Digital Commons Network^™

Evolutionary Theory: Establishing Positive Learning Environments, Lawrence C. Scharmann

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

A simple but effective technique for self-assessing readiness to teach a particular topic is to explicitly reflect on the student questions, ‘Why do I need toknow this stuff?’ and ‘What’s in it for me?’ Faced with these questions, real or implied, instructional decisions should be made to better address and reflect the needs of target learners. If the teacher’s response does not have sufficient perceived relevance to the target learner, students find it quite easy to dismiss the ‘stuff’ as unimportant – something to be memorised for a test and forgotten. Preparation to teach evolution often carries with it an …

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.

Distr6: R6 Object-Oriented Probability Distributions Interface In R, Raphael Sonabend, Franz J. Király

The R Journal

distr6 is an object-oriented (OO) probability distributions interface leveraging the extensibility and scalability of R6 and the speed and efficiency of Rcpp. Over 50 probability distributions are currently implemented in the package with ‘core’ methods, including density, distribution, and generating functions, and more ‘exotic’ ones, including hazards and distribution function anti-derivatives. In addition to simple distributions, distr6 supports compositions such as truncation, mixtures, and product distributions. This paper presents the core functionality of the package and demonstrates examples for key use-cases. In addition, this paper provides a critical review of the object-oriented programming paradigms in R and describes some …

Dchaos: An R Package For Chaotic Time Series Analysis, Julio E. Sandubete, Lorenzo Escot

The R Journal

Chaos theory has been hailed as a revolution of thoughts and attracting ever-increasing attention of many scientists from diverse disciplines. Chaotic systems are non-linear deterministic dynamic systems which can behave like an erratic and apparently random motion. A relevant field inside chaos theory is the detection of chaotic behavior from empirical time-series data. One of the main features of chaos is the well-known initial-value sensitivity property. Methods and techniques related to testing the hypothesis of chaos try to quantify the initial-value sensitive property estimating the so-called Lyapunov exponents. This paper describes the main estimation methods of the Lyapunov exponent from …

Exprior: An R Package For The Formulation Of Ex-Situ Priors, Falk Heße, Karina Cucchi, Nura Kawa, Yoram Rubin

The R Journal

The exPrior package implements a procedure for formulating informative priors of geostatistical properties for a target field site, called ex-situ priors and introduced in Cucchi et al. (2019). The procedure uses a Bayesian hierarchical model to assimilate multiple types of data coming from multiple sites considered as similar to the target site. This prior summarizes the information contained in the data in the form of a probability density function that can be used to better inform further geostatistical investigations at the site. The formulation of the prior uses ex-situ data, where the data set can either be gathered by the …

Changes In R 4.0–4.1, Tomas Kalibera, Sebastian Meyer, Kurt Hornik

The R Journal

We give a selection of the most important changes in R 4.1.0. Some statistics on source code commits and bug tracking activities are also provided.

Paul Austin Johnsgard: Memories Of An Exceptional Naturalist, Allison E. Johnson, Charles R. Brown

Nebraska Bird Review

On May 28, 2021 the world lost one of its most dogged advocates, and we lost an amazing teacher, naturalist, and friend. Paul has told you in his own words in the previous pages where he was from, where he was educated, about the immense number of scholarly articles and books he published, and about his beautiful art that brought the wild to all of us (https://digitalcommons.unl.edu/zeabook/30/), but we wanted to share the person we knew Paul to be, and to relive some of our memories of him. While Paul’s body of work will continue to impact the ornithological and …

Incorrectly Aged, Identified And Classified: Revisiting Nebraska’S 1968 ‘Barnacle Goose’ Record, Joel G. Jorgensen, Stephen J. Brenner, W. Ross Silcock

Nebraska Bird Review

On 2 November 1968 in northeastern Otoe County, Nebraska, Milton Muncie harvested a bird (herein referred to as the 1968 specimen), subsequently identified as an immature Barnacle Goose (Branta leucopsis), from a flock of about 40 Cackling Geese (Branta hutchinsii; Cortelyou 1969). The occurrence was reported not only as the first record of a Barnacle Goose for Nebraska, but also the first record for the North American Interior and West (Cortelyou 1969). Cortelyou’s (1969) brief article also included a photograph of the mounted specimen. At the time and when subsequently reviewed by various authors, the identity of the 1968 specimen …

