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The R Journal (June 2021) 13(1): Complete Issue, The R Foundation

The R Journal

Editorial, Dianne Cook

Contributed Research Articles

SEEDCCA: An Integrated R-Package for Canonical Correlation Analysis and Partial Least Squares, Bo-Young Kim, Yunju Im, and Jae Keun Yoo

npcure: An R Package for Nonparametric Inference in Mixture Cure Models, Ana López-Cheda, M. Amalia Jácome, and Ignacio López-de-Ullibarri

A Method for Deriving Information from Running R Code, Mark P. J. van der Loo

JMcmprsk: An R Package for Joint Modelling of Longitudinal and Survival Data with Competing Risks, Hong Wang, Ning Li, Shanpeng Li, and Gang Li

Wide-to-tall Data Reshaping Using Regular Expressions and the nc Package, Toby Dylan Hocking

Linear Regression with …

Incompatibility Group I1 (Inci1) Plasmids: Their Genetics, Biology, And Public Health Relevance, Steven L. Foley, Pravin R. Kaldhone, Steven C. Ricke, Jing Han

United States Food and Drug Administration: Publications

Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple Enterobacteriaceae of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA …

Nebline, June 2021

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Choosing Quality Child Care: Guidance For Parents

Eastern Carpenter Bees

Eating for Brain Health

Recipe of the Month

Naturally Occurring Contaminants, Part 4 of a Series — Arsenic

Efficiency Is Key To Profit On Stocker Cattle

Common Grub Control Questions

Garden Guide: Things to do This Month

Heart of 4-H Volunteer Award: Jen & Jesse Metcalf

4th Graders Learn About “Farm to Fork” During Virtual Ag Festival

Statewide 4-H Companion Animal Challenge Results

Extension News

Extension Calendar

STEM Zoom Workshops in June

Seeking Lancaster County Fair Historic Memorabilia and Stories

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 …

Seedcca: An Integrated R-Package For Canonical Correlation Analysis And Partial Least Squares, Bo-Young Kim, Yunju Im, Jae Keun Yoo

The R Journal

Canonical correlation analysis (CCA) has a long history as an explanatory statistical method in high-dimensional data analysis and has been successfully applied in many scientific fields such as chemometrics, pattern recognition, genomic sequence analysis, and so on. The so-called seedCCA is a newly developed R package that implements not only the standard and seeded CCA but also partial least squares. The package enables us to fit CCA to large-p and small-n data. The paper provides a complete guide. Also, the seeded CCA application results are compared with the regularized CCA in the existing R package. It is believed that the …

Rocnreg: An R Package For Receiver Operating Characteristic Curve Inference With And Without Covariates, María Xosé Rodríguez-Álvarez, Vanda Inácio

The R Journal

This paper introduces the package ROCnReg that allows estimating the pooled ROC curve, the covariate-specific ROC curve, and the covariate-adjusted ROC curve by different methods, both from (semi) parametric and nonparametric perspectives and within Bayesian and frequentist paradigms. From the estimated ROC curve (pooled, covariate-specific, or covariate-adjusted), several summary measures of discriminatory accuracy, such as the (partial) area under the ROC curve and the Youden index, can be obtained. The package also provides functions to obtain ROC-based optimal threshold values using several criteria, namely, the Youden index criterion and the criterion that sets a target value for the false positive …

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, …

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 …

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 …

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 …

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 …

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 …

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 …

Survivorship Of Soybean Aphid Biotypes (Hemiptera: Aphididae) On Winter Hosts, Common And Glossy Buckthorn, Doris M. Lagos-Kutz, Glen L. Hartman

Insecta Mundi

The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), is a major pest of soybean, Glycine max (L.) Merr., both in Asia where it is native, and in the USA where it is adventive. The rapid spread and establishment of the soybean aphid in the USA since its discovery in 2000 was successful because of extensive soybean production in the Midwest and the wide distribution of common buckthorn, Rhamnus cathartica (L.), its preferred primary winter host. The survivorship of four soybean aphid biotypes on com­mon and glossy buckthorn, Frangula alnus Mill., were compared. Our study showed that nymph oviparae of soybean …

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 …

Component Causes Of Infectious Bovine Keratoconjunctivitis—Non-Moraxella Organisms In The Epidemiology Of Infectious Bovine Keratoconjunctivitis, John Dustin Loy, Kristin A. Clothier, Gabriele Maier

School of Veterinary and Biomedical Sciences: Faculty Publications

• Non-Moraxella organisms are associated with infectious bovine keratoconjunctivitis (IBK).

