NCCC_old170: Research Advances in Agricultural Statistics

(Multistate Research Coordinating Committee and Information Exchange Group)

Status: Inactive/Terminating

Project Menu

SAES-422 Reports

Annual/Termination Reports:

[08/21/2017] [08/17/2018] [08/09/2019] [08/23/2020] [08/16/2021]

Date of Annual Report: 08/21/2017

Report Information

Annual Meeting Dates: 06/22/2017 - 06/23/2017
Period the Report Covers: 10/01/2016 - 09/30/2017

Participants

MEMBERS: Nora Bello (KS), Bruce Craig (IN, Admin.), Philip Dixon (IA), Sara Duke (USDA-ARS), Susan Durham (UT), Ed Gbur (AR), Carla Goad (OK), Matt Kramer (UDSA-ARS), Nick Keuler (WI), Neil Paton (Cargill), Raul Macchiavelli (PR), Larry Madden (OH), Bahram Momen (MD), Julia Sharp (SC), John Stevens (UT), Rob Tempelman (MI), Kathy Yeater (USDA-ARS),

OTHERS: William Bridges (SC), JungAe Lee (AR), Kelci Miclaus (SAS), Jason Osborne (NC), Aaron Rendahl (MN), Brian Rice (IL), Esperanza Shenstone (IL), Qiong Hu(Cargill), Tatiana Lust (Cargill), Andrea Ostrom (Cargill), Travis Wolter (Cargill)

Brief Summary of Minutes

Minutes Attachment:

