Digital Commons Network^™

Analyzing Dependence Between Point Processes In Time Using Indtestpp, Ana C. Cebrián, Jesús Asín

The R Journal

The need to analyze the dependence between two or more point processes in time appears in many modeling problems related to the occurrence of events, such as the occurrence of climate events at different spatial locations or synchrony detection in spike train analysis. The package IndTestPP provides a general framework for all the steps in this type of analysis, and one of its main features is the implementation of three families of tests to study independence given the intensities of the processes, which are not only useful to assess independence but also to identify factors causing dependence. The package also …

Robustness In Network (Robin): An R Package For Comparison And Validation Of Communities, Valeria Policastro, Dario Righelli, Annamaria Carissimo, Luisa Cutillo, Italia De Feis

The R Journal

In network analysis, many community detection algorithms have been developed. However, their implementation leaves unaddressed the question of the statistical validation of the results. Here, we present robin (ROBustness In Network), an R package to assess the robustness of the community structure of a network found by one or more methods to give indications about their reliability. The procedure initially detects if the community structure found by a set of algorithms is statistically significant and then compares two selected detection algorithms on the same graph to choose the one that better fits the network of interest. We demonstrate the use …

Benchmarking R Packages For Calculation Of Persistent Homology, Eashwar V. Somasundaram, Shael E. Brown, Adam Litzler, Jacob G. Scott, Raoul R. Wadhwa

The R Journal

Several persistent homology software libraries have been implemented in R. Specifically, the Dionysus, GUDHI, and Ripser libraries have been wrapped by the TDA and TDAstats CRAN packages. These software represent powerful analysis tools that are computationally expensive and, to our knowledge, have not been formally benchmarked. Here, we analyze runtime and memory growth for the 2 R packages and the 3 underlying libraries. We find that datasets with less than 3 dimensions can be evaluated with persistent homology fastest by the GUDHI library in the TDA package. For higher-dimensional datasets, the Ripser library in the TDAstats package is the fastest. …

The Bdpar Package: Big Data Pipelining Architecture For R, Miguel Ferreiro-Díaz, Tomás R. Cotos-Yáñez, José R. Méndez, David Ruano-Ordás

The R Journal

In the last years, big data has become a useful paradigm for taking advantage of multiple sources to find relevant knowledge in real domains (such as the design of personalized marketing campaigns or helping to palliate the effects of several fatal diseases). Big data programming tools and methods have evolved over time from a MapReduce to a pipeline-based archetype. Concretely the use of pipelining schemes has become the most reliable way of processing and analyzing large amounts of data. To this end, this work introduces bdpar, a new highly customizable pipeline-based framework (using the OOP paradigm provided by R6 …

Conference Report Of Why R? Turkey 2021, Mustafa Cavus, Olgun Aydin, Ozan Evkaya, Ozancan Ozdemir, Deniz Bezer, Ugur Dar

The R Journal

The Why R? Turkey 2021 as a three-day online conference was organized to bring together researchers and professionals from Turkey on April 16-17-18, 2021. We hereby aimed to promote the R community in Turkey by bringing R users with different backgrounds such as genetics, sociology, finance, economy, bio-statistics. There were 8 thematic sessions and 18 invited speakers. In this article, it is aimed to describe the preparation phase, technical details, and the impact of the conference on audience.

Rlumcarlo: Simulating Cold Light Using Monte Carlo Methods, Sebastian Kreutzer, Johannes Friedrich, Vasilis Pagonis, Christian Laag, Ena Rajovic, Christoph Schmidt

The R Journal

The luminescence phenomena of insulators and semiconductors (e.g., natural minerals such as quartz) have various application domains. For instance, Earth Sciences and archaeology exploit luminescence as a dating method. Herein, we present the R package RLumCarlo implementing sets of luminescence models to be simulated with Monte Carlo (MC) methods. MC methods make a powerful ally to all kinds of simulation attempts involving stochastic processes. Luminescence production is such a stochastic process in the form of charge (electron-hole pairs) interaction within insulators and semiconductors. To simulate luminescence-signal curves, we distribute single and independent MC processes to virtual MC clusters. RLumCarlo comes …

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor 3.13 was released on 20 May, 2021. It is compatible with R 4.1.0 and consists of 2042 software packages, 406 experiment data packages, 965 up-to-date annotation packages, and 29 workflows.