Young Women’S Body Attitudes And Sexual Satisfaction: Examining Dehumanization And Communication As Serial Multiple Mediators, Kathryn J. Holland, Kristen E. Silver, Allison E. Cipriano, Rebecca L. Brock

Department of Psychology: Faculty Publications

Women’s bodies are frequent sites of stigmatization. The internalization of negative attitudes toward the body can have negative implications for women’s sexual well-being. In the current study, we examined the relationships between young women’s internalization of body stigma—including body shape, genitals, and menstrual periods—and sexual satisfaction. Additionally, we tested two mechanisms that may mediate the relationship between body attitudes and sexual satisfaction: dehumanization (i.e., feelings of a loss of autonomy and subjectivity) and communication with a sexual partner (e.g., expressing needs and desires). We collected and analyzed survey data from 569 undergraduate women. We tested serial mediation models, such that …

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 …

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) …

Swissenveo: A Fair National Environmental Data Repository For Earth Observation Open Science, Gregory Giuliani, Hugues Cazeaux, Pierre-Yves Burgi, Charlotte Poussin, Jean-Philippe Richard, Bruno Chatenoux

Copyright, Fair Use, Scholarly Communication, etc.

Environmental scientific research is highly becoming data-driven and dependent on high performance computing infrastructures to process ever increasing large volume and diverse data sets. Consequently, there is a growing recognition of the need to share data, methods, algorithms, and infrastructure to make scientific research more effective, efficient, open, transparent, reproducible, accessible, and usable by different users.

However, Earth Observations (EO) Open Science is still undervalued, and different challenges remains to achieve the vision of transforming EO data into actionable knowledge by lowering the entry barrier to massive-use Big Earth Data analysis and derived information products. Currently, FAIR-compliant digital repositories cannot …

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 …

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 …

Chlamydastis Meyrick Of Costa Rica: Barcodes, Biology, And Descriptions Of 36 New Species (Lepidoptera: Depressariidae), Eugenie Phillips-Rodríguez, John W. Brown, Winnie Hallwachs, Daniel H. Janzen

Insecta Mundi

We recognize and review 40 species of Chlamydastis Meyrick, 1916 (Lepidoptera: Depressari­idae) from Costa Rica, including four previously described (i.e., C. vividella (Busck, 1914), revived status; C. phytoptera (Busck, 1914); C. orion Busck, 1920; and C. ungulifera (Meyrick, 1929)) and 36 new species: C. abelulatei Phillips and Brown, new species; C. carolinagodoyae Phillips and Brown, new species; C. angelsolisi Phillips and Brown, new species; C. lindapitkinae Phillips and Brown, new species; C. iangauldi Phillips and Brown, new species; C. anniapicadoae Phillips and Brown, new species; C. antonioazofeifai Phillips and Brown, new species; …

Ruminal Protozoal Populations Of Angus Steers Differing In Feed Efficiency, Brooke A. Clemmons, Sung B. Shin, Timothy P.L. Smith, Mallory M. Embree, Brynn H. Voy, Liesel G. Schneider, Dallas R. Donohoe, Kyle J. Mclean, Phillip R. Myer

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Feed accounts for as much as 70% of beef production costs, and improvement of the efficiency with which animals convert feed to product has the potential to have substantial financial impact on the beef industry. The rumen microbiome plays a key role in determining feed efficiency; however, previous studies of rumen microbiota have not focused on protozoal communities despite the estimation that these organisms represent approximately 50% of rumen content biomass. Protozoal communities participate in the regulation of bacterial populations and nitrogen cycling—key aspects of microbiome dynamics. The present study focused on identifying potential associations of protozoal community profiles with …

