NCCC_old170: Research Advances in Agricultural Statistics

(Multistate Research Coordinating Committee and Information Exchange Group)

Status: Inactive/Terminating

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SAES-422 Reports

Annual/Termination Reports:

[08/06/2012] [08/09/2013] [09/12/2014] [07/31/2015] [08/04/2016]

Date of Annual Report: 08/06/2012

Report Information

Annual Meeting Dates: 06/28/2012 - 06/29/2012
Period the Report Covers: 10/01/2011 - 09/01/2012

Participants

See minutes section for list of participants

Brief Summary of Minutes

Annual meeting held at SAS Institute, Cary, NC
June 28-29, 2012
Joint meeting with SCC-013 (USSES)

Official Members Present: John Aleong (VT), Nora Bello (KS), Bruce Craig (IN, Admin.), Xin Dai (UT), Sara Duke (USDA-ARS), Susan Durham (UT), Ed Gbur (AR), Carla Goad (OK), Ken Koehler (IA), Raul Macchiavelli (PR), Larry Madden (OH), Kevin McCarter (LA), Bahram Momen (MD), Bahman Shafii (ID), Julia Sharp (SC), John Stevens (UT), Walt Stroup (NE), Rob Tempelman (MI), Mark West (USDA-ARS), Kathy Yeater (USDA-ARS), Linda Young (FL), Jun Zhu (WI)

Official Members Absent: German Bollero (IL), Don Bullock (IL), Mark Hinds (Pioneer Hi-Bred), David Meek (USDA retired), Margaret Nemeth (Monsanto), Dan Schmoldt (USDA, Admin.)

USSES and Others Present: 16 USSES members and local visitors, several SAS employees in addition to the speakers

2009 Officers: Ed Gbur, Chair; Bruce Craig, Program Chair; Susan Durham, Secretary

NCCC-170 Website: http://www.uark.edu/misc/ncr170/

Minutes:

Technical program:

The meeting began at 8:30 a.m. on Thursday, June 28, 2012 with opening remarks by Jerry Oglesby (USSES program chair). Presentations on Thursday ended at 4:40 p.m. The final presentation by Russ Wolfinger was given on Friday morning before the business meetings.

The technical program consisted of the following presentations.

Radhika Kulkarni - High performance analytics: Competing in the 21st century

Bradley Jones - A class of three level designs for definitive screening in the presence of second order effects

Frances Giesbrecht - Constructing plans for experiments: A package of SAS modules

Michael Speed - Is variable selection in PROC REG obsolete?

Min Zhu - Bias adjustment methods for small sample inference in mixed models

Maura Stokes - Look out: After SAS/STAT 9.3 comes SAS/STAT 12.1

Russell Wolfinger - Update on JMP Genomics

The technical program ended with announcements from Jerry Oglesby on Friday at 9:45 a.m. Jason Osborne (USSES chair) and Jerry Oglesby were thanked for organizing a productive and enjoyable meeting.

Business meeting:

The business meeting began at 10:10 a.m. on Friday, June 29, 2012. Ed Gbur presided. Ed invited all participants to send him any photographs taken during the meeting for posting on the project web site. Jerry Oglesby will check with the speakers about posting their presentations on the project website.

The following items were discussed:

(1) Ed announced that John Boyer has retired from Kansas State and resigned as our Administrative Advisor. Bruce Craig has been appointed as our new Administrative Advisor.

(2) The annual report and impact statement are due shortly after the annual meeting. Participants need to send Ed (egbur@uark.edu) accountings of all activities (workshops, papers, presentations, grants, teaching related items, etc.) from October 1, 2011 to September 30, 2012 (or since last years report) that are related to or inspired by their participation in NCCC-170 as soon as possible.

(3) The 2013 annual meeting will be held during the last week of June to avoid conflicts with the July 4 holiday and the Animal Sciences annual meetings the week after that. Rob Tempelman will host the meeting at Michigan State and serve as local arrangements chair. Bruce Craig will serve as program chair. The tentative site for the 2014 meeting is Nebraska with Walt Stroup as host. The 2015 meeting is tentatively planned as a joint meeting with USSES to be held in Puerto Rico with Raul Macchiavelli serving as the host.

(4) Ed Gbur reported that the generalized linear mixed model (GLMM) book was published in January 2012 by the American Society of Agronomy. The title is "Analysis of Generalized Linear Mixed Models in the Agricultural and Natural Resources Sciences" and can be purchased directly from the Society or on Amazon. The book had sold 312 copies as of July 6. Project members involved in the writing were Mary Christman, Susan Durham, Ed Gbur, Matt Kramer, Kevin McCarter, Walt Stroup, Mark West and Linda Young.

(5) The group reviewed progress toward the goals identified at the 2011 meeting. The first goal has been met with the publication of the GLMM book. Nora Bello and Bruce Craig have extensively revised the mixed model workshop to include a section on GLMMs and have introduced the use of PROC GLIMMIX. Attention turned to the specific goals for the next three years. Discussion about expanding the information on generalized linear mixed models in the mixed models workshop led to a proposal to break the workshop into two components, one focusing on linear mixed models and the other on GLMMs. A new goal was added to create a workshop on data analysis for genomics researchers. The effort would be led by Kathy Yeater and Sara Duke.

(6) Bruce and Nora invited project members to become involved in the mixed model workshops presented at the annual Animal Sciences meetings. Presenter costs are covered by the workshop registration fee and the workshops are well attended. Following up on the discussion of breaking the workshop into two components, Walt Stroup suggested that a workshop for the Animal Sciences meetings be presented annually, alternating between linear mixed and generalized linear mixed models. Several members expressed interest in participating.

(7) Kathy Yeater reported that the Biometry and Statistical Computing Section of the American Society of Agronomy is collaborating with the Agronomy Journal Statistics Committee to put together an invited series of eleven papers on statistical topics that would be compiled into a special publications monograph. Several NCCC-170 members including Kathy Yeater, Sara Duke and Walt Stroup have been asked to contribute to the collection on the topics of multivariate analysis and non-normal data, respectively.

The meeting adjourned at approximately 10:50 a.m. A group photograph for the project web site was taken immediately afterward.

Accomplishments

Statisticians who consult and do research in an Agricultural Experiment Station environment enable land grant institutions to perform their agricultural research missions more effectively and efficiently than would otherwise be possible. However, most stations have at most one or two professional statisticians who are not, and can not be expected to be, experts in every area of statistics. This multi-state committee brings together statisticians to work cooperatively to determine the best current approaches to common statistical problems and to help guide future directions of sound statistical practice. In addition to producing group outputs such as workshops, the committee serves as a resource for its members and a sounding board for new ideas in their applied statistical research. As a result, all members are able to provide more effective assistance to agricultural researchers addressing national research priorities than they would be without NCCC-170. Specific goals for the next three years: (1) Complete the revision of the mixed model workshop to include generalized linear mixed models and the use of new software. (2) Offer the mixed model and generalized linear mixed model workshops upon request from subject matter groups. (3) Develop a workshop on data analysis techniques for genomics researchers. (4) Educate project members in statistical issues and methodology related to statistical problems in which large number of variables are collected on relatively few experimental units. Application areas include biotechnology, precision agriculture and chemometrics. Outputs: Workshops: Walt Stroup and Matt Kramer presented a workshop entitled "Introduction to Generalized Linear Mixed Models for Horticultural Research" at the American Society of Horticultural Sciences in Wailoloa, HI in September 2011. Rob Tempelman presented an invited workshop entitled "Quantitative Genetic Inference in Generalized Linear Mixed Models" for INTA (Instituto Nacional de Tecnologia Agropecuaria), Buenos Aires, Argentina in October 2011. Sara Duke and Kathy Yeater along with colleagues at SAS Institute planned and facilitated two 3-day training workshops entitled "Linkage Mapping and Association Mapping using JMP Genomics Software."The first was for oat researchers and was held in College Station, TX in October 2011. The second was for rice researchers and was held in Stuttgart, AR in November 2011. There were 25 participants at each training workshop. Rob Tempelman presented a workshop entitled "Introduction to SAS for the Analysis of Research Data" at the Center for Statistical Training and Consulting, Michigan State University, East Lansing, MI in November 2011. Walt Stroup presented a workshop entitled "The Next Generation Of Statistics In Aquaculture - Mixed Models" at the Aquaculture America Conference in Las Vegas, NV in February 2012. Rob Tempelman presesnted a one-day invited workshop entitled "Applied Bayesian Inference for Agricultural Statisticians" at the Kansas State University Conference on Applied Statistics in Agriculture in April 2012. Rob Tempelman presented a three day workshop entitled "Applied Bayesian Inference for Agricultural Statisticians and Animal Geneticists" to the Department of Animal Science at the University of Maryland, College Park, MD in May 2012. Larry Madden presented a half-day workshop entitled "Meta-Analysis for Research Synthesis in Plant Pathology" at the Annual Meeting of the North Central Division of the American Phytopathological Society (APS) in Wooster, OH in June 2012. There were 40 registrants. Bruce Craig co-presented a two day workshop entitled "Statistical design of experiments and linear mixed models and their applications in the context of bioinformatics" at the 8th International Purdue University Symposium on Statistics in June 2012. Raul Macchiavell and F. Casanoves presented a half-day short course entitled "Applications of Linear Mixed Models" at the XXII Colombian Statistical Symposium, Bucaramanga, Colombia in July 2012. Larry Madden presented a one-day workshop entitled "Mixed Models for Analysis of Factorials in Plant Pathology" at the Annual Meeting of the American Phytopathological Society in Providence, RI in August 2012. There were 60 registrants. Raul Macchiavelli, J. Di Rienzo and F. Casanoves taught a 40 hour short course entitled "Linear Mixed Models" at CATIE (Tropical Agronomic Center for Research and Teaching) in Turrialba, Costa Rica in August 2012. Presentations: Macchiavelli, R.Use of Nonlinear Mixed Models in Forestry Studies. XXII Colombian Statistical Symposium, Bucaramanga, Colombia in July 2012 (Invited). Stevens, J.R. Gene Set Testing to Characterize Multivariately Differentially Expressed Genes. Purdue University Statistical Bioinformatics Seminar in November 2011. (Invited). Tempelman, R.J.Beyond the Linear Mixed Model, A Hierarchical Bayes Perspective. Conference on Applied Statistics in Agriculture, Kansas State University, Manhattan, KS in April 2012. (Keynote address). Tempelman, R.J. A Bayesian Antedependence Model for Whole Genome Prediction. University of Maryland, College Park, MD in May 2012. (Rotary Leclerg Lecture). Aleong, J. Global spatial modeling. Joint Statistics Meetings, San Diego, CA in August 2012. Ayala Godoy, J., Macchiavelli, R. Properties of generalized linear mixed models with a negative binomial conditional distribution. XIII Conferencia Española y III Encuentro Iberoamericano de Biometría in Barcelona, Spain in September 2011. Cull, C.A., D.G. Renter, Z.D. Paddock, N.M. Bello, A.H. Babcock and T.G. Nagaraja. Efficacy of a vaccine and a direct-fed microbial on fecal shedding of E. coli O157:H7 in a randomized field trial of a commercial feedlot cattle fed distiller's grains. Conference of Research Workers in Animal Diseases in Chicago, IL in December 2011. Di Rienzo, J.A., R. Macchiavelli, F. Casanoves. A Friendly Interface to the LME4 Library in R. XXVI International Biometric Conference, Kobe, Japan in August 2012. Ellick, R., S. Fitzgerald, J. Newsted, N.M. Bello and S. Bursian. The examination of mandibular and maxillary squamous cell proliferation in mink (Mustela vison). Society of Environmental Toxicology and Chemistry North America Annual Meeting in Boston, MA in November 2011. García Saavedra, Y., Macchiavelli, R., J. Chavarría Carvajal.Using nonlinear mixed models with beta distribution to fit disease progress curves to model black Sigatoka epidemics in banana in Puerto Rico. XXVI International Biometric Conference, Kobe, Japan in August 2012. Gray, M., H. Tetreault, C. Rodewald, P. St. Amand, S. Baer, B. Maricle, T. Morgan, N.M. Bello, R. Goad, J. Olsen, L. Wheeler, E. Akhunov, K. Garrett, G. Bai and L. Johnson. Evidence for Local Adaptation and Genetic Differentiation across Andropogon gerardii (big bluestem) Tall Grass Ecotypes Occurring along a Precipitation Gradient. Ecological Genomics Symposium in Kansas City, KS in November 2011. Gray, M., P. St Amand, H. Tetreault, K. Garrett, E. Ahkunov, N.M. Bello, J. Bryant, A. deLaCruz, N. An, T. Morgan, S. Baer, B. Maricle, R. Goad, J. Olsen and L. Johnson. Ecotypic variation in drought tolerance and genetic diversity of the ecologically dominant grass big bluestem (Andropogon gerardii) across the Great Plains precipitation gradient. 97th Annual Meeting of the Ecological Society of America in Portland, OR in August 2012. Isom, S.C., J.R. Stevens, R. Li, W. Spollen, and R.S. Prather.Transcriptional profiling by high-throughput sequencing of porcine pre- and peri-implantation embryos (poster). Annual Conference of the International Embryo Transfer Society, Phoenix, AZ in January 2012. Kramer, M. Crossover designs in nutrition: New methodology accounting for individually varying responses. Whole Grains Summit, Minneapolis, MN in May 2012. Kriss, A.B., Gottwald, T.R., Paul, P.A., and Madden, L.V. Wavelet analysis as a statistical tool for spatial and temporal analysis of epidemics. Annual Meeting of the American Phytopathological Society in Providence, RI in August 2012. Kriss, A.B., Paul, P.A., and Madden, L.V. Climate patterns as predictors of Stagonospora nodorum blotch in Ohio. Annual Meeting of the American Phytopathological Society in Providence, RI in August 2012. Macchiavelli, R. and Ayala, J. Negative binomial-normal generalized mixed models. 6th Biennial Meeting Caribbean and Central American Region, International Biometric Society in Kingston, Jamaica in November 2011. Macchiavelli, R., Y. García Saavedra, J. Chavarría Carvajal.Modeling black Sigatoka disease severity in banana crops in Puerto Rico using nonlinear mixed models with beta distribution. XIII Conferencia Española y III Encuentro Iberoamericano de Biometría in Barcelona, Spain in September 2011. Macchiavelli, R., Martínez, G., Sotomayor, D. Statistical Properties of Water Quality Criteria for Lakes in Puerto Rico. XXVI International Biometric Conference, Kobe, Japan in August 2012. Martinez Suárez, A., Macchiavelli, R. Statistical Methods for the Detection of Contamination Thresholds in Fresh Water Aquatic Ecosystems. XXII Colombian Statistical Symposium, Bucaramanga, Colombia in July 2012. Piccardi, M., Balzarini, M., Macchiavelli, R., Capitaine Funes, A., Bó, G.A. Modeling Lactation Curves in Dairy Cows with Linear, Non-Linear and Mixed Models. XXVI International Biometric Conference, Kobe, Japan in August 2012. Pucket, J.D., R.A. Allbaugh, A.J. Rankin, Z. Ou and N.M. Bello. Comparison of efficacy and duration of topical anesthetics on corneal sensitivity in clinically normal horses. Conference of the American College of Veterinary Ophthalmologists in Hilton Head, SC in October 2011. Ramos Santana. R., E. Valencia, R. Macchiavelli. Valor nutritivo y ganancia en peso del Morus alba (morera) en la alimentación de cabras de reemplazo en Puerto Rico. Sociedad Puertorriqueña de Ciencias Agrícolas, Reunión Científica Anual in Puerto Rico in November 2011. Renter, D.G., C. Cull, Z. Paddock, N.M. Bello, A. Babcock and T.G. Nagaraja. Efficacy of the SRP® vaccine and/or low-dose Bovamine against fecal shedding of E. coli O157:H7 in a randomized field trial of commercial feedlot cattle. Beef Industry Safety Summit in Tampa, FL in March 2012. Rubio, N., Giménez, G., R. Macchiavelli, A. Lavalle.Ajuste de un modelo lineal generalizado mixto para la caracterización de las clases diamétricas de árboles en un bosque tropical. XV Reunión Argentina de Biometría, Salta, Argentina in October 2011. Samarakoon, T.N., J.M. Shelton, R. Jeannotte, Z. Song, N.M. Bello, B. Nikolau, R. Welti, L. Johnson. Gas Chromatography/Mass Spectrometry Reveals Contrasts in Epicuticular Wax Composition of Big Bluestem (Andropogon gerardii) and Edaphic Variety Sand Bluestem (A. gerardii var halli.). American Society of Plant Biologists Meeting in Lincoln, NE in March 2012. Stevens, J.R. Gene Set Testing to Characterize Multivariately Differentially Expressed Genes. Conference on Applied Statistics in Agriculture in Manhattan, KS in May 2012. Stevens, J.R.Gene Set Testing to Characterize Multivariately Differentially Expressed Genes. Joint Statistical Meetings in San Diego, CA in July 2012. Tempelman, R.J. A Bayesian Antedependence Model for Whole Genome Prediction. Section of Statistical Genetics, Department of Biostatistics, University of Alabama-Birmingham in November 2011. Veachgs, A.M., E.C. Martings, N.M. Bello, K.B. Gido and W.K. Dodds. Consumer effects on stream metabolism at decimeter and reach scales. Society for Freshwater Science 2012 Meeting in Louisville, KY in May 2012. Yeater, K.M. Data Visualization and New Stat Tools. USDA-ARS Knipling-Bushland U.S. Livestock Insects Research Laboratory, Kerrville, TX in October 2011. Yeater, K.M. and Duke, S.E. Introduction to JMP Genomics. USDA-ARS Grain Marketing Laboratory, Manhattan, KS in May 2012. Other project related activities: Bruce Craig has incorporated portions of the material from the NCCC-170 linear and generalized linear mixed model workshops into his course entitled "Statistical consulting and collaboration" in the Department of Statistics at Purdue University. Kathy Yeater served as Presiding Chair of the Biometry and Statistical Computing Section of the American Society of Agronomy. She is also an ad-hoc member of the Agronomy Journal Statistics Committee. Walt Stroup directed PhD student Martin Frenzel whose dissertation was entitled "Frequentist Approaches To Overdispersed Repeated Measures Count Data" in the University of Nebraska Department of Statistics. Frenzel successfully defended his work in July 2012. Walt Stroup taught a reading class entitled "R and SAS as tools for GLMM analysis - a comparison" to University of Nebraska Statistics PhD students using examples from his generalized linear mixed model book and the generalized linear mixed model book by Gbur et al. The students compared implementation of the analysis of the examples using R and SASs PROC GLMMIX. They presented a seminar to the department as part of their course work and a draft summary of their findings was distributed to NCCC170 & SCC-13 members at the joint 2012 meeting. Walt Stroup is the Principal Investigator on an NSF Research, Evaluation and Technical Assistance (RETA) Grant entitled "Data Connections" whose purpose is to develop value-added models to characterize the impact of Math-Science Partnerships on K-12 student learning in Math and Science. Value-added models are mixed models whose roots go back to Bill Sanders work with S-189 (the project that led to SAS's PROC MIXED). There is a close interconnection between value-added models for education and mixed models in genomics. The models that he is working on in the RETA grant will also contribute to the University of Nebraskas strategic plan objective to "Create a knowledgeable workforce with significant intellectual capacity within scientific fields that drive the economic progress and productivity of the agbioscience industry." Walt attributes his generalized linear mixed model work with NCCC-170 and S-189 as a big factor in obtaining the grant.