NCCC-170_ 2017_Report.pdf

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: Larry Madden taught a one-day workshop entitled “Meta-analysis for evidence synthesis” at the Annual Meeting of the American Phytopathological Society (APS), August 2017. San Antonio, TX.  Nora Bello, Nick Keuler, and Kevin McCarter taught a one and a half day workshop in conjunction with the Joint Annual Meetings of the American Dairy Science Association and American Society of Animal Sciences with focus on the application of general and generalized linear mixed models to research problems in the animal and food sciences. 61 participants. June 2017. Pittsburgh, PA.  Nora Bello taught three day workshop on the application of general and generalized linear mixed models for experimental design and data analysis of research problems in animal health and production. 25 participants. May 31 to July 2, 2017. Kansas State University. The workshop was sponsored by Shell US.  Nora Bello taught two day workshop on mixed models for repeated measures data at the XXI Annual Meeting of the Argentinean Chapter of the International Biometrics Society (Grupo Argentino de Biometria). Approximately 50 participants. September 2016. Corrientes, Argentina.  Kathy Yeater and Maria Villamil presented a half-day workshop entitled “Multivariate Analysis: Tools for understanding complex systems” at the ASA-CSSA-SSSA Meetings. November 2016. Phoenix, AZ.  Kathy Yeater presented an introduction to JMP for researchers at the U.S. Meat Animal Research Center, Clay Center, NE. February 2017.  Rob Templeman presented a half-day workshop entitled “An introduction to SAS” at the Center for Statistical Training and Consulting at Michigan State. November 2016.  Rob Templeman presented a half-day workshop entitled “Introduction to generalized linear models” at the Center for Statistical Training and Consulting at Michigan State. February 2017.  Rob Templeman presented a half-day workshop entitled “Determining the right standard errors and statistical tests using mixed models” at the Center for Statistical Training and Consulting at Michigan State. March 2017.  Presentations: Bello N.M., Gonclaves M. On linear and non-linear mixed modeling of dose responses: Lessons learnt. David H. Baker Amino Acid Symposium, 2016 Midwest Chapter Meetings of the American Society of Animal Sciences. DesMoines, Iowa. March 2016. (Invited Keynote Address)  Bello N.M. Brief tour of Structural Equation Models: Rethinking causal inference in beef cattle. Kansas State University Center for Outcomes Research and Education. February 2016. (Invited)  Bello N.M. Towards reproducible research in animal health and production: Thoughts from Statistics. Center for Outcomes Research and Epidemiology. Kansas State University. February 2017. (Invited)  Bello N.M. Further thoughts for reproducible research in animal health and production (Part II). Center for Outcomes Research and Epidemiology. Kansas State University. May 2017. (Invited)  Bello N.M. A closer look at low-expression RNASeq transcripts: Motivations from the prairie. Department Seminar Series at the University of Kansas Cancer Center. Kansas City, Kansas. July 2016. (Invited)  Madden, L. V. Network meta-analysis for evidence synthesis in the plant and agricultural sciences. Central European Network of the International Biometric Society (IBS), August 2017. Vienna, Austria. (Invited)  Stevens J.R. Annotation Tools for Multivariate Gene Set Testing in Non-Model Organisms. Animal Reproduction and Biotechnology Laboratory Seminar, Colorado State University Department of Biomedical Sciences, October 2016. (Invited)  Bishop M.O., Stevens J.R., and Isom S.C. Statistical Methods for Assessing Individual Oocyte Viability Through Gene Expression Profiles. ENAR Spring Meeting, Washington DC, March 2017.  Bishop M.O., Stevens J.R., and Isom S.C. Statistical Methods for Assessing Individual Oocyte Viability Through Gene Expression Profiles. Kansas State University Conference on Applied Statistics in Agriculture, April 2017.  Pillai S.M., Hoffman M.L., Jones A.K., McFadden K.K., Stevens J.R., Zinn S.A., Reed S.A., and Govoni K.E. Poor maternal nutrition during gestation alters muscle gene expression in fetal offspring. Annual meeting of the American Society of Animal Science, July 2017.  Stevens J.R. The academic applied statistician -- transitioning domain-specific data into statistics research.  Joint Statistical Meetings, Baltimore MD, August 2017.  Bello N.M. Honing in on low-expression RNASeq transcripts: Motivations from the prairie. Applied Bioinformatics Seminar Series at Kansas State University. February 2016.  Yeater, K.M.  Introduction to JMP. U.S. Meat Animal Research Center, Clay Center, NE. February 2017.  Yeater, K.M.  Tools for Researchers: Omics using JMP Genomics Software.  VA SAS Users’ Group, Richmond, VA. May 2017.  Yeater, K.M.  What is a GLMM? And, how do I analyze it?  U.S. Meat Animal Research Center, Clay Center, NE.  June 2017.  Craig, B.A., Hurwitz, S, Sampson, P.D., Smith, H.S., and Wiest, M.  Teaching a Statistical Consulting Course. Joint Statistical Meetings, Chicago, Illinois, August 2016. (Panel discussion)  Craig, B.A., Chen, N., and Wijayawardana, S.R. Assessing Inter-rater Agreement of Immunohistochemistry Scores. 28th International Biometric Conference, Victoria, Canada, July 2016.  Lawrence, G.B., Sabo, R., Scanga. S.E., Momen, B. Is recovery of forest soils from acidic deposition accelerating watershed release of atmospherically deposited nitrogen accumulated over past decades? American Geophysical Union, Fall General Assembly 2016.  Macchiavelli, R.; P. Torres-Saavedra, J. Chavarría-Carvajal, A. Calvo-Alfaro, Liz Terán-Herrera. Semi-parametric mixed beta regression models for disease severity in plants: Modelling Black Sigatoka in banana crops. 61st ISI World Statistics Congress, Marrakech, Morocco, July 2017.  Casanoves, F.; R. Macchiavelli; J. Di Rienzo. Non-linear mixed model implementation in InfoStat: an Interface with the nmle Library. 61st ISI World Statistics Congress, Marrakech, Morocco, July 2017.  Giménez, G., Rubio, N., Haique, A., Macchiavelli, R.. Métodos alternativos para predecir categorías de frutos en base a curvas de crecimiento simuladas: modelo generalizado mixto multicategórico y support vector machine (SVM). XXI Reunión Científica del Grupo Argentino de Biometría., Corrientes, Argentina. 2016.  Piccardi, M., Macchiavelli, R., Balzarini, M. Ajuste de curvas de lactancia que derivan de un aborto. XXI Reunión Científica del Grupo Argentino de Biometría, Corrientes, Argentina. 2016.  Padilla, Ingrid Y., Vilda L. Rivera, Norma I. Torres, Raul Macchiavelli, Jose Cordero, David Kaeli, and Akram Alshawabkeh. Assessment of Links Between Contamination in Karst Groundwater and Water Quality in Drinking Water Systems., NIEHS Environmental Health Science FEST, Durham, NC, December 2016.  Di Rienzo, J.; R. Macchiavelli; Casanoves, F. Non-linear mixed model implementation in InfoStat. XXVIII International Biometric Conference, Victoria, Canada, July 2016.  Murphy, M., D. Hodgson, N. M. Bello. On accuracy and precision of oxygen flow meters. International Veterinary Emergency and Critical Care Symposium. September 2017. Nashville, TN  Sharpe, S., L. Johnson, N. M. Bello, O. Parrish and M. Galliart. Rapid evolution in a disturbed environment: Evolutionary response of native grass Andropogon virginicus to heavy metals in an abandoned mine site. Switchgrass IV: Prairie and Native Grass International Conference. Lincoln, NE. August 2017.  Sharpe, S., L. Johnson, N. M. Bello, M. Galliart and O. Parrish. Rapid adaptation in a contaminated environment: Evolutionary adaptive response of old field grass Andropogon virginicus to heavy metals in abandoned lead and zinc mines. Joint Annual Conference of the American Society of Naturalists, the Society for the Study of Evolution and the Society of Systematic Biologists. Portland, OR. June 2017.  Sharpe, S., L. Johnson, N. M. Bello, M. Galliart and O. Parrish. Rapid adaptation in a disturbed environment: Evolutionary adaptive response of native grass Andropogon virginicus to heavy metals in an abandoned mine site. 2017 Botany Conference. Fort Worth, TX. June 2017.  Chitakasempornkul, K. , E. Cha, M. Sanderson, A. Jager, N. Cernicchiaro, T. Schroeder, D. G. Renter and N.M. Bello. Accounting for data architecture on structural‐equation‐based modeling of feedlot performance outcomes. Kansas State University Conference on Applied Statistics in Agriculture. April 2017.  Chitakasempornkul, K., M. B. Menegatgs, S. S. Dritz, M. A. D. Goncalves, A. Jager, M.D. Tokach, R. D.Goodband and N.M. Bello. Exploring biological relationships between reproductive outcomes in high‐performing gilts and sows following nutritional management during late gestation. Kansas State University Conference on Applied Statistics in Agriculture. April 2017.  Cha, E., M. Sanderson, N.M. Bello, N. Cernicchiaro, A. Jager and D. G. Renter Network assessment of the relationship between Bovine Respiratory Disease Morbidity and performance in feedlot cattle. Kansas State University Conference on Applied Statistics in Agriculture. April 2017.  Books: Di Rienzo, Julio Alejandro; Raúl E. Macchiavelli; Fernando Casanoves 2017. Modelos lineales generalizados mixtos: aplicaciones en InfoStat. Córdoba: Digital Book, PDF (InfoStat Software Estadístico / Di Rienzo, Julio Alejandro) ISBN 978-987-42-4985-2  Other project related activities: Larry Madden maintains a website with statistical software code (SAS) and PowerPoint presentations on a range of data-analytic subjects. Material based heavily on previously presented workshops. <a href="http://www.oardc.ohio-state.edu/aps-statsworkshop/default.htm">www.oardc.ohio-state.edu/aps-statsworkshop/default.htm</a> Current specific goals for the 2016-2021 project: (1)        To identify, foster and coordinate cooperative research efforts in statistics among statisticians serving food and agriculture research programs.  (2)        To provide continuing education and statistical support to the scientific community in the review and editorial process.  (3)        To address the statistical design and analysis issues associated with studies involving technologies that typically produce a large number of spatially and/or temporally correlated variables per observations but small sample sizes (e.g.,-omics, informatics, and -metrics).  (4)        To address concerns associated with the development and implementation of generalized linear mixed model techniques and software used by statisticians and researchers.  (5)        To address meta-analysis issues associated with multi-location, multi-investigator projects including those in which study treatments and/or designs may differ by location.

