Digital Commons Network^™

The R Quest: From Users To Developers, Simon Urbanek

The R Journal

R is not a programming language, and this produces the inherent dichotomy between analytics and software engineering. With the emergence of data science, the opportunity exists to bridge this gap, especially through teaching practices.

The R Developer Community Does Have A Strong Software Engineering Culture, Maëlle Salmon, Karthik Ram

The R Journal

There is a strong software engineering culture in the R developer community. We recommend creating, updating and vetting packages as well as keeping up with community standards. We invite contributions to the rOpenSci project, where participants can gain experience that will shape their work and that of their peers.

American Burying Beetle, Plant Richness, And Soil Property Responses To Collapse Of Juniperus Virginiana Woodlands With Fire, Alison K. Ludwig

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Grasslands are declining in the Great Plains due to land use changes, woody plant encroachment, and loss of historic fire cycles. Prescribed burn associations have utilized prescribed fire to collapse invading woodlands and allow the restoration of grasslands. This fire is considered “extreme” because it is capable of changing the structure and function of an ecosystem. Our study site is the Loess Canyons Experimental Landscape, a long-term, ecoregion-scale experiment to apply prescribed fire across the region to restore grasslands. The Nebraska Natural Legacy Project established the Loess Canyons ecoregion as a Biologically-Unique Landscape in 2005 with the state’s wildlife action …

Voltage Controlled Néel Vector Rotation In Zero Magnetic Field, Ather Mahmood, Will Echtenkamp, Mike Street, Jun Lei Wang, Shi Cao, Takashi Komesu, Peter Dowben, Pratyush Buragohain, Haidong Lu, Alexei Gruverman, Arun Parthasarathy, Shaloo Rakheja, Christian Binek

Peter Dowben Publications

Multi-functional thin films of boron (B) doped Cr₂O₃ exhibit voltage-controlled and nonvolatile Néel vector reorientation in the absence of an applied magnetic field, H. Toggling of antiferromagnetic states is demonstrated in prototype device structures at CMOS compatible temperatures between 300 and 400 K. The boundary magnetization associated with the Néel vector orientation serves as state variable which is read via magnetoresistive detection in a Pt Hall bar adjacent to the B:Cr₂O₃ film. Switching of the Hall voltage between zero and non-zero values implies Néel vector rotation by 90 degrees. Combined magnetometry, spin resolved inverse …

Comparative Analysis Of Kmer Counting And Estimation Tools, Ankitha Vejandla

School of Computing: Dissertations, Theses, and Student Research

The rapid development of next-generation sequencing (NGS) technologies for determining the sequence of DNA has revolutionized genome research in recent years. De novo assemblers are the most commonly used tools to perform genome assembly. Most of the assemblers use de Bruijn graphs that break the sequenced reads into smaller sequences (sub-strings), called kmers, where k denotes the length of the sub-strings. The kmer counting and analysis of kmer frequency distribution are important in genome assembly. The main goal of this research is to provide a detailed analysis of the performance of different kmer counting and estimation tools that are currently …

Agent Based Modeling Of The Spread Of Social Unrest Based On Infectious Disease Spread Model, Anup Adhikari

School of Computing: Dissertations, Theses, and Student Research

Social unrest activities are the tools for people to show dissatisfaction, and often people are motivated by similar unrest activities in another region. This causes a spread of unrest activities across space and time. In this thesis, we model the spread of social unrest across time and space. The underlying novel methodology is to model the regions as agents that transition from one state to another based on changes in their environment. The methodology involves (1) creating a region vector for each agent based on socio-demographic, cultural, economic, infrastructural, geographic, and environmental (SCEIGE) factors, (2) formulating neighborhood distance function to …

Algorithmic Trading And Market Quality: International Evidence, Ekkehart Boehmer, Kingsley Fong, Juan (Julie) Wu

Department of Finance: Faculty Publications

We study the effect of algorithmic trading (AT) on market quality between 2001 and 2011 in 42 equity markets around the world. We use exchange co-location service that increases AT as an exogenous instrument to draw causal inferences of AT on market quality. On average, AT improves liquidity and informational efficiency but increases short-term volatility. Importantly, AT also lowers execution shortfalls for buy-side institutional investors. Our results are surprisingly consistent across markets and thus across a wide range of AT environments. We further document that the beneficial effect of AT is stronger in large stocks than in small stocks.