Gofcopula: Goodness-Of-Fit Tests For Copulae, Ostap Okhrin, Simon Trimborn, Martin Waltz

The R Journal

The last decades show an increased interest in modeling various types of data through copulae. Different copula models have been developed, which lead to the challenge of finding the best fitting model for a particular dataset. From the other side, a strand of literature developed a list of different Goodness-of-Fit (GoF) tests with different powers under different conditions. The usual practice is the selection of the best copula via the p-value of the GoF test. Although this method is not purely correct due to the fact that non-rejection does not imply acception, this strategy is favored by practitioners. Unfortunately, …

The Nebraska Bird Review, Volume 89 June 2021 Number 2

Nebraska Bird Review

Spring Field Report, March - May 2021, by W. Ross Silcock … 50

Incorrectly Aged, Identified and Classified: Revisiting Nebraska’s 1968 ‘Barnacle Goose’ Record, by Joel G. Jorgensen, Stephen J. Brenner, and W. Ross Silcock …80

Paul A. Johnsgard by Paul A. Johnsgard … 92

Paul Austin Johnsgard: Memories of an Exceptional Naturalist by Allison E. Johnson and Charles R. Brown …94

Breeding Status of Louisiana Waterthrush (Parkesia motacilla) in the Niobrara River Valley, North-central Nebraska by W. Ross Silcock … 97

Remembering Elaine Bachel 1946-2021, by Ruthie Stearns …101

Subscription and Organization Information …103

Rhizosphere Microbiomes In A Historical Maize-Soybean Rotation System Respond To Host Species And Nitrogen Fertilization At The Genus And Subgenus Levels, Michael A. Meier, Martha G. Lopez-Guerrero, Ming Guo, Marty Schmer, Josh Herr, James Schnable, James R. Alfano, Jinliang Yang

Department of Agronomy and Horticulture: Faculty Publications

Root-associated microbes are key players in plant health, disease resistance, and nitrogen (N) use efficiency. It remains largely unclear how the interplay of biological and environmental factors affects rhizobiome dynamics in agricultural systems. In this study, we quantified the composition of rhizosphere and bulk soil microbial communities associated with maize (Zea mays L.) and soybean (Glycine max L.) in a long-term crop rotation study under conventional fertilization and low-N regimes. Over two growing seasons, we evaluated the effects of environmental conditions and several treatment factors on the abundance of rhizosphere- and soil-colonizing microbial taxa. Time of sampling, host plant species, …

Using Thermal Imaging To Measure Water Stress In Creeping Bentgrass Putting Greens, Joseph G. Foral Jr.

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

Thermal imaging is a developing tool that can help turf managers reduce water consumption and improve irrigation scheduling, but in-depth studies are needed to maximize this potential. This study evaluated the ability of thermal imaging to identify water stress in a creeping bentgrass (Agrostis stolonifera ‘007’) putting green. Water use and canopy temperature (T_c) were measured for plots subjected to three levels of measured water replacement (full, half, and none) to evaluate changes over a range of soil water potentials (SWP). Water use was consistent across the irrigation treatments up to several days before observed wilt …

Real-Life Conundrums In The Struggle For Institutional Transformation, Julia Mcquillan, Nestor Hernandez

Department of Sociology: Faculty Publications

Intersecting systems of inequality (i.e., gender and race/ethnicity) are remarkably resistant to change. Many universities, however, seek National Science Foundation Institutional Transformation awards to change processes, procedures, and cultures to make science, technology, engineering, and mathematics (STEM) departments more inclusive. In this article we describe a case study with observations for eight years of before (2000–2007), five during (2008–2013), and seven after (2014–2020) intensive efforts to increase women through reducing barriers and increasing access to women. Finally, we reflect on flawed assumptions built into the proposal, the slow and uneven change in the proportion of women over time, the strengths …

Comparing Management Programs To Reduce Red–Tailed Hawk Collisions With Aircraft, Brian Washburn, Craig K. Pullins, Travis L. Guerrant, Gregory J. Martinelli, Scott F. Beckerman

United States Department of Agriculture Wildlife Services: Staff Publications

Wildlife-aircraft collisions (wildlife strikes) pose a serious safety risk to aircraft. Raptors (i.e., hawks and owls) are one of the most frequently struck guilds of birds within North America. Although raptors (most notably red-tailed hawks [Buteo jamaicensis]) are commonly managed at most airports and military bases, there is no scientific information available regarding comparisons of the efficacy of raptor management programs for reducing raptor-aircraft collisions. Therefore, we conducted a study to examine the efficacy of 2 raptor hazard management programs implemented at Chicago's O'Hare International Airport (ORD). The first raptor management program (Phase I) occurred during January 2010–June 2013 and …