Publications

Bello, NM, Kramer, M, Tempelman, RJ, Stroup, WW, St-Pierre, NR, Craig, BA, Young, LJ, and Gbur, EE. 2016. Short communication: On recognizing the proper experimental unit in animal studies in the dairy sciences. Journal of Dairy Science 99, 8871-8879. [Article highlighted in Journal of Dairy Sciences as “Best Research Practices”]  Mohammadi, S., S.S. French, L.A. Neuman-Lee, S.L. Durham, Y. Kojima, A. Mori, E.D. Brodie, Jr., and A. Savitzky 2017. Corticosteroid responses of snakes to toxins from toads (bufadienolides) and plants (cardenolides) reflect differences in dietary specializations. General and Comparative Endocrinology 247, 16-25. doi: 10.1016/j.ygcen.2017.03.015  Skinner, H.M., A.M. Durso, L.A. Neuman-Lee, S.L. Durham, S.D. Mueller, and S.S. French 2016. Effects of diet restriction and diet complexity on life history strategies in side-blotched lizards (Uta stansburiana). Journal of Experimental Zoology 325(9), 626-637. doi: 10.1002/jez.2056  Tepedino, V.J., L.C. Arneson, and S.L. Durham 2016. Pollen removal and deposition by pollen- and nectar-collecting specialist and generalist bee visitors to Iliamna bakeri (Malvaceae). Journal of Pollination Ecology 19(8), 50-56.  Ogata, E.M., W. W. Wurtsbaugh, T.N. Smith, and S.L. Durham 2017. Bioassay analysis of nutrient and Artemia franciscana effects of trophic interactions in the Great Salt Lake, USA. Hydrobiologia 788(1), 1-16. doi: 10.1007/s10750-016-2881-9  Denlinger, D.S., A.Y. Li, S.L. Durham, P.G. Lawyer, J.L. Anderson, and S.A. Bernhardt 2016. Comparison of in vivo and in vitro methods for blood feeding of Phlebotomus papatasi (Diptera: Psychodidae) in the laboratory. Journal of Medical Entomology 53(5), 1112-1116. doi: 10.1093/jme/tjw074  Messina, F.J., and S.L. Durham 2015. Loss of adaptation following reversion suggests trade-offs in host use by a seed beetle. Journal of Evolutionary Biology 28, 1882-1891. doi: 10.1111/jeb.12704  Flint, C.G., X. Dai, D. Jackson-Smith, J. Endter-Wada, S.K. Yeo, R. Hale and M.K. Dolan 2017. Social and Geographic Contexts of Water Concerns in Utah. Society & Natural Resources 30(8), 885 - 902. DOI: 10.1080/08941920.2016.1264653.  Bushman, B.S., L. Wang, X. Dai, A. Joshi, J.G. Robins and P.G. Johnson. 2016. Responses of Tolerant and Susceptible Kentucky Bluegrass Germplasm to Salt Stress. Hort Science 141(5), 449 - 456. Hass, Z, DePalma G, Craig, BA, Xu, H, and Sands, LP. 2017. Unmet Need for Help With Activities of Daily Living Disabilities and Emergency Department Admissions Among Older Medicare Recipients. Gerontologist 57(2), 206 - 210. Rivera, RL, Maulding, MK, Abbott, AR, Craig, BA, and Eicher-Miller, HA. 2016. SNAP-Ed (Supplemental nutrition assistance program-education) increases long-term food security among Indiana households with children in a randomized controlled study. Journal of Nutrition 146(11), 2375 - 2382. Xavier, A, Muir, WM, Craig, BA, and Rainey, KM. 2016. Walking through the statistical black boxes of plant breeding. Theoretical and Applied Genetics 129(10), 1933-1949. Osei-Boadi Anguah, K, Lovejoy, JC, Craig, BA, Gehrke, MM, Palmer, PA, Eichelsdoerfer, PE, and McCrory, MA 2017. Can the palatability of healthy, satiety-promoting foods increase with repeated exposure during weight loss? Foods In press. Cabezòn, FA, Schinckel, AP, Leòn, YL, and Craig, BA. 2017. Analysis of lactation feed intakes for sows with extended lactation lengths. Translational Animal Science. In press. Gallagher, P, Craig, BA, Luttermoser, T, and Buczkowski, G. 2017.  Paired Competition Analysis using Mixed Models. Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. In press. Lakshmikantha H. Channaiaha, Minto Michaelb, Jennifer C. Acuffb, Randall K. Phebusb, Harshavardhan Thippareddic, Maureen Olewnika, George Milliken 2017. Validation of the baking process as a kill-step for controlling Salmonella in muffins. International Journal of Food Microbiology 250(5), 1-6 Michaela A. Schenkelberg, Richard R. Rosenkranz, George A. Milliken, Kristi Menear, David A. Dzewaltowski 2017. Implications of Social Groups on Sedentary Behavior of Children with Autism: A Pilot Study. Journal of Autism and Developmental Disorders 47 (4), 1223–1230.  Dale E. Bauman, Normand R. St-Pierre, George A. Milliken, Robert J. Collier, Joseph S. Hogan, Jan K. Shearer, K. Larry Smith, William W. Thatcher. 2016. Recombinant bovine somatotropin: Overview and results from a recent meta-analysis of effects on health and welfare of dairy cows. The AABP Proceedings 48, 73-78.  Channaiah, L.H., E.S. Holmgren, M. Michael, N.J. Sevart, D. Milke, C.L. Schwan, M. Krug, A. Wilder, R.K. Phebus, H. Thippareddi, and G. Milliken. 2016. Validation of baking to control Salmonella serovars in hamburger bun manufacturing, and evaluation of Enterococcus faecium ATCC 8459 and Saccharomyces cerevisiae as nonpathogenic surrogate indicators. Journal of Food Protection. DOI: 10.4315/0362-028X.JFP-15-241.  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. DOI: 10.1371/journal.pone.0156851.  