Publications

Books and Book Chapters: Carroll, J.F., A. Zhang and M. Kramer. 2011. Using Lone Star Ticks, Amblyomma americanum (Acari: Ixodidae), in In Vitro Laboratory Bioassays of Repellents: Dimensions, Duration, and Variability. In: Recent Developments in Invertebrate Repellents, ACS Symposium Series, volume 1090, G.E. Paluch and J.R. Coats, ed.. Chapter 7, 97-120. Cutler, A., D.R. Cutler and J.R. Stevens. 2012. Random Forests. In: Ensemble Machine Learning: Methods and Applications, Cha Zhang and Yunqian Ma, ed., 157-175. Springer Verlag, NY.. Gbur, E.E., W.W. Stroup, K.S. McCarter, S. Durham, L.J. Young, M. Christman, M. West and M. Kramer. 2012. Analysis of Generalized Linear Mixed Models in the Agricultural and Natural Resources Sciences. ASA-SSSA-CSSA, Madison, WI. 283pp. Malone, R., D. Meek, L. Ma., D. Jaynes, B. Nolan and D. Karlen. 2011. Chapter 10. Quality assurance of weather data for agricultural system model input: A case study using the Walnut Creek Watershed in Central Iowa. In: Methods for introducing system models into agricultural research. L. Ahuja and L. Ma, ed. ASA-SSSA-CSSA, Madison, WI. 283-295. Stroup, W.W. 2012. Generalized Linear Mixed Models: Modern Concepts, Methods and Applications. CRC Press, Boca Raton, FL. Available Sept 2012 Journal Publications: Bangarwa, S.K., J.K. Norsworthy, E.E. Gbur, J. Zhang and T. Habtom. 2011. Allyl isothiocyanate: A methyl bromide replacement in polyethylene-mulched bell pepper. Weed Technology, 25: 90-96. Bangarwa, S.K., J.K. Norsworthy, J.D. Mattice and E.E. Gbur. 2011. Yellow nutsedge interference in polyethylene-mulched bell pepper as influenced by turnip soil amendment. Weed Technology, 25: 466-472. Bello, N.M., J.P. Steibel, and R.J. Tempelman. 2012. Hierarchical Bayesian modeling of heterogeneous cluster and subject level associations between continuous and binary outcomes in dairy production. Biometrical Journal 54:230-248. Bello, N.M., J.P. Steibel, R.M. Erskine, and R.J. Tempelman. 2012. Inferring upon heterogeneous associations in dairy cattle performance using a bivariate hierarchical model. Journal of Agricultural, Biological, and Environmental Statistics 17:142-161. Bryant, R.J., Yeater, K.M., Miller, H.B. 2012. The effect of induced yellowing on the physicochemical properties of specialty rices. Journal of the Science of Food and Agriculture. In press. Carroll, J.F., Kramer, M. 2012. Responses of lone star tick (Acari: Ixodidae) nymphs to the repellent deet applied in acetone and ethanol solutions in vitro bioassays. Journal of Entomological Science 47(2): 193-196. Coetzee J.F., L.N. Edwards, R.A. Moshergs, N.M. Bello, A.M. O'Connor, B. Wang, B. KuKanich and D. A. Blasi. 2012. Effect of oral meloxicam on health and performance of beef steers relative to bulls castrated upon arrival at the feedlot. Journal of Animal Science 90: 1026-1039. Cross, R., McCarty, L.B., Estes, A.G., Sharp, J.L. and Toler, J.E. 2012. Annual bluegrass control in overseeded golf course fairways when mitosis-inhibiting herbicides are not effective. Applied Turfgrass Science, doi: 10.1094/ATS-2012-0523-01-RS. Cull, C.A, Z.D. Paddock, T.G. Nagaraja, N.M. Bello, A.H. Babcock and D.G. Renter. 2012. Efficacy of a vaccine and a direct-fed microbial against fecal shedding of Escherichia coli O157:H7 in a randomized pen-level field trial of commercial feedlot cattle. Vaccine. http://dx.doi.org/10.1016/j.vaccine.2012.05.080. Font, E., P. Carazo, G. P. de Lanuza and M. Kramer. 2011. Predator-elicited foot shakes in wall lizards (Podarcis muralis): Evidence for a pursuit-deterrent function. Journal of Comparative Psychology 126: 87-96. Golden, B.R., N.A. Slaton, R.J. Norman, E.E. Gbur and C.E. Wilson. 2011. Nitrogen release from Environmentally Smart Nitrogen Fertilizer as influenced by soil series, temperature, moisture and incubation method. Communications in Soil Science and Plant Analysis, 42: 1809-1824. Granger L.A., L.J. Armburst, D.C. Rankin, R. Ghering, N.M. Bello and K. Alexander. 2012. Estimation of glomerular filtration rate in healthy cats using single-slice dynamic computed tomography and Patlak plot analysis. Veterinary Radiology and Ultrasound 53(2): 181-188. Hinchliffe, D.J., Turley, R.B., Naoumkina, M.A., Kim, H.J., Tang, Y., Yeater, K.M., Li, P., Fang, D.D. 2011. A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.). Biomed Central (BMC) Genomics, 12: 445. Isom, S.C., J.R. Stevens, R. Li, W. Spollen, and R.S. Prather. Transcriptional profiling by high-throughput sequencing of porcine pre- and peri-implantation embryos. Reproduction, Fertility and Development 2012, 24(1): 184-184. Jia, L., Yan, W., Zhu, C., Agrma, H.A., Jackson, A.K., Yeater, K.M., Li, X., Huang, B., Hu, B., Mcclung, A.M., Wu, D. 2012. Allelic analysis of sheath blight resistance with association mapping in rice. PLoS One, 7(3):e32703. Kim, J-S., K.A. Artymovich, D.F. Hall, E.J. Smith, D. Wilson, R. Fulton, J. Bell, L. Dybas, L.S. Mansfield, R. Tempelman, and J. Linz. 2012. Passage of Campylobacter jejuni through the chicken reservoir or mice promotes phase variation in contingency genes Cj0045 and Cj0170 that strongly associates with colonization and disease in a mouse model. Microbiology 158:1304-1316. Kriss, A.B., Paul, P.A., and Madden, L.V. 2012. Variability in Fusarium head blight epidemics in relation to global climate fluctuations as represented by the El Niño Southern Oscillation and other atmospheric patterns. Phytopathology 102: 55-64. Kriss, A.B., Paul, P.A., Xu, X., Nicholson, P., Doohan, F.M., Hornok, L., Rietini, A., Edwards, S.G., and Madden, L.V. 2012. Quantification of the relationship between the environment and Fusarium head blight, Fusarium pathogen density, and mycotoxins in winter wheat in Europe. European Journal of Plant Pathology 133: 975-993. Li, B., Madden, L.V., and Xu, X.-M. 2012. An alternative SADIE local clustering index for studying spatial patterns. Methods in Ecology and Evolution 3: 368-377. Li, X., Yan, W., Agrama, H., Jia, L., Jackson, A.K., Moldenhauer, K., Yeater, K.M., Mcclung, A.M., Wu, D. 2012. Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.) PLoS One, 7(1):e29350. Loch, T.P., K. Scribner, R. Tempelman, G. Whelan and M. Faisal. 2012. Bacterial infections of Chinook salmon, Oncorhynchus tshawytscha, (Walbaum) returning to gamete-collecting weirs in Michigan. Journal of Fish Diseases 35:39-50. Meek, D., C. Hoang, R. Malone, R. Kanwar, G. Fox, J. Guzman, M. Shipitalo. 2012. Rational polynomial functions for modeling E. Coli and bromide breakthrough. Transactions of ASABE. In press. Nita, M., Ellis, M.A., and Madden, L.V. 2012. Spatial distribution of Phomopsis cane and leaf spot symptoms in commercial vineyards in Ohio. Journal of Phytopathology 160: 26-36. Pucket, J. D., R.A. Allbaugh, A.J. Rankin, Z. Ougs and N.M. Bello. 2012. Comparison of efficacy and duration of topical anesthetics on corneal sensitivity in clinically normal horses. American Journal of Veterinary Research. In press. Rankin, A. J., L. Sebbagpd, N.M. Bello, W.R. Crumley and R.A. Allbaugh. 2012. Inhibition of paracentesis-induced blood-aqueous barrier breakdown by oral administration of anti-inflammatory medications in normal cats. American Journal of Veterinary Research. In press. Rezac, D.J., K.N. Grigsby, N.M. Bello and B.J. Bradford. 2012. Effects of varying rates of tallgrass prairie hay and wet corn gluten feed on productivity of lactating dairy cows. Journal of Dairy Science 95(2): 842-849. Sales, M.A., N.R. Burgos, V.K. Shivrain, B. Murphy and E.E. Gbur. 2011. Morphological and physiological responses of weedy red rice (Oryza sativa L.) and cultivated rice (O. sativa) to N supply. American Journal of Plant Science, 2: 569-577. Savarino P., M. Borgarelli, A. Tarducci, S. Crosara, N.M. Bello and M.L. Margiocco. 2012. Diagnostic performance of P wave duration in the identification of left atrial enlargement in dogs. Journal of Small Animal Practice 53(5): 267-272. Sharp, J.L., Sojda, R.S., Greenwood, M., Rosenberry, D.O. and Warren, J.M. 2012. Statistical classification of water levels and hydraulic gradients in a northern Rocky Mountain wetland complex. Ecohydrology. doi: 10.1002/eco.1252. Simko, I., R.J. Hayes and M. Kramer. 2012. Computing integrated ratings from heterogeneous phenotypic assessments: A case study of lettuce postharvest quality and downy mildew resistance. Crop Science 52: 2131-2142. Singer C., N.M. Bello and B.A. Snyder. 2012. Characterizing prevalence and ecological impact of non-native terrestrial isopods (Isopoda: Oniscidea) in tallgrass prairie. Crustaceana. In press. Singer, J.W. and D.W. Meek. 2012. Relationship between inter-seeded red clover biomass and plant number. Crop Science 52(2): 981-985. Stevens, J.R. and G. Nicholas. 2012. Assessing Numerical Dependence in Gene Expression Summaries with the Jackknife Expression Difference. PLoS ONE. In press. Turechek, W.W., Madden, L.V., Gent, D.H., and Xu, X.-M. 2011. Comments regarding the binary power law for heterogeneity of disease incidence. Phytopathology 101: 1396-1407. Yang, W. and R.J. Tempelman. 2012. A Bayesian antedependence model for whole genome prediction. Genetics 190:1491-1501. You, Q., Chen, F., Sharp, J.L., Wang, X., You, Y. and Zhang, C. 2012. High-performance liquid chromatography-mass spectrometry and evaporative light-scattering detector to compare phenolic profiles of muscadine grapes. Journal of Chromatography A, 1240: 96-103.

Impact Statements

NCCC-170 fosters research to identify and develop statistical methodology applicable to agricultural research and provides a forum for sharing and educating both statisticians and subject-matter scientists in the agricultural, environmental and natural sciences. As a result, all members are able to provide more effective assistance to agricultural researchers addressing national research priorities than they would be without NCCC-170.

Date of Annual Report: 08/09/2013

Report Information

Annual Meeting Dates: 06/27/2013 - 06/28/2013
Period the Report Covers: 10/01/2012 - 09/01/2013

Participants

Nora Bello (KS), Bruce Craig (IN, Admin.), Xin Dai (UT), Sara Duke (USDA-ARS), Ed Gbur (AR), Carla Goad (OK), Ken Koehler (IA), Matt Kramer (USDA-ARS), Raul Macchiavelli (PR), Larry Madden (OH), David Meek (USDA retired), Bahram Momen (MD), Margaret Nemeth (Monsanto retired), Bahman Shafii (ID), John Stevens (UT), Walt Stroup (NE), Rob Tempelman (MI), Kathy Yeater (USDA-ARS)

Brief Summary of Minutes

Remote participation:

Arrangements had been made to enable members to remotely connect to the meeting. Six members participated remotely in all or parts of the technical program and business meeting. One presentation was given by a remote participant. The most common reason given for remote participation was the lack of available travel funds.

Technical program:

The meeting began at 8:45 a.m. on Thursday, June 27, 2013 with opening remarks by Rob Tempelman and Doug Buhler (Director of MSU AgBioResearch). Presentations ended at approximately 5:10 p.m. The technical program consisted of the following presentations.

Cen Wu. High dimensional variable selection in gene-environment interactions

David Meek. Rational polynomial functions for modeling E. coli and bromide breakthrough (Remote presentation)

Bruce Craig. Assessing inter-observer agreement for multivariate observations

Vince Melfi. Quantitative and statistical literacy of undergraduates

Heng Wang. A hidden Markov approach for ascertaining SNP genotypes from Next Generation Sequencing data in the presence of allelic imbalance

Ed Gbur. Small sample inference in the beta distribution

Walt Stroup. Comparing alternative analyses for non-normal data: An update

Business meeting:

The business meeting began at 9:05 a.m. on Friday, June 28, 2013. Ed Gbur presided. Ed invited all participants to send him any photographs taken during the meeting for posting on the project web site.

The following items were discussed:

(1) Rob Tempelman and Bruce Craig were thanked for organizing a productive and enjoyable meeting. Nora Bello was thanked for arranging for remote access by project members.

(2) The annual report and impact statement are due shortly after the annual meeting. Participants need to send Ed Gbur (egbur@uark.edu) accountings of all activities (workshops, papers, presentations, grants, teaching related items, etc.) from October 1, 2012 to September 30, 2013 (or since last years report) that are related to or inspired by their participation in NCCC-170 as soon as possible.

(3) The 2014 meeting will be held at Nebraska with Walt Stroup as host. After some discussion about conflicts with other meetings, the choices were narrowed to July 14-15 or July 18-19. The other option would be the last half of June at a time that did not conflict with the USSES meeting. Bahman Shafii will serve as program chair. The 2015 meeting is tentatively planned as a joint meeting with USSES to be held in Puerto Rico with Raul Macchiavelli serving as the host.

(4) The group reviewed progress toward the goals identified at the 2012 meeting. The first goal has been met with the completion of the revision of the mixed model workshop to include generalized linear mixed models and the use of new software. The goal will be removed from the list for next year. Kathy Yeater indicated that the genomics workshop which she and Sara Duke are developing currently covers QTL mapping and association mapping using JMP/Genomics. They are planning to add a section on Next Gen RNA-Seq gene expression analysis. It was decided that the three remaining goals from this year will be listed again for next year.

(5) Bruce Craig and Nora Bello invited project members to become involved in the mixed model workshops presented at the annual Animal Sciences meetings. Presenter costs are covered by the workshop registration fee and the workshops are well attended.

(6) The NCCC-170 impact statement from the previous project renewal (2006-2011) edited and designed by Sara Delheimer was reviewed. After much discussion it was decided that more details related to Accomplishments and Needed Research sections should be included in the annual impact statement. It was also suggested that we submit some photographs related to project activities. This was not done previously and as a result, the figures used in the 2006-2011 statement did not directly relate to the projects accomplishments.

(7) The group discussed the issue of remote access participation. The members using remote access at this meeting agreed that it worked acceptably well but was not as desirable as being present. They would not choose remote access if they had the option to be present. Some indicated that they were not as comfortable asking questions during the presentations and missed the in-person interaction with other attendees. Suggestions for improvements included having a moderator, creating an instruction sheet for remote access, and having a training session before the meeting began. The possibility of purchasing a good quality microphone and external speakers was discussed without a final resolution. Members agreed that there should be a reduced registration fee for remote participation if there were costs related to providing such access.

The meeting adjourned at approximately 10:25 a.m. A group photograph for the project web site was taken immediately afterward.

Accomplishments

Statisticians who consult and do research in an Agricultural Experiment Station environment enable land grant institutions to perform their agricultural research missions more effectively and efficiently than would otherwise be possible. However, most stations have at most one or two professional statisticians who are not, and can not be expected to be, experts in every area of statistics. This multi-state committee brings together statisticians to work cooperatively to determine the best current approaches to common statistical problems and to help guide future directions of sound statistical practice. In addition to producing group outputs such as workshops, the committee serves as a resource for its members and a sounding board for new ideas in their applied statistical research. As a result, all members are able to provide more effective assistance to agricultural researchers addressing national research priorities than they would be without NCCC-170. Outputs: Workshops, Symposia, Short Courses, etc.: Kathy Yeater chaired a symposium entitled "Statistical Concepts and Tools to Aid in Publishing Proper Research Conclusions" at the 2012 ASA-CSSA-SSSA meetings in Cincinnati in October, 2012. The Biometry and Statistical Computing Section which is chaired by Kathy Yeater cosponsored the symposium. Kathy Yeater and Sara Duke presented "Multivariate Analysis: Greater Insight in Complex Systems" at a symposium entitled "Statistical Concepts and Tools to Aid in Publishing Proper Research Conclusions" during the 2012 ASA-CSSA-SSSA meetings in Cincinnati in October, 2012. Linda Young presented workshops on "Applied Mixed Models" on behalf of the American Statistical Associations Council of Chapters Traveling Course program. Workshops were provided to requesting chapters in 2012 (5 chaptersHarrisburg, Pittsburgh, San Antonio, Houston, New Jersey), and 2013 (1 chapterHawaii). She had provided the workshops in 2010 and 2011 as well. Bruce Craig, Jun Zhu and Nora Bello presented a one and a half day workshop for the Federation of Animal Science Societies (FASS) in conjunction with the Joint Annual Meetings of the American Dairy Science Association and the American Society of Animal Sciences in July, 2013 in Indianapolis as a venue for continuing education for affiliated researchers. The workshop focused on the application of general and generalized linear mixed models to research problems in the animal and food sciences. There were approximately 80 participants of whom 40% returned the workshop survey. The written comments indicated that participants felt that the presenters were well prepared and informative. They found the data driven example approach helpful for them to be able to apply the material to their own research. 86% of the respondents gave the workshop a rating of 8 or higher on a 1 to 10 scale. Linda Young and Kenneth Lopiano presented a workshop entitled "Change of Support: Statistical Issues and Methods" to the US-International Association for Landscape Ecology in April, 2012 in Newport, Rhode Island. Mark West presented "Mixed Model Analysis for a Real Data Set" as part of a workshop "R for Recovering SAS Users - Introduction to the Statistical Software Package R" at the ASA-CSSA-SSSA Meeting in Cincinnati on October, 2012. Rob Tempelman presented a workshop entitled "Introduction to SAS for Statistical Analysis of Research Data" for faculty, staff, and graduate students at Michigan State University, September, 2012. He also presented a second workshop entitled "Determining the Right Standard Errors & Statistical Tests Using Mixed Models" for faculty, staff, and graduate students in March, 2013. Raul Macchiavelli, J. Di Rienzo and F. Casanoves taught a 40 hour short course entitled "Advanced Statistical Modeling" at CATIE (Tropical Agronomic Center for Research and Teaching) in Turrialba, Costa Rica (July, 2013). Raul Macchiavelli, J. Di Rienzo and F. Casanoves taught a three hour short course entitled "Generalized Linear Mixed Models in InfoStat" at X CLATSE, Latin American Conference of Statistical Societies (October 2012, Córdoba, Argentina). Bruce Craig gave a series of four one hour presentations to faculty and students in the Ingestive Behavior Research Center at Purdue in June and July, 2013 that followed the same structure as our mixed model workshop. The lecture topics were general linear mixed models, generalized linear mixed models, handling missing observations in longitudinal studies, and sample size/power calculations for mixed models. Attendance ranged from 30 to 50 participants. Presentations: Abreu, D.A., K.K. Lopiano, S.C. Garber, A.C. Lamas and L.J. Young. Estimating the number of U.S. farms with adjustment for misclassification at the Joint Statistical Meetings. July, 2012. San Diego, California. Bello, N.M. Statistics: Catalyst for Interdisciplinary Interactions. at the College of Arts and Sciences Deans Advisory Council Meeting, Kansas State University in October, 2012 (Invited). Bello, N. M., J. P. Steibel and R. J. Tempelman. Accounting for heterogeneous pleiotropy in whole genome selection models as a poster at the Joint Annual Meeting of the American Dairy Science Association and the American Society of Animal Science. Indianapolis, July, 2013. (Their abstract was one of 30 selected from 2,200 abstracts as an American Society of Animal Science Presidential Pick. Selection criteria included scientific merit and overall interest.) Cox L., Ward A., Saunders G., Stevens J.R., and Isom S.C. Gene expression analysis of in vivo- and in vitro-matured porcine metaphase II oocytes (poster) at the International Plant and Animal Genome XXI, San Diego in January, 2013. Di Rienzo, J; R. Macchiavelli; F. Casanoves. Una interfaz amigable para la librería lme4 de R at the Tenth Latin American Conference of Statistical Societies (CLATSE) in Córdoba, Argentina, October 2012. Holt, N. M., L.J. Young and C.A. Gotway. Moran-type ratio of quadratic forms for assessing spatio-temporal associations at the International Biometric Conference. August, 2012. Kobe, Japan. Hyman, M.. and L.J. Young. On the inference for the K-function for spatial point patterns at the Joint Statistical Meetings. July, 2012. San Diego, California. Leary, E., L.J. Young, C. DuClos and M. Jordan. Climate change and heat-related health effects for Florida at the Joint Statistical Meetings. July, 2012. San Diego, California. Lopiano, K.K., L.J. Young and C.A. Gotway. Two-stage methods for regression with spatially misaligned data at the Joint Statistical Meetings. July, 2012. San Diego, California. Madden, L.V. Predicting plant disease epidemics: A case study with Fusarium head blight of wheat at the 50th Anniversary Meeting of the Chinese Society of Plant Protection (CSPP), Beijing, China. October, 2012 (Plenary Session). Madden, L.V. The cost of plant disease prediction a seminar at Kansas State University, Manhattan, KS. November, 2012. Madden, L.V. The cost of predicting plant diseases: A Bayesian Perspective a seminar at University of California, Davis. Davis, CA. January, 2013. Piccardi M.; R. Macchiavelli; M. Balzarini. Comparación de modelos para el ajuste de curvas de lactación en tambos at the Tenth Latin American Conference of Statistical Societies (CLATSE) in Córdoba, Argentina, October, 2012. Rubio, N.; G. Giménez; R. Macchiavelli; A. Lavalle. Aplicación de diferentes herramientas gráficas en R para el análisis descriptivo en el ajuste de un modelo logit acumulado mixto at the Tenth Latin American Conference of Statistical Societies (CLATSE) in Córdoba, Argentina, October, 2012. Rubio, N.; G. Giménez; R. Macchiavelli; A. Lavalle. Aplicación de dos técnicas numéricas para la estimación de un modelo lineal generalizado mixto con datos multinomiales at the Tenth Latin American Conference of Statistical Societies (CLATSE) in Córdoba, Argentina, October, 2012. Saunders G., Stevens J.R., and Isom S.C. An Improved FWER Controlling Method in Gene Ontology Graphs (poster) at the Conference on Applied Statistics in Agriculture, Manhattan, KS, in April, 2013. Saunders G., Stevens J.R., and Isom S.C. An Improved FWER Controlling Method in Gene Ontology Graphs (poster) at the Joint Statistical Meetings, Montreal, QB, in August, 2013. Stevens J.R., Jones T.R., and Lefevre M. SigTree: An Automated Meta-Analytic Approach to Find Significantly Responsive Branches in a Phylogenetic Tree at the Joint Statistical Meetings, Montreal, QB, in August, 2013. Tempelman, R.J. A Bayesian Antedependence Model for Whole Genome Prediction at the University of Guelph, Guelph, Canada, April, 2013. Thompson, K. and E.E. Gbur. A simulation study of the small sample properties of likelihood based inference for the beta distribution (poster) at the Conference on Applied Statistics in Agriculture in Manhattan, KS, in April, 2013. Wang, Shu and L.J. Young. Inference for map comparisons at the Joint Statistical Meetings. July, 2012. San Diego, California. Young, L. J. 2012. Relating public health to environmental factors: Quantifying uncertainty when exposure is predicted. ENAR Spring Meeting April, 2012. Washington, D.C.. (Invited). Other project related activities: Larry Madden organized and chaired an invited paper session on "Modeling in Plant Disease Epidemiology" at the International Congress of Plant Pathology, Beijing, China. August, 2013. Larry Madden led a discussion session on "The application of new statistical methods in plant disease epidemiology" at the Eleventh International Epidemiology Workshop, Beijing, China. August, 2013. Kathy Yeater is a team member on the Specific Cooperative Agreement New Statistical Tools to Study Aflatoxin Genetic Resistance in Maize. Kathy Yeater will be co-facilitating "Statistics Workshops for Regional Meeting and Web-Based Platforms" for the American Society of Agronomy. This two-year grant from the professional society beginning November 1, 2013 will expand statistics workshops and training opportunities from the usual one-time event at Annual Meetings to Specialty/Regional meetings and a web-based platform. NCCC-170 members including Walt Stroup, Nora Bello, Bruce Craig, Kathy Yeater and Sara Duke will assist with the development of initial workshop topics such as sample size and power calculations, mixed models for normal and non-normal data, and multivariate analysis applications. John Stevens is a co-investigator on a grant entitled "Genome reprogramming and embryo survivability in porcine somatic cell nuclear transfer embryos" funded by the USDA under the AFRI Foundational Program. The award period is August 2013 - July 2016. Using statistical bioinformatics tools John has learned and refined through discussions with members of the NCCC-170 group, he will help the principal investigators consider a novel, noninvasive means to evaluate reprogramming efficiency and survivability in porcine embryos produced using somatic cell nuclear transfer. Application of this bioassay could significantly enhance the efficiency of reproductive cloning by nuclear transfer in agriculturally relevant species. Bruce Craig continues to use portions of the material from the NCCC-170 linear and generalized linear mixed model workshops in his course entitled "Statistical consulting and collaboration" in the Department of Statistics at Purdue University. Bahram Momen teaches a graduate course in Experimental Design and Advanced Statistical Analysis at the University of Maryland attended by students from the University as well as other educational and research institutions in the Washington D.C. area. The course content, particularly the laboratory component, has been influenced by his association with NCCC-170. The statistical consulting component of his faculty appointment has also been enhanced by his participation in the project. Specific goals for the next three years: (1) Offer the mixed model and generalized linear mixed model workshops upon request from subject matter groups. (2) Develop a workshop on data analysis techniques for genomics researchers. (3) Educate project members in statistical issues and methodology related to statistical problems in which large numbers of variables are collected on relatively few experimental units. Application areas include biotechnology, precision agriculture and chemometrics.