Presence-Absence Sampling Plans For Stink Bugs (Hemiptera: Pentatomidae) In The Midwest Region Of The United States, Rafael Carlesso Aita, Daniela T. Pezzini, Eric C. Burkness, Christina D. Difonzo, Deborah L. Finke, Thomas E. Hunt, Janet J. Knodel, Christian H. Krupke, Lia Marchi-Werle, Brian Mccornack, Andrew P. Michel, Christopher R. Philips, Nicholas J. Seiter, Adam J. Varenhorst, Robert J. Wright, William D. Hutchison, Robert L. Koch

Department of Entomology: Faculty Publications

Stink bugs represent an increasing risk to soybean production in the Midwest region of the United States. The current sampling protocol for stink bugs in this region is tailored for population density estimation and thus is more relevant to research purposes. A practical decision-making framework with more efficient sampling effort for management of herbivorous stink bugs is needed. Therefore, a binomial sequential sampling plan was developed for herbivorous stink bugs in the Midwest region. A total of 146 soybean fields were sampled across 11 states using sweep nets in 2016, 2017, and 2018. The binomial sequential sampling plans were developed …

Maize Tassel Detection From Uav Imagery Using Deep Learning, Aziza Alzadjali, Mohammed H. Alali, Arun Narenthiran Weeranampalayam Sivakumar, Jitender S. Deogun, Stephen Scott, James C. Schnable, Yeyin Shi

Department of Mechanical and Materials Engineering: Faculty Publications

The timing of flowering plays a critical role in determining the productivity of agricultural crops. If the crops flower too early, the crop would mature before the end of the growing season, losing the opportunity to capture and use large amounts of light energy. If the crops flower too late, the crop may be killed by the change of seasons before it is ready to harvest. Maize flowering is one of the most important periods where even small amounts of stress can significantly alter yield. In this work, we developed and compared two methods for automatic tassel detection based on …

Morphophysiological And Molecular Characterization Of Millet (Panicum Miliaceum L.) Varieties For Crop Improvement In Western Europe, Massimo Vischi, Nicola Zorzin, Maria Bernhart, Johanna Winkler, Dipak Santra, Carla Pappalardo, Stefano Marchetti

Department of Agronomy and Horticulture: Faculty Publications

Background

Global warming and issues in favour of a more sustainable agriculture suggest a reconsideration of minor cereals in European agrosystems. Compared to other summer crops, proso millet has a remarkable drought resistance and could be used to improve crop rotation and biodiversity. Proso millet is also increasingly sought by industry to produce novel foods such as those designed for celiac patients. In this study, a thorough characterization of 11, commercially available, proso millet (Panicum milliaceum L.) varieties was carried out as a preliminary step for crop reintroduction and breeding in Western Europe.

Methods

The cultivars under evaluation were …

James Davidson Fawcett (1933–2020): Imbibing With The Kiwi, Louis A. Somma

Papers in Herpetology

An obituary and summary of the life of James D. Fawcett (1933-2020), herpetologist and instructor and professor of Biology at University of Nebraska at Omaha, 1972-2015. Includes bibliography of his works, list of master's theses chaired, and recollections of former students.

Modeling Vadose Zone Hydrology [Lecture Notes], Derek M. Heeren, Dean E. Eisenhauer

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Modeling Vadose Zone Hydrology is a graduate-level course offered biennially in the Department of Biological Systems Engineering. Topics included hydraulic properties of porous media, application of Darcy's Law in variably saturated media, hydrologic and transport processes in the vadose zone, and solution of steady and unsteady flow problems using numerical techniques. A graphical approach for characterizing vertical one-dimensional problems with energy head profiles was emphasized. Common one-dimensional flow and transport problems were solved analytically. The course was taught using a combination of lecture notes and PowerPoint presentations. The lecture notes from 2021, captured using the Microsoft Whiteboard app with a …

Dynamic Observers For Unknown Populations, Chris Guiver, Nathan Poppelreiter, Richard Rebarber, Brigitte Tenhumberg, Stuart Townley

Brigitte Tenhumberg Papers

Dynamic observers are considered in the context of structuredpopulation modeling and management. Roughly, observers combine a known measured variable of some process with a model of that process to asymptotically reconstruct the unknown state variable of the model. We investigate the potential use of observers for reconstructing population distributions described by density-independent (linear) models and a class of density-dependent (nonlinear) models. In both the density-dependent and -independent cases, we show, in several ecologically reasonable circumstances, that there is a natural, optimal construction of these observers. Further, we describe the robustness these observers exhibit with respect to disturbances and uncertainty in …

Longitudinal Study Of Pogonomyrmex Occidentalis (Hymenoptera: Formicideae), Western Harvester Ant, Colony Survival In Western Nebraska, Kathleen H. Keeler

School of Biological Sciences: Faculty Publications

I observed individual western harvester ant (Pogonomyrmex occidentalis) colonies, marked between 1977 and 1994, to live a mean of 15.65 years (n = 112). The longest-lived colony lived 42 years.