Cartwright J, Dzantor EK, Momen B. 2016. Soil microbial community profiles and diversity in limestone cedar glades. CATENA 147, 216-224. lsen 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, DOI: 10.1111/jfr3.12257. Yu M, Kearney M, Momen B. 2017. Drought associated phenological changes of coastal marshes in Louisiana. Ecosphere. DOI: 10.1002/ecs2.18. Rogers, C.W., R.J. Norman, T.J. Siebenmorgen, B.C. Grigg, J.T. Hardke, K.R. Brye and E.E. Gbur 2016. Rough rice and milling yields as affected by nitrogen, harvest moisture, and cultivar. Agronomy Journal 108, 813-821. Chitwood, J., A. Shi, M. Evans, C. Rom, E.E. Gbur, D. Motes, P. Chen and D. Hensley 2016. Effect of temperature on seed germination in spinach (Spinaciaoleracea L.). Hort Science 51, 1475-1478. Suhartono, M.C. Savin and E.E. Gbur 2016. Genetic redundancy and persistence of plasmid-mediated trimethoprim/sulfamethoxazole resistant effluent and stream water Escherichia coli. Water Research 103, 197-204. Weeks, W., M.P. Popp, M. Salmeron, L.C. Purcell, E.E. Gbur, F.M. Bourland, N.W. Buehring, L. Earnest, F.B. Fritschi, B.R. Golden, D. Hathcoat, J. Lofton, A.T. McClure, T.D. Miller, C. Neely, G. Shannon, T.K.  Udeigwe, D.V. Verbree, E.D. Vories and W.J. Weibold 2016. Diversifying soybean production risk using maturity group and planting date choices. Agronomy Journal 108, 1917-1929. Singh, V., N. Burgos, S. Singh, D. Gealy and E. Gbur 2017. Impact of volunteer rice infestation on yield and grain quality of rice. Pest Management Science 73, 604-615. DOI: 10.1002/ps.4343. Jones, J., M.C. Savin, C.R. Rom and E. Gbur 2017. Denitrifier community response to seven years of ground cover and nutrient management in an organic apple orchard soil. Applied Soil Ecology 112, 60-70. Burgos, N., Singh, V., S. Singh, H. Black, V. Boyett, S. Basu, D. Gealy, E. Gbur, A. Pereira, R.C. Scott and A. Caicedo 2017. Introgression of ClearfieldTM rice crop traits into weedy red rice outcrosses. Field Crops Research 207, 13-23. Brennan, R.B., J.T. Scott, A.N. Sharpley, H.T. Lally, H.P. Jarvie, M.J. Bowes, Haggard, M. and E.E. Gbur 2017. Linking soil erosion to instream dissolved P cycling and periphyton growth. Journal of the American Water Resources Association, 1-13. DOI: 10.1111/1752-1688.12534. Cobb, Adam B., Gail W. T. Wilson, Carla L. Goad, Jeff D. Wilson 2017. Assessing the influence of farm fertility amendments, field management, and sorghum genotypes on soil microbial communities and grain quality. Applied Soil Ecology 119, 367-364. DOI: 10.1016/j.apsoil.2017.06.010. Basyouni, Rania, B. L. Dunn, Carla Goad 2016. Use of Nondestructive Sensors to Assess Nitrogen Status in Potted Dianthus (Dianthus chinensis L.) Production. Canadian Journal of Plant Science 97(1). DOI: 10.1139/CJPS-2016-0059. Chang, Dan, Yanqi Wu, Linglong Liu, Shuiyi Lu-Thames, Hongxu Dong, Carla Goad 2016. Quantitative trait mapping for tillering-related traits in two switchgrass populations, The Plant Genome, 9(2). DOI: 10.3835/plantgenome2016.01.0010. Cobb, Adam B., Gail W. T. Wilson, Carla L. Goad, Scott R. Bean, Rhett C. Kaufman, Thomas J. Herald, Jeff D. Wilson 2016. The role of arbuscular mycorrhizal fungi in grain production and nutrition of sorghum genotypes: Enhancing sustainability through plant-micorbial partnership. Agriculture, Ecosystems & Environment 233, 432-440. <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__dx.doi.org_10.1016_j.agee.2016.09.024&d=DwMFAg&c=7ypwAowFJ8v-mw8AB-SdSueVQgSDL4HiiSaLK01W8HA&r=vUvzplQw5LUYeuaEIq_Elw&m=Cjj11c6pt8RYeRjIUN6bqNbUof-hz0wMmXqOkRo7fdo&s=sJ94D1PQX6f6up36mpn1SgZ-0brpnF8rsMFeL_AklDs&e=">http://dx.doi.org/10.1016/j.agee.2016.09.024</a>. Akehi, K, Long, B, Warren, AJ, Goad, C. 2016. Ankle joint angle and lower leg musculotendinous unit responses to cryotherapy. The Journal of Strength and Conditioning Research 30(9), 2482-92. Dunn, Bruce 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. http://dx.doi.org/10.1080/01904167.2015.1086791 Hanzlicek, A. S., J. H. Meinkoth, J. S. Renschler, Carla Goad, L. J. Wheat, 2016. Antigen concentrations as an indicator of clinical remission and disease relapse in cats with histoplasmosis. Journal of Veterinary Internal Medicine 30(4). DOI: 10.111/jvim.13962 Jiang, Li, Bruce Dunn, Yunwen Wang, Carla Goad 2016. Responses to Propagation Substrate and Rooting Hormone Products to Facilitate Asexual Propagation of Silene chalcedonica and Silene coronaria. Journal of Environmental. Horticulture 34(3): 80-83. Jeger, M. J., Stevenson, K. L., and Madden, L. V. 2017. Plant disease epidemiology. Oxford Bibliographies. http://oxfordbibliographiesonline.com/.  