Publications

Anaya, A.; I. Padilla; R. Macchiavelli; D. Vesper; J. Meeker; A. Alshawabkeh 2013. Estimating preferential flow in karstic aquifers using statistical mixed models. Groundwater (doi: 10.1111/gwat.12084) In press. Anco, D. J., Madden, L. V., and Ellis, M. A. 2012. Effects of temperature and wetness duration on the sporulation of Phomopsis viticola on infected grape canes. Plant Health Progress (on-line journal). doi:10.1094/PHP-2012-0723-02-RS. (http://www.plantmanagementnetwork.org/sub/php/symposium/ melhus/2011/grape/). Anco, D. J., Madden, L. V., and Ellis, M. A. 2013. Effects of temperature and wetness duration on the sporulation rate of Phomopsis viticola on infected grape canes. Plant Disease 97: 579-589. Bangarwa, S.K., J.K. Norsworthy and E.E. Gbur. 2012. Herbicidal performance of phenyl isothiocyanate in polyethylene-mulched bell pepper. Weed Technology 26: 763-768 Bangarwa, S.K., J.K. Norsworthy and E.E. Gbur. 2012. Effects of shoot clipping-soil disturbance frequency and tuber size on above-ground and below-ground growth of purple and yellow nutsedge (Cyperus rotundus and Cyperus esculentus). Weed Technology 26: 813-817. Bello N. M., J. S. Stevenson and R. J. Tempelman. 2012. Invited review: Milk production and reproductive performance - Modern multidisciplinary insights into an enduring axiom. Journal of Dairy Science 95(10): 5461-5475. Bello, N.M., J.S. Stevenson, and R.J. Tempelman. 2012. Invited Review: Milk production and reproductive performance: Modern interdisciplinary insights into an enduring axiom. Journal of Dairy Science 95: 5461-5475. Bello, N.M., J.P. Steibel, R.M. Erskine, and R.J. Tempelman. 2013. Cows and Herds Constitute Distinct Hierarchical Levels of Heterogeneity in the Variability of and Association between Milk Yield and Pregnancy Outcome in Dairy Cows. Journal of Dairy Science 96: 2314-2326. Bello, N. M., J. P. Steibel, R. J. Erskine and R. J. Tempelman. 2013. Cows and herds constitute distinct hierarchical levels of heterogeneity in the variability of and association between milk yield and pregnancy outcome in dairy cows. Journal of Dairy Science 96 (4):14-26. Bryant, R.J., K.M. Yeater, and H.B. Miller. 2012. The effect of induced yellowing on the physicochemical properties of specialty rices. Journal of the Science of Food and Agriculture. (wileyonlinelibrary.com) DOI 10.1002/jsfa.5751. Bursian, S. J., J. Moore, J. L. Newsted, J. E. Link, S. D. Fitzgerald, N. M. Bello, V. S. Bhat, D. Kay, X. Zhang, S. Wiseman, R. A. Budinsky, J. P. Giesy and M. J. Zwiernik. 2012. Incidence of jaw lesions and activity and gene expression of hepatic P4501A enzyme in mink (Mustela vison) exposed to dietary 2,3,7,8-tetrachlorodibenzo-p-dioxin, 2,3,7,8-tetrachlorodibenzofuran and 2,3,4,7,8-pentachlorodibenzofuran. Environmental Toxicology and Chemistry. 31(11): 2545-2556. Cardoso, F.F., and R.J. Tempelman. 2012. Linear reaction norm models for the prediction of genetic merit of Angus cattle with genotype by environment interaction. Journal of Animal Science 90: 2130-2141. Cernicchiaro, N., D. Renter, S. Xiang, B.J. White and N.M. Bello. 2013. Hierarchical Bayesian modeling of heterogeneous variances in performance of commercial feedlot cattle. Journal of Animal Science 91(6): 2910-2919. Cull, C.A, Z.D. Paddock, T.G. Nagaraja, N. M. Bello, A. H. Babcock and D. G. Renter. 2012. Efficacy of a vaccine and a direct-fed microbial against fecal shedding of Escherichia coli O157:H7 in a randomized pen-level field trial of commercial feedlot cattle. Vaccine 30(43): 6210 - 6215. Hesler, L.S., M.V. Chiozza, M.E. O'Neal, G.C.MacIntosh, K.J. Tilmon, D.I. Chandrasena, N.A. Tinsley, S.R. Cianzio, A.C. Costamagna, E.Cullen, C.D. DiFonzo, B.D. Potter, D.W. Ragsdale, K.Steffey, and K.J. Koehler. 2013. Performance and prospects of Rag genes for management of soybean aphid. Entomologia Experimentalis et Applicata. 147(3): 201-216. Isom S.C., Stevens J.R., Li R., Spollen W., Cox L., Spate L., Murphy C., and Prather R. 2013. Transcriptional profiling by RNA-Seq of peri-attachment porcine embryos generated using a variety of assisted reproductive technologies (ART). Physiological Genomics 45(14): 577-589. Kriss, A. B., Paul, P. A., and Madden, L. V. 2012. Characterizing heterogeneity of disease incidence in a spatial hierarchy: A case study from a decade of observations of Fusarium head blight of wheat. Phytopathology 102: 867-877. Kriss, A. B., Madden, L. V., Paul, P. A., and Xu, X. 2012. Heterogeneity of Fusarium head blight of wheat: Multi-scale distributions and temporal variation in relation to environment. Plant Health Progress (on-line journal). doi:10.1094/PHP-2012-0723-01-RS. (http://www.plantmanagementnetwork.org/ sub/php/symposium/melhus/2011/wheat/). Lawlor MR, Craig BA, Schinckel AP, Einstein ME, Matthews JO, Fields B, Booher C, Dreadin T, Fralick C, Tabo S, Sosnicki A, Wilson E, and Boyd RD. 2012. Development of a procedure to reproduce the variances and relationships amongst carcass measurements and the weight of primal and subprimal lean cuts. The Professional Animal Scientist, 29, 83-88. Li, X., W. Yan, H. Agrama, L. Jia, A.K. Jackson, K. Moldenhauer, K.M. Yeater, A.M. Mcclung, and D. Wu. 2012. Unraveling the complex trait of harvest index with association mapping in rice (Oryza sativa L.). PLoS One. 7(1): e29350. doi:10.1371/journal.pone.0029350. Lopiano, K.K., L.J. Young and C.A. Gotway. 2012. Estimated generalized least squares in spatially-misaligned regression models with Berkson error. Biostatistics. In Press. Miller, R., A. Estrada-Pena, C. Almazan, K.M. Yeater, M. Messenger, D. Ellis, and A.A. Perez De Leon. 2012. Exploring the use of anti-tick vaccine as tool for integrated eradication of the cattle fever tick, Rhipicephalus (Boophilus) annulatus. Vaccine. 30(38):5682-5687. Olbricht G., B.A. Craig and R.W. Doerge. 2012. Incorporating Genomic Annotation into a Hidden Markov Model for DNA Methylation Tiling Array Data. Statistical Applications in Genetics and Molecular Biology, 11(5), ISSN (Online) 1544-6115. Ostoja, S.M., E.W. Schupp, S. Durham, and R. Klinger. 2013. Seed harvesting is influenced by associational effects in mixed seed neighbourhoods, not just by seed density. Functional Ecology 27: 775-785. Piepho, H.-P., Williams, E. R., and Madden, L. V. 2012. The use of two-way linear mixed models in multi-treatment meta-analysis. Biometrics 68: 1269-1277. Pucket, J. D., R. A. Allbaugh, A. J. Rankin, Z. Ou and N. M. Bello. 2013. Comparison of efficacy and duration of topical anesthetics on corneal sensitivity in clinically normal horses. American Journal of Veterinary Research 74(3): 459-464. Rankin, A. J., L. Sebbag, N. M. Bello, W.R. Crumley and R. A. Allbaugh. 2013. Inhibition of paracentesis-induced blood-aqueous barrier breakdown by oral administration of anti-inflammatory medications in normal cats. American Journal of Veterinary Research 74(2): 262-267. Reid-Bush, T., L. Bix, N. M Bello and J. Fair. 2013. Differences in kinematics of restrained and unrestrained conditions of opening for two sizes of glass jars. Packaging Technology and Science 26:105-113. Rothrock, C. S., Winters, S. A., Miller, P. K., Gbur, E., Verhalen, L. M., Greenhagen, B. E., Isakeit, T. S., Batson, W. E., Jr., Bourland, F. M., Colyer, P. D., Wheeler, T. A., Kaufman, H. W., Sciumbato, G. L., Thaxton, P. M., Lawrence, K. S., Gazaway, W. S., Chambers, A. Y., Newman, M. A., Kirkpatrick, T. L., Barham, J. D., Phipps, P. M., Shokes, F. M., Littlefield, L. J., Padgett, G. B., Hutmacher, R. B., Davis, R. M., Kemerait, R. C., Sumner, D. R., Seebold, K. W. Jr., Mueller, J. D., and Garber, R. H. 2012. Importance of fungicide seed treatment and environment on seedling diseases of cotton. Plant Disease 96: 1805-1817. Singer C., N. M. Bello and B. A. Snyder. 2012. Characterizing prevalence and ecological impact of non-native terrestrial isopods (Isopoda: Oniscidea) in tallgrass prairie. Crustaceana 85(12/13): 1499-1511 Stevens J.R. and Isom S.C. 2013. Gene Set Testing to Characterize Multivariately Differentially Expressed Genes. In Proceedings of Conference on Applied Statistics in Agriculture 2012, pp. 125-137. Sundar, R. P., L. Bix, N. M. Bello and M. W. Becker. 2012. Quantifying age-related differences in information processing behaviors when viewing prescription drug labels. PLoS One 7(6):e38819. Tomer, M.D., P.C. Beeson, D.W. Meek, D.N. Moriasi, C.G. Rossi, and A.M. Sadeghi 2013. Evaluating simulations daily discharge from large watersheds using autoregression and an index of flashiness. Trans. ASABE. In Press. Torres, S., D. U. Thompson, N. M. Bello, B. Nosky and C. D. Reinhardt. 2013. Field study of the comparative efficacy of gamithromycin and tulathromycin for the control of undifferentiated bovine respiratory disease complex in beef feedlot calves at high risk calves of developing respiratory tract disease. American Journal of Veterinary Research 74 (6): 839-846. Torres, S., D. U. Thompson, N. M. Bello, B. Nosky and C. D. Reinhardt. 2013. Field study of the comparative efficacy of gamithromycin and tulathromycin for the treatment of undifferentiated bovine respiratory disease complex in beef feedlot calves. American Journal of Veterinary Research 74 (6): 847-853. Willyerd, K.T., Li, C., Madden, L.V., Bradley, C.A., Bergstrom G.C., Sweets, L.E., McMullen, M., Ransom, J. K., Grybauskas, A., Osborne, L., Wegulo, S. N., Hershman, D.E., Wise, K., Bockus, W.W., Groth, D., Dill-Macky, R., Milus, E., Esker, P.D., Waxman, K.D., Adee, E.A., Ebelhar, S.E., Young, B.G., and Paul, P.A. 2012. Efficacy and stability of integrating fungicide and cultivar resistance to manage Fusarium head blight and deoxynivalenol in wheat. Plant Disease 96: 957-967. Xu H, Black M, and Craig, BA. 2012. Evaluating Accuracy of Diagnostic Tests with Intermediate Results in the Absence of a Gold Standard. Statistics in Medicine, 32(15), 2571-2584.

Impact Statements

NCCC-170 fosters research to identify and develop statistical methodology applicable to agricultural research and provides a forum for sharing and educating both statisticians and subject-matter scientists in the agricultural, environmental and natural sciences. As a result, all members are able to provide more effective assistance to agricultural researchers addressing national research priorities than they would be without NCCC-170.
Project members provide continuing education for scientists in agriculturally related disciplines in modern statistical analyses of designed experiments in general and specifically in the areas of generalized linear mixed models and statistical techniques in genomics applications. Examples of such activities and their immediate impacts for the current reporting period are listed in the Accomplishments section of this report.
Project members collaborate in research projects with scientists in agricultural related disciplines to develop and use proper statistical design and analysis methodology well beyond standard textbook applications. These efforts often result in competitive grant participation and refereed publications. Examples these impacts are listed in the Accomplishments and Publications sections of this report.

Date of Annual Report: 09/12/2014

Report Information

Annual Meeting Dates: 07/17/2014 - 07/18/2014
Period the Report Covers: 10/01/2013 - 09/01/2014

Participants

Aleong, John (VT)
Bello, Nora (KS)
Craig, Bruce (IN, Admin.)
Durham, Susan (UT)
Gbur, Edward (AR)
Goad, Carla (OK)
Macchiavelli, Raul (PR)
Madden, Larry (OH)
Momen, Bahram (MD)
Shafii, Bahman (ID)
Stroup, Walt (NE)
Clarke, Jennifer (NE)
Keuler, Nick (WI)
Kramer. Matt (USDA-ARS)
Milliken, George (KS)
Nettleton, Dan (IA)
Olbricht, Gayla (MO Sci&Tech)

Brief Summary of Minutes

Minutes:

Technical program:

The meeting began at 8:30 a.m. on Thursday, July 17, 2014 with opening remarks by Walt Stroup and Archie Clutter (Dean/Director of Agricultural Research Division, UNL). Presentations ended at approximately 5:00 p.m. The technical program consisted of the following presentations.

Jennifer Clarke - The new reality of Big Data

Bahram Momen - Non-linear mixed model analysis of photosynthetic-light responses to N and Ca additions

Dan Nettleton - Using quasi-likelihood analysis of RNA-Seq data to identify differentially expressed genes

Gayla Olbricht - Exploratory analysis of sleep and wake bouts in Drosophila melanogaste

Matthew Kramer - A new general diagnostic/goodness-of-fit tool for GLMMs

Nora Bello - A hierarchical Bayesian approach to assess fit of generalized linear mixed models

Walt Stroup - Fixed/random block effect dilemma, edition 64+. Valid caution or die-hard urban legend?

Bahman Shafii - Bayesian approaches for estimation of an unknown dose

Business meeting:

The business meeting began at 9:10 a.m. on Friday, July 18, 2014. Ed Gbur presided. The following items were discussed:

(1) Ed Gbur thanked several people for organizing a productive and enjoyable meeting: Walt Stroup for local arrangements; Bahman Shafii for the technical program; Ellen Paparozzi and Walt Stroup for the cookout/mixer at their home; Stacy Herceg for support and refreshments.

(2) The annual report and impact statement are due shortly after the annual meeting. Participants need to send Ed Gbur (egbur@uark.edu) accountings of all activities (workshops, papers, presentations, grants, teaching related items, etc.) from October 1, 2013 to September 30, 2014 (or since last year’s report) that are related to or inspired by their participation in NCCC-170 as soon as possible.

(3) The 2015 meeting will be held in Mayagüez, Puerto Rico on June 25-26 with Raul Macchiavelli as host. This will be a joint meet with USSES (SCC-013). After some discussion, Mayagüez was chosen as the location over San Juan. Bahman Shafii will serve as program chair. Bahram Momen is the USSES program chair. The 2016 meeting is set for Maryland with Bahram Momen serving as the host. The 2017 meeting is tentatively planned for Arkansas.

(4) Ed Gbur noted that we successfully navigated the mid-term review and that NCCC-170 has been approved to continue through 2016. The notification letter is posted on the project website under this year’s meeting.

(5) The group reviewed progress toward the goals identified at the 2013 meeting. The mixed model workshop materials have been updated and expanded to include generalized linear mixed models and the use of new software. The focus of the genomics workshops has shifted to more current topics and continues to evolve over time. Anyone interested in participating in this endeavor should contact Kathy Yeater. Goals for the next three years were revised based on the discussion.

