of Physics and Astronomy: Faculty Publications

The double differential cross sections of the Drell–Yan lepton pair (ℓ ⁺ ℓ ⁻, dielectron or dimuon) production are measured as functions of the invariant mass m_ℓℓ, transverse momentum p_T(ℓℓ), and ϕ^∗_η. The ϕ^∗_η observable, derived from angular measurements of the leptons and highly correlated with p_T(ℓℓ), is used to probe the low-p_T(ℓℓ) region in a complementary way. Dilepton masses up to 1 TeV are investigated. Additionally, a measurement is performed requiring at least one jet in the final state. To benefit from partial cancellation …

Editorial: Function And Formation Of Mitochondrial Metalloproteome, Michał Wasilewski, Vishal M. Gohil, Oleh Khalimonchuk

Department of Biochemistry: Faculty Publications

No abstract provided.