Digital Commons Network^™

News From The Forwards Taskforce, Heather Turner

The R Journal

Forwards is an R Foundation taskforce working to widen the participation of underrepresented groups in the R project and in related activities, such as the useR! conference. This report rounds up activities of the taskforce during the first half of 2021.

Towards A Grammar For Processing Clinical Trial Data, Michael J. Kane

The R Journal

The goal of this paper is to help define a path toward a grammar for processing clinical trials by a) defining a format in which we would like to represent data from standardized clinical trial data b) describing a standard set of operations to transform clinical trial data into this format, and c) to identify a set of verbs and other functionality to facilitate data processing and encourage reproducibility in the processing of these data. It provides a background on standard clinical trial data and goes through a simple preprocessing example illustrating the value of the proposed approach through the …

Package Wsbackfit For Smooth Backfitting Estimation Of Generalized Structured Models, Javier Roca-Pardiñas, María Xosé Rodríguez-Álvarez, Stefan Sperlich

The R Journal

A package is introduced that provides the weighted smooth backfitting estimator for a large family of popular semiparametric regression models. This family is known as generalized structured models, comprising, for example, generalized varying coefficient model, generalized additive models, mixtures, potentially including parametric parts. The kernel-based weighted smooth backfitting belongs to the statistically most efficient procedures for this model class. Its asymptotic properties are well-understood thanks to the large body of literature about this estimator. The introduced weights allow for the inclusion of sampling weights, trimming, and efficient estimation under heteroscedasticity. Further options facilitate easy handling of aggregated data, prediction, and …

Jmcmprsk: An R Package For Joint Modelling Of Longitudinal And Survival Data With Competing Risks, Hong Wang, Ning Li, Shanpeng Li, Gang Li

The R Journal

In this paper, we describe an R package named JMcmprsk, for joint modelling of longitudinal and survival data with competing risks. The package in its current version implements two joint models of longitudinal and survival data proposed to handle competing risks survival data together with continuous and ordinal longitudinal outcomes respectively (Elashoff et al., 2008; Li et al., 2010). The corresponding R implementations are further illustrated with real examples. The package also provides simulation functions to simulate datasets for joint modelling with continuous or ordinal outcomes under the competing risks scenario, which provide useful tools to validate and evaluate …

R Medicine 2020: The Power Of Going Virtual, Elizabeth J. Atkinson, Peter D. Higgins, Denise Esserman, Michael J. Kane, Steven J. Schwager, Joseph B. Rickert, Daniella Mark, Mara Alexeev, Stephan Kadauke

The R Journal

The third annual R/Medicine conference was planned as a physical event to be held in Philadelphia at the end of August 2020. However, a nationwide lockdown induced by the COVID-19 pandemic required a swift transition to a virtual conference. This article describes the challenges and benefits we encountered with this transition and provides an overview of the conference content.

Wide-To-Tall Data Reshaping Using Regular Expressions And The Nc Package, Toby Dylan Hocking

The R Journal

Regular expressions are powerful tools for extracting tables from non-tabular text data. Capturing regular expressions that describe the information to extract from column names can be especially useful when reshaping a data table from wide (few rows with many regularly named columns) to tall (fewer columns with more rows). We present the R package nc (short for named capture), which provides functions for wide-to-tall data reshaping using regular expressions. We describe the main new ideas of nc, and provide detailed comparisons with related R packages (stats, utils, data.table, tidyr, tidyfast, tidyfst, reshape2, cdata).

Stratamatch: Prognostic Score Stratification Using A Pilot Design, Rachael C. Aikens, Joseph Rigdon, Justin Lee, Michael Baiocchi, Andrew B. Goldstone, Peter Chiu, Y Joseph Woo, Jonathan H. Chen

The R Journal

Optimal propensity score matching has emerged as one of the most ubiquitous approaches for causal inference studies on observational data. However, outstanding critiques of the statistical properties of propensity score matching have cast doubt on the statistical efficiency of this technique, and the poor scalability of optimal matching to large data sets makes this approach inconvenient if not infeasible for sample sizes that are increasingly commonplace in modern observational data. The stratamatch package provides implementation support and diagnostics for ‘stratified matching designs,’ an approach that addresses both of these issues with optimal propensity score matching for large-sample observational studies. First, …

Automating Reproducible, Collaborative Clinical Trial Document Generation With The Listdown Package, Michael Kane, Xun Jiang, Simon Urbanek