(6) As part of Kathy Yeater’s project on “Statistics Workshops for Regional Meetings and Web-Based Platforms” that she is facilitating for the American Society of Agronomy, Carla Goad discussed the web based introductory course that Julia Sharp taught and the experimental design/ANOVA course that she taught. Both courses were well received by society members.

As part of the same project, Kathy is looking for volunteers to develop a short course for the Society that introduces the use of statistical analyses in R. Anyone interested should contact Kathy. Carla and Kathy both indicated that there are financial incentives related to this project’s participants.

(7) Nora Bello invited project members to become involved in the mixed model workshops presented at the annual Animal Sciences meetings. Next year’s workshop is July 15-16, 2015 in Orlando. Presenter travel and housing expenses are covered by the Society. The workshops have been well attended with an average of about 80 participants each time it has been presented. Bruce Craig noted that he can make workshop materials available to project participants. The materials can be used with proper acknowledgment of NCCC-170.

(8) The group discussed the issue of remote access participation. Nora Bello volunteered to purchase a good quality microphone and noted that she has access through KSU to Zoom software for facilitating remote participation. Members agreed that there should be a reduced registration fee of $10 for remote participation, with funds being used to reimburse expenses such as the microphone purchase.

(9) Nora Bello solicited suggestions about a topic and speaker for the 2015 Conference on Applied Statistics in Agriculture at Kansas State. She was also interested in input on ways to increase attendance at the conference. Nora encouraged people to send ideas and in particular would welcome statements of support for an alternative date as a way to increase attendance.

The meeting adjourned at approximately 10:55 a.m. A group photograph for the project web site was taken immediately afterward.

Accomplishments

Accomplishments: Statisticians who consult and do research in an Agricultural Experiment Station environment enable land grant institutions to perform their agricultural research missions more effectively and efficiently than would otherwise be possible. However, most stations have at most one or two professional statisticians who are not, and cannot be expected to be, experts in every area of statistics. This multi-state committee brings together statisticians to work cooperatively to determine the best current approaches to common statistical problems and to help guide future directions of sound statistical practice. In addition to producing group outputs such as workshops, the committee serves as a resource for its members and a sounding board for new ideas in their applied statistical research. As a result, all members are able to provide more effective assistance to agricultural researchers addressing national research priorities than they would without NCCC-170. Outputs: Workshops: Bruce Craig, Jun Zhu and Nora Bello presented a one and a half day workshop on the application of general and generalized linear mixed models to research problems in the animal and food sciences at the joint annual national meetings of the American Dairy Science Association and the American Society of Animal Sciences. There were approximately 80 participants. Raul Macchiavelli, J. Di Rienzo and F. Casanoves taught a 40 hour short course entitled “Advanced Statistical Modeling: Mixed Models Applications”, at CATIE (Tropical Agronomic Center for Research and Teaching) in Turrialba, Costa Rica in August 2014. Larry Madden presented a workshop entitled “An introduction to meta-analysis for the synthesis of evidence” at the University of Salzburg in Salzburg, Austria in July 2014. Larry Madden presented a workshop entitled “Introduction to Bayesian analysis in plant pathology” at the annual meeting of the American Phytopathological Society (APS) in Minneapolis in August 2014. Sara Duke and Kathy Yeater presented a workshop entitled “Aquaculture Statistics Workshop – Multivariate Statistics” at Aquaculture America 2014 in Seattle, WA in February 2014. Kathy Yeater facilitated the program “Statistics Workshops for Regional Meeting and Web-Based Platform” for the American Society of Agronomy. Two short courses have been developed and presented once, each consisting of 4 weekly 2 hour sessions using a distance learning platform. Julia Sharp developed and instructed “Introductory Statistics Refresher Course” and Carla Goad developed and instructed “Introduction to Experimental Design and Analysis.” Presentations: Nora Bello. “Inferring upon heterogeneous associations in dairy cow performance using a bivariate hierarchical model” at the International Biometric Conference in Florence, Italy in July 2014. (Invited) Nora Bello, J. P. Steibel and Rob Tempelman. “Accounting for heterogeneous pleiotropy in whole genome selection models” at the 2013 Joint Annual Meeting of the American Dairy Science Association and the American Society of Animal Science in Indianapolis in July 2013. (This presentation was one of 30 selected out of 2,200 abstracts submitted for the American Society of Animal Science Presidential Pick. Selection criteria included scientific merit and overall interest.) Bruce Craig and Z. Hass. “Developing prediction equations for carcass lean mass in the presence of proportional measurement error” at the the Kansas State University Conference on Applied Statistics in Agriculture in April 2014. Z. Ou, Rob Tempelman, J. P. Steibel, C. Ernst, R. Bates and Nora Bello. “Genomic prediction accounting for residual heteroskedasticity” at the Kansas State University Conference on Applied Statistics in Agriculture in April 2014. J. Schroeder, Walt Stroup and Nora Bello. “Hierarchical Bayesian implementation of generalized linear mixed models for count data” at the Kansas State University Conference on Applied Statistics in Agriculture in April 2014. Saunders G., Fu G., and John Stevens. “A Hierarchical Weighted-Bonferroni Multiplicity Correction in Linkage Disequilibrium Based QTL Mapping” at the Kansas State University Conference on Applied Statistics in Agriculture in April 2014. John Stevens, Ganesan B., Lefevre M., and Weimer B.C. “SigTree: Identifying and Visualizing Significantly Responsive Branches in a Phylogenetic Tree” at the Kansas State University Conference on Applied Statistics in Agriculture in April 2014. Matt Kramer. “Use of the posterior predictive distribution as a diagnostic tool for mixed models” at the Kansas State University Conference on Applied Statistics in Agriculture in April 2014. Noral Bello. “Heterogeneous Pleiotropy in Whole-Genome Selection Models” at departmental seminars for the Departments of Statistics and Animal Science at the University of Nebraska in November 2013. Noral Bello. “Heterogeneous Pleiotropy in Whole-Genome Selection Models” at the Bioinformatics Seminar, Department of Statistics at Purdue University in November 2013. Taylor, I., Julia Sharp,, White, D. L., Hallstrom, J. O., von Oehsen, J. B., Duffy, E., Eidson, G., Privette, C., Cook, C. T., Sampath, A., Radhakrishnan, G. “Monitoring Sensor Measurement Anomalies of Streaming Environmental Data Using a Local Correlation Score” at the 4th International Conference on Computing for Geospatial Research & Application in San Jose, CA in July 2013. Drennan, K., Wiesinghe, D., White, S., White, D., Menchyk, N., Julia Sharp, Vincent, E. and Park, D.M. “Soil Temperature and Moisture Differentials from Concrete Sidewalks” at the 14th American Ecological Engineering Society Meeting in Charleston, SC. in June 2014. Larry Madden. “The cost of plant disease prediction” at Pennsylvania State University in April 2014. Larry Madden. “Predicting plant diseases: A case study with Fusarium head blight of wheat” at Cornell University in Geneva, NY and in Ithaca, NY in May 2014. J. Gaffney, M. Galliart, S. Sabates, S. Baer, B. Maricle, E. McCrea, Nora Bello and L. C. Johnson. “Variations in polyploidy in big bluestem (Andropogongerardii) ecotypes across the Great Plains” at the annual meeting of the Botanical Society of America, Boise, Idaho in July 2014. M. Galliart, L. Johnson, S. Sabates, H. Tetreault, A. DeLaCruz, J. Bryant, T. J. Morgan, M. Knapp, Nora Bello, S. G. Baer, D. Gibson, L. Wilson, B. R. Maricle. “Adaptive potential and trait variation of a widespread grass Andropogongerardii across a Great Plains climate gradient: Implications for climate change” at the annual meeting of the Botanical Society of America, Boise, Idaho in July 2014. J. Craver, C. Miller, K. Williams and Nora Bello. “UVB radiation affects intumescence development in Ipomoea batatas (ornamental sweet potato)” at the American Society for Horticultural Science annual conference in Orlando, Florida in July 2014. Raul Macchiavelli. “Nonlinear mixed models for disease incidence and severity: Modelling plant diseases in tropical crops” at the59th World Statistics Congress in Hong Kong (China) in 2013. Information Bulletin 2, 149. http://www.statistics.gov.hk/wsc/IPS105-P2-S.pdf Casanoves, F., M. Nime, Raul Macchiavelli, C. Mattoni. “Application of generalized linear models to study the surface activity of scorpions” at the 59th World Statistics Congress in Hong Kong (China) in 2013. Information Bulletin 2, 135. Mark West. “Generalized Linear Mixed Models: Seeking Better Inferences” at a symposium for “Advanced Statistical Approaches to Reach Strong Inferences from Agronomic and Environmental Studies” at the Tri-Societies (ASA-CSA-SSSA) annual meeting in Tampa, FL in November 2013. Di Rienzo, J.; Raul Macchiavelli; F. Casanoves. “New functionalities for the InfoStat interface to LME4 library” at the XXVIIth International Biometric Conference in Florence, Italy in July 2014. Torres-Saavedra, P.; Raul Macchiavelli.”Mixed Beta Regression with Penalized Splines For Disease Severity” at the XXVIIth International Biometric Conference in Florence, Italy in July 2014. Macchiavelli, Raul. “Uso de Modelos Estadísticos para Combinar Información Longitudinal y Transversal en Estudios Forestales: Aplicaciones de Modelos no Lineales Mixtos en Curvas de Índice de Sitio para teca” at the X Congreso Internacional de Investigación Científica (X CIC) at the Universidad Autónoma de Santo Domingo, Dominican Republic in June 2014. Momen, Bahram. “Use of nonlinear mixed regression models in factorial experiments involving repeated measurements.” Annual meeting of SCC-013 (USSES) at Clemson University in June 2014. Momen, Bahram., Behling S., Sullivan J.H., Lawrence G.B. “Non-linear mixed model analysis of photosynthetic-light response of sugar maple to calcium and nitrogen addition in the Catskills Mountain, NY.” At the Ecological Society of America annual meeting in Sacramento, CA. Craig. Bruce. “Sample size/power calculations” at the Department of Psychology weekly clinical symposia and at the Ingestive Behavior Research Center (IBRC) at Purdue University. Craig. Bruce. “Linear mixed models and repeated measures” at the Ingestive Behavior Research Center (IBRC) at Purdue University. Other project related activities: Nora Bello received a President’s Faculty Development Award from the Office of Research and Sponsored Programs, Kansas State University, in partial support for professional travel to present the 2012 winner of the “Best Paper in JABES by an IBS Member” at the International Biometric Conference in Florence, Italy in July 2014. ($4,500) Nora Bello is a co-PI on a grant from Micronutrients entitled “The effects of SID Lysine and Intellibond C (TBCC) feeding strategy in finishing pigs on growth performance, carcass characteristics and economics” with PI Steve Dritz, College of Veterinary Medicine, Kansas State University. The award period is 2014-2015. ($25,000) Nora Bello is a co-PI on a grant from Morris Animal Foundation entitled “The effects of ophthalmic prednisolone and diclofenac on diabetes mellitus regulation in dogs” with PI Amy Rankin, College of Veterinary Medicine, Kansas State University. The award period is 2014-2015. ($35,000) John Stevens is a co-PI on a grant entitled “Genome reprogramming and embryo survivability in porcine somatic cell nuclear transfer embryos” with PIs C. Isom and A. Benninghoff from USDA (USDA-NIFA-AFRI-003958). The award period is 2013-2016. ( $484,266) Larry Madden maintains a website with SAS code and instructions for many statistical analyses, especially for mixed-model analyses at the Ohio State University. http://oardc.osu.edu/APS-statsworkshop/default.htm . Bahram Momen credits NCCC-170 in improving the content of his graduate course in experimental design and advanced statistical analysis (BIOM602) course at the University of Maryland and in his consulting and mentoring of graduate students and faculty.

Publications

Allbaugh, R., S. Keil, Z. Ou and N. M. Bello. 2014. “Intraocular pressure changes in equine athletes during endurance competitions”. Veterinary Ophthalmology. 17, Suppl.1, 154-159. DOI: 10.1111/vop.12182. Bello, N. M., J. P. Steibel, R. J. Erskine and R. J. Tempelman. 2013. “Cows and herds constitute distinct hierarchical levels of heterogeneity in the variability of and association between milk yield and pregnancy outcome in dairy cows.” Journal of Dairy Science 96 (4):14-26. Bryant, R.J., A.K. Jackson, K.M. Yeater, W. Yan, A.M. McClung, and R.G. Fjellstrom. 2013. “Genetic Variation and Association Mapping of Protein Concentration in Brown Rice Using a Diverse Rice Germplasm Collection”. Cereal Chemistry http://cerealchemistry.aaccnet.org/doi/abs/10.1094/cchem-09-12-0122-R. Carroll JF, Kramer M, Bedoukian RH. 2014. “Solvent, drying time, and substrate affect the responses of lone star ticks (Acari: Ixodidae) to the repellents deet and picaridin”. Journal of Medical Entomology 51: 629-637. Cernicchiaro, N., D. Renter, S. Xiang, B. J. White and N. M Bello. 2013. “Hierarchical Bayesian modeling of heterogeneous variances in performance of commercial feedlot cattle.” Journal of Animal Science 91 (6): 2910-2919. Davidson, J.B., S.L. Durham, and P.G. Wolf. 2014. “Breeding system of the threatened endemic Primula cusickiana var. maguirei (Primulaceae)”. Plant Species Biology (in press). Eizenga, G.C., L.M. Ali, R.J. Bryant, K.M. Yeater, A.M. McClung, and S. McCouch. 2013. “Registration of the ‘Rice Diversity Panel I’ Genome_Wide Association Mapping Studies”. Journal of Plant Registrations: 8:109-116. Fallahi, E., B. Fallahi, B. Shafii, Z. Zamani. 2014. “Long-term yield and harvest time fruit quality attributes in various Fuji apple strains.” Horticultural Science 49(3): 281–284. Feldlaufer, MF, Ulrich, KR, Kramer, M. 2013. “No Sex-Related Differences in Mortality in Bed Bugs (Hemiptera: Cimicidae) Exposed to Deltamethrin, and Surviving Bed Bugs Can Recover”. Journal of Economic Entomology 106(2): 988-994. Fu G., Saunders G., and Stevens J.R. 2014. “Holm multiple correction for large-scale gene-shape association mapping”. BMC Genetics (Suppl 1): S5. Holt, E.A., B. Fagerheim, and S. Durham. 2014. “Online plagiarism training falls short in biology classrooms”. CBE—Life Sciences Education 13: 83-89. Imai, I., J.A. Kimball, B. Conway, K.M. Yeater, S.R. McCouch, and A.M. McClung. 2013. “Validation of yield enhancing QTLs from a low-yielding wild ancestor of rice”. Molecular Breeding: 32(1):101-120. Kaume, L., E.E. Gbur, R. DiBrezzo, L.R. Howard and L. Devareddy (2014). Antioxidant rice berries exert modest bone protective effects in postmenopausal smokers without improving biomarkers of bone metabolism. Journal of Functional Foods 9: 201-210. Kulmatiski A., Anderson-Smith A., Beard K., Doucette-Riise S., Mazzacavallo M., Monal N., Ramirez R. and Stevens J.R. 2014. “Most soil trophic guilds increase plant growth: a meta-analytical review”. Oikos. (In press) Klun, JA, Kramer, M, Debboun, M. 2013.” Four simple stimuli that induce host-seeking and blood-feeding behaviors in two mosquito species, with a clue to DEET's mode of action”. Journal of Vector Ecology 38: 143-153. Larrabee, B., H. M. Scott and N. M. Bello. 2014. “Ordinary least squares regression of ordered categorical data: Inferential implications.” Journal of Agricultural, Biological and Environmental Statistics. DOI: 10.1007/s13253-014-0176-z. Lass, L.W., S. P. Cook, B. Shafii, and T. S. Prather. 2014. “Development of a dispersal model for balsam woolly adelgid, Adelges piceae Ratzeburg (Hemiptera: Adelgidae), to facilitate landscape-level management planning.” International Journal of Forestry Research. Vol. 2014: Article ID 519010. 8 pp. Messina, F.J. and S.L. Durham. 2013. “Adaptation to a novel host by a seed beetle (Coleoptera: Chrysomelidae: Bruchinae): effect of source population”. Environmental Entomology 42(4): 733-742. Mikhailova, E.A., D.J.R. Cherney, L.U. Snyder, S.M. Kelly, C.J. Post, J.L. Sharp, and S.K. Cox. 2013. “Evaluation of nutritive value of Pueraria montana (kudzu) during the drought-prone growing season”. Communications in Soil Science and Plant Analysis 44: 1-11. Minshall, G.W, B. Shafii, C. Holderman, W.J. Price, P. J. Anders, G. Lester, and P. Barrett. 2014. “Effects of nutrient replacement on benthic macroinvertebrates in an ultra-oligotrophic reach of the Kootenai River, 2003-2010.” Freshwater Science (In press). Momen B, Behling S, Sullivan JH. 2014. “Non-linear modeling of photosynthetic response of sugar-maple mature trees and seedlings to calcium and nitrogen additions in the Catskills Mountains, NY.” JSM Environmental Science and Ecology (In press). Naoumkina, M.A., G.N. Thyssen, D.D. Fang, D.J. Hinchliffe, C.B. Florane, K.M. Yeater, J.J. Page, and J.A. Udall. 2014. “The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.)”. PLoS One: 9(3):e90830. Norswothy, J.K., G. Griffith, T. Griffin, M. Bagavathiannan and E.E. Gbur (2014). In-field movement of glyphosate resistant Palmer Amaranth and its impact on cotton lint yield ? Evidence for a zero threshold. Weed Science 62: 237-249. Norsworthy, J.K., M.J. Wilson, R.C. Scott and E.E. Gbur (2014). Herbicidal activity on acetolactate synthase-resistant barnyardgrass (Echinochloa crus-galli) in USA rice. Weed Biology and Management 14: 50-58. Phillips PL, Welch JB, Kramer M. 2014. “Development of a spatially targeted field sampling technique for the southern cattle tick, Rhipicephalus microplus, by mapping white-tailed deer, Odocoileus virginianus, habitat in South Texas”. Journal of Insect Science 14(88). Pinson, S.R., L. Tarpley, W. Yan, K.M. Yeater, M. Zhang, M. Geurinot, and D.E. Salt. 2014. “Diversity for concentrations of mineral nutrients and trace elements in rice grains”. Crop Science doi:10.2135/cropsci2013.10.0656. Pirk CWW, de Miranda JR, Kramer M, Murray TE, Nazzi F, Shutler D, van der Steen JJM, van Dooremalen C. 2013. “Statistical guidelines for Apis mellifera research”. Journal of Apicultural Research 52(4). doi 10.3896/IBRA.1.52.4.1. Rawal S., Bauer M.M., Mendoza K.M., El-Nezami H., Hall J.O., Kim J.E., Stevens J.R., Reed K.M., and Coulombe R.A. 2014. “Aflatoxicosis Chemoprevention by Probiotic Lactobacillius and its Impact on BG Genes of the Major Histocompatibility Complex”. Research in Veterinary Science. (In press) Reid-Bush, T., L. Bix, N. M Bello and J. Fair. 2013. “Differences in kinematics of restrained and unrestrained conditions of opening for two sizes of glass jars.” Packaging Technology and Science 26:105-113. Rogers, C.W., K.R. Brye, A.D. Smartt, R.J. Norman, E.E. Gbur and M.A. Evans-White (2014). Cultivar and previous crop effects on methane emissions from drill-seeded, delayed flood rice production on a silt loam soil. Soil Science, 179, 28-36. Shafii, Bahman, W.J. Price, T.S. Prather and L.W. Lass. 2014. “Modeling dispersal of yellow starthistle in the canyon grasslands of northern Idaho.” International Journal of Plant Biology and Research 2(2):1011. Shah, Binay K., A. Bista and B. Shafii. 2014. “Disparities in receipt of radiotherapy and survival by age, sex and ethnicity among patients with Stage I Diffuse Large B-Cell Lymphoma.” Leukemia & lymphoma (In press). Shah, D.A., Molineros, J.E., Paul, P.A., Willyerd, K.T., Madden, L.V., and De Wolf, E.D. 2013. “Predicting Fusarium head blight epidemics with weather-driven pre- and post-anthesis logistic regression models.” Phytopathology 103: 906-919. Shah, D., and Madden, L.V. 2013. A comment on Mendes and Yigit. 2013. “Type I error and test power of different tests for testing interaction effects in factorial experiments”, Statistica Neerlandica, 67:1-26. Statistica Neerlandica 67: 397-399. Shah J., Desai P.T., Chen D., Stevens J.R., and Weimer B.C. 2013. “Pre-adaptation to cold-stress in Salmonella Typhimurium increases survival during subsequent acid-stress exposure”. Applied and Environmental Microbiology 79(23): 7281-7289. Shah, D.A., De Wolf, E.D., Paul, P.A., and Madden, L.V. 2014. “Predicting Fusarium head blight epidemics with boosted regression trees.” Phytopathology 104: 702-714. Stoner, D.C., M.L. Wolfe, C. Mecham, M.B. Mecham, S.L. Durham, and D.M. Choate. 2013. “Dispersal behavior of a polygynous carnivore: do cougars Puma concolor follow source-sink predictions?” Wildlife Biology 19: 289-301. Stoner, D.C., M.L. Wolfe, W.R. Rieth, K.D. Bunnell, S.L. Durham, and L.L. Stoner. 2013. “De facto refugia, ecological traps and the biogeography of anthropogenic cougar mortality in Utah.” Diversity and Distributions 19: 1114-1124. Tabanca, N., Wang, M., Avonto, C., Chittiboyina, A.G., Parcher, J.F., Carroll, J.F., Kramer, M., and Khan, I.A. 2013. “Bioactivity-guided investigation of geranium essential oils as natural tick repellents”. Journal of Agricultural Food Chemistry 61: 4101-4107. Tomer, M.D., P. C. Beeson, D. W. Meek, D. N. Moriasi, C. G. Rossi, A. M. Sadeghi. 2013. “Evaluating simulations of daily discharge from watersheds using autoregression and an index of flashiness”. Transactions of ASABE 56(4): 1317-1326. Trier, T., N. M. Bello, T. R. Bush and L. Bix. 2014. “Role of packaging on contamination rates during simulated presentation to a sterile field.” PLoS One 9(7): e100414. Tucker R.M, Edlinger C, Craig B.A., and Mattes R.D. 2014 Associations between BMI and fat taste sensitivity in humans. Chemical Senses 39(4): 349-357. Vega FE, Simpkins A, Bauchan G, Infante F, Kramer M, Land MF. 2014. “On the eyes of male coffee berry borers as rudimentary organs”. PLoS One 9(1): e85860. doi:10.1371/journal.pone.0085860 Yeater, K.M., S.E. Duke, and W.E. Riedell. 2014. “Multivariate Analysis: Greater Insights into Complex Systems.” Agronomy Journal. doi:10.2134/agronj14.0017. Xu, X., Madden, L.V., Edwards, S.G., Doohan, F.M., Moretti, A., Hornok, L., Nicholson, P., and Ritieni, A. 2013. “Developing logistic models to relate the accumulation of DON associated with Fusarium head blight to climatic conditions in Europe.” European Journal of Plant Pathology 137: 689-706. Xu, X., Madden, L.V., and Edwards, S.G. 2014. “Relating HT2 and T2 toxin accumulation in field oat grains to environmental conditions.” Phytopathology 104: 57-66. Xie, L., and Madden, L.V. 2014. “%HPGLIMMIX, a high performance SAS macro for GLMM estimation.” Journal of Statistical Software 58(8): 1-25. http://www.jstatsoft.org/