DOI: 10.1093/OBO/9780199830060-0166. Mila, A. L. and Madden, L. V. 2017. Introduction to Bayesian analysis of Phytopathological data using SAS. Plant Health Instructor. http://www.apsnet.org/edcenter/Pages/phi.aspx. DOI: 10.1094/PHI-A-2017-0603-01. Thomson, J., K.M. Yeater, L. Zurek, and D. Nayduch 2016. Abundance and accumulation of Escherichia coli and Salmonella Typhimurium procured by male and female house flies (Diptera: Muscidae) exposed to cattle manure. Annals of the Entomological Society of America 110, 37-44. Crippen, T.L., C.L. Sheffield, J.A. Byrd, J.F. Esquivel, R.C. Beier, and K.M.Yeater 2016. Poultry litter and the environment: Physiochemical properties of litter and soil during successive flock rotations and after remote site deposition. Science of the Total Environment 553, 650-661. <a href="https://www.cambridge.org/core/search?filters%5BauthorTerms%5D=Monica%20Piccardi&eventCode=SE-AU">Piccardi</a>, M., <a href="https://www.cambridge.org/core/search?filters%5BauthorTerms%5D=Ra%C3%BAl%20Macchiavelli&eventCode=SE-AU">R. Macchiavelli</a>, <a href="https://www.cambridge.org/core/search?filters%5BauthorTerms%5D=Ariel%20Capitaine%20Funes&eventCode=SE-AU">Ariel Capitaine Funes</a>, <a href="https://www.cambridge.org/core/search?filters%5BauthorTerms%5D=Gabriel%20A%20B%C3%B3&eventCode=SE-AU">Gabriel A Bó</a> and Monica Balzarini 2017. Fitting milk production curves through nonlinear mixed models. Journal of Dairy Research 84 (2), 146-153. DOI: <a href="https://doi.org/10.1017/S0022029917000085">https://doi.org/10.1017/S0022029917000085</a> Flores, C., R. Macchiavelli, O. Bosques, and R. Toledo 2016. Calidad y Estado Fisiológico del Café al momento de la Cosecha y su Efecto en el Rendimiento en Puerto Rico. Journal of Agriculture of the University of Puerto Rico 100: 27-41. Stevens J.R., Al Masud A., and Suyundikov A. 2017. A comparison of multiple testing adjustment methods with block-correlation positively-dependent tests. PLOS ONE 12(4):e0176124. Belmont P., Stevens J.R., Czuba J.A., Kumarasamy K., and Kelly S.A. 2016. Comment on ‘Climate and agricultural land use change impacts on streamflow in the upper midwestern United States’ by Satish C. Gupta et al. Water Resources Research 52,7523-7528. Polejaeva I., Ranjan R., Davies C.J., Regouski M., Hall J., Olsen A.L., Meng Q., Rutigliano H.M., Dosdall D.J., Angel N.A., Sachse F.B., Seidel T., Thomas A.J., Stott R., Panter K.E., Lee P.M., Van Wettere A.J., Stevens J.R., Wang Z., MacLeod R.S., Marrouche N.F., and White K.L. 2016. Increased Susceptibility to Atrial Fibrillation Secondary to Atrial Fibrosis in Transgenic Goats Expressing Transforming Growth Factor-beta1. Journal of Cardiovascular Electrophysiology 27(10),1220-1229. Ruppert D, Needelman BA, Kleinman PJA, Rabenhorst MC, Momen B, Wester DB. 2017. Hydrology and soil manipulations of iron-rich ditch mesocosms provide little evidence of phosphorus capture within the profile. Journal of Environmental Quality 46, 596-604. Kivett, 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 51(4), 274-291. doi: 10.18474/JES16-07.1 Goncalves, 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 95(5), 1993-2003. doi: 10.2527/jas.2015-0087 Martin, 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 61(6), 887-898. doi: 10.1111/fwb.12752. Becker, M. W., R. P. Sundar, 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. Fissekis, S., D. S. Hodgson and N. M. Bello 2017. Effect of cleaning on accuracy and precision of oxygen flow meters on anesthetic machines of various ages. Veterinary Anaesthesia and Analgesia http://dx.doi.org/10.1016/j.vaa.2016.10.002. Delph, K., E. G. Davis, N. M. Bello, K. Hankins, M. J. Wilkerson, C. Ewen 2017. Comparison of immunologic responses following intranasal and oral administration of a USDA-approved, live-attenuated Streptococcus equi vaccine. Journal of Equine Veterinary Science doi: 10.1016/j.jevs.2016.08.015 Tempelman, R.J. 2016. Editorial: The frontier spirit and reproducible research in animal breeding. Journal of Animal Breeding and Genetics 133, 441-442. doi: 10.1111/jbg.12244.  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. de Haas, and R.J. Tempelman 2017.  Modeling genetic and non-genetic variation of feed efficiency and its partial relationships between component traits as a function of management and environmental factors. Journal of Dairy Science 100, 412-427. doi: 10.3168/jds.2016-11491.  Yao, C., G. de los Campos, M. J. Vandehaar, D.M. Spurlock, L.E. Armentano, M. Coffey, Y. deHaas, R.F. Veerkamp, C.R. Staples, E.E. Connor, Z. Wang, M.D. Hanigan, R.J. Tempelman, and K.A. Weigel  2017. Use of genotype × environment interaction model to accommodate genetic heterogeneity for residual feed intake, dry matter intake, net energy in milk, and metabolic body weight in dairy cattle. Journal of Dairy Science 100, 2007-2016. doi: 10.3168/jds.2016-11606.  Mmongoyo, J.A., F. Wu, J.E. Linz, M.G. Nair, J.K. Mugula, R.J. Tempelman and G.M. Strasburg 2017. Aflatoxin levels in sunflower seeds and cakes collected from micro- and small-scale sunflower oil processors in Tanzania. PLOS One 12(4), e0175801. doi: 10.1371/journal.pone.0175801  Mota, R.R., B.P. Sollero, P.S. Lopes, R.J. Tempelman, I. Aguilar, and F. F. Cardoso 2017.  Analyses of Reaction Norms Reveal New Chromosome Regions Associated with Tick Resistance in Cattle.  Animal July 13, 1-10. doi: 10.1017/S1751731117001562.  Chen, C., J.P. Steibel, and R.J. Tempelman 2017. Genome wide association analyses based on broadly different specifications for prior distributions, genomic windows, and estimation methods. Genetics 206, 1791-1806. doi: 10.1534/genetics.117.202259

