Digital Commons Network^™

Aquadtree: An R Package For Quadtree Anonymization Of Point Data, Raymond Lagonigro, Ramon Oller, Joan Carles Martori

The R Journal

The demand for precise data for analytical purposes grows rapidly among the research community and decision makers as more geographic information is being collected. Laws protecting data privacy are being enforced to prevent data disclosure. Statistical institutes and agencies need methods to preserve confidentiality while maintaining accuracy when disclosing geographic data. In this paper we present the AQuadtree package, a software intended to produce and deal with official spatial data making data privacy and accuracy compatible. The lack of specific methods in R to anonymize spatial data motivated the development of this package, providing an automatic aggregation tool to anonymize …

Six Years Of Shiny In Research: Collaborative Development Of Web Tools In R, Peter Kasprzak, Lachlan Mitchell, Olena Kravchuk, Andy Timmins

The R Journal

The use of Shiny in research publications is investigated over the six and a half years since the appearance of this popular web application framework for R, which has been utilised in many varied research areas. While it is demonstrated that the complexity of Shiny applications is limited by the background architecture, and real security concerns exist for novice app developers, the collaborative benefits are worth attention from the wider research community. Shiny simplifies the use of complex methodologies for people of different specialities, at the level of proficiency appropriate for the end user. This enables a diverse community of …

Assembling Pharmacometric Datasets In R: The Puzzle Package, Mario González-Sales, Olivier Barrière, Pierre Olivier Tremblay, Guillaume Bonnefois, Julie Desrochers, Fahima Nekka

The R Journal

Pharmacometric analyses are integral components of the drug development process. The core of each pharmacometric analysis is a dataset. The time required to construct a pharmacometrics dataset can sometimes be higher than the effort required for the modeling per se. To simplify the process, the puzzle R package has been developed aimed at simplifying and facilitating the time consuming and error prone task of assembling pharmacometrics datasets.

Puzzle consist of a series of functions written in R. These functions create, from tabulated files, datasets that are compatible with the formatting requirements of the gold standard non-linear mixed effects modeling …

Rngforgpd: An R Package For Generation Of Univariate And Multivariate Generalized Poisson Data, Hesen Li, Hakan Demirtas, Ruizhe Chen

The R Journal

This article describes the R package RNGforGPD, which is designed for the generation of univariate and multivariate generalized Poisson data. Some illustrative examples are given, the utility and functionality of the package are demonstrated; and its performance is assessed via simulations that are devised around both artificial and real data.

Species Distribution Modeling Using Spatial Point Processes: A Case Study Of Sloth Occurrence In Costa Rica, Paula Moraga

The R Journal

Species distribution models are widely used in ecology for conservation management of species and their environments. This paper demonstrates how to fit a log-Gaussian Cox process model to predict the intensity of sloth occurrence in Costa Rica, and assess the effect of climatic factors on spatial patterns using the R-INLA package. Species occurrence data are retrieved using spocc, and spatial climatic variables are obtained with raster. Spatial data and results are manipulated and visualized by means of several packages such as raster and tmap. This paper provides an accessible illustration of spatial point process modeling that can …

Testing The Equality Of Normal Distributed And Independent Groups’ Means Under Unequal Variances By Doex Package, Mustafa Cavus, Berna Yazıcı

The R Journal

In this paper, we present the doex package contains the tests for equality of normal distributed and independent group means under unequal variances such as Cochran F, Welch-Aspin, Welch, Box, Scott-Smith, Brown-Forsythe, Johansen F, Approximate F, Alexander-Govern, Generalized F, Modified Brown-Forsythe, Permutation F, Adjusted Welch, B2, Parametric Bootstrap, Fiducial Approach, and Alvandi Generalized F-test. Most of these tests are not available in any package. Thus, doex is easy to use for researchers in multidisciplinary studies. In this study, an extensive Monte-Carlo simulation study is conducted to investigate the performance of the the tests for equality of normal distributed group means …

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 3.12 was released on 28 October, 2020. It is compatible with R 4.0.3 and consists of 1974 software packages, 398 experiment data packages, 968 up-to-date annotation packages, and 28 workflows. Books are a new addition, built regularly from source and therefore fully reproducible; an example is the community-developed Orchestrating Single-Cell Analysis with Bioconductor.