Impact Statements

NCCC-170 fosters research to identify and develop statistical methodology applicable to agricultural research and provides a forum for sharing and educating both statisticians and subject-matter scientists in the agricultural, environmental and natural sciences. As a result, all members are able to provide more effective assistance to agricultural researchers addressing national research priorities than they would be without NCCC-170.
Project members provide continuing education for scientists in agriculturally related disciplines in modern statistical analyses of designed experiments in general and specifically in the areas of generalized linear mixed models and statistical techniques in genomics applications. Examples of such activities and their immediate impacts for the current reporting period are listed in the Accomplishments section of this report.
Project members collaborate in research projects with scientists in agricultural related disciplines to develop and use proper statistical design and analysis methodology well beyond standard textbook applications. These efforts often result in competitive grant participation and refereed publications. Each of these impacts is listed in the Accomplishments and Publications sections of this report.

Date of Annual Report: 07/31/2015

Report Information

Annual Meeting Dates: 06/25/2015 - 06/26/2015
Period the Report Covers: 10/01/2014 - 09/01/2015

Participants

Nora Bello (KS), Bruce Craig (IN, Admin.), Xin Dai (UT), Sara Duke (USDA-ARS), Ed Gbur (AR), Carla Goad (OK), Nick Keuler (WI), Matt Kramer (USDA-ARS), Alex Lipka (IL), Raul Macchiavelli (PR), Bahram Momen (MD), Dan Nettleton (IA), Gayla Olbricht (MOSci&Tech), Neil Paton (Cargill), Bahman Shafii (ID), Julia Sharp (SC), John Stevens (UT), Walt Stroup (NE), Rob Tempelman (MI), Mark West (USDA-ARS), Kathy Yeater (USDA-ARS)

Brief Summary of Minutes

Technical program:

The meeting began at 9:00 a.m. on Thursday, June 25, 2015 with opening remarks by Raul Macchiavelli (Interim Dean and Interim Experiment Station Director as well as Local Arrangements Chair). Presentations ended at approximately 4:15 p.m. The technical program consisted of the following presentations.

Walt Stroup and Ellen Paparozzi A glimpse of GLMMIX (with a peek at R) for use in horticultural research

Matt Kramer, Ellen Paparozzi and Walt Stroup Statistical issues in a horticultural journal: Misunderstanding and misapplication of fundamental concepts

Dan Nettleton A glimpse inside the random forest black box

Gayla Olbricht Investigating differences in sleep properties between Alzheimer’s and normal fruit flies

Bruce Craig, Ningning Chen and Sameera Wijayawardana Assessing inter-observer agreement for multivariate IHC scoring data

Elizabeth Claassen Mixed and generalized models in JMP

John Stevens The bivariate null kernel method for LD-based QTL mapping

Ed Gbur Inference issues related to the two sample test for means of beta distributions

Raul Macchiavelli Application of non-linear mixed models to combine information from different sources to estimate site index curves in forestry studies

Business meeting:

The business meeting began at 9:12 a.m. on Friday, June 26, 2015. Ed Gbur presided. The following items were discussed:

(1) The organizers were thanked for a productive and enjoyable meeting: Raul Macchiavelli for local arrangements with assistance from Ms. Lucy Serrano and Bahman Shafii for the technical program. Ed Gbur was thanked for his work as chair and webmaster of the committee.

(2) Presenters who wish to post their talk on the project website should send a pdf of the talk to Ed Gbur (egbur@uark.edu).

(3) The annual report and impact statement are due shortly after the annual meeting. Participants need to send Ed Gbur (egbur@uark.edu) accountings of all activities (workshops, papers, presentations, grants, teaching related items, etc.) from October 1, 2014 to September 30, 2015 (or since last year’s report) that are related to or inspired by their participation in NCCC-170 as soon as possible.

(4) The 2016 meeting will be held in Maryland with Bahram Momen as the local host. Tentative dates are June 23-24, 2016. This will be a joint meet with USSES (SCC-013). Kathy Yeater will serve as program chair. The 2017 meeting is tentatively planned for Elk River, Minnesota at the Cargill Experiment Station with Neil Paton as the local host. The 2018 meeting is tentatively planned for Arkansas.

(5) The current NCCC-170 project is scheduled to end on September 30, 2016. Ed Gbur announced that the initial deadline for the renewal proposal is September 15, 2015. His goal is to submit the proposal no later than September 1. More information and reminders along with deadlines for various steps in the process will be distributed shortly. It is important that all individuals sign up as official members. This includes current members because membership does not automatically roll over into the renewal. Organizationshave the option of allowing multiple official members but only one member can be the voting member.

(6) Kathy Yeater announced that on-line statistics trainings, facilitated by American Society of Agronomy’s as part of their program “Statistics Workshops for Regional Meeting and Web-Based Platform,” had three successful presentations over the last academic year that were taught by NCCC-170 members Julia Sharp and Carla Goad. Each course lasted 4 weeks, with 2 hours of contact time per week. Approximately 150 ASA members and industry partners enrolled in the courses. The society is very supportive of the online statistics courses and is open to facilitating more applied statistics courses.

(7) Kathy Yeater also announced that at the upcoming Annual Meeting for ASA-CSSA-SSSA in November activities are scheduled for meta-analysis and data stewardship topics. There will be a symposium entitled “Meta-Analysis Applications in Agricultural Research” and a partnered workshop “Meta-Analysis for the Synthesis of Evidence in Agriculture.” Larry Madden will be presenting the workshop. The Plenary special session is “Getting More from Data: Science for Sustainable Solutions.”

(8) Lastly, Kathy Yeater called for volunteer(s) or nomination(s) to present invited statistics workshop(s) for the Aquaculture America conference in February 2016. The topics of multiple comparison procedures, regression approaches, and categorical data analysis were requested.

(9) Debbie Boykin announced an upcoming opening for an ARS Area Statistician to be located in Athens, Georgia. She encouraged interested individuals to apply as soon as possible after the announcement is posted.

(10) Nora Bello announced that the mixed models workshop will be presented at the annual Animal Science meeting on July 15-16, 2015 in Orlando, Florida. The workshop has already reached the 100 participant limit. Since the Animal Science and Dairy Science annual meetings are being planned as separate meetings in the future, there was discussion about presenting the workshop for both societies, possibly alternating years between them.

(11) The group reviewed progress toward the goals identified at the 2014 meeting. In addition, based on the discussion generated by the first two presentations of the technical program, the group agreed that incorporating ideas for providing statistical support to the scientific community in the review and editorial process of publications was important to include in the Goals, Impacts, and Outcomes sections of the annual report and renewal proposal. A few other changes regarding wording of application areas were also suggested.

(12) The group discussed USSES (SCC-013) meeting jointly with NCCC-170 yearly. Previously the two groups met together every three years. For the immediate future, the administrative structure of the individual groups would not change. Meeting jointly would allow both groups to benefit from the presentations and experience of the combined group. Concern was expressed that the combined groups may eventually become too large.

The meeting adjourned at approximately 10:50 a.m. A group photograph for the project web site was taken during a break in the meeting.

Accomplishments

Outputs: Workshops: Walt Stroup and Ellen Paparozzi presented a workshop entitled “A glimpse of GLIMMIX (with a peek at R) for use in horticultural research” at the International Horticulture Congress in Brisbane, Australia in August 2014. The presentation has been accepted to appear in refereed proceedings that will be published in ActaHorticultura. Ken Koehler and Kevin McCarter taught the mixed model workshop focusing on the application of general and generalized linear mixed models to research problems in the animal and food sciences at the Annual American Dairy Science Association and American Society of Animal Sciences National Meetings in Orlando, FL in July 2015. Jennifer Clarke presented a workshop on statistics and “big data” at the Annual Meeting of the Snake River Chapter of the American Statistical Association in May 2015 in Meridian, ID. The workshop included invitees from universities in Idaho and Utah, as well as members of NCCC-170. Presentations: Larry Madden. Meta-analysis of 19 years of fungicide trials for the control of Fusarium head blight of wheat. Keynote presentation at the National Fusarium Head Blight Forum, December 2014. St. Louis, MO. Bruce Craig. Consensus development for public health guidelines: a critical approach. Women's Global Health Institute High Tea Symposium. Purdue University, November 7, 2014. Bruce Craig. Assessing inter-observer agreement for multivariate IHC scoring data. Department of Statistics, University of Georgia, September 4, 2014 and at the Department of Biostatistics, Indiana University, November 21, 2014. Macchiavelli, R.; A. Calvo; P. Torres-Saavedra; J. Chavarría-Carvajal. Semiparamentric Mixed Beta Regression with Penalized Splines for Disease Severity in Plants. XXVIIth Annual Conference on Applied Statistics in Agriculture.26-29 April, 2015, Manhattan, KS. Calvo, A.; R. Macchiavelli. Regresión semi-paramétrica con Distribución Beta y efectosaleatorios. XXXSeminario Interuniversitario de Investigación Matemática (SIDIM). 27-28 Febrero 2015, Mayagüez, PR. Torres-Saavedra, P.; R. Macchiavelli. Semiparametric Mixed Beta Regression with Penalized Splines for Disease Severity. XXX Seminario Interuniversitario de Investigación Matemática (SIDIM). 27-28 Febrero 2015, Mayagüez, PR. Piccardi, M, R. Macchiavelli, M. Balzarini. Modelos no lineales mixtos para la producción de lechediaria. XIX Reunión Científicadel Grupo Argentino de Biometría. 10-12 September, 2014, Santiago del Estero, Argentina. Willems, P., R. Macchiavelli, C. Robles. Comparación de formas de aplicación de la vacuna Brucellaabortus cepa 19 en bovinos: Aplicación de modelos no lineales mixtos. XIX Reunión Científicadel Grupo Argentino de Biometría. 10-12 September, 2014, Santiago del Estero, Argentina. John Stevens, Mecham D, Isom SC, and Saunders G. mvGST: Multivariate and Directional Gene Set Testing. Kansas State University Conference on Applied Statistics in Agriculture in April 2015 and at the Joint Statistical Meetings in Seattle, WA in August 2015. Yu M, Kearney M, Momen B, Riter, JCA. Correlating peak NDVIs of salt marshes with environmental conditions in Louisiana, USA, using principal component analysis. IGARSS, 2015. Nora Bello. Experimental design basics. Kansas State University Honors Undergraduate Program on General Agriculture. February 2015. Ou, Z., R.J. Tempelman, J.P. Steibel, C.W. Ernst, R.O. Bates and N.M. Bello. Breeding implications of heteroskedastic whole-genome prediction of genetic merit. Joint Annual Meetings of the American Dairy Science Association and the American Society of Animal Science. Orlando, FL. July 12-16, 2015. Lu, Y., M.J. Vandehaar, D.M. Spurlock, K.A. Weigel, L.E. Armentano, C.R. Staples, E.E. Connor, Z. Wang, M. Coffey, R.F. Veerkamp, Y. deHass, N.M. Bello and R.J. Tempelman. Hierarchical Bayesian inference on genetic and non-genetic components of partial efficiencies determining feed efficiency in dairy cattle. Joint Annual Meetings of the American Dairy Science Association and the American Society of Animal Science. Orlando, FL. July 12-16, 2015. Delph, K., E.G. Davis, N.M. Bello, K. Hankins, M.J. Wilkenson and C. Ewen. Comparison of immunologic responses following intranasal and oral vaccination with a USDA-approved, live-attenuated Streptococcus equi vaccine. 2015 American College of Veterinary Internal Medicine Forum. Indianapolis, IN. June 4-6, 2015. Johnson, L., M.M. Gray, P. St. Amand, M. Galliart, S. Brown, J. Poland, K. Garret, E. Ekhunov, N.M. Bello, T. Morgan, S.G. Baer and B. Maricle. Genetic differentiation, transcriptome variation, and local adaptation of dominant prairie grass Andropogongerardii along the climate gradient of the US Midwest: Implications for climate change. Society for Molecular Biology and Evolution Satellite Meeting. Montepellier, France. May 26-29, 2015. Galliart, M., P. St. Amand, J. Polland, N.M. Bello, S. Sabates, H. Tetreault, A. DeLaCruz, J. Bryant, T.J. Morgan, M. Knapp, S.G. Baer, D. Gibson, L. Wilson, B.R. Maricle and L. Johnson. Trait variation and genetic divergence of a widespread grass Andropogon gerardii across a Great Plains climate gradient. American Society of Plant Biologists Midwestern Section Meeting. Lincoln, NE. March 24-25, 2015. Goncalves, M.A D., S.S. Dritz, M.D. Tokach, N.M. Bello, J.M. DeRouchey, R.D. Goodband and J.C. Woodworth. Effect of lysing and energy intake during late gestation on weight gain and reproductive performance of gilts and sows under commercial conditions. Joint Midwest Meeting of the American Dairy Science Association and American Society of Animal Science. Des Moines, IA. March 15-18, 2015. Cull, C., D. Renter, N.M. Bello, A. Babcock, S. Ives and T.G. Nagaraja. Efficacy of a vaccine and a direct-fed microbial against fecal shedding of Escherichia coli O157:H7 and corresponding impacts on cattle performance in a commercial feedlot. Kansas State University Cattlemen's Day. Manhattan, KS. March 6, 2015. Johnson, L., J. Shelton, N.M. Bello, S. Raithel, M. Galliert, S.J. Brown, N. Herndon, R. Welti, B. Nikolau, T. Samarakoon, Z. Song and R. Jeannotte. Divergent epicuticular wax and transcriptome of edaphically differentiated Andropogon grasses in the US Midwest prairies. XXIII International Plant & Animal Genome Conference. San Diego, CA. January 10-14, 2015. Galliart, M., P. St. Amand, J. Polland, N.M. Bello, S. Sabates, H. Tetreault, A. DeLaCruz, J. Bryant, T. J. Morgan, M. Knapp, S.G. Baer, D. Gibson, L. Wilson, B.R. Maricle and L. Johnson. Trait variation and genetic divergence of a widespread grass Andropogon gerardii across a Great Plains climate gradient. XXIII International Plant & Animal Genome Conference. San Diego, CA. January 10-14, 2015. Kivett, J., N.M. Bello and R. Cloyd. Efficacy of rotation programs against the western flower thrips, Frankliniella occidentalis that include entomopathogenic fungi. Entomological Society of America Annual Meeting. Portland, OR. November 16-19, 2014. Raithel, S., L. Johnson, M. Galliart, S. Brown, J. Shelton, N. Herndon and N.M. Bello. Assessing gene filtering strategies in RNA-Seq differential expression analysis of an edaphic subspecies of dominant prairie grass Andropogon gerardii.10thAnnualEcological Genomics Symposium. Kansas City, MO. October 31 - November 2, 2014. Cull, C.A., D.G. Renter, N.M. Bello, A.H. Babcock and T.G Nagaraja. Efficacy of a vaccine and a direct-fed microbial against fecal shedding of Escherichia coli O157:H7 and corresponding impacts on cattle performance in a commercial feedlot. 10thAnnual Applied Animal and Public Health Research and Extension Symposium. Kansas, City, MO. October 18, 2014. Gardhouse, S., D. Eshar, N.M. Bello and D. Mason. Evaluation of changes in critical care blood analytes during isoflurane anesthesia in zoo-kept black-tailed prairie dogs (Cynomysludovicianus). American Association of Zoo Veterinarians Annual Conference. Orlando, FL. October 18-24, 2014. Gerard, P., Wrenn, J., and Sharp, J.L. Identifying the perceived value of statistical consulting in a university setting. Joint Statistics Meetings, Boston, MA. August 2-7, 2014. Drennan, K., Wiesinghe, D., White, S., White, D., Menchyk, N., Sharp, J., Vincent, E. and Park, D.M. Soil Temperature and Moisture Differentials from Concrete Sidewalks. 14th American Ecological Engineering Society Meeting. Charleston, SC. June 10, 2014. Lund, R.L., Bowman, D.D., Brown, H., Malone, J.B., McMahan, C., Sharp, J.L. Wang, D. Identifying relevant canine heartworm factors. American Association of Veterinarian Parasitologists. Denver, CO.July 26-29, 2014. Solomons, A.G., Mikhailova, E.A., Post, C.J., and Sharp, J. L. Using low-cost thermal cameras to validate LiDAR-based predictions. Clemson Biological Sciences 7th Annual Student Symposium. Clemson, SC. February 28, 2015. Sharp, J.L., Smith, J., Park, D. Exploring Challenges Encountered With Streaming Data Analyses. Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KSApril27-28, 2015. West, Mark. Three presentations entitled Introduction to R with RStudio; Experiments, designs and models; Introduction to mixed model analysis. Natural Resource Management Research Center, Mandan, ND. March 11, 2014. West, Mark. How to mess up experiments, designs and models. Red River Valley Agricultural Research Center, Fargo, ND. September 24, 2014. Thompson, K.T. and Gbur, E.E. Small sample properties of the two independent sample test for means from beta distributions. Conference on Applied Statistics in Agriculture. Manhattan, KS April 27-28, 2015. Olbricht G.R. Analyzing DNA Methylation Data in Plants: The Importance of Sequence Context. University of Missouri – Kansas City, Mathematics and Statistics Department Colloquia. Kansas City, MO, April 24, 2015. Baumann D. and Olbricht G.R. Statistical Analysis of DNA Methylation in Plants. Conference on Applied Statistics in Agriculture. Manhattan, KS, April 27-28, 2015. Goad, Carla. Experimental design basics. Oklahoma State University Department of Horticulture and Landscape Architecture seminar (Invited). January 2015. Clarke, J. The Challenge of Big Data. USDA-ARS Big Data Workshop. George Washington Carver Center, Beltsville, MD. July 15-16, 2015. Snelling, W.M., Kuehn, L.A., Sinha, R., Wells, J.E., Bono, J.L., Berry,, E.D., Kim, M.S., Clarke, J., Kachman, S.D., Moriyama, E., Wilson, D., Benson, A. Geneomic heritabilities and SNP associated with lower gastrointestinal tract microflora taxonomic groups and E. coli O157:H7 shedding. Joint Midwest Meeting of the American Dairy Science Association and American Society of Animal Science. Des Moines, IA. March 15-18, 2015. Kuehn, L.A., Snelling, W.M., Sinha, R., Wells, J.E., Bono, J.L., Freetly, H.C., Kim, M.S., Clarke, J., Kachman, S.D., Moriyama, E., Wilson, D. and Benson, A. Genetic correlations of lower gastrointestinal tract microflora taxonomic groups with animal intake and gain. Joint Midwest Meeting of the American Dairy Science Association and American Society of Animal Science. Des Moines, IA. March 15-18, 2015. Clarke, B., Valdes, C., Dobra, A. and Clarke, J. A Bayes testing approach to metagenomic profiling in bacteria. ICSA Annual Meeting, Colorado State University, Ft. Collins, CO, June 17-18, 2015. (Invited) Other project related activities: As part of the American Society of Agronomy’s on-line statistics training initiative Julia Sharp taught “Introduction to Statistics for Agricultural Researchers” in Fall 2014 and Carla Goad taught the follow-up “Introduction to Experimental Design and Analysis.” Carla Goad’s course included 24 Pakistani participants from partner organizations United States Agency for International Development (USAID) and International Maize and Wheat Improvement Center (CIMMYT). In Spring 2015 Julia Sharp taught “Introduction to Statistics Using R.” Walt Stroup’s invited paper “Rethinking the Analysis of Non-Normal Data in Plant and Soil Science” in Agronomy Journal has been the tenth mostread paper of 2015 for that journal. Four of the top ten papers were invited statistics manuscripts. The invited Statistics Series manuscripts for Agronomy Journal have elicited an out-growth to a textbook being prepared for ASA-CSSA-SSSA Publications. Nora Bello is a co-PI on a USDA-AFRI Foundational Program A1221 grant proposal entitled“Risk Management Strategies to Reduce the Impacts of Bovine Respiratory Disease Complex in Commercial Feeder Cattle.” Principal Investigator is David Renter, College of Veterinary Medicine, Kansas State University.The proposal was funded for2014-2018 at $498,500. It was ranked as Outstanding and the #1 ranked grant for this review panel. John Stevens has maintained the R package mvGST on Bioconductor since its acceptance there in October 2014. This package facilitates multivariate and directional gene set testing, was primarily motivated by collaboration with animal science reproduction researchers, and was co-authored with former students Dennis Mecham and Garrett Saunders. NCCC-170 has helped Bahram Momen improve the content of his graduate course in experimental design and advanced statistical analysis (BIOM602) course at the University of Maryland. It has also helped him substantially in consulting and mentoring many graduate students and faculty members in designing their research and analyzing the data. Walt Stroup developed and taught a course on non-normal data for entomology and ecology graduate students at the University of Nebraska in the Fall 2014 semester. In addition, his graduate level Design of experiments and Statistical modeling courses have been influenced by his participation in NCCC-170. The audiences for both courses include agriculture graduate students. Approximately half of the students in the Design class were from agricultural disciplines. Jennifer Clarke developed and is co-director of a new doctoral program in Complex Biosystems at the University of Nebraska. She is director of the program specialization in Systems Analysis. The program has accepted its inaugural class of students and will begin teaching courses in Fall 2015. Entering students have undergraduate degrees in analytical as well as agricultural areas of study. The program design was influenced by the NCCC-170 and includes required courses in statistics and specializations in integrated plant biology, microbial interactions, and computational ecology, evolution, and organismal biology. Specific goals for the next three years: (1) Educate project members in statistical issues and methodology related to statistical problems related to new complex data types collected on relatively few experimental units. Application areas include agricultural analytics, informatics, -omics, and -metrics. (2) Continue to offer updated and expanded mixed model and generalized linear mixed model workshops upon request from subject matter groups. (3) Develop web-based educational materials and workshops for agricultural scientists including statistical assistance in the review and editorial process of agricultural publications.