Genome Annotation Using Average Mutual Information, Garin P. Newcomb

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

Advancements in high-throughput DNA sequencing technologies and ambitious goals for their use are resulting in the generation of a deluge of unannotated sequenced genomes. This makes computational tools that can aid in annotation increasingly valuable.

Here, we provide a detailed exploration of the utility as well as the limitations of average mutual information (AMI) in several steps of genome annotation. For a genomic sequence, AMI is a measure of the information a base contains about the base separated by a fixed lag. A profile is constructed by calculating AMI at multiple lags. In addition to traditional AMI, we employ two …

Risk-Based Machine Learning Approaches For Probabilistic Transient Stability, Umair Shahzad

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

Power systems are getting more complex than ever and are consequently operating close to their limit of stability. Moreover, with the increasing demand of renewable wind generation, and the requirement to maintain a secure power system, the importance of transient stability cannot be overestimated. Considering its significance in power system security, it is important to propose a different approach for enhancing the transient stability, considering uncertainties. Current deterministic industry practices of transient stability assessment ignore the probabilistic nature of variables (fault type, fault location, fault clearing time, etc.). These approaches typically provide a conservative criterion and can result in expensive …

Novel Peridynamic Models For Material Degradation And Mass Transport, Jiangming Zhao

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

Fracture and corrosion are two major causes of structure failure. They can interact with each other, leading to faster material degradation. They are also under the influence of environmental conditions. The corrosion rate highly depends on the transportation rate of involving substances, while the fracture can be accelerated significantly due to fluid flow. These complex mechanisms involved in structure failure have troubled classical models for decades. The peridynamic (PD) theory introduced in 2000 has shown great potential in modeling such problems. In this work, we develop novel PD models for fracture, corrosion, mass transport, and viscous flow, which are building …

How Do Genetic Relatedness And Spatial Proximity Shape African Swine Fever Infections In Wild Boar?, Tomasz Podgórski, Kim M. Pepin, Anna Radko, Angelika Podbielska, Magdalena Łyjak, Grzegorz Woźniakowski, Tomasz Borowik

United States Department of Agriculture Wildlife Services: Staff Publications

The importance of social and spatial structuring of wildlife populations for disease spread, though widely recognized, is still poorly understood in many host-pathogen systems. In particular, system-specific kin relationships among hosts can create contact heterogeneities and differential disease transmission rates. Here, we investigate how distance-dependent infection risk is influenced by genetic relatedness in a novel host-pathogen system: wild boar (Sus scrofa) and African swine fever (ASF).We hypothesized that infection risk would correlate positively with proximity and relatedness to ASF-infected individuals but expected those relationships to weaken with the distance between individuals due to decay in contact rates and …

Moisture Transport Associated With Southwest Monsoon Rainfall Over Sri Lanka In Relatively Wet And Dry Rainfall Years, Sherly Shelton

Department of Earth and Atmospheric Sciences: Faculty Publications

Atmospheric moisture transportation associated with the occurrence of relatively wet and dry southwest monsoon (SWM) years over Sri Lanka is still not fully understood. This study focused on investigating the role of moisture transport in contrast SWM years. We selected seven wet (SWM_Wet) and nine dry (SWM_Dry) years for 1985-2015 and found that the whole country experiences above-average (below average) rainfall in SWM_Wet (SWM_Dry) years. In SWM_Wet years, strengthening moisture-laden low-level jets (LLJ) from the Arabian Sea bring a large amount of moisture towards Sri Lanka. In contrast, the weakening of the …