Editorial, Michael J. Kane

The R Journal

On behalf of the editorial board, I am pleased to present Volume 12 Issue 2 of the R Journal. This is my third and final issue as the Editor-in-Chief. In the last year, we have made some substantial changes to the journal that I believe will continue to increase our capacity to support the growing data science and computational statistics communities, and continue to raise the visibility of the journal. In the last few months we recruited 10 Associate Editors and we are continuing the recruitment process. I’d like to publicly welcome our new Associate Editors, and thank each of …

Miwqs: Multiple Imputation Using Weighted Quantile Sum Regression, Paul M. Hargarten, David C. Wheeler

The R Journal

The miWQS package in the Comprehensive R Archive Network (CRAN) utilizes weighted quantile sum regression (WQS) in the multiple imputation (MI) framework. The data analyzed is a set/mixture of continuous and correlated components/chemicals that are reasonable to combine in an index and share a common outcome. These components are also interval-censored between zero and upper thresholds, or detection limits, which may differ among the components. This type of data is found in areas such as chemical epidemiological studies, sociology, and genomics. The miWQS package can be run using complete or incomplete data, which may be placed in the first quantile, …

Shedding Of Marburg Virus In Naturally Infected Egyptian Rousette Bats, South Africa, 2017, Janusz T. Pawęska, Nadia Storm, Wanda Markotter, Nicholas Di Paola, Michael R. Wiley, Gustavo Palacios, Petrus Jansen Van Vuren

University of Nebraska's National Strategic Research Institute: Publications

We detected Marburg virus RNA in rectal swab samples from Egyptian rousette bats in South Africa in 2017. This finding signifies that fecal contamination of natural bat habitats is a potential source of infection for humans. Identified genetic sequences are closely related to Ravn virus, implying wider distribution of Marburg virus in Africa.

The genus Marburgvirus, family Filoviridae, comprises 1 species, Marburg marburgvirus, which comprises 2 marburgviruses, Marburg virus (MARV) and Ravn virus (RAVV) (1). Marburgviruses cause sporadic but often fatal MARV disease in humans and nonhuman primates (2). The Egyptian rousette bat (Rousettus aegyptiacus) …

Preparing For A Driverless Future, Daniel P. Piatkowski, Santosh Pitla, Joe Luck, Josephine K. Hazelton

Nebraska Department of Transportation: Research Reports

Autonomous vehicles (AVs) are widely considered to be the future of surface transportation in the United States, but little is understood about how people will interact with these vehicles, what they will use them for, and how they will impact our roads. However, farmers have been interacting with some degree of AV technology, primarily auto-guidance, in Nebraska for at least the last 10 years. The research in Section 1 first utilizes in-depth qualitative interviews to understand farmers’ experiences with using highly automated technology in order to inform adoption and diffusion patterns of AVs. The findings in Section 1 lead to …

Neonicotinoid Pesticide And Nitrate Removal In Floating Treatment Wetlands, Julia Lindgren

Department of Environmental Engineering: Theses and Other Student Research

Nutrient and pesticide concentrations in surface water are a growing concern in the Midwest. Floating treatment wetlands (FTWs) are often used to remove excess nutrients from surface water and should be considered for removal of emerging contaminants, such as neonicotinoids. Therefore, the objectives for this research project were: 1) Determine FTW neonicotinoid removal capacity, 2) Quantify neonicotinoid incorporation into floating macrophytes, and 3) Explore potential implications of neonicotinoids on microbial denitrification. A microcosm and mesocosm experiment was completed. The mesocosm experiment evaluated 3 treatments: 1) FTW mesocosm with neonicotinoids, 2) FTW without neonicotinoids, and 3) mesocosm with neonicotinoids and without …

Struggling Student Teachers: Interventions For Support And Success, Sheree Moser

Department of Teaching, Learning, and Teacher Education: Theses and Other Student Research

Teacher shortages in K-12 schools have created unique challenges for teacher preparation programs. University instructors face the task requirements of supporting candidates from a wide variety of backgrounds at the undergraduate and graduate level. While some of these candidates enter higher education programs skilled, eager, and committed, others are less prepared, requiring significant attention to make it through the program. Exams required by state departments of education and minimum grade point averages influence each candidate’s ability to move forward within the program, causing some students to experience additional struggles related to mental health and financial burdens.