Publications

Easson, M.W., S.A. Wojkowski, B.D. Condon, K.M. Yeater, R.P. Slopek, and C.A. Fortier (2015). Ultrasound-enhanced bioscouring of greige cotton: regression analysis of process factors. American Association of Textile Chemists and Colorists Journal of Research 2(1):16-23. Gealy, D., N.R. Burgos, K.M. Yeater, A.K. Jackson (2015). Outcrossing Potential between U.S. Blackhull Red Rice and Indica Rice Cultivars. Weed Science (in press, Accepted February 12, 2015). doi: http://dx.doi.org/10.1614/WS-D-14-00150.1. Guerrero, F.D., R. Andreotti, K.G. Bendele, R.C. Cunha, R.J. Miller, K. Yeater, and A.A. Perez de Leon (2014). Rhipicephalus (Boophilus) microplus aquaporin as an effective vaccine antigen to protect against cattle tick infestations. Parasite Vectors 7:475. Published online 2014 Oct. 12. Doi: 10.1186/s13071-014-0475-9. Kim, H.J., D.J. Hinchliffe, B.A. Triplett, K.M. Yeater, H.S. Moon, M.K. Gilbert, G.N. Thyssen, R.B. Turley, and D.D. Fang (2015). Phytohormonal networks promote differentiation of fiber initials on pre-anthesis cotton ovules grown in vitro and in planta. PLoS One 10(4):e0125046. Sheffield, C.L., T.L. Crippen, J.A. Byrd, R.C. Beier, and K.M. Yeater (2015). Canonical discrimination of the effect of a new broiler production facility on soil chemical profiles as related to current management practices. PLoS One 10:1-13. Neuman-Lee, L.A., H.B. Fokidis, A.R. Spence, M. Van der Walt, G.D. Smith, S. Durham, and S.S. French (2015). Food restriction and chronic stress alter energy use and affect immunity in an infrequent feeder. Functional Ecology (in press). Ranglack, D.H., S. Durham, and J.T. du Toit (2015). Competition on the range: science vs. perception in a bison-cattle conflict in the western USA. Journal of Applied Ecology 52: 467-474. Tepedino, V.J., S. Durham, S.A. Cameron, and K. Goodell (2015). Documenting bee decline or squandering scarce resources. Conservation Biology 29: 280-282. Ramos-Santana, R., Y. Quijano-Cabrera, R. Macchiavelli (2014). Evaluación del rendimiento y la calidad del forraje Maralfalfa en tres vaquerías del norte de Puerto Rico en la época de días cortos. Journal of Agriculture of the University of Puerto Rico 98: 49-56. Ramos-Santana, R., E. Valencia-Chin, R. Macchiavelli (2014). Potencial de Morus alba (Morera) en la alimentación de cabras de reemplazo en Puerto Rico. Journal of Agriculture of the University of Puerto Rico 98: 79-82. Anaya, A.; I. Padilla; R. Macchiavelli; D. Vesper; J. Meeker; A. Alshawabkeh (2014). Estimating preferential flow in karstic aquifers using statistical mixed models. Groundwater 52:584-596 (doi: 10.1111/gwat.12084). Klun, JA and Kramer, M. (2014). Klun & Debboun modules: uses and data analysis. In Insect Repellents Handbook, 2nd ed. Eds: Debboun, M; Frances, SP; Strickman, DA. CRC Press, Boca Raton, FL. pp. 267-281. Baldos, OC; DeFrank, J; Kramer, M; Sakamoto, GS. (2014). Storage humidity and temperature affect dormancy loss and viability of tanglehead (Heteropogoncontortus) seeds. HortScience 49: 1328-1334. Ulrich, KR; Feldlaufer, MF; Kramer, M; St. Leger, RJ. (2014). Exposure of bed bugs to Metarhiziumanisopliae at different humidities. J. Economic Entomology 107: 2190-2195. Ulrich, KR; Feldlaufer, MF; Kramer, M; St. Leger, RJ. (2015). Inhibition of the entomopathogenic fungus Metarhiziumanisopliaes ensulato in vitro by the bed bug defensive secretions (E)-2-hexenal and (E)-2-octenal. BioControl 60: 517–526 Apps, PJ, Weldon, PJ, Kramer, M. (2015). Chemical signals in terrestrial vertebrates: search for design features.Nat. Prod. Rep. 32: 1131-1153. Saunders G., Fu G., and Stevens J.R. (2014). A graphical weighted power improving multiplicity correction approach for SNP selections. Current Genomics 15(5):380-389. Saunders G., Stevens J.R., and Isom S.C. (2014). A shortcut for multiple testing on the directed acyclic graph of gene ontology. BMC Bioinformatics 15:349. Walsh, S.W., F. Mossa, S.T. Butler, D.P. Berry, D. Scheetz, F. Jimenez-Krassel, R.J. Tempelman, F. Carter, P. Longergan, A.C.O. Evans, and J.J. Ireland (2014). Heritability and impact of environmental effects during pregnancy on antral follicle count in cattle. Journal of Dairy Science 97:4503-4511. Tempelman, R.J., D.M. Spurlock, M. Coffey, R.F. Veerkamp, L.E. Armentano, K.A. Weigel, Y. de Haas, C.R. Staples, E.E. Connor, Y. Lu, and M.J. Vandehaar (2015). Heterogeneity in genetic and non-genetic variation and energy sink relationships for residual feed intake across research stations and countries.Journal of Dairy Science 98:2013-2026. Yang, W., C. Chen, and R.J. Tempelman (2015). Improving the computational efficiency of fully Bayes inference and assessing the effect of misspecification of hyperparameters in whole genome prediction models. Genetics, Selection, Evolution 47(1):13. Jimenez-Krassel, F., D. Scheetz, L. Neuder, J. Ireland, J.R. Pursley, G. Smith, R.J. Tempelman, T. Ferris, W. Roudehush, W. F. Mossa, and P. Lonergan (2015). Anti-Müllerian hormone concentration indairy heifers is positively associated with productive herd life. Journal of Dairy Science 98:3036-3045. Yang, W.,, C. Chen, J.P. Steibel, C.W. Ernst, R.O. Bates, L. Zhou, and R.J. Tempelman (2015). A comparison of alternative random regression and reaction norm models for whole genome predictions. Journal of Animal Science 93: 2678-2692. Chen C., H. Wang, W. Yang and R.J. Tempelman (2014). Exploring extensions and properties of expectation-maximization methods for whole genome prediction. Proceedings of the 10th World Congress on Genetics Applied to Livestock Production.August 17-22, 2014, Vancouver, Canada, ASAS, Champaign, IL. Spurlock, D. M., Tempelman, R. J.,Weigel, K. A., Armentano, L. E., Wiggans, G. R., Veerkamp, R. F., deHaas, Y., Coffee, M. P., Connor, E. E., Hanigan, M. D., Staples, C., and Vandehaar, M. (2014). Genetic architecture and biological basis of feed efficiency in dairy cattle. Proceedings of the 10th World Congress on Genetics Applied to Livestock Production. August 17-22, 2014, Vancouver, Canada, ASAS, Champaign, IL. Lu, Y., Vandehaar, M., Weigel, K., Armentano, L., Spurlock, D., Staples, C., Connor, E., and Tempelman, R. J. (2014). An alternative approach to modeling genetic merit of feed efficiency in dairy cattle. 2014. Proceedings of the 10th World Congress on Genetics Applied to Livestock Production. August 17-22, 2014, Vancouver, Canada, ASAS, Champaign, IL. Weigel, K. A., Yao, C., Hoffman, P. C., Armentano, L. E., Spurlock, D. M., Tempelman, R. J., and Vandehaar, M. (2014) Improving biological and economic aspects of production efficiency through genetic selection and genome-guided replacement management. Proceedings of the 10th World Congress on Genetics Applied to Livestock Production. August 17-22, 2014, Vancouver, Canada, ASAS, Champaign, IL. Mota, R., Tempelman, R. J., Cardoso, F., Aguilar, I., & Lopes, P. (2014). Genomic Wide-Selection for Tick Resistance in Hereford and Braford Cattle via Reaction Norm Models. 2014. Proceedings of the 10th World Congress on Genetics Applied to Livestock Production. August 17-22, 2014, Vancouver, Canada, ASAS, Champaign, IL. Cladis, DP, Zhang, R, Tan, Xi, Craig, BA, and Santerre, CR. (2015). Postharvest Correlation between Swordfish (Xiphius gladius) Size and Mercury Concentration in Edible Tissues. Journal of Food Protection 78(2), 396--401. Janle, E, Freiser, H, Mangnais, C, Chen, T-Y, Craig BA, and Santerre, C. (2014). Green tea increase the concentration of total mercury in the blood of rats following an oral fish tissue bolus. BioMed Research International, Article ID 320936. Running CA, Craig BA, and Mattes RD (2015). Oleogustus: The Unique Taste of Fat. Chemical Senses, 2015, 1–10 doi:10.1093/chemse/bjv036. Haas, Z and Craig, BA (2014). Developing prediction equations for carcass lean mass in the presence of proportional measurement error. Proceedings of the Conference on Applied Statistics in Agriculture Conference. Ed. W. Song. K.M. Webb, R.M. Harveson, M.S. West (2015). Evaluation of Rhizoctoniazeae as a potential biological control option for fungal root diseases of sugar beet. Annals of Applied Biology 167: 75–89. Rebecca L. Phillips, Mikki R. Eken, Mark S. West (2015). Soil Organic Carbon Beneath Croplands and Re-established Grasslands in the North Dakota Prairie Pothole Region. Environmental Management 55(4). Rao S, Stolle EC, Sher S, Lin CW, Momen B, Nahabedian MY (2014). A multiple logistic regression of complications following microsurgical breast reconstruction. Gland Surgery 3:226-31. DOI: 10.3978/j.issn.2227-684X.2014.10.03. Yu M, Momen B, Kearney M. (2015). Quantifying moderate resolution remote sensing phenology of Louisiana coastal marshes. Ecological Modeling 312: 191-199. Johnson, L., J.T. Olsen, H. Tetreault, R.K. Goad, M.M. Mendola, A. DeLaCruz, H. Bryant, T. Morgan, M. Knapp, N.M. Bello, S. Baer and B. Maricle (2015). Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains’ precipitation gradient: Implications for grassland restoration with climate change. Evolutionary Applications. DOI: 10.1111/eva.12281 Higbie, C.T., D. Eshar and N.M. Bello (2015). Evaluation of three point-of-care meters and a portable chemistry analyzer for measurement of blood glucose concentrations in black-tailed prairie dogs (Cynomysludovicianus). American Journal of Veterinary Research 76(6): 532-539. Horne, E.A., S. Foulks, N. M. Bello (2015). Visual display in Blanchard's cricket frogs (Acrisblanchardi). The Southwestern Naturalist 59(3): 409-413. Gray, M., P. St. Amand, N.M. Bello, M.B. Galliart, M. Knapp, K. Garrett, T.J. Morgan, S.G. Baer, B.R. Maricle, E. Akhunov and L. Johnson (2014). Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands environmental gradient. Molecular Ecology 23(24): 6011-28. DOI: 10.1111/mec.12993. Miller, C., J.K. Craver, K.A. Williams and N.M. Bello (2014). UVB radiation affects intumescence development in ornamental sweet potato (Ipomoea batatas). HortScience 49(10):1277-1283. Davis, E.G., N.M. Bello, A.J. Bryan, K. Hankins, M. Wilkerson (2014). Characterization of immune responses in healthy foals when a multivalent vaccine protocol was initiated at 90 and 180 days of age. Equine Veterinary Journal. doi: 10.1111/evj.12350. Wesselowski, S., M. Borgarelli, N. M. Bello and J. Abbott (2014). Discrepancies in identification of left atrial enlargement in dogs using left atrial volume versus left atrial to aortic root ratio. Journal of Veterinary Internal Medicine 28(5): 1527-33. DOI: 10.1111/jvim.12410. Douhit, T.L., J.M. Bormann, N.M. Bello (2014). Assessing the association between hoof thermography and hoof doppler ultrasonography for the diagnosis of lameness in horses. Journal of Equine Veterinary Science 34: 275-280. Xu, X., and Madden, L.V. 2014. The limits of the binary power law describing spatial variability for incidence data. Plant Pathology 63: 973-982. Salgado, J. D., Madden, L. V., and Paul, P. A. 2014. Efficacy and economics of integrating in-field and harvesting strategies to manage Fusarium head blight of wheat. Plant Disease 98: 1407-1421. Anderson, K.F., Madden, L.V., and Paul, P.A. 2015. Fusarium head blight development and deoxynivalenol accumulation in wheat as influenced by post-anthesis moisture patterns. Phytopathology 105: 210-219. Salgado, J. D., Madden, L. V., and Paul, P. A. 2015. Quantifying the effects of Fusarium head blight on grain yield and test weight in soft red winter wheat. Phytopathology 105: 295-306. Piepho, H.-P., Madden, L.V., and Williams, E.R. 2015. Multiplicative interaction in network meta-analysis. Statistics in Medicine 34: 582-594. Wang, D., Bowman, D.D., Brown, H., Harrington, L.C., Kaufman, P.E., McKay, T, Nelson, C.T., Sharp, J.L. and Lund, R. (2014). Factors influencing U.S. canine heartworm (Dirofilariaimmitis) prevalence. Parasites and Vectors 7:264. Stroup, W.W. 2015. Rethinking the Analysis of Non-Normal Data in Plant and Soil Science. Agronomy Journal 107: 811-827. Salmeron, M., E.E. Gbur, F.M. Bourland, N.W. Buehring, L.Ernest, F.B. Fritschi, B.R. Golden, D. Hathcoat, J. Lofton, T.D. Miller, C.Nelly, G. Shannon, T.K. Udeigwe, D.A. Verbree, E.D. Vories, W.J. Wiebold, and L.C. Purcell (2014). Soybean maturity group choices for early and late plantings in the U.S. Midsouth. Agronomy Journal, 106, 1893-1901. Smith, F., K.R. Brye, P. Chen, E.E. Gbur and K. Korth (2014). Residue and water management effects on aggregate stability and aggregate associated carbon and nitrogen in a wheat-soybean double crop system. Soil Science Society of America Journal, 78: 1378-1391. Smith, A., M. Popp, D. Philipp, K. Coffey and E.E. Gbur (2014). Overseeding bermudagrass pastures with ryegrass and clovers: Estimating partial returns. Journal of the American Society of Farm Managers and Rural Appraisers. 108-123. McMullen, R.L., K.R. Brye, A.L. Daigh, B.C. Menjoulet, A.L. Pirani, E.E. Gbur, D.M. Miller, M.A. Evans-White and R.E. Mason (2014). Long term runoff water quality as affected by broiler litter application to a Udult in the Ozark Highlands. Soil Science Society of America Journal, 78, 2017-2031. Ballesteros, D.C., R.E. Mason, C.K. Addison, A.A. Acuña, N.A. Arguello, N. Subramanian, R.G. Miller, H. Slater, E.E. Gbur, D. Miller, C.A. Griffey, M.D. Barnett and D. Tucker (2015). Tolerance of wheat to vegetative stage soil waterlogging is conditioned by both constitutive and adaptive QTL. Euphytica 201(3), 329-343. DOI 10.1007/s10681-014-1184-3. Motschenbacher, J.M., K.R. Brye, M.M. Anders and E.E. Gbur (2014). Long term rice rotation, tillage, and fertility effects on near-surface chemical properties in a silt-loam soil. Nutrient Cycling in Agroecosystems. DOI 10.1007/s10705-014-9628-7. Nam, S., R. Slopek, D. Wolf, M. Warnock, B.D. Condon, P. Sawhney, E. Gbur, M. Reynolds and C. Allen (2015). Comparison of biodegradation of low-weight hydroentangled raw cotton nonwoven fabric and that of commonly used disposable nonwoven fabrics in aerobic Captina silt loam soil. Textile Research Journal. DOI 10.1177/0040517514551468. Motschenbacher, J.M., K.R. Brye, M.M. Anders, E.E. Gbur, N.A. Slaton and M.A. Evans-White (2015). Daily soil surface CO2 flux during non-flooded periods in flood irrigated rice rotations. Agronomy for Sustainable Development, 35, 771-782. McMullen, R.L., K.R. Brye, A.L. Daigh, D.M. Miller, E.E. Gbur, A.L. Pirain, M.A. Evans-White and R.E. Mason (2014). Long term leachate water quality trends from a broiler litter amended Udult in the Ozark Highlands. Vadose Zone. DOI 10.2136/vzj2014.06.0064. Barriga, P.A., C.F. Dormann, E.E. Gbur and C.L. Sagers (2015). Community structure and ecological specialization in plant-ant interactions. Journal of Tropical Ecology. DOI 10.1017/S0266467415000139. Luján-Rhenals, D.E., R. Morawicki, E. Gbur and S.C. Ricke (2015). Fermentation of soybean meal hydrolyzates with Saccharomyces cerevisiae and Zymomonasmobilis for ethanol production. Journal of Food Science, 80, E1512-E1518. Olbricht G.R., Samaranayake V.A., Injamuri S., Wang L., Fiebelman C., and Thimgan M.S. (2014). Modeling Sleep and Wake Bouts in Drosophila melanogaster. Proceedings of the Conference on Annual Applied Statistics in Agriculture. ed. W. Song. Manhattan, KS: Kansas State University. 58-70. Dunn, Bruce L., Carla Goad (2015) Effect of Foliar Nitrogen and Optical Sensor Sampling Method and Location for Determining Ornamental Cabbage Fertility Status. 74 HortScience, 50(1), 74-77. Dunn, B.L., A. Shrestha, and C. Goad (2015). Use of Non-Destructive Sensors to Quantify Ornamental Kale Nitrogen Status. Journal of Plant Nutrition. DOI: 10.1080/01904167.2015.1069342. Al Sharqi, S., N.T. Dunford, C. Goad (2014). Evaluation of Water Degumming for Wheat Germ Oil. Transactions of the ASABE, 57(6): 1707-1715. DOI 10.13031/trans.57.10617. Gifford, C.A., K.A. Branham, J.O. Ellison, B.I. Gomez, C.O. Lemley, G.G. Hart, C.R. Krehbiel, B.C. Bernhard, C.L. Maxwell, C.L. Goad, D.M. Hallford, J.A. Hernandez Gifford (2014). Effect of anabolic implants on adrenal cortisol synthesis in feedlot beef cattle implanted early or late in the finishing phase. Physiology & Behavior, DOI: 10.1016/j.physbeh.2014.10.025. Clarke, J. and Clarke, B. (2014). Deconvolution of gene expression from mixed samples. STAT, 3 (1), 313-325. Clarke, B., Valdes, C., Dobra, A. and Clarke, J. (2015) A Bayes testing approach to metagenomic profiling in bacteria. Statistics and Its Interface, 8 (2): 173-185.