The R Journal

the conveyance of clinical trial explorations and analysis results from a statistician to a clinical investigator is a critical component of the drug development and clinical research cycle. Automating the process of generating documents for data descriptions, summaries, exploration, and analysis allows the statistician to provide a more comprehensive view of the information captured by a clinical trial, and efficient generation of these documents allows the statistican to focus more on the conceptual development of a trial or trial analysis and less on the implementation of the summaries and results on which decisions are made. This paper explores the use …

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, …

How Can Public Child Welfare Agencies Get And Keep A Great Workforce?, Quality Improvement Center For Workforce Development

QIC-Tips

Public child welfare agencies continue to face complex challenges including high workforce turnover. An examination of federal data found that, from 2003 to 2015, states experienced 14-22% annual turnover rates, with caseworkers staying on the job for an average of 1.8 years. Such turnover increases workloads for remaining workers and negatively impacts children and families. The QIC-WD is working with eight jurisdictions to better understand turnover and test interventions to improve workforce retention. The following tips were compiled based on the experience of QIC-WD sites. They are intended to help child welfare administrators, state legislators, or other local policymakers consider …

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 …

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 …

What Does The Research Teach Feminists About The Possibility Of Organizational Change?, Barbara J. Risman, Julia Mcquillan

Department of Sociology: Faculty Publications

At the winter meeting of SWS [Sociologists for Women in Society] in 2019, Barbara [Risman] heard Julia [McQuillan] give her SWS Feminist Lecture and was totally fascinated. The U.S. National Science Foundation had been spending millions of dollars each year to promote gender transformation on college campuses, hoping to increase the participation of women in science, technology, engineering, and math (STEM) disciplines. What had we learned about the organizational policies that were changed to overcome gender bias? What interventions made the most change? What did not seem to make any difference? Julia presented data on 19 years (at the time) …

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 …

Associations Between Community Nutrition Environments And Early Care And Education Classroom Nutrition Practices, Bethany Williams, Susan B. Sisson, Bryce Lowery, Dipti Dev, Diane M. Horm, Janis Campbell, Denise Finneran, Jennifer Graef-Downard

Department of Child, Youth, and Family Studies: Faculty Publications

Poor child diet is influenced by nutrition environments surrounding schools and homes; influence of these environments on Early Care and Education (ECE) settings is not understood. The purpose of this study was to determine associations between community nutrition environments and ECE classroom nutrition practices, by ECE context [Head Starts, community-based childcare (CBCs), and family child care homes (FCCHs)].

Conclusions: Contrary to studies in residential areas and schools, nutrition environments were not related to nutrition practices in ECEs. This suggests that ECEs may serve as protective microenvironments supporting health for children more vulnerable to the health environments of their nearby residing …

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.

Peanut Allergen Reaction Thresholds During Controlled Food Challenges In 2 Canadian Randomized Studies (Canada-Arm1 And Pisces), Derek K. Chu, Joseph L. Baumert, Steve L. Taylor, Julie A. Nordlee, Tina Nham, Jonathan Bramson, Sébastien La Vieille, Michael A. Abbott, Paul Spill, Andrea Marrin, Manel Jordana, Susan Waserman

Department of Food Science and Technology: Faculty Publications

In 2 randomized studies addressing peanut allergy (Canada-Food Allergy Risk Management 1 [NCT01812798] and Peanut Immunotherapy Starting in Canada, Evaluation and DiScovery [NCT0 1601522]), we quantified peanut allergen thresholds to food challenge using Bayesian stacked model averaging to inform policy and clinical practice. About 50% of patients tolerated more than 70 mg (~ ¼ peanut).

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 …

Urbanization Of The Salt Plains: Early Industry And Material Culture Of The Kauffman Neighborhood, June Weber

Department of Anthropology: Theses and Student Research

The material history of Lincoln, Nebraska has previously been addressed through several theses and papers, however, the Kauffman collection up to this point has not been thoroughly analyzed and summarized as a whole. Through this thesis, the results of data from the features excavated will be compared with the analysis of artifact collections revealing the social dynamics of both the individual household and the neighborhood itself. Census data and Sanborn maps will be integrated in order to better visualize changes in household composition and size throughout time. Primarily by analyzing glass bottles and ceramic assemblages found within individual privies, cisterns, …

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 …

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 …

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 …

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

Department of Agricultural and Biological Systems 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 …

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 …

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 …

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 …