The problem of practice …

Struggling Student Teachers: Interventions For Support And Success, Sheree Moser

Department of Teaching, Learning, and Teacher Education: Theses and Other Student Research

Teacher shortages in K-12 schools have created unique challenges for teacher preparation programs. University instructors face the task requirements of supporting candidates from a wide variety of backgrounds at the undergraduate and graduate level. While some of these candidates enter higher education programs skilled, eager, and committed, others are less prepared, requiring significant attention to make it through the program. Exams required by state departments of education and minimum grade point averages influence each candidate’s ability to move forward within the program, causing some students to experience additional struggles related to mental health and financial burdens.

The problem of practice …

A Musical Analysis Of The Improvisational Bebop Style Of Nat Adderley (1955–1964), Kyle Granville

Glenn Korff School of Music: Dissertations, Theses, Student Creative Work, and Performances

Nathaniel Carlyle Adderley was an American jazz artist active in New York City, Florida and Europe throughout his extensive musical career. A prominent cornet player and composer, Adderley was highly respected by many of his peers in New York City, Florida, as well as all over Europe. He spent a lot of time during his career performing with and composing for many renowned jazz musicians: Horace Silver, Oscar Pettiford, Johnny Griffin, Yusef Lateef and most notably his older brother, Cannonball Adderley. Collaborations with these notable musicians and many others, help cement Nat Adderley a well deserving spot in the jazz …

Packet Delivery: An Investigation Of Educational Video Games For Computer Science Education, Robert Lafferty

School of Computing: Dissertations, Theses, and Student Research

The field of educational video games has rapidly grown since the 1970s, mostly producing video games to teach core education concepts such as mathematics, natural science, and English. Recently, various research groups have developed educational games to address elective topics such as finance and health. Educational video games often target grade school audiences and rarely target high school students, college students, or adults. Computer science topics are not a common theme among educational video games; the games that address Computer Science topics teach computer fundamentals, such as typing or basic programming, to young audiences.

Packet Delivery, an educational video …

Effects Of Career Courses On Career Self-Efficacy And Outcome Expectations, Celeste Spier

Department of Educational Administration: Dissertations, Theses, and Student Research

The purpose of this study was to examine two required career courses to determine if they produced an increase in career self-efficacy and outcome expectations, and which components of the learning theory from Social Cognitive Career Theory have the strongest influence. Participants were undergraduate business students at a midsized, Midwestern university enrolled in two required career courses and a comparison group of students not yet enrolled in the courses. Students took four measures (i.e., Career Exploration and Decisional Self-Efficacy Scale, Career Search Self-Efficacy Scale, Career Expectations Survey Scale, and Career Exploration and Decision Learning Experiences Scale) at two points in …

The Role Of Faculty In Fostering Psychosocial Wellbeing Among University Students, Kelley Wick

College of Education and Human Sciences: Dissertations, Theses, and Student Research

The transition to college represents a major life event, and successfully navigating this shift has implications for students’ psychosocial wellbeing. While there is ample support for the idea that social relationships can facilitate student wellbeing during the transition to college, there is limited understanding of the unique role faculty may play in supporting students. The aim of this study was to determine the relation of faculty support to student wellbeing and self-efficacy, independent of peer support and student level of stress. Additionally, the primary questions were to examine whether self-efficacy mediated the relation of faculty support to student wellbeing, and …

Relationship Between Personal Distress And Aggression Is Moderated By Nucleus Accumbens Volume, Yuan Ta Poh