Amilorides Inhibit Sars-Cov-2 Replication In Vitro By Targeting Rna Structures, Martina Zafferani, Christina Haddad, Le Luo, Jesse Davila-Calderon, Liang-Yuan Chiu, Christian Shema Mugisha, Adeline G. Monaghan, Andrew A. Kennedy, Joseph D. Yesselman, Robert J. Gifford, Andrew W. Tai, Sebla B. Kutluay, Mei-Ling Li, Gary Brewer, Blanton S. Tolbert, Amanda E. Hargrove

Department of Chemistry: Faculty Publications

The SARS-CoV-2 pandemic, and the likelihood of future coronavirus pandemics, emphasized the urgent need for development of novel antivirals. Small-molecule chemical probes offer both to reveal aspects of virus replication and to serve as leads for antiviral therapeutic development. Here, we report on the identification of amiloride-based small molecules that potently inhibit OC43 and SARS-CoV-2 replication through targeting of conserved structured elements within the viral 5′-end. Nuclear magnetic resonance–based structural studies revealed specific amiloride interactions with stem loops containing bulge like structures and were predicted to be strongly bound by the lead amilorides in retrospective docking studies. Amilorides represent the …

Nuscon: A Community-Driven Platform For Quantitative Evaluation Of Nonuniform Sampling In Nmr, Yulia Pustovalova, Frank Delaglio, D. Levi Craft, Haribabu Arthanari, Ad Bax, Martin Billeter, Mark J. Bostock, Hesam Dashti, D. Flemming Hansen, Sven G. Hyberts, Bruce A. Johnson, Krzysztof Kazimierczuk, Hengfa Lu, Mark Maciejewski, Tomas M. Miljenović, Mehdi Mobli, Daniel Nietlispach, Vladislav Orekhov, Robert Powers, Xiaobo Qu, Scott Anthony Robson, David Rovnyak, Gerhard Wagner, Jinfa Ying, Matthew Zambrello, Jeffrey C. Hoch, David L. Donoho, Adam D. Schuyler

Department of Chemistry: Faculty Publications

Although the concepts of nonuniform sampling (NUS) and non-Fourier spectral reconstruction in multidimensional NMR began to emerge 4 decades ago (Bodenhausen and Ernst, 1981; Barna and Laue, 1987), it is only relatively recently that NUS has become more commonplace. Advantages of NUS include the ability to tailor experiments to reduce data collection time and to improve spectral quality, whether through detection of closely spaced peaks (i.e., “resolution”) or peaks of weak intensity (i.e., “sensitivity”). Wider adoption of these methods is the result of improvements in computational performance, a growing abundance and flexibility of software, support from NMR spectrometer vendors, and …

Comment On “Intensity Interference In A Coherent Spin-Polarized Electron Beam”, Herman Batelaan, Sam Keramati, T. J. Gay

Department of Physics and Astronomy: Faculty Publications

No abstract provided.

Feasibility Discussion Of Potential Carbon Offsetting Options For Nebraska, Andrew Mwape

School of Natural Resources: Faculty Publications

Conclusion

Highlighting the advantages and disadvantages of carbon offsetting options in the context of the state of Nebraska, this discussion shows that the choice and decisions about which option is better than the other depends on the interests at play and expected outcomes of the participation in carbon markets. However, irrespective of the motive to engage in emission reduction projects for carbon marketing, factors such as cost, and project efficiency can never be overlooked. Given the options discussed in this report, Nebraska has a lot of potential for carbon offsetting or emission reduction projects that would not only reduce and …

Primordial Black Holes From A Cosmic Phase Transition: The Collapse Of Fermi-Balls, Kiyoharu Kawana, Ke-Pan Xie

Department of Physics and Astronomy: Faculty Publications

We propose a novel primordial black hole (PBH) formation mechanism based on a first-order phase transition (FOPT). If a fermion species gains a huge mass in the true vacuum, the corresponding particles get trapped in the false vacuum as they do not have sufficient energy to penetrate the bubble wall. After the FOPT, the fermions are compressed into the false vacuum remnants to form non-topological solitons called Fermi-balls, and then collapse to PBHs due to the Yukawa attractive force. We derive the PBH mass and abundance, showing that for a [](GeV)FOPT the PBHs could be ∼10¹⁷ g and explain …