• Mycoplasma bovoculi can cause conjunctivitis and has a potential role in IBK pathogenesis.

• Other Non-Mycoplasma agents can cause disease that resembles IBK but is clinically different.

• Genomics and molecular technology are advancing research in this area.

• Classification and determination of pathogenesis potential of these organisms may be better understood through metagenomics and whole genome sequencing.

Coleoptile Length Comparison Of Three Winter Small Grain Cereals Adapted To The Great Plains, M. Alam, M. Kashif, Amanda Easterly, F. Wang, J. D. Boehm Jr., P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Successful crop stand establishment is critical to realize high yield potential, which is dependent on depth of seed placement to access soil moisture. The coleoptile determines sowing depth by its length and ability to emerge from depth. This study was conducted to assess coleoptile length among three sets of three Great Plains winter small grain cereals—wheat (Triticum aestivum L.), barley (Hordeum vulgare L.) and triticale (X triticosecale Wittm.)—and to evaluate the effect of the Rht-B1b dwarfing allele on coleoptile length in wheat and triticale. Fifty seeds of each genotype were sown in wet germination paper in two …

Multi-Strategy Engineering Greatly Enhances Provitamin A Carotenoid Accumulation And Stability In Arabidopsis Seeds, Tianhu Sun, Qinlong Zhu, Ziqing Wei, Lauren A. Owens, Tara Fish, Hyojin Kim, Theodore W. Thannhauser, Edgar B. Cahoon, Li Li

Department of Biochemistry: Faculty Publications

Staple grains with low levels of provitamin A carotenoids contribute to the global prevalence of vitamin A deficiency and therefore are the main targets for provitamin A biofortification. However, carotenoid stability during both seed maturation and postharvest storage is a serious concern for the full benefits of carotenoid biofortified grains. In this study, we utilized Arabidopsis as a model to establish carotenoid biofortification strategies in seeds. We discovered that manipulation of carotenoid biosynthetic activity by seed-specific expression of Phytoene synthase (PSY) increases both provitamin A and total carotenoid levels but the increased carotenoids are prone to degradation during …

Nile Tilapia (Oreochromis Niloticus) Fried In Recycled Palm Oil: Implications For Nutrition And Health, Aemiro Tadesse Zula, Derese Tamiru Desta, Mary S. Willis

Department of Food Science and Technology: Faculty Publications

Fish constitutes a occasional food for the Sidama people of Hawassa, the capital city of Ethiopia’s Sidama Region and the site of a large endorheic lake. Freshly-caught fish, especially Nile tilapia or koroso in Local name, are typically fried prior to consumption. Despite the sensory qualities, fried foods are not always advisable due to the impact of frying on the nutritional quality of food. This study was designed to assess the nutritional quality of Nile tilapia that had been fried in the same palm oil over six consecutive frying cycles. The raw fish were purchased from the Lake Hawassa fish …

Short Term Safety, Immunogenicity, And Reproductive Effects Of Combined Vaccination With Anti-Gnrh (Gonacon) And Rabies Vaccines In Female Feral Cats, Shiri Novak, Boris Yakobson, Shir Sorek, Liat Morgan, Smadar Tal, Ran Nivy, Roni King, Lauren Jaebker, Douglas C. Eckery, Tal Raz

United States Department of Agriculture Wildlife Services: Staff Publications

Overpopulation of free-roaming cats is a major problem leading to negative impacts on animal health and welfare, public nuisance, transmission of zoonotic diseases, and well-documented harm to wildlife. Surgical sterilization had failed to provide a practical solution to free-roaming cats’ overpopulation under field conditions; therefore, efficient and safe non-surgical immunocontraception methods are aspired. Rabies is a deadly virus that may infect people and animals. However, the safety and efficacy of combined vaccination with anti-GnRH and rabies vaccines in feral cats, which often suffer from disrupted health conditions and experienced high stress level, has never been studied. Therefore, our objective was …

Short Term Safety, Immunogenicity, And Reproductive Effects Of Combined Vaccination With Anti-Gnrh (Gonacon) And Rabies Vaccines In Female Feral Cats, Shiri Novak, Boris Yakobson, Shir Sorek, Liat Morgan, Smadar Tal, Ran Nivy, Roni King, Lauren Jaebker, Douglas C. Eckery, Tal Raz