Novel 3d Imaging Systems For High-Throughput Phenotyping Of Plants, Tian Gao, Feiyu Zhu, Puneet Paul, Jaspreet Sandhu, Henry Akrofi Doku, Jianxin Sun, Yu Pan, Paul Staswick, Harkamal Walia, Hongfeng Yu

School of Computing: Faculty Publications

The use of 3D plant models for high-throughput phenotyping is increasingly becoming a preferred method for many plant science researchers. Numerous camera-based imaging systems and reconstruction algorithms have been developed for the 3D reconstruction of plants. However, it is still challenging to build an imaging system with high-quality results at a low cost. Useful comparative information for existing imaging systems and their improvements is also limited, making it challenging for researchers to make data-based selections. The objective of this study is to explore the possible solutions to address these issues. We introduce two novel systems for plants of various sizes, …

Three-Dimensional Shape Analysis Of Peripapillary Retinal Pigment Epithelium-Basement Membrane Layer Based On Oct Radial Images, Junfei Tong, Pengfei Dong, Sachin Kedar, Deepta Ghate, Linxia Gu

Department of Mechanical and Materials Engineering: Faculty Publications

The peripapillary retinal pigment epithelium-basement membrane (ppRPE/BM) layer angle was recently proposed as a potential index for estimating intracranial pressure noninvasively. However, the ppRPE/BM layer angle, measured from the optical coherence tomography (OCT) scans, varied across the radial directions of the optic disc. This made the ppRPE/BM layer angle difficult to be utilized in its full potential. In this study, we developed a mathematical model to quantify the ppRPE/BM layer angles across radial scans in relation to the ppRPE/BM 3D morphology in terms of its 3D angle and scanning tilt angles. Results showed that the variations of the ppRPE/BM layer …

Setting Empirically Informed Policy Benchmarks For Physical Science Teaching, Elizabeth B. Lewis, Ana Rivero, Lyrica L. Lucas, Aaron Musson, Brandon Helding

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

In the United States, research on beginning science teachers provides little guidance regarding empirical minimum levels of discipline-specific science coursework for sufficient subject matter knowledge to teach science. Accordingly, in this study we analyzed secondary physical science teachers' science coursework for subject matter knowledge (SMK) and resulting misconceptions of chemistry and physics concepts. Findings were compared with state-level science teacher certification policies. Participants had either: (a) completed a master's level teacher preparation program with an undergraduate degree in science, (b) completed an undergraduate teacher preparation program with a minor degree or more in science, or (c) were undergraduate students enrolled …

Towards A Machine Learning Based Generalizable Framework For Detecting Covid-19 Misinformation On Social Media, Yuanzhi Chen

School of Computing: Dissertations, Theses, and Student Research

Since the beginning of the COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, online social media has become a conduit for the rapid propagation of misinformation. The misinformation is a type of fake news that is created inadvertently without the intention of causing harm. Yet COVID-19 misinformation has caused serious social disruptions including accidental death and destruction of public property. Timely prevention of the propagation of online misinformation requires the development of automated detection tools. Machine learning (ML) based models have been used to automate techniques for identifying fake news. These techniques involve converting text data …

Multiphysics Modeling And Analysis Of A Solar Desalination Process Based On Vacuum Membrane Distillation, Benjamin N. Shuldes, Mona Bavarian, Siamak Nejati

Department of Chemical and Biomolecular Engineering: Faculty Publications

A hollow fiber vacuum membrane distillation (VMD) module was modeled using finite element analysis, and the results were used to conduct an exergy efficiency analysis for a solar-thermal desalination scheme. The performance of the VMD module was simulated under various operating conditions and membrane parameters. Membrane porosity, tortuosity, pore diameter, thickness, and fiber length were varied, along with feed temperature and feed configuration. In all cases, polarization phenomena were seen to inhibit the performance of the module. Under VMD operation, polarization of salt concentration was seen to be the main determining factor in the reduction of permeate flux. Within the …

Using An Integrative Machine Learning Approach To Study Microrna Regulation Networks In Pancreatic Cancer Progression, Roland Madadjim