Impact Statements

Members continuing to offer workshops and, where appropriate, alternative means of continuing education and support for subject matter scientists, reviewers, and technical editors on valid design and statistical analysis of studies.

Date of Annual Report: 08/17/2018

Report Information

Annual Meeting Dates: 06/28/2018 - 06/29/2018
Period the Report Covers: 10/01/2017 - 09/30/2018

Participants

Nora Bello (KS), Bruce Craig (IN, Admin.), Sara Duke (USDA-ARS), Susan Durham (UT), Ed Gbur (AR), Carla Goad (OK), Nick Keuler (WI), Alex Lipka (IL), Raul Macchiavelli (PR), Larry Madden (OH), Gayla Olbricht (MO), Guilherme Rosa (WI), Julia Sharp (SC), John Stevens (UT), Walt Stroup (NE), Rob Tempelman (MI), Kathy Yeater (USDA-ARS)

Brief Summary of Minutes

Technical program: The meeting began at 8:30 a.m. on Thursday, June 28, 2018 with opening remarks by Dr. Nathan McKinney, Assistant Director of the Arkansas Agricultural Experiment Station.

Presentations ended at approximately 4:15 p.m. and were followed by two group discussions and the business meeting, ending at 5:15 p.m. The technical program consisted of the following presentations:

Alex Lipka, Univ. of Illinois	Quantification of the genomic contribution towards food and energy related crop traits
Nora Bello, Kansas State Univ.	Searching for causal networks in experimental data: A swine production application
JungAe Lee-Bartlett, Univ. of Arkansas	Discrete time survival analysis applied to experimental data
Walter Stroup, Univ. of Nebraska-Lincoln	Pseudo-likelihood or quadrature? What we thought we knew, what we think we know, and what we are still trying to figure out
Raul Macchiavelli, Unvi. of Puerto Rico-Mayagüez	A Bayesian semi-parametric mixed beta regression model for disease severity in plants
Rob Tempelman, Michigan State Univ.	Using genetic relationships to improve on the design and analysis of animal science studies
Larry Madden, Ohio State Univ.	Multi-treatment (“network”) meta-analysis in agriculture
Bruce Craig, Arman Sabbaghi, and Mark Ward, Purdue Univ.	Bayesian analysis of partial cladograms resulting from free-sorting tasks
Nicholas Keuler and Jun Zhu, Univ. of Wisconsin	Revising an introductory statistics curriculum from the ground up – Challenges, solutions, and lessons learned.

The first group discussion was centered on the use of error bars by researchers to visualize significant differences among treatment group means. Since the use of error bars can easily be misinterpreted, discussion centered on meaningful and easily interpreted alternatives.

The second discussion addressed the question of whether or not current journals, in particular, the Journal of Agricultural, Biological, and Environmental Statistics (JABES) which individuals from our group played a role in establishing, meet our publication needs and expectations. Agricultural applications have been almost non-existent in JABES for the last several years. The group discussed the lack of a current editorial board member who works with agricultural applications and concluded that we need to be more engaged in manuscript submissions as well as the editorial and review processes. It was suggested that the group draft the letter to the editorial board and the incoming editor-in-chief who will begin their term in January, 2019.

Business meeting: The business meeting began at about 4:50 p.m. Ed Gbur presided. The following items were discussed:

(1) The organizers were thanked for a productive and enjoyable meeting.

(2) Ed may several announcements concerning events involving project participants since last year’s meeting.

On January 5, 2018 the American Statistical Association Board of Directors endorsed our position paper entitled “Statistics as a Scientific Discipline and Practical Implications for Evaluation of Faculty Excellence.” Development and acceptance of the paper was led by Walt Stroup, Nora Bello, Bruce Craig and William Bridges. The paper can be accessed using the link www.amstat.org/asa/files/pdfs/POL-Statistics-as-a-Scientific-Discipline.pdf .

The University of Maryland’s student newspaper The Diamondback published an obituary for long time member Bahram Momen who died on March 13, 2018. A copy of the obituary can be found on our project website. Matt Kramer represented our group at the funeral.

The USSES project is scheduled to end in September of this year. The participants do not plan to renew the project but instead to become members of NCCC-170.

Presenters who wish to post their talk on the project website should send a pdf of the talk to Ed.

(3) The annual report and impact statement are due this Fall. 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, 2017 to September 30, 2018 (or since last year’s report) that are related to or inspired by their participation in NCCC-170 as soon as possible. Please see the July 5 e-mail from Ed for more details. A copy of the e-mail is posted on the project website.

(4) The 2019 meeting will be held at the University of Illinois with Alex Lipka as the local host. Tentative dates are June 20-21, 2019. Larry Madden will serve as program chair. The 2020 meeting is tentatively planned for Oklahoma State with Carla Goad as the local host. Colorado State was suggested as a tentative site for 2021.

(5) 2017-2018 is the second year of the current project that is scheduled to end in 2021. Progress toward those objectives as they relate to the expected outcomes and impacts, especially providing continuing education and statistical support to the scientific community in the review and editorial process have become more important than ever.

(6) Several individuals who participate in the annual meetings are not official participants according to NIMSS. Several other individuals listed have not participated in annual meetings. 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 only if they intend to participate.

The business meeting adjourned at approximately 5:15 p.m.