Impact Statements

(1) NCCC-170 fosters research to identify and develop statistical methodology applicable to agricultural research and provides a forum for sharing and educating both statisticians and subject-matter scientists in the agricultural, environmental and natural sciences. As a result, all members are able to provide more effective assistance to agricultural researchers addressing national research priorities than they would be without NCCC-170.
(2) Project members provide continuing education for scientists in agriculturally related disciplines in modern statistical analyses of designed experiments in general and specifically in the areas of generalized linear mixed models, statistical techniques in genomics applications, and meta-analysis. Examples of such activities and their immediate impacts for the current reporting period are listed in the Accomplishments section of this report.
(3) Project members collaborate in research projects with scientists in agricultural related disciplines to develop and use proper statistical design and analysis methodology well beyond standard textbook applications. These efforts often result in competitive grant participation and refereed publications. Each of these impacts is listed in the Accomplishments and Publications sections of this report.

Date of Annual Report: 08/04/2016

Report Information

Annual Meeting Dates: 06/23/2016 - 06/24/2016
Period the Report Covers: 10/01/2015 - 09/30/2016

Participants

Nora Bello (KS), Bruce Craig (IN, Admin.), Sara Duke (USDA-ARS), Susan Durham (UT), Ed Gbur (AR), Carla Goad (OK), Alex Lipka (IL), Larry Madden (OH), Bahram Momen (MD), Walt Stroup (NE), Mark West (USDA-ARS), Kathy Yeater (USDA-ARS), William Bowerman (MD), Elizabeth Claassen (SAS), Nick Keuler (WI), Matt Kramer (USDA-ARS), Yu Mo (MD), Dan Nettleton (IA), Neil Paton (Cargill), Ellen Paparozzi (NE), Perla Reyes (KS), Bryan Vinyard (USDA-ARS)

Brief Summary of Minutes

Technical program: The meeting began at 8:30 a.m. on Thursday, June 23, 2016 with opening remarks by Dr. William Bowerman, Chair of the Dept. of Environmental Science and Technology at the University of Maryland. Presentations ended at approximately 5:00 p.m. The technical program consisted of the following presentations:

Elizabeth Claassen JMP Analytical Development -- Predictive Modeling in an n < p World

Sara Duke USDA ARS -- Where is Research Going: Long Term Agro-Ecosystem Research Initiativ

W. Bowerman, H. Pittman, L. Fuentes Univ. of Maryland, K. F. Leith, M. C. Wierda, Clemson Univ., F. Bourland Univ. of Arkansas, D. Jones Cotton Inc, W. Bridges Clemson Univ. -- Evaluating and Improving Eagle Monitoring and Cotton Variety Testing

Yu Mo, Bahram Momen, Michael S. Kearney Univ. of Maryland -- Quantify remote sensing phenology using a nonlinear mixed model

N. M. Bello, A. Jager, E. Cha, M. Sanderson, N. Cernicchiaro, D. Renter Kansas State Univ. -- Rethinking Causal Inference from Observational Data: a structural equation modeling approach

Walt Stroup, Univ. of Nebraska, Matt Kramer USDA-ARS -- P-value Controversy – in preparation for JSM

Business meeting: The business meeting began at about 9:00 a.m. on Friday, June 24, 2016. Ed Gbur presided. The following items were discussed:

(1) The organizers were thanked for a productive and enjoyable meeting: Bahram Momen for local arrangements and Kathy Yeater for the technical program. Ed Gbur was thanked for his work as chair and webmaster of the committee.

(2) Presenters who wish to post their talk on the project website should send a pdf of the talk to Ed Gbur (egbur@uark.edu).

(3) The annual report and impact statement are due shortly after the annual meeting. Participants need to send Ed Gbur (egbur@uark.edu) accountings of all activities (workshops, papers, presentations, grants, awards, teaching related items, etc.) from October 1, 2015 to September 30, 2016 (or since last year’s report) that are related to or inspired by their participation in NCCC-170 as soon as possible.

(4) The current NCCC-170 project is scheduled to end on September 30, 2016. The project renewal has been approved for October 1, 2016 through September 30, 2021.

(5) The 2017 meeting will be held in Elk River, Minnesota at the Cargill Experiment Station with Neil Paton as the local host. Tentative dates are June 22-23, 2017. Nora Bello will serve as program chair. The 2018 meeting is tentatively planned for Idaho and for Arkansas in 2019. Illinois will serve as a backup location if needed and otherwise as a tentative site for 2020.

(6) The group reviewed progress toward objectives of the current project.

(7) The group reviewed objectives of the new project. The new project retains four objectives from the current project and adds an objective identified during the 2015 meeting to provide continuing education and statistical support to the scientific community in the review and editorial process. The “Expected Outcomes and Impacts” section identifies “the sort of things we should be thinking about.”

(8) With a new project comes a new participant list. Several persons who participate in the annual meetings are not official participants in the project, and not everyone from the current project is listed as a participant in the new project. The same state and institution can be represented by multiple people, only one of whom is designated as a voting member. Ed encouraged people to join if they intend to participate.

(9) Elizabeth Claassen announced the JMP Discovery Summit, to be held at SAS headquarters in Cary, NC on September 19-23, 2016.

The business meeting adjourned at approximately 9:40 a.m. After break, the group reconvened for a discussion on how to train and advance applied statisticians in professional and academic settings. We forgot to take the annual group photograph for the project web site.

Accomplishments

Accomplishments: Statisticians who consult and do research in an Agricultural Experiment Station environment enable land grant institutions to perform their agricultural research missions more effectively and efficiently than would otherwise be possible. However, most stations have at most one or two professional statisticians who are not, and cannot be expected to be, experts in every area of statistics. This multi-state committee brings together statisticians to work cooperatively to determine the best current approaches to common statistical problems and to help guide future directions of sound statistical practice. In addition to producing group outputs such as workshops, the committee serves as a resource for its members and a sounding board for new ideas in their applied statistical research. As a result, all members are able to provide more effective assistance to agricultural researchers addressing national research priorities than they would without NCCC-170.  Outputs:  Workshops: George Milliken taught a short course entitled “Experimental Design and Analysis of Mixed Models” at the FDA Center for Veterinary Medicine in Washington D.C., September 30-October 1, 2015.  Julia Sharp presented a webinar module entitled “Introductory Statistics” to the American Dairy Science Association’s Fatty Acid Form in November 2016. She and Billy Bridges presented a webinar module entitled “What is Meta-analysis” to the same group in April 2016.  Larry Madden presented a one day workshop entitled “Meta-analysis for evidence based agriculture” at the ASA-CSSA-SSSA International Meetings in Minneapolis, MN. November 2015. Kathy Yeater presented a workshop entitled “So you want to do a: RNAseq experiment, Differential Gene Expression Analysis” at the USDA Meat Animal Research Center, Clay Center, NE. August 16, 2016.  Larry Madden presented a one day workshop entitled “Generalized linear mixed models for data analysis in plant pathology” at the Annual Meeting of the American Phytopathological Society. July 2016.  Walt Stroup presented the American Statistical Association (ASA) Traveling Course entitled “Introduction to Generalized Linear Mixed Models using SAS” twice in October, 2015, one in Dallas, TX and one in San Antonio, TX; two courses in November 2015, one in Indianapolis, IN, one in Cincinnati, OH. Each was to local ASA Chapter   Presentations: Lipka, A.E. Exploration, embellishment, and implementation of statistical approaches for genome-wide association studies and genomic selection. Corn Breeding Research Meeting, Jacksonville, FL March 17, 2016. (Invited)  Lipka, AE, AH Chen, W Metcalf and LS Mainzer Introducing elements of high performance computing and two-way epistasis into genome-wide association studies with stepwise model selection. Plant and Animal Genome Maize Workshop, San Diego, CA. January 9, 2016. (Invited)  Yeater, K. Multivariate Analysis: Tools for Understanding Complex Systems. Agroecosystem Management and Grain, Forage, and Bioenergy Research Units, Lincoln, NE (April 26, 2016), U.S. Meat Animal Research Center, Clay Center, NE (April 28, 2016), and Center for Grain and Animal Health Research, Manhattan, KS (May 2, 2016).  Villena, O.C, E. Landa, B. Momen, P.T. Leisnham, and J.H. Sullivan JH. The effects of UV radiation on tire deterioration and pollutant release on competition between Aedes albopictus and Culex pipiens mosquitoes. 2015 Ecological Society of America Annual Meeting. Baltimore, MD.  Zhou, L. and R.J. Tempelman. 2015.Strategies for estimating hyperparameters based on single-step Bayesian models (Abstract: Journal of Dairy Science 98 (Suppl. 2): 579).  Chen, C., J.P. Steibel, and R.J. Tempelman. 2015.Reassessing hierarchical Bayesian genome-wide association analyses (Abstract: Journal of Dairy Science 98(Suppl. 2): 580).  Lu, Y., M.J. Vandehaar, D.M. Spurlock, K.A. Weigel, L.E. Armentano, C.R. Staples, E.E. Connor, Z. Wang, M. Coffey, R. Veerkamp, Y deHaas, N.M. Bello, and R.J. Tempelman. 2015. Hierarchical Bayesian inference on genetic and non-genetic components of partial efficiencies determining feed efficiency in dairy cattle (Abstract: Journal of Dairy Science 98(Suppl. 2): 573).  Chen, C., J.P. Steibel, and R.J. Tempelman. 2016. Exploring sparsities of genome wide association analyses based on different sparsities of prior specifications. 5th International Conference on Quantitative Genetics, Madison, WI, USA, June 12-17, 2016 (Poster).  Lu, Y., M.J. Vandehaar, D.M. Spurlock, K.A. Weigel, L.E. Armentano, C.R. Staples, E.E. Connor, Z. Wang, M. Coffey, R.F. Veerkamp, Y deHaas, M.D. Hanigan, and R.J. Tempelman. 2016.Genome-wide association analyses based on alternative strategies for modeling feed efficiency. 5th International Conference on Quantitative Genetics, Madison, WI, June 12-17, 2016 (Poster).  Lu, Y., M.J. Vandehaar, D.M. Spurlock, K.A. Weigel, L.E. Armentano, C.R. Staples, E.E. Connor, Z. Wang, M.D. Hanigan, and R.J. Tempelman. 2016. Modeling genotype by environment interaction over multiple covariates for feed efficiency in dairy cattle. Poster presented at the 5th International Conference on Quantitative Genetics, Madison, WI, June 12-17, 2016.  Johnson, L., J. Alsdurf, N.M. Bello, A. Smith and M. Knapp. Phenotypic variation of the dominant prairie grass Andropogon gerardii and its predicted response to climate change across Midwest grasslands. 2016 Botany Conference. Savannah, GA. July 30 - August 3, 2016.  Johnson, L., M. Galliart, N.M. Bello, M.J. Polland, P. St. Amand, M. Knapp, B.R. Maricle, S.G. Baer and D. Gibson. Adaptive ecotypic variation and genetic divergence of an ecologically dominant prairie grass across the Great Plains precipitation gradient. 2016 Botany Conference. Savannah, GA. July 30 - August 3, 2016.  Galliart, M., P. St. Amand, J. Polland, N.M. Bello, M. Knapp, S.G. Baer, D. Gibson, B.R. Maricle and L. Johnson. Adaptive ecotypic variation and genetic divergence of a widespread grass, big bluestem, across a Great Plains climate gradient. 2016 American Genetic Association Annual Meeting. Asilomar, CA. July 14-17, 2016.  Ou, Z., R.J. Tempelman, J.P. Steibel, C.W. Ernst, R.O. Bates, C. Chen and N.M. Bello. Heteroskedastic extensions for genome-wide association studies. Joint Annual Meetings of the American Society of Animal Sciences and the American Dairy Science Association. Salt Lake City, UT. July 19-23, 2016.  Craig, B.A. Disk Diffusion Breakpoint Determination Using an Errors-in-Variables Model Approach, University of Texas Medical Branch at Galveston, April 2016.  Craig, B.A., Chen, N., and Wijayawardana, S.R. Assessing Inter-rater Agreement of Immuno-histochemistry Scores, University of Texas Medical Branch at Galveston, April 2016.  Sanchez, DL, Hu S, V AE, Lipka AE, and Lubberstedt T. A comparison between GBS and SNP chip marker systems in molecular profiling of doubled haploid exotic introgression lines in maize. 58th Annual Maize Meeting, Jacksonville, FL; March 17-20, 2016.  Hu, S, Wang Cuiling, Sanchez DL, Lipka AE, Liu P, Yin Y, Xu M, and Lubberstedt T. Brassinosteroid and Gibberellin control of plant height in a phenotypic selected introgression library in maize. 58th Annual Maize Meeting, Jacksonville, FL; March 17-20, 2016.  Chen, AH, and Lipka AE. Genome-Wide Association Study (GWAS) Using Targeted Marker Subsets to Account for Population Structure and Relatedness Identifies More Genomic Signals Associated with Polygenic Traits in Maize (Zea mays L.). ASA, CSSA, SSSA International Annual Meetings, Minneapolis, MN; November 15-18, 2015.  Kramer M and Font E. Strategies for reducing control group size in experiments using live animals. Conference on Applied Statistics in Agriculture, April 2016. Kansas State Univ., Manhattan KS.  Kramer M. P-value Controversy. Annual Joint Statistics Meetings, Aug 2016.  Duke, S. Practical Statistics: Real Data in Agriculture. Symposium of Practical Statistics, University of the Incarnate Word in San Antonio, TX, January 15, 2016.  Other project related activities: Kathy Yeater is co-editing a book for ACSESS (ASA-CSSA-SSSA Publications) currently titled Applied statistics in agricultural, biological, and environmental sciences. All chapters are submitted and under final review. It is anticipated that final editing will commence near the end of FY16 and full publication will occur in early FY17. Current members and/or recent attendees of NCCC-170 that are chapter authors include: Philip Dixon, Kevin McCarter, Walt Stroup, Maria Villamil, and Kathy Yeater.  Dan Nettleton and Rob Tempelman were guest editors of a special issue on “Statistical Genomics and Transcriptomics in Agriculture” for the December, 2015 issue of Journal of Agricultural, Biological, and Environmental Statistics (http://link.springer.com/journal/13253/20/4/page/1).  Nora Bello is a co-PI on a USDA AFRI grant in the Foundational Program A1221 entitled Risk Management Strategies to Reduce the Impacts of Bovine Respiratory Disease Complex in Commercial Feeder Cattle". PI is David Renter, College of Veterinary Medicine, Kansas State University. The grant award was $489,466 for 2015-2019. The grant was ranked the number 1 proposal by its review panel.  Walt Stroup participated in a Roundtable Luncheon entitled On P-values at the 2015 Joint Statistics Meetings (JSM) to consider an American Statistical Association (ASA) policy of use of P-values in research publications. He was also an invited participant on a panel discussion entitled With Great Power Comes Great Responsibility: Harnessing the Extraordinary Power of Statistics on this topic at JSM 2016. ASA has since published a policy statement on the topic.  Larry Madden maintains a website (<a href="http://www.oardc.ohio-state.edu/aps-statsworkshop/default.htm">http://www.oardc.ohio-state.edu/aps-statsworkshop/default.htm</a>) with statistical software code (SAS) and PowerPoint presentations on a range of data-analytic subjects. The material is based heavily on previously presented workshops.  Bruce Craig directed an Undergraduate Research Experience (URE) Purdue-Columbia during the Summer and Fall 2015 for Yinneth Lorena Leon Velasco on the topic of Applications of linear and nonlinear mixed models: a) Semantic Richness and Word Learning in Children with Autism Spectrum Disorder, and b) Feed Intakes of Sows Lactation. He also directed a URE during the Fall 2015 and Spring 2016 for Patrick Gallagher on the topic of Mixed model analysis of paired competition studies (entomology).  Bruce Craig hosted of Olusanya Olubusoye, LISA 20/20 Fellow, from the University of Ibadan, Nigeria, in March 2016 during his visit to the Purdue Statistics Department’s consulting service.  Bruce Craig participated in a panel discussion entitled The Non-Technical Skills Needed to Be an Effective Statistical Consultant at the 2015 Joint Statistical Meetings in Seattle, WA. Other panelists were C. Holloman, M. Clayton and M. Wiest.  Bruce Craig participated in a panel discussion entitled Teaching a Statistical Consulting Course at the 2016 Joint Statistical Meetings in Chicago. Other panelists were S. Hurwitz, P.D. Sampson, H.S. Smith, and M. Wiest.  Bahram Momen reported that NCCC-170 activities have helped him in his consulting and mentoring of many graduate students and faculty members in designing their research and analyzing the data.  Sara Duke is a co-PI on a USDA-NIFA grant with the University of the Incarnate Word in San Antonio, TX entitled Strengthening the Agricultural Statistics Pipeline at Hispanic-Serving Institutions. The grant was funded for September 2015 to August 2019.