School of Computing: Dissertations, Theses, and Student Research

With advances in genomic discovery tools, recent biomedical research has produced a massive amount of genomic data on post-transcriptional regulations related to various transcript factors, microRNAs, lncRNAs, epigenetic modifications, and genetic variations. In this direction, the field of gene regulation network inference is created and aims to understand the interactome regulations between these molecules (e.g., gene-gene, miRNA-gene) that take place to build models able to capture behavioral changes in biological systems. A question of interest arises in integrating such molecules to build a network while treating each specie in its uniqueness. Given the dynamic changes of interactome in chaotic systems …

Characterizing Genetic Regulatory Elements In Ovine Tissues, Kimberly M. Davenport, Alisha T. Massa, Suraj Bhattarai, Stephanie D. Mckay, Michelle R. Mousel, Maria K. Herndon, Stephen N. White, Noelle E. Cockett, Timothy P L Smith, Brenda M. Murdoch

Roman L. Hruska U.S. Meat Animal Research Center: Reports

The Ovine Functional Annotation of Animal Genomes (FAANG) project, part of the broader livestock species FAANG initiative, aims to identify and characterize gene regulatory elements in domestic sheep. Regulatory element annotation is essential for identifying genetic variants that affect health and production traits in this important agricultural species, as greater than 90% of variants underlying genetic effects are estimated to lie outside of transcribed regions. Histone modifications that distinguish active or repressed chromatin states, CTCF binding, and DNA methylation were used to characterize regulatory elements in liver, spleen, and cerebellum tissues from four yearling sheep. Chromatin immunoprecipitation with sequencing (ChIP-seq) …

On The Comparison Of Flow Physics Between Minimal And Extended Flow Units In Turbulent Channels, Ethan A. Davis, Siamak Mirfendereski, Jae Sung Park

Department of Mechanical and Materials Engineering: Faculty Publications

Direct numerical simulations were performed to study the effects of the domain size of a minimal flow unit (MFU) and its inherent periodic boundary conditions on flow physics of a turbulent channel flow in a range of 200 ≤ Re_τ ≤ 1000. This was accomplished by comparing turbulent statistics with those computed in sub-domains (SD) of extended domain simulations. The dimensions of the MFU and SD were matched, and SD dynamics were set to minimize artificial periodicities. Streamwise and spanwise dimensions of healthy MFUs were found to increase linearly with Reynolds number. It was also found that both MFU …

Early Detection Of Encroaching Woody Juniperus Virginiana And Its Classification In Multi-Species Forest Using Uas Imagery And Semantic Segmentation Algorithms, Lin Wang, Yuzhen Zhou, Qiao Hu, Zhenghong Tang, Yufeng Ge, Adam Smith, Tala Awada, Yeyin Shi

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Woody plant encroachment into grasslands ecosystems causes significantly ecological destruction and economic losses. Effective and efficient management largely benefits from accurate and timely detection of encroaching species at an early development stage. Recent advances in unmanned aircraft systems (UAS) enabled easier access to ultra-high spatial resolution images at a centimeter level, together with the latest machine learning based image segmentation algorithms, making it possible to detect small-sized individuals of target species at early development stage and identify them when mixed with other species. However, few studies have investigated the optimal practical spatial resolution of early encroaching species detection. Hence, we …

Research And Education For Optimizing The Development And Implementation Of An Unmanned Aircraft Program At The Nebraska Department Of Transportation, Wayne Woldt, Jon Starr, Christopher M. U. Neale

Nebraska Department of Transportation: Research Reports

This report describes the development and implementation of an Unmanned Aircraft System Program at the Nebraska Department of Transportation (NDOT). The project involved the selection and purchase of appropriate UAS and imaging systems for NDOT, education and training for NDOT personnel with classroom and hands-on operation of UAS with the goal of obtaining proficiency and pilot licenses. In addition, the development of policy for the use of UAS within NDOT was accomplished as well as standard operating procedures (SOP) documentation and the development of example case studies of interest to NDOT using the purchased systems and technology.