Paul Johnsgard, Nebraska's Internationally Respected Naturalist, Dies At 89, Nancy Gaarder

Paul Johnsgard Collection

An internationally respected naturalist and ornithologist, Johnsgard wrote more than 100 books and numerous scholarly papers, many of them about the landscape and wildlife of his adopted home, Nebraska. Johnsgard’s decades of writing, photography, artwork and educational endeavors helped bring to the public consciousness the value of Nebraska wildlife, especially the unique spectacle that is the sandhill crane migration. That, in turn, contributed to conservation efforts along the Platte River and a thriving tourism economy in central Nebraska.

Overview Of The Microbiome Among Nurses Study (Micro-N) As An Example Of Prospective Characterization Of The Microbiome Within Cohort Studies, Christine Everett, Chengchen Li, Jeremy E. Wilkinson, Long H. Nguyen, Lauren J. Mciver, Kerry Ivey, Jacques Izard, Natalia Palacios, A. Heather Eliassen, Walter C. Willett, Alberto Ascherio, Qi Sun, Shelley S. Tworoger, Andrew T. Chan, Wendy S. Garrett, Curtis Huttenhower, Eric B. Rimm, Mingyang Song

Department of Food Science and Technology: Faculty Publications

A lack of prospective studies has been a major barrier for assessing the role of the microbiome in human health and disease on a population-wide scale. To address this significant knowledge gap, we have launched a large-scale collection targeting fecal and oral microbiome specimens from 20,000 women within the Nurses’ Health Study II cohort (the Microbiome Among Nurses study, or Micro-N). Leveraging the rich epidemiologic data that have been repeatedly collected from this cohort since 1989; the established biorepository of archived blood, urine, buccal cell, and tumor tissue specimens; the available genetic and biomarker data; the cohort’s ongoing follow-up; and …

Alfaxalone Successfully Immobilizes Small Indian Mongooses (Urva Auropunctata): A Field Report, Caroline C. Sauvé, Yves Rondenay, Are R. Berentsen, Mel J. Rivera-Rodriguez, Patrick A. Leighton

United States Department of Agriculture Wildlife Services: Staff Publications

We investigated intramuscular administration of alfaxalone (5.3–10.0 mg/kg) as an immobilizing agent in free-ranging small Indian mongooses (Urva auropunctata) on the island of St. Kitts, West Indies. From 5–11 January 2020, we successfully immobilized 10 of 11 mongooses. Alfaxalone provided rapid onset (median = 3 min) of immobilization. Mean duration of immobilization was 16.8 ± 3 min. Mean recovery time was 5.6 ± 1 min. There was no effect of dose administered on induction, anesthesia, or recovery times at the dose range used. We concluded that alfaxalone represents an effective alternative to dissociative agents for the immobilization of free-ranging mongooses. …

Strategic Testing Approaches For Targeted Disease Monitoring Can Be Used To Inform Pandemic Decision-Making, James D. Nichols, Tiffany L. Bogich, Emily Howerton, Ottar N. Bjørnstad, Rebecca K. Borchering, Matthew Ferrari, Murali Haran, Christopher Jewell, Kim M. Pepin, William J.M. Probert, Juliet R.C. Pulliam, Michael C. Runge, Michael Tildesley, Cecile Viboud, Katriona Shea

United States Department of Agriculture Wildlife Services: Staff Publications

More than 1.6 million Servere Acute Respiratory Syndrome Cronovirus 2(SARS-COV-2)tests were administered daily in the United States at the peak of the epidemic, with a significant focus on individual treatment. Here, we show that objective-driven, strategic sampling designs and analyses can maximize information gain at the population level, which is necessary to increase situational awareness and predict, prepare for, and respond to a pandemic, while also continuing to inform individual treatment. By focusing on specific objectives such as individual treatment or disease prediction and control (e.g., via the collection of population- level statistics to inform lockdown measures or vaccine rollout) …

An Evaluation Of Body-Grip Trap Trigger Configurations For Reducing River Otter Take Incidental To Beaver Trapping, Alec J. Sundelius, Nicholas Forman, Nathan M. Roberts, Shawn T. Rossler, David B. Ruid, Robert C. Willging