Prosopis Glandulosa Persistence Is Facilitated By Differential Protection Of Buds During Low- And High-Energy Fires, Heath D. Starns, Carissa L. Wonkka, Matthew B. Dickinson, Alexandra G. Lodge, Morgan L. Treadwell, Kathleen L. Kavanagh, Douglas R. Tolleson, Dirac L. Twidwell Jr, William E. Rogers

Department of Agronomy and Horticulture: Faculty Publications

Rangelands worldwide have experienced significant shifts from grass-dominated to woody-plant dominated states over the past century. In North America, these shifts are largely driven by overgrazing and landscape-scale fire suppression. Such shifts reduce productivity for livestock, can have broad-scale impacts to biodiversity, and are often difficult to reverse. Restoring grass dominance often involves restoring fire as an ecological process. However, many resprouting woody plants persist following disturbance, including fire, by resprouting from protected buds, rendering fire ineffective for reducing resprouting woody plant density. Recent research has shown that extreme fire (high-energy fires during periods of water stress) may reduce resprouting …

Experimental Observation Of Polarization-Resolved Nonlinear Thomson Scattering Of Elliptically Polarized Light, Colton Fruhling, Junzhi Wang, Donald Umstadter, Christoph Schulzke, Mahonri Romero, Michael Ware, Justin Peatross

Department of Physics and Astronomy: Faculty Publications

We report experimental results from a study of nonlinear Thomson scattering of elliptically polarized light. Polarization-resolved radiation patterns of the scattered light are measured as a function of the elliptical polarization state of the incident laser light. The relativistic electron trajectory in intense elliptically polarized fields leads to the formation of unique radiated polarization states, which are observed by our measurements and predicted by a theoretical model. The polarization of Thomson scattered light depends strongly on the intensity of the incident light due to nonlinearity. The results are relevant to high-field electrodynamics and to research and development of light sources …

Multi-Proxy Record Of Holocene Paleoenvironmental Conditions From Yellowstone Lake, Wyoming, Usa, Sabrina R. Brown, Rosine Cartier, Christopher M. Schiller, Petra Zahajská, Sherilyn C. Fritz, Lisa A. Morgan, Cathy Whitlock, Daniel J. Conley, Jack H. Lacey, Melanie J. Leng, W.C. Pat Shanks Iii

Department of Earth and Atmospheric Sciences: Faculty Publications

A composite 11.82 m-long (9876e-67 cal yr BP) sediment record from Yellowstone Lake, Wyoming was analyzed using a robust set of biological and geochemical proxies to investigate the paleoenvironmental evolution of the lake and its catchment in response to long-term climate forcing. Oxygen isotopes from diatom frustules were analyzed to reconstruct Holocene climate changes, and pollen, charcoal, diatom assemblages, and biogenic silica provided information on terrestrial and limnological responses. The long-term trends recorded in the terrestrial and limnic ecosystems over the last 9800 years reflect the influence of changes in the amplification of the seasonal cycle of insolation on regional …

Level And Gorenstein Projective Dimension, Laila Awadalla, Thomas Marley

Department of Mathematics: Faculty Publications

We investigate the relationship between the level of a bounded complex over a commutative ring with respect to the class of Gorenstein projective modules and other invariants of the complex or ring, such as projective dimension, Gorenstein projective dimension, and Krull dimension. The results build upon work done by J. Christensen [7], H. Altmann et al. [1], and Avramov et al. [4] for levels with respect to the class of finitely generated projective modules.

The concept of level in a triangulated category, first defined by Avramov, Buch- weitz, Iyengar, and Miller [4], is a measure of how many mapping cones …

Interspecific And Local Variation In Tern Chick Diets Across Nesting Colonies In The Gulf Of Maine, Keenan Yakola, Adrian Jordaan, Stephen Kress, Paula Shannon, Michelle D. Staudinger