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Studies into the relationship between empathy and aggression has found that the effect is weak (Vachon et al., 2014). This weak relationship is observed through aspects of empathy interacting with aspects of aggression in different ways depending on the types of empathy and aggression being measured. The present study utilized neuroimaging approach to examine the relationship among empathy, aggression and nucleus accumbens (NAc) volume. Forty nine college students underwent magnetic resonance imaging scans and completed the Interpersonal Reactivity Index as well as the Reactive-Proactive Questionnaire. Using FreeSurfer, bilateral NAc volumes were obtained for statistical analysis. Hierarchal regression analyses were utilized …

Through Their Eyes: Photo Stories About Family Strengths In Johannesburg, South Africa, Megan Ribbens

College of Education and Human Sciences: Dissertations, Theses, and Student Research

A study by DeFrain, Asay and Geggie (2010) outlines six characteristics of strong families. This qualitative case study investigates one of the six qualities. Using an adapted photovoice research method, 12 parents in Johannesburg, South Africa describe what spending enjoyable time looks like in their personal and community context. Additionally, they outline the barriers that keep families from enjoyable activities. Qualitative data for analysis included: photographs, written descriptions, compiled activity lists, and focus group discussion. Open, axial, and selective codes and theme analysis were used to analyze the data. This study hopes to contribute to the understanding of the strengths …

The Influence Of Proximal And Distal Familial Factors On Preschool Children's Inhibitory Control And Social Emotional Skills, Amy Encinger

College of Education and Human Sciences: Dissertations, Theses, and Student Research

Children in the United States experience higher rates of poverty than any other age group, including elderly adults and the poverty rate of young children (0-5 years) is considerably higher than that of older children (Proctor et al., 2016). There is an extensive body of research examining familial socioeconomic status (SES) and the influence on the skills and behaviors of young children; however, common key indicators of family SES may not fully depict the ways in which children living in poverty/low-income homes are influenced by economic disadvantage. The focus of the current study is to explore the ways in which …

Assessment Of Grain Safety In Developing Nations, Jose R. Mendoza

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Grains are the most widely consumed foods worldwide, with maize (Zea mays) being frequently consumed in developing countries where it feeds approximately 900 million people under the poverty line of 2 USD per day. While grain handling practices are acceptable in most developed nations, many developing nations still face challenges such as inadequate field management, drying, and storage. Faulty grain handling along with unavoidably humid climates result in recurrent fungal growth and spoilage, which compromises both the end-quality and safety of the harvest. This becomes particularly problematic where there is little awareness about health risks associated with poor …

Strategic Audit Of Optum, Connor Crow

Honors Program: Senior Projects (Public)

Optum is a large American-based pharmacy benefit manager, healthcare consultant, healthcare delivery service, and business analytics corporation that has dominated the industry with sister-company UnitedHealthcare underneath the umbrella UnitedHealthGroup. This report seeks to understand through internal and external analyses how Optum’s business model and strategies have allowed them to gain and sustain competitive advantages in the everchanging, volatile environment of healthcare. Specific tools used to highlight this include Porter’s Five Forces, PESTEL, and SWOT analyses. Additionally, strategic recommendations are given for Optum’s next steps.

Investing In Bicycle Infrastructure To Spur Statewide Economic Growth Through Bicycle Tourism, Pedro Aguero Arroyo, Daniel P. Piatkowski, F. Alsaleem

Nebraska Department of Transportation: Research Reports

Bicycle tourism is a growing industry that has been shown by prior studies to contribute significantly to the economy of numerous states. The economic benefits of recreational bicycling are not limited to the direct effects of the transactions of bicyclists in related industries, but also spillover effects such as the reduction of automobile activity and its associated costs to society, or the decrease of the costs of obesity and inactivity to the healthcare system. This study focuses on the former and provides a qualitative and quantitative analysis of the economic impacts derived from recreational bicycling expenditure, as well as an …

A Big Data Approach For Improving Nebraska Cycling Routes, Fadi Alsaleem, Ali Al-Ramini, Mohammad Ali Takallou, Daniel P. Piatkowski

Nebraska Department of Transportation: Research Reports

More people are becoming interested in creating healthy lifestyle habits for themselves. It has been proved that cycling has several health benefits. Therefore, governments are planning towards more cycling-friendly infrastructures and environments. To understand the cycling activities in Nebraska, we analyze Strava data for the last three years, providing valuable insight into cycling activities for urban planning purposes.