United States Department of Agriculture Wildlife Services: Staff Publications

River otter (Lontra canadensis) populations in North America have been the focus of significant restoration efforts. Wildlife management agencies, concerned about the unintentional take of river otters incidental to beaver (Castor canadensis) trapping, may recommend techniques to avoid capturing river otters. River otter avoidance techniques that are ineffective or diminish trap performance for beavers are undesirable. We conducted a field evaluation in 2015 and 2016 in Wisconsin to assess how two trigger configurations (offset and center) on body-grip traps would affect the incidental capture rate of river otters during beaver trapping. We also evaluated effects of …

Quantifying High-Temperature Stress On Soybean Canopy Photosynthesis: The Unique Role Of Sun-Induced Chlorophyll Fluorescence, Hyungsuk Kimm, Kaiyu Guan, Charles H. Burroughs, Bin Peng, Elizabeth A. Ainsworth, Carl J. Bernacchi, Caitlin E. Moore, Etsushi Kumagai, Xi Yang, Joseph A. Berry, Genghong Wu

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

High temperature and accompanying high vapor pressure deficit often stress plants without causing distinctive changes in plant canopy structure and consequential spectral signatures. Sun-induced chlorophyll fluorescence (SIF), because of its mechanistic link with photosynthesis, may better detect such stress than remote sensing techniques relying on spectral reflectance signatures of canopy structural changes. However, our understanding about physiological mechanisms of SIF and its unique potential for physiological stress detection remains less clear. In this study, we measured SIF at a high-temperature experiment, Temperature Free-Air Controlled Enhancement, to explore the potential of SIF for physiological investigations. The experiment provided a gradient of …

Brown Treesnake Mortality After Aerial Application Of Toxic Baits, Scott M. Goetz, Eric T. Hileman, Melia G. Nafus, Amy A. Yackel Adams, Amanda R. Bryant, Robert N. Reed, Shane R. Siers

United States Department of Agriculture Wildlife Services: Staff Publications

Quantitative evaluation of control tools for managing invasive species is necessary to assess overall effectiveness and individual variation in treatment susceptibility. Invasive brown treesnakes (Boiga irregularis) on Guam have caused severe ecological and economic effects, pose a risk of accidental introduction to other islands, and are the greatest impediment to the reestablishment of extirpated native fauna. An aerial delivery system for rodent‐based toxic baits can reduce brown treesnake abundance and heterogeneity among individuals may influence bait attraction or toxicant susceptibility. Previous baiting trials have either been simulated aerial treatments or relied on slightly different bait capsule compositions and the results …

Improved Taste And Texture In Novel Popcorn Varieties Compared To Conventional Lines, Leandra Parsons, Oscar Rodriguez, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Abstract Quality Protein Popcorn (QPP) varieties were bred out of a unique germplasm pool derived from Quality Protein dent Maize and conventional popcorn lines. To identify and compare distinctive characteristics within this population, a new sensory method was employed that coupled hedonic numeric rankings of common sensory traits appearance, aroma, texture, and taste with an “overall likability” score while requiring the selection of specific descriptors for taste and texture. Participants tasted six popcorn cultivars, rated each sample based on sensory factors, and offered specific descriptors for taste and texture. This sensory method identified two QPP hybrids with higher overall likability …

Genomics-Guided Refinement Of Butterfly Taxonomy, Jing Zhang, Qian Cong, Jinhui Shen, Paul A. Opler, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Continuing with comparative genomic exploration of worldwide butterfly fauna, we use all proteincoding genes as they are retrieved from the whole genome shotgun sequences for phylogeny construction. Analysis of these genome-scale phylogenies projected onto the taxonomic classification and the knowledge about butterfly phenotypes suggests further refinements of butterfly taxonomy that are presented here. As a general rule, we assign most prominent clades of similar genetic differentiation to the same taxonomic rank, and use criteria based on relative population diversification and the extent of gene exchange for species delimitation. As a result, 7 tribes, 4 subtribes, 14 genera, and 9 subgenera …

Uavs For Vegetation Monitoring: Overview And Recent Scientific Contributions, Ana I. De Castro, Yeyin Shi, Joe Mari Maja, Jose M. Pena

Department of Mechanical and Materials Engineering: Faculty Publications

This paper reviewed a set of twenty-one original and innovative papers included in a special issue on UAVs for vegetation monitoring, which proposed new methods and techniques applied to diverse agricultural and forestry scenarios. Three general categories were considered: (1) sensors and vegetation indices used, (2) technological goals pursued, and (3) agroforestry applications. Some investigations focused on issues related to UAV flight operations, spatial resolution requirements, and computation and data analytics, while others studied the ability of UAVs for characterizing relevant vegetation features (mainly canopy cover and crop height) or for detecting different plant/crop stressors, such as nutrient content/deficiencies, water …