United States Geological Survey: Staff Publications

The Gulf of Maine, USA is home to four colonial co-nesting tern species: Least Tern (Sternula antillarum), Common Tern (Sterna hirundo), Arctic Tern (Sterna paradisaea), and the federally endangered Roseate Tern (Sterna dougallii). Over three decades of visual observations of chick provisioning were compiled for a comparative dietary study in the region, including the first detailed descriptions of Least and Roseate Tern chick diets. Three prey groups comprised the majority of chick diets among tern species between 1986–2017: hake (Urophycis spp. or Enchelyopus cimbrius) 28–37% frequency of occurrence (FO), sand lance …

Exposure Of Predatory And Scavenging Birds To Anticoagulant Rodenticides In France: Exploration Of Data From French Surveillance Programs, Meg-Anne Moriceau, Sébastien Lefebvre, Isabelle Fourel, Etienne Benoit, Florence Buronfosse-Roque, Pascal Orabi, Barnett A. Rattner, Virginie Lattard

United States Geological Survey: Staff Publications

Wild raptors are widely used to assess exposure to different environmental contaminants, including anticoagulant rodenticides (ARs). ARs are used on a global scale for rodent control, and act by disruption of the vitamin K cycle that results in haemorrhage usually accompanied by death within days. Some ARs are highly persistent and bioaccumulative, which can cause significant exposure of non-target species.We characterized AR exposure in a heterogeneous sample of dead raptors collected over 12 years (2008–2019) in south-eastern France. Residue analysis of 156 liver samples through LC-MS/MS revealed that 50% (78/156) were positive for ARs, with 13.5% (21/156) having summed second-generation …

Issue Of False Amphetamine Field Test Positives Caused By Sugar: Use Of Baeyer Test As A Secondary Test Solution, Reed A. Knutson, Jennah Duncan, Kara Peightal, Samuel Thomas

Department of Chemistry: Dissertations, Theses, and Student Research

The Marquis reagent is a well-established and widely used chemical presumptive test for 3,4-Methylenedioxymethamphetamine (MDMA) and methamphetamine. It is composed of concentrated sulfuric acid and 40% formaldehyde, which act upon alkaloids causing them to complex into larger molecules. This complexation causes a color change that can be visually interpreted as a positive or negative result. Almost any sugar molecule can be complexed in this way as well, due to their many OH groups. Experimentally it was found that the sugar molecules did complex with one another when the Marquis test was administered. The color produced by this reaction was brownish-red. …

Higher Sound Levels In K-12 Classrooms Correlate To Lower Math Achievement Scores, Laura Caroline Brill, Lily M. Wang

Durham School of Architectural Engineering and Construction: Faculty Publications

Sound levels from occupied classrooms have been gathered from 220 classrooms across four grade levels (3, 5, 8 and 11) over six school days each and processed with k-means clustering into speech and non-speech clusters. Three metrics describing the classroom acoustics, including the average daily A-weighted equivalent level for non-speech, the average daily difference between the A-weighted equivalent levels for speech and nonspeech (a signal to noise ratio), and the mid-frequency averaged reverberation time, were analyzed against classroom-aggregated standardized reading and math achievement test scores, while controlling for classroom demographics including socioeconomic status. Interactions between the metrics and demographics were …

Correlated Evolution Of Distinct Signals Associated With Increased Social Selection In Female White-Shouldered Fairywrens, John Anthony Jones, Karan J. Odom, Ian R. Hoppe, Doka Nason, Serena Ketaloya, Jordan Karubian

School of Natural Resources: Faculty Publications

Conspicuous female signals have recently received substantial scientific attention, but it remains unclear if their evolution is the result of selection acting on females independently of males or if mutual selection facilitates female change. Species that express female, but not male, phenotypic variation among populations represents a useful opportunity to address this knowledge gap. White-shouldered fairywrens (Malurus alboscapulatus) are tropical songbirds with a well-resolved phylogeny where female, but not male, coloration varies allopatrically across subspecies. We explored how four distinct signaling modalities, each putatively associated with increased social selection, are expressed in two populations that vary in competitive pressure on …

Salient Experiences In Student Development: Impact Of An Undergraduate Stem Teacher Preparation Program, Amie S. Sommers, Kelly Gomez Johnson, Paula Jakopovic, Julio Rivera, Neal Grandgenett, John A. Conrad, William E. Tapprich, Christine E. Cutucache