We analyze commute and recreational cycling patterns varying between weekdays and weekends to identify peak hours. Moreover, we study the effect of weather on cycling activity patterns for the last three years. Also, we use the impact of the outside temperature as …

Utilizing Kryton Kim Technology In Bridge Deck And Rail Construction To Protect Against Chloride Ion Penetration, Mick Syslo, Wally Heyen, Lieska Halsey, David Hansen, Tim Kranson

Nebraska Department of Transportation: Research Reports

No abstract provided.

Quantification Of Nitric Oxide Via Single-Walled Carbon Nanotubes, Jakob Meier

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Nitric oxide (NO), a free radical present in biological systems, can have many beneficial and detrimental effects on the body. Due to NO’s short half-life, its detection and quantification is difficult. This inability to quantify NO has hindered researchers that are trying to understand NO’s impact in healthy and diseased conditions. Single-walled carbon nanotubes (SWNT), can become selective to various analytes when wrapped in specific single-stranded DNA strands. The presence of the analyte of interest can change the wavelength and/or intensity of the SWNT’s fluorescence, allowing the SWNT to be used as a sensor. One type of SWNT sensor, 6,5 …

The Role Of Liver Sinusoidal Endothelial Cells In Liver Malady Homeostasis, Fatima Cabral

Department of Biochemistry: Dissertations, Theses, and Student Research

Current literature described techniques for the purification of liver cell types through text alone. The techniques described for the isolation of liver sinusoidal endothelial cells as well as hepatocytes described here are modified from a published article in the Journal of Visualized experiments. The video protocol allows for the user to successfully isolate cells as the most difficult parts of the procedure are demonstrated visually. The detection of liver maladies such as the non-alcoholic fatty liver disease, the stage if this disease and differentiation between non-alcoholic and alcoholic fatty liver disease is demonstrated in the development of a unique panel …

Women In Beekeeping: Impacts Of A Beekeeper Educational Program, Bridget Gross

Department of Entomology: Dissertations, Theses, and Student Research

The decline in honey bee populations over the past two decades in the United States is alarming. The management provided by beekeepers to their honey bee colonies influences the survival of the colony. However, there is a lack of information on the experiences of beekeepers, specifically women beekeepers. The Center for Rural Affairs (CFRA) in Nebraska hosted the “Honey Bees on the Farm: Connecting Women Beekeepers and Women Farmers for Environmental and Economic Benefit” program that provided informal, educational events to women beekeepers and landowners. Using a convergent mixed methods design, the first research question examines the impacts of the …

The Gut Bacterium Extibacter Muris Produces Secondary Bile Acids And Influences Liver Physiology In Gnotobiotic Mice, Theresa Streidl, Isabel Karkossa, Rafael R. Segura Munoz, Claudia Eberl, Alex Zaufel, Johannes Plagge, Robert Schmaltz, Kristin Schubert, Marijana Basic, Kai Markus Schneider, Mamdouh Afify, Christian Trautwein, Rene Tolba, Barbel Stecher, Heidi L. Doden, Jason M. Ridlon, Josef Ecker, Tarek Moustafa, Martin Von Bergen, Amanda Ramer-Tait, Thomas Clavel

Department of Food Science and Technology: Faculty Publications

Extibacter muris is a newly described mouse gut bacterium which metabolizes cholic acid (CA) to deoxycholic acid (DCA) via 7α-dehydroxylation. Although bile acids influence metabolic and inflammatory responses, few in vivo models exist for studying their metabolism and impact on the host. Mice were colonized from birth with the simplified community Oligo-MM¹² with or without E. muris. As the metabolism of bile acids is known to affect lipid homeostasis, mice were fed either a low- or high-fat diet for eight weeks before sampling and analyses targeting the gut and liver. Multiple Oligo-MM¹² strains were capable of deconjugating …