United States Department of Agriculture Wildlife Services: Staff Publications

Overpopulation of free-roaming cats is a major problem leading to negative impacts on animal health and welfare, public nuisance, transmission of zoonotic diseases, and well-documented harm to wildlife. Surgical sterilization had failed to provide a practical solution to free-roaming cats' overpopulation under field conditions; therefore, efficient and safe non-surgical immunocontraception methods are aspired. Rabies is a deadly virus that may infect people and animals. However, the safety and efficacy of combined vaccination with anti-GnRH and rabies vaccines in feral cats, which often suffer from disrupted health conditions and experienced high stress level, has never been studied. Therefore, our objective was …

Techniques To Improve The Volume, Texture And Nutritional Quality Of Gluten-Free Bread, Zachary Christman

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

This article highlights the use of soy flour to improve the protein and fiber of gluten free bread. Also, the use of an extrusion process on soybean and corn flour blends improves the volume and texture of the bread. A full listing of the ingredients and method for production of higher quality gluten free bread is included.

Building Scene: Translations Between Text And Architecture, Joseph Synek

Masters in Architecture Program: Theses

This thesis explores the translation between text and architecture to construct architectural scene. By foregrounding the richness of the scene, these processes engage the kinesthetic, material, emotional, and temporal qualities of architectural space.

Advisor: Zachary Tate Porter

Marketing Agroforestry Products: Lessons From Producers

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

This publication shares producer experiences with marketing agroforestry products, including how producers entered — or created — the markets for their products. These individual stories highlight a diversity of experiences, from family-run farms to intermediaries assisting with market access. United States Department of Agriculture (USDA) and other federal, state, and local programs can provide capital or technical assistance to farmers at different phases of market development. The case studies in this publication highlight programs and resources available through USDA.

While marketing tree crops and non-timber forest products can be a challenge for producers, there is room for growth and opportunities …

Museum Exploration Club, Celeste Kenworthy, Aurora Kenworthy

Honors Program: Expanded Learning Clubs

Afterschool club that virtually visits museums in order to help students gain an appreciation for museums and learn about concepts related to art, history, and science.

Tree-Mendous Fun With Nature Club, Ashley Mcrae

Honors Program: Expanded Learning Clubs

Tree-Mendous Fun with Nature was a kids club run for kids ages 6-10. We enjoyed this club and the curriculum we created so here we offer our lesson plans so others can duplicate our club. Each lesson revolves around a different topic of nature. By the end of the club, students will be able to understand nature on a much more intimate level.

Nebline, May 2021

NEBLINE Newsletter Archive from Nebraska Extension in Lancaster County

Building Health Equity in Lincoln: Extension Launches Health Equity Coalition

Recipe of the Month

Intensive Gardening Techniques

Garden Guide Things to Do This Month

Naturally Occurring Elements in Groundwater--Part 3 of a Series — Fluoride

Cash Rent Survey

Preparing for the Inevitable: Japanese Beetles

Challenge Accepted! Children Thrive Outside

Heart of 4-H Volunteer Award: Rusty & Heidi Hanley

4-H Announcements for 4-H'ers and Volunteers

Clover College: June 15–18, 2021

EXTENSION CALENDAR

4-H’ers Qualify for State Speech & PSA Contest

4-H Horse Stampede Results

An Intron Variant Of The Gli Family Zinc Finger 3 (Gli3) Gene Differentiates Resistance Training-Induced Muscle Fiber Hypertrophy In Younger Men, Christopher G. Vann, Robert W. Morton, Christopher B. Mobley, Ivan J. Vechetti, Brian K. Ferguson, Cody T. Haun, Shelby C. Osburn, Casey L. Sexton, Carlton D. Fox, Matthew A. Romero, Paul A. Roberson, Sara Y. Oikawa, Chris Mcglory, Kaelin C. Young, John J. Mccarthy, Stuart M. Phillips, Michael D. Roberts

Department of Nutrition and Health Sciences: Faculty Publications

We examined the association between genotype and resistance training-induced changes (12 wk) in dual x-ray energy absorptiometry (DXA)-derived lean soft tissue mass (LSTM) as well as muscle fiber cross-sectional area (fCSA; vastus lateralis; n = 109; age = 22 ± 2 y, BMI = 24.7 ± 3.1 kg/m2). Over 315 000 genetic polymorphisms were interrogated from muscle using DNA microarrays. First, a targeted investigation was performed where single nucleotide polymorphisms (SNP) identified from a systematic literature review were related to changes in LSTM and fCSA. Next, genome-wide association (GWA) studies were performed to reveal associations between novel SNP targets with …