Research And Education For Optimizing The Development And Implementation Of An Unmanned Aircraft Program At The Nebraska Department Of Transportation, Wayne Woldt, Jon Starr, C.M.U. Neale

Nebraska Department of Transportation: Research Reports

This report describes the development and implementation of an Unmanned Aircraft System Program at the Nebraska Department of Transportation (NDOT). The project involved the selection and purchase of appropriate UAS and imaging systems for NDOT, education and training for NDOT personnel with classroom and hands-on operation of UAS with the goal of obtaining proficiency and pilot licenses. In addition, the development of policy for the use of UAS within NDOT was accomplished as well as standard operating procedures (SOP) documentation and the development of example case studies of interest to NDOT using the purchased systems and technology.

Landscape Genetics Of American Beaver In Coastal Oregon, Clinton W. Epps, Vanessa M. Petro, Tyler G. Creech, Rachel S. Crowhurst, Matthew J. Weldy, Jimmy D. Taylor

United States Department of Agriculture Wildlife Services: Staff Publications

American beaver (Castor canadensis) have been translocated for population restoration, reduction of human‐wildlife conflict, and enhancement of ecosystem function. Yet few studies have assessed dispersal of beaver, making it difficult to determine at what scale translocations are appropriate. Genetic studies can provide inferences about gene flow, and thus dispersal. We used a landscape genetic approach to evaluate whether landscape features influenced gene flow among beaver in the Coast Range of western Oregon, USA, using samples collected April–September 2014. We collected genetic samples from live‐captured (n=232), road‐killed (n=2) and trapper‐provided (n=58) tissue samples and genotyped them at 10 microsatellite loci. We …

Representativeness Of Eddy-Covariance Flux Footprints For Areas Surrounding Ameriflux Sites, Housen Chu, Xiangzhong Luo, Zutao Ouyang, W. Stephen Chan, Sigrid Dengel, Sébastien C. Biraud, Margaret S. Torn, Stefan Metzger, Jitendra Kumar, M. Altaf Arain, Tim J. Arkebauer, Dennis Baldocchi, Carl Bernacchi, Dave Billesbach, T. Andrew Black, Peter D. Blanken, Gil Bohrer, Rosvel Bracho, Shannon Brown, Nathaniel A. Brunsell, Jiquan Chen, Xingyuan Chen, Kenneth Clark, Ankur R. Desai, Tomer Duman, David Durden, Silvano Fares, Inke Forbrich, John A. Gamon, Christopher M. Gough, Timothy Griffis, Manuel Helbig, David Hollinger, Elyn Humphreys, Hiroki Ikawa, Hiroki Iwata, Yang Ju, John F. Knowles, Sara H. Knox, Hideki Kobayashi

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

Large datasets of greenhouse gas and energy surface-atmosphere fluxes measured with the eddy-covariance technique (e.g., FLUXNET2015, AmeriFlux BASE) are widely used to benchmark models and remote-sensing products. This study addresses one of the major challenges facing model-data integration: To what spatial extent do flux measurements taken at individual eddy-covariance sites reflect model- or satellite-based grid cells? We evaluate flux footprints—the temporally dynamic source areas that contribute to measured fluxes—and the representativeness of these footprints for target areas (e.g., within 250–3000 m radii around flux towers) that are often used in flux-data synthesis and modeling studies. We examine the land-cover composition …

Feature-Based Point Cloud-Based Assessment Of Heritage Structures For Nondestructive And Noncontact Surface Damage Detection, Richard L. Wood, Mohammad Ebrahim Mohammadi

Department of Civil and Environmental Engineering: Faculty Publications

Assessment and evaluation of damage in cultural heritage structures are conducted primarily using nondestructive and noncontact methods. One common deployment is laser scanners or ground-based lidar scanners that produce a point cloud containing information at the centimeter to the millimeter level. This type of data allows for detecting surface damage, defects, cracks, and other anomalies based only on geometric surface descriptors using a single dataset, which does not rely on a change detection approach. Moreover, geometric features are not influenced by color, which is essential for heritage structures because they are nonuniform in color due to anthropologic and environmental effects …