Accomplishments

Publications

Workshops: Guilherme Rosa taught a short course on “Quantitative Genetics and Prediction of Complex Traits” (co-taught with Dr. Dan Gianola) at the China Agricultural University, Beijing, China. October 18-22, 2017.  Guilherme Rosa taught a short course on “Statistical Modeling in Animal Breeding and Genetics” at Sao Paulo State University (UNESP), Jaboticabal, Brazil. November 6-10, 2017.  Nora Bello taught a workshop on an “Introduction to structural equation modeling for production systems in animal agriculture” at the Department of Agronomy and Department of Economics and Statistics, National University of Cordoba, Argentina. December 22, 2017.  Rob Tempelman taught an “Introduction to SAS” workshop for the MSU Center for Statistical Training and Consulting. February 9, 2018.  Walt Stroup taught a three workshop on generalized linear mixed models at the Finnish Natural Resources Institute. March, 2018.  Alex Lipka taught a series of three workshops entitled “GWAS to identify targets for MAS”, “Implementing genomic selection”, and “Comparing GS to MAS” at the African Plant Breeding Academy, Class III, Session 3, World Agroforestry Centre, Nairobi, Kenya. May 17-19, 2018.  Guilherme Rosa taught a 1-day workshop on “Introduction to Graphical Modeling for Agricultural Data” at the 30th Conference on Applied Statistics in Agriculture, Kansas State University, Manhattan, KS. May 6, 2018.  Bruce Craig led a day-long workshop titled “An Overview of Linear Mixed Models” as part of the 9th International Purdue Symposium on Statistics. June 5, 2018.  Guilherme Rosa taught a short course on “Quantitative Genetics” (co-taught with Dr. Bruce Walsh) at the 23rd Summer Institute in Statistical Genetics, University of Washington, Seattle, WA. July 16-18, 2018.  Guilherme Rosa taught a short course on “Mixed Models in Quantitative Genetics” (co-taught with Dr. Bruce Walsh) at the 23rd Summer Institute in Statistical Genetics, University of Washington, Seattle, WA. July 18-20, 2018.  Kathy Yeater presented a training workshop entitled “Learning the Essential Steps to Non-Gaussian Data Analysis” to the USDA Biosciences Research Laboratory, Insect Genetics and Biochemistry Research Unit, Fargo, ND.  July 16-17, 2018.  Nora Bello taught a workshop on “Application of general and generalized linear mixed models for experimental design and data analysis of research problems in animal health and production” at a Summer Workshop on Mixed Models, Kansas State University. Sponsored by Shell U.S. August 7-8, 2018.  Books: Glaz, B. and K.M. Yeater (ed.) 2018. Applied Statistics in Agricultural, Biological, and Environmental Sciences. ASA, CSSA, and SSSA, Madison, WI. doi: 10.2134/appliedstatistics  Dixon, P.M., K.J. Moore, and E. van Santen. 2018. The Analysis of Combined Experiments. In Applied Statistics in Agricultural, Biological, and Environmental Sciences. Glaz and Yeater (ed.). pp 201-234. ASA, CSSA, and SSSA, Madison, WI. doi: 10.2134/appliedstatistics.2016.0004  Burgueno, J., J. Crossa, F. Rodriguez, and K.M. Yeater. 2018. Augmented Designs-Experimental Designs in which all Treatments are Not Replicated. In Applied Statistics in Agricultural, Biological, and Environmental Sciences. Glaz and Yeater (ed.) pp 345-370. ASA, CSSA, and SSSA, Madison, WI. doi: 10.2134/appliedstatistics.2016.0005  Yeater, K.M. and M.B. Villamil. 2018. Multivariate Methods for Agricultural Research. In Applied Statistics in Agricultural, Biological, and Environmental Sciences. Glaz and Yeater (ed.). pp 371-400. ASA, CSSA, and SSSA, Madison, WI. doi: 10.2134/appliedstatistics.2015.0083  Stroup, W.W. 2018. Analysis of Non-Gaussian Data. In Applied Statistics in Agricultural, Biological, and Environmental Sciences. Glaz and Yeater (ed.) pp 449-510. ASA, CSSA, and SSSA, Madison, WI. doi:10.2134/appliedstatistics.2015.0081  Presentations: Bello, N.M. Searching for causal networks in experimental data: a swine application. Biometry Seminar, Dept. of Statistics, University of Wisconsin – Madison. April 27, 2018. (Invited)  Bello, N.M. Exploring biological relationships between reproductive outcomes in a swine production system. Department of Agronomy and Department of Economics and Statistics, National University of Cordoba, Argentina. December 22, 2017. (Invited)  Bello, N.M. Data architecture and related considerations for big data analytics. USDA National Animal Genome Research Program (NAGRP) Meeting on Livestock High-Throughput Phenotyping and Big Data Analytics, Beltsville, Maryland. November 13-14, 2017. (Invited)  Bello, N.M. Statistical principles for reproducible research in the Animal Sciences. Department Seminar Series, Department of Animal Sciences, University of Wisconsin – Madison. September 26th, 2017. (Invited)  Tempelman, R.J. Using genetic relationships to improve the design and analysis of animal science studies. Midwestern section of the American Society of Animal Science. March 13, 2018. (Invited)  Lipka A.E. Quantification of Non-Additive Genomic Contribution towards Food and Energy-related Crop Traits. 9th International Purdue Symposium on Statistics. June 7, 2018. (Invited)       Lipka A.E. Quantification of the Genomic Contribution towards Food and Energy-related Crop Traits. Bioinformatics Seminar, Department of Statistics, Purdue University. April 10, 2018. (Invited)  Lipka A.E. Quantification of the Genomic Contribution towards Food and Energy-related Crop Traits. Spring Seminar Series, Interdisciplinary Plant Group, University of Missouri. April 2, 2018. (Invited)  Lipka A.E. Quantification of the Genomic Contribution towards Food and Energy-related Crop Traits at the Data Driven Crop Design Technology workshop, Kyushu University, Japan. February 20, 2018. (Invited)  Shenstone, E. and Lipka A.E. Genome Wide Association Study for Binomially Distributed Traits: A Case Study for Stalk Lodging in Maize. Genomes to Fields G2F Collaborator’s Meeting, Chicago. December 5, 2017. (Invited)  Rosa, G.J.M. Leveraging on High-Throughput Phenotyping Technologies to Optimize Livestock Genetic Improvement and Husbandry. 