Publications

Bryant, R.J., K.M. Yeater, and A.M. McClung (2015). Effect of nitrogen rate and the environment on physicochemical properties of selected high amylose rice cultivars. Cereal Chemistry. 92(6):604-610. Eizenga, G.C., J.D. Edwards, K.M. Yeater, S.R. McCouch, and A.M. McClung (2016). Transgressive variation for yield components measured throughout the growth cycle of Jefferson rice (Oryza sativa) X O. rufipogon introgression lines. Crop Sci. 56. In press. Funk, P.A., K. Elsayed, K.M. Yeater, G.A. Holt, and D.P. Whitelock (2015). Could cyclone performance improve with reduced inlet velocity? J Powder Technology 280:211-218. Yeater, K.M., and M.B. Villamil (2016). Multivariate Methods for Agricultural Research. In Applied statistics in agricultural, biological, and environmental sciences. B. Glaz et al (ed.). ASA, CSSA, and SSSA, Madison, WI. In press. Neuman-Lee, L.A., H.B. Fokidis, A.R. Spence, M. Van der Walt, G.D. Smith, S. Durham, and S.S. French (2015). Food restriction and chronic stress alter energy use and affect immunity in an infrequent feeder. Functional Ecology. In press. Ranglack, D.H., S. Durham, and J.T. du Toit (2015). Competition on the range: science vs. perception in a bison-cattle conflict in the western USA. Journal of Applied Ecology 52: 467-474. Tepedino, V.J., S. Durham, S.A. Cameron, and K. Goodell (2015). Documenting bee decline or squandering scarce resources. Conservation Biology 29: 280-282. Momen B, Behling SJ, Sullivan JH, Lawrence GB. (2015). Photosynthetic and growth response of sugar maple (Acer saccharum, Marsh) mature trees and seedlings to calcium, magnesium, and nitrogen additions in the Catskill Mountains, NY, USA. PLoS ONE, 10:1-14. DOI:10.1371/journal.pone.0136148. Khan S, Jackson RT, Momen B. (2016). Impact of acculturation and its factors on metabolic syndrome on South Asian American adults in community health centers. Journal of Public Health. DOI: 10.1007/ s10389-016-0726-7. Khan S, Jackson RT, Momen B. (2016). The relationship between diet quality and acculturation of immigrated South Asian American adults and their association with metabolic syndrome. PLoS ONE. In press. Cartwright J, Dzantor EK, Momen B. (2016). Soil microbial community profiles and diversity in limestone cedar glades. CATENA. In press. Olsen VBK, Momen B, Langsdale S, Galloway G, Link E, Brubaker K, Matthias R, Hill R. (2016). An approach for improving flood risk communication using realistic interactive visualization. Journal of Flood Risk Assessment. In Press.  Hu, X., Edwards, S., Madden, L.V., and Xu, X. (2015). Combining models is more likely to give better predictions than single models. Phytopathology 105: 1174-1182.  Willyerd, K. T., Bradley, C. A., Chapara, V., Conley, S. P., Esker, P. D., Madden, L. V., Wise, K. A., and Paul, P. A. (2015). Revisiting fungicide-based management guidelines for leaf blotch diseases in soft red winter wheat. Plant Disease 99: 1434-1444.  Madden, L.V., Shah, D.A., and Esker, P.D. (2015). Does the P value have a future in plant pathology? Phytopathology 105: 1400-1407.    Madden, L.V., Piepho, H.-P., and Paul, P.A. (2016). Statistical models and methods for network meta-analysis. Phytopathology 106: 792-806.  Yang, W., C. Chen, J.P. Steibel, C.W. Ernst, R.O. Bates, L. Zhou, and R.J. Tempelman (2015). A comparison of alternative random regression and reaction norm models for whole genome predictions. Journal of Animal Science 93: 2678-2692.  Lu, Y., M.J. Vandehaar, D.M. Spurlock, K.A. Weigel, L.E. Armentano, C.R. Staples, E.E. Connor, Z. Wang, N.M. Bello, and R.J. Tempelman (2015). An alternative approach to modeling genetic merit of feed efficiency in dairy cattle. Journal of Dairy Science 98:6535-6551.  Chen, C. and R.J. Tempelman (2015). An integrated approach to empirical Bayesian whole genome prediction modeling. Journal of Agricultural, Biological, and Environmental Statistics 20:491-511.  Tempelman R.J. (2015). Statistical and computational challenges in whole genome prediction and genome wide association analyses for plant and animal breeding. Journal of Agricultural, Biological, and Environmental Statistics 20:442-466.  Manzanilla-Pech, C.I.V., R.F. Veerkamp, R.J. Tempelman, M.L. van Pelt, K.A. Wiegel, M.J. Vandehaar, T.J. Lawlor, D.M. Spurlock, L.E. Armentano, C.R. Staples, M. Hanigan, and Y. deHaas (2016). Correlations between feed intake-related traits and conformation traits in two separate dairy populations: the Netherlands and United States. Journal of Dairy Science 99:443-457.  Ou, Z., R.J. Tempelman, J.P. Steibel, C.W. Ernst, R.O. Bates, and N.M. Bello (2016).Genomic prediction accounting for residual heteroskedascity. Genes, Genomes, Genetics 6(1):1-13.  Mota, R.R., R.J. Tempelman, P.S. Lopes, I. Aguilar, F.F. Silva, and F.F. Cardoso (2016).Genotype by environment interaction for tick resistance of Hereford and Braford beef cattle using reaction norm models. Genetics, Selection Evolution 48:3  Vandehaar, M.J., L.E. Armentano, K. Weigel, D.M. Spurlock, R.J. Tempelman, and R.F. Veerkamp (2016). Harnessing the genetics of the modern dairy cow to continue improvements in feed efficiency. Journal of Dairy Science 99:4941-4954.  Mota, R.R., P.S. Lopes,R.J. Tempelman, F.F. Silva, I. Aguilar, C.C.G. Gomes, and F.F. Cardoso (2016). Genome-enabled prediction for tick resistance in Hereford and Braford beef cattle via reaction norm models. Journal of Animal Science 94:1834-1843.  DePalma, G., Turnidge, J, and Craig BA (2016). Determination of disk diffusion susceptibility testing interpretive criteria using model-based analysis: development and implementation. Diagnostic Microbiology and Infectious Disease. In press  Dhillon, J, Craig, BA, Leidy, HJ, Amankwaah, AF, Osei-BoadiAnguah, K, Jacobs, A, Jones, BL, Jones, JB, Keeler, CL, Keller, CEM, McCrory, MA, Rivera, RL, Slebodnik, M, Mattes, RD, and Tucker, RM (2016). The effect of increased protein intake on fullness: A meta-analysis and its limitations. Journal of the Academy of Nutrition and Dietetics. In press.  Dhawan, D, Paoloni, M, Shukradas, S, Choudhury, DR, Craig, BA, Ramos-Vara, JA, Hahn, N, Bonney, PL, Khanna, C and Knapp, D. (2015). Comparative gene expression analyses identify luminal and basal subtypes of canine invasive urothelial carcinoma that mimic patterns in human invasive bladder cancer. PLoS ONE 10(9): e0136688.  Running CA, Craig, BA, Mattes, RD (2015). Oleogustus: The unique taste of fat, Chemical Senses 40(7), 501–516.  Smartt, A.D., K.R. Brye, C.W. Rogers, R.J. Norman, E.E. Gbur, J.T. Hardke and T.L. Roberts (2015). Chamber size effects on methane emissions from rice production. Open Journal of Soil Science 5, 227-235.  Brye, K., M. Helton, H. Liechty, M. Blazier, C. West, E. Gbur, M. Savin, and E. Mason (2015). Carbon dioxide emissions from switchgrass and cottonwood grown as bioenergy crops in the Lower Mississippi River Alluvial Valley. Biomass and Bioenergy. 83, 383-392.  Norman, C.R., K.R. Brye, E.E. Gbur, P. Chen and J. Rupe (2015). Long term effects of alternative residue management practices on soil water retention in a wheat-soybean, double crop system in Eastern Arkansas. Open Journal of Soil Science 5, 199-209.  Salmeron, M., E. Gbur, F. Bourland, N. Buehring, L. Earnest, F. Fritschi, B. Golden, D. Hathcoat, J. Lofton, A. Thompson, T. Miller, C. Neely, J.G. Shannon, T. Udeigwe, D. Verbree, E. Vories, W. Wiebold and L. Purcell (2016). Yield response to planting date among soybean maturity groups for irrigated production in the U.S. Midsouth. Crop Science 56, 747-759. DOI:10.2135/cropsci2015.07.0466.  Singh, V., N. Burgos, S. Singh, S. Abugho, L. Earnest, E. Gbur and R. Scott (2016). Herbicide and winter flood treatments for controlling volunteer rice off-season. Crop Protection 79, 87-96.  Rogers, C.W., R.J. Norman, T.J. Siebenmorgen, B.C. Grigg, J.T. Hardke, K.R. Brye and E.E. Gbur (2016). Nitrogen, harvest moisture, and cultivar selection effects on rough rice and milling yields. Agronomy Journal 108, 1-9.  Brye, K.R., R.L. McMullen, M.L. Silveira, J.M.D. Motschenbacher, S.F. Smith, E.E. Gbur and M.L. Helton (2016). Environmental controls on soil respiration across a southern US climate gradient: A meta-analysis. Geoderma Regional 7, 110-119.  Smartt, A.D., K.R. Brye, C.W. Rogers, R.J. Norman, E.E. Gbur, J.T. Hardke and T.L. Roberts (2016). Characterization of methane emissions from rice production on a clay soil in Arkansas. Soil Science 181, 57-67.  Smartt, A.D., K.R. Brye, C.W. Rogers, R.J. Norman, E.E. Gbur, J.T. Hardke and T.L. Roberts (2016). Previous crop and cultivar effects on methane emissions from drill-seeded, delayed-flood rice grown on a clay soil. Applied and Environmental Soil Science. DX.DOI.ORG/10.1.1155/2016/9542361. 13 pp.  Hill, Z.T., J.K. Norsworthy, L.T. Barber, T.L. Roberts and E.E. Gbur (2016). Assessing the potential for Fluridone carryover to six crops rotated with cotton. Weed Technology 30(2), 346-354.  Akehi, K, Long, B, Warren, AJ, Goad, C. (2016). Ankle joint angle and lower leg musculotendinous unit responses to cryotherapy. Journal of Strength and Conditioning Research. In press.  Dunn, B.L., T. Cavins and C. Goad (2016). Effect of applying calcium chloride and three milk supplements to poinsettia ‘Prestige Red’. Journal of Plant Nutrition 39(1), 45-50. <a href="http://dx.doi.org/10.1080/01904167.2015.1086791">http://dx.doi.org/10.1080/01904167.2015.1086791</a>  Al Sharqi, S., N. T. Dunford and C. Goad (2015). Acid and enzymatic degumming of wheat germ oil. Transactions of the ASABE 58(6): 1861-1866 DOI 10.13031/trans.58.11031.  Al Sharqi, S., N. T. Dunford and C. Goad (2015) Enzymatic wheat germ oil degumming, Transactions of the ASABE 58(6): 1867-1872. DOI 10.13031/trans.58.11032.  Basyouni, R., B. L. Dunn and Carla Goad (2015). Use of Nondestructive Sensors to Assess Nitrogen Status in Potted Poinsettia (Euphorbia pulcherrima L. (Willd. Ex Klotzsch)) Production. Scientia Horticulturae 192: 47–53. Dunn, B.L. and Carla Goad (2015). Effect of Foliar Nitrogen and Optical Sensor Sampling Method and Location for Determining Ornamental Cabbage Fertility Status. 74 Hortscience 50(1). Dunn, B.L., A. Shrestha and C. Goad (2015). Use of Non-Destructive Sensors to Quantify Ornamental Kale Nitrogen Status. J. Plant Nutrition. DOI: 10.1080/01904167.2015.1069342 Raithelgs, S., L. Johnson, M. Galliartgs, S. Brown, J. Shelton, N. Herndon and N. M. Bello (2016). Inferential considerations for low-count RNA-seq transcripts: a case study of dominant prairie grass Andropogon gerardii. BMC Genomics 17(1):140. doi: 10.1186/s12864-016-2442-7 Goncalvesgs, M.A.D., N.M. Bello, S.S. Dritz, M.D. Tokach, J.M. DeRouchey, J.C. Woodworth and R.D. Goodband (2016). An update on modeling dose-response relationships: accounting for correlated data structures and heterogeneous variances in linear and non-linear mixed models. Journal of Animal Science 94(5): 1940-1950. doi:10.2527/jas.2015-0106. Kivettgs, J.M., R.A. Cloyd and N.M. Bello (2016). Evaluation of entomopathogenic fungi against Western flower thrips (Thysanoptera: thripidae) under laboratory conditions. Journal of Entomological Science. In press. Goncalvesgs, M.A.D., K.M. Gourley, S.S. Dritz, M.D. Tokach, N.M. Bello, J.M. DeRouchey, J.C. Woodworth and R.D. Goodband (2016). Effects of amino acids and energy intake during late gestation of high-performing gilts and sows on litter and reproductive performance under commercial conditions. Journal of Animal Science. doi: 10.2527/jas.2015-0087 Martings, E.C., K. Gido, N.M. Bello, W.K. Dodds and A. Veach (2016). Increasing fish taxonomic and functional richness affects ecosystem properties of small headwater prairie streams. Freshwater Biology DOI: 10.1111/fwb.12752. Becker, M.W., R.P. Sundargs, N.M. Bello, R. Alahabi, L. Weatherspoon and L. Bix (2016) Assessing attentional prioritization of front-of-pack nutritional labels using change detection. Journal of Applied Ergonomics 54:90-99. doi:10.1016/j.apergo.2015.11.014. Bix, L., R.P. Sundargs, N.M. Bello, C. Peltier, L. Weatherspoon and M. Becker (2015). To see or not to see: Do front of pack nutrition labels affect attention to overall nutritional information. PLoS ONE 10(10): e0139732. doi: 10.1371/journal.pone.0139732. Becker, M., N.M. Bello, R. Sundargs, C. Peltiergs and L. Bix (2015). Front of package labels enhance attention to nutritional information in novel and commercial brands. Food Policy 56:76-86. doi: 10.1016/j.foodpol.2015.08.001.  Goncalvesgs, M.A.D., S. Nitikanchanapd, M.D. Tokach, S.S. Dritz, N.M. Bello, R.D. Goodband, J. Usry, K.J. Touchette, J.M. DeRouchey and J.C. Woodworth (2015) Effect of standardized ileal digestible tryptophan:lysine ratio on growth performance of nursery pigs. Journal of Animal Science 93(8): 3909-3918  Kivettgs, J.M., R.A. Cloyd and N.M. Bello (2015). Insecticide rotation programs with entomopathogenic organisms for suppression of Western flower thrips (Thysanoptera thripidae) populations under greenhouse conditions. Journal of Economic Entomology 108(4): 1936-1946. DOI: 10.1093/jee/tov155.  Gardhouserd, S.M., D. Eshar, N.M. Bello and D. Mason (2015). Venous blood gas analytes during isoflurane anesthesia in black-tailed prairie dogs (Cynomys ludovicianus). Journal of the American Veterinary Medicine Association 247(4): 404-408.  DeHenaugs, C., M.W. Becker, N.M. Bello, S. Liu and L. Bix (2015). Tallman lettering as a strategy for differentiation in look-alike sound-alike drug names: the role of familiarity in differentiating drug dopplegangers Journal of Applied Ergonomics 52:77-84.  Cullgs, C.A., D.G. Renter, N.M. Bello and A.H. Babcock (2015). Performance and carcass characteristics of commercial feedlot cattle from a study on vaccine and direct-fed microbial effects on E.coli O157:H7 fecal shedding. Journal of Animal Science 93: 3144-3151.  Johnson, L., J.T. Olsenug, H. Tetreaultgs, R.K. Goad, M.M. Mendola, A. DeLaCruz, H. Bryant, T. Morgan, M. Knapp, N.M. Bello, S. Baer and B. Maricle (2015). Intraspecific variation of a dominant grass and local adaptation in reciprocal garden communities along a US Great Plains’ precipitation gradient: Implications for grassland restoration with climate change. Evolutionary Applications 8:705-723. DOI: 10.1111/eva.12281.  Chen AH and Lipka AE. (2016) The Use of Targeted Marker Subsets to Account for Population Structure and Relatedness in Genome-Wide Association Studies of Maize (Zea mays L.). G3: Genes, Genomes, Genetics. In press.  Hagler JR, Erica E. Tassone EE, Coffelt TA, and Lipka AE. (2016) Host plant preference of Lygus hesperus exposed to three desert-adapted industrial crops. Industrial Crops and Products. In press.  Jenkins WD, Lipka AE, Fogleman A, Delfino KR, Malhi RS, and Hendricks BD (2016). Variance in disease risk: rural populations and genetic diversity. Genome. In press.  Arruda MP, Lipka AE, Brown PJ, Krill AM, Thurber C, Brown-Guedira G, Dong Y, Foresman J, and Kolb FL (2016). Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum). Molecular Breeding 36(7): 1-11.  Gonzalez-Jorge S, Mehrshahi P, Magallanes-Lundback M, Lipka AE, Angelovici R, Gore MA, and DellaPenna D (2016). ZEAXANTHIN EPOXIDASE activity potentiates carotenoid degradation in maturing Arabidopsis seed. Plant Physiology: pp-00604.  Chang HX, Lipka AE, Domier L, and Hartman G (2016). Characterization of Disease Resistance Loci in the USDA Soybean Germplasm Collection using Genome-wide Associations. Phytopathology. In press.  Pauli D, Andrade-Sanchez P, Carmo-Silva AE, Gazave E, French AN, Heun J, Hunsaker DJ, Lipka AE, Setter TL, Strand RJ, Thorp KR, Wang S, White JW, and Gore MA (2016). Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton”. G3: Genes, Genomes, Genetics 6(4): 865-879.  Tang Y, Liu X, Wang J, Li M, Wang Q, Tian F, Su Z, Pan Y, Liu D, Lipka AE, Buckler ES, and Zhang Z (2016). GAPIT Version 2: Enhanced Integrated Tool for Genomic Association and Prediction. The Plant Genome. In press.  Rincker K, Lipka AE, and Diers BW (2016). Genome-wide association study of brown stem rot resistance in soybean across multiple populations. The Plant Genome. In press.  Chang HX, Brown PJ, Lipka AE, Domier LL, and Hartman GL (2016). Genome-wide association and genomic prediction identifies associated loci and predicts the sensitivity of Tobacco ringspot virus in soybean plant introductions. BMC Genomics 17(1): 1.  Tassone EE, Lipka AE, Tomasi P, Lohrey GT, Qian W, Dyer JM, Gore MA, and Jenks MA (2016). Chemical variation for leaf cuticular waxes and their levels revealed in a diverse panel of Brassica napus L. Industrial Crops and Products 79: 77-83.  Ilut DC, Lipka AE, Jeong N, Bae DN, Kim DH, Kim JH, Redekar N, Yang K, Park W, Kang ST, Kim N, Moon JK, Saghai Maroof MAS, Gore MA, and Jeong SC (2015). Identification of haplotypes at the Rsv4 genomic region in soybean associated with durable resistance to soybean mosaic virus. Theoretical and Applied Genetics: 1-16. Arruda MP, Brown PJ, Lipka AE, Krill AM, Thurber C, and Kolb FL (2015). Genomic selection for predicting fusarium head blight resistance in a wheat breeding program. The Plant Genome 8(3). Fatima T, AP Sobolev, JR Teasdale, M Kramer, J Bunce, AK Handa, AK Mattoo. (2016). Fruit metabolite networks in engineered and non-engineered tomato genotypes reveal fluidity in a hormone and agroecosystem specific manner. Metabolomics 12:103 (15 pp), doi: 10.1007/s11306-016-1037-2. Poffenbarger HJ, Mirsky SB, Weil RR, Kramer M, Spargo JT, Cavigelli MA. (2015). Legume proportion, poultry litter, and tillage effects on cover crop decomposition. Agronomy Journal 107(6):2083-2096. Poffenbarger HJ, Mirsky SB, Kramer M, Weil RR, Meisinger JJ, Cavigelli MA, Spargo JT. (2015). Cover crop and poultry litter management influence spatiotemporal availability of topsoil nitrogen. Soil Science Society of America Journal 79:1660-1673. doi:10.2136/sssaj2015.03.0134 Kramer M & Font E. (2015). Reducing sample size in experiments with animals: historical controls and related strategies. Biology. Reviews. doi: 10.1111/brv.12237 Greene SL, Kesoju SR, Martin RC, Kramer M (2015) Occurrence of Transgenic Feral Alfalfa (Medicago sativa subsp. sativa L.) in Alfalfa Seed Production Areas in the United States. PLoS ONE 10 (12): e0143296. doi:10.1371/journal.pone.0143296  Poffenbarger, HJ; Mirsky, SB; Teasdale, JR; Spargo, JT; Cavigelli, MA; Kramer, M. (2015). Nitrogen competition between corn and weeds in soils under organic and conventional management. Weed Science 63: 461-476.  Guo, Y; Olsen, RT; Kramer, M; Pooler, M. (2015). Effective bioassays for evaluating boxwood blight susceptibility using detached stem inoculations. HortScience 50: 268-271.  Kramer, E. T. Paparozzi and W. W. Stroup. (2016) Statistics in a Horticultural Journal: Problems and Solutions. Journal of the American Society for Horticultural Science. In press.

Impact Statements

Project members collaborate in research projects with scientists in agricultural related disciplines to develop and use proper statistical design and analysis methodology well beyond standard textbook applications. These efforts often result in competitive grant participation and refereed publications. Each of these impacts is listed in the Accomplishments and Publications sections of this report.