School of Natural Resources: Faculty Publications

The need for a comprehensive, high-quality pipeline for the development of undergraduate pre-service teachers, especially those that represent a diverse student body, within STEM disciplines is acute. Here, we studied the NoyceSCIENCE program to determine the most impactful experiences offered to undergraduates through the lens of student development theory. We used qualitative coding to analyze data collected from journals (n = 29) written by students of varying backgrounds, and at varying levels within the program (i.e., the Scholar and Intern level) over a 3-year program running period. We observed that faculty mentorship, the ability of undergraduates to mentor others, volunteer …

Monitoring Agroecosystem Productivity And Phenology At A National Scale: A Metric Assessment Framework, Dawn M. Browning, Eric S. Russell, Guillermo E. Ponce-Campos, Nicole Kaplan, Andrew D. Richardson, Bijan Seyednasrollah, Sheri Spiegal, Nicanor Saliendra, Joseph G. Alfieri, John Baker, Carl Bernacchi, Brandon T. Bestelmeyer, David Bosch, Elizabeth H. Boughton, Raoul K. Boughton, Pat Clark, Gerald Flerchinger, Nuria Gomez-Casanovas, Sarah Goslee, Nick M. Haddad, David Hoover, Abdullah Jaradat, Marguerite Mauritz, Gregory W. Mccarty, Gretchen R. Miller, John Sadler, Amartya Saha, Russell L. Scott, Andrew Suyker, Craig Tweedie, Jeffrey D. Wood, Xukai Zhang, Shawn D. Taylor

School of Natural Resources: Faculty Publications

Effective measurement of seasonal variations in the timing and amount of production is critical to managing spatially heterogeneous agroecosystems in a changing climate. Although numerous technologies for such measurements are available, their relationships to one another at a continental extent are unknown. Using data collected from across the Long-Term Agroecosystem Research (LTAR) network and other networks, we investigated correlations among key metrics representing primary production, phenology, and carbon fluxes in croplands, grazing lands, and crop-grazing integrated systems across the continental U.S. Metrics we examined included gross primary productivity (GPP) estimated from eddy covariance (EC) towers and modelled from the Landsat …

The R Journal (December 2021) 13(2): Complete Issue, The R Foundation

The R Journal

On behalf of the R Foundation and the Editorial board, I am pleased to present Volume 13 Issue 2 of the R Journal. This is the biggest issue ever!

First, some news from the Editorial board. A big thank you to Mike Kane, who has finished his term. As Editor-in-Chief in 2020, Mike expanded operations to include Associate Editors in the reviewing process. The R Journal now has a team of 20 Associate Editors. This has helped to manage the increasing number of submissions. We welcome new Associate Editors, Przemek Biecek, Chris Brunsdon, Mine Çetinkaya-Rundel, Kieran Healy, Adam Loy, Priyanga …

The U.S. Inland Creel And Angler Survey Catalog (Creelcat): Development, Applications, And Opportunities, Abigail J. Lynch, Nicholas A. Sievert, Holly S. Embke, Ashley M. Robertson, Bonnie J.E. Myers, Micheal S. Allen, Zachary S. Feiner, Frederick Hoogakker, Scott Knoche, Rebecca M. Krogman, Stephen R. Midway, Chelsey L. Nieman, Craig P. Paukert, Kevin L. Pope, Mark W. Rogers, Lyndsie S. Wszola, T. Douglas Beard

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

Inland recreational fishing, defined as primarily leisure-driven fishing in freshwaters, is a popular pastime in the USA. State natural resource agencies endeavor to provide high-quality and sustainable fishing opportunities for anglers. Managers often use creel and other angler survey data to inform state- and waterbody-level management efforts. Despite the broad implementation of angler surveys and their importance to fisheries management at state scales, regional and national coordination among these activities is minimal, limiting data applicability for larger-scale management practices and research. Here, we introduce the U.S. Inland Creel and Angler Survey Catalog (CreelCat), a first-of-its-kind, publicly available national database of …