69th Annual Meeting of the European Federation of Animal Science (EAAP). Dubrovnik, Croacia, August 27-31, 2018. (Invited)  Rosa, G.J.M. Harnessing Operational Farm Data to Enhance Advancement of Agricultural Sciences. 63rd Annual Meeting of the Brazilian Region (RBRAS) of the International Biometric Society, Curitiba, Brazil, May 23-25, 2018. (Invited)  Rosa, G.J.M. Harnessing Operational Farm Data to Enhance Advancement of Agricultural Sciences. KSU Conference on Applied Statistics in Agriculture, Manhattan, KS. May 07-08, 2018. (Invited)  Rosa, G.J.M. Modeling Networks for Prediction and Causal Inference in Quantitative Genetics and Genomics. Symposium on Genomic Prediction. Beijing, China, October 17, 2017. (Invited)  Chitakasempornkul, K., A. Jager, N. M. Bello. Hierarchical Bayesian structural equation modeling of heterogeneous relationships between performance outcomes in animal production systems. International Biometrics Conference. Barcelona, Spain. July 8-13, 2018.  Johnson, L.C., M. Galliart, N. M. Bello, J. Polland, P. St Amand, M. Knapp, B. Maricle, S. Baer. Experimental natural selection of big bluestem grass ecotypes across the Great Plains’ climate gradient. Population, Evolutionary and Quantitative Genetics Conference PEQG18. Madison, WI. May 13-17. 2018.  Chitakasempornkul, K., M. B. Menegat, M. A. D. Goncalves, S. S. Dritz, A. Jager, M. D. Tokach, R. D. Goodband, N. M. Bello. Exploring causal biological relationships between reproductive traits in high-performing gilts and sows. Midwest Meetings of the American Society of Animal Sciences. Omaha, NE. March 12-14, 2018.  Shawk, D. J., K. N. Nemechek, R. D. Goodband, J. C. Woodworth, M. D. Tokach, S. S. Dritz,  Chitakasempornkulgs, N. M. Bello and J. M. DeRouchey. Effect of increasing chloride concentration on 7 to 12 kg nursery pig growth performance. Midwest Meetings of the American Society of Animal Sciences. Omaha, NE. March 12-14, 2018.  Wu, F., M. D. Tokach, J. M. DeRouchey, S. S. Dritz, J. C. Woodworth, R. D. Goodband, K. Capp, S. Remfry, K. Chitakasempornkul, N. M. Bello, T. G. Nagaraja, R. G. Amachawadi. Effects of tylosin administration route on the development of antimicrobial resistance in fecal enterococci of finishing swine. Midwest Meetings of the American Society of Animal Sciences. Omaha, NE. March 12-14, 2018.  Sharpe, S., L. Johnson, N. M. Bello, O. Parrish and M. Galliart. Rapid evolution in a contaminated environment: evolutionary response of native grass Andropogon virginicus to heavy metals in an abandoned mine site. Annual Conference of the oSTEM professional society (Out in Science, Technology, Engineering and Mathematics). Chicago, IL. November 16-18, 2017.  Rankin, A. J., T. O. Schermerhorn, K. S. KuKanich, N. M. Bello, J. A. S. Huey, K. A. Fentiman and J. A. Meekins. The effects of ophthalmic prednisolone and diclofenac on diabetes mellitus regulation in dogs.  American College of Veterinary Ophthalmologists Conference. Baltimore, MD. October 11-14, 2017.  Murphy, M., D. Hodgson, N. M. Bello. On accuracy and precision of oxygen flow meters. International Veterinary Emergency and Critical Care Symposium. September 13-17, 2017. Nashville, TN. Macchiavelli, R. Oportunidades de Investigación en Biometría. VI Reunión Iberoamericana de Biometría. Quito, Ecuador, November 15-17, 2017.  Madden, L. V. Is disease intensity a good surrogate for yield loss or toxin contamination? A case study with Fusarium head blight of wheat using surrogacy models. The 12th International Epidemiology Workshop. Lillehammer, Norway. June 10-14, 2018.  Yeater, K.M. What is a GLMM? And, how do I analyze it? USDA Northern Crop Science Laboratory, Fargo, ND. March 28, 2018.  Yeater, K.M. Best Practices for Data Spreadsheet Organization. USDA Biosciences Research Laboratory, Insect Genetics and Biochemistry Research Unit, Fargo, ND. July 16, 2018.  Yeater, K.M. Introduction to JMP. USDA Biosciences Research Laboratory, Insect Genetics and Biochemistry Research Unit, Fargo, ND. July 18, 2018.  Torres, P.; Macchiavelli, R.; Teran, L, Chavarria Carvajal, J. Semi-parametric mixed beta regression model for disease severity in plants. XXIX International Biometric Conference, Barcelona, Spain, July 9-13, 2018.  Alhojaily, S., Stott, R., Rutigliano, H., Stevens, J.R., and Isom, S.C. Effects of lactation and negative energy balance on endometrial expression of selected transcripts of Holstein dairy cows at day 7 post-ovulation.  Annual meeting of the American Society of Animal Science, Vancouver, Canada, July 2018.  Publications: Leone, C. M., Dharmasena, M., Tang, C., DiCaprio, E., Ma, Y., Araud, E., Bolinger, H., Rupprom, K., Yeargin, T., Li, J., Schaffner, D., Jiang, X. Sharp, J. L., Vinje, J., and Fraser, A. 2018. Prevalence of human noroviruses in commercial food establishment bathrooms. Journal of Food Protection, 81(5): 719-728.  Vernon, K.L., Cloy, S., Boone, L.H., Coverdale, J.A., Jenkins, T. C., and Sharp, J. L. 2017. Dietary supplementation of conjugated linoleic acid in horses: establishment of baseline values on bone turnover, synovial prostaglandin E2, and gait kinematics. Comparative Exercise Physiology, 13 (2): 71-78.  Mikhailova, E., Hagan, D., Sharp, J. L., Ritter, B., Stiglitz, R., Mealing, V., Allerton, T., Burdette, K., and Solomons, A. 2017. Landscape, soil and plant analysis of Japanese stiltgrass (Microstegium vimineum) invasion in Piedmont region, SC. Communications in Soil Science and Plant Analysis, 48 (9): 1068-1077.  0.1080/00103624.2017.1323099  Bello, N. M., V. C. Ferreira, D. Gianola and G. J. M. Rosa. 2018. Invited review: Conceptual framework for investigating causal effects from observational data in livestock. Journal of Animal Science. In press.  Bello, N. M. and D. Renter. 2018. Invited review: Reproducible research from noisy data: revisiting key statistical principles for the animal sciences Journal of Dairy Science 101 (7):1-23.  Lamsal, A., S. Welch, J. White, K. Thorp and N. M. Bello. 2018. Estimating Parametric Phenotypes that Determine Anthesis Date in Zea mays: Challenges in Combining Ecophysiological Models with Genetics. PLoS One 13(4): e0195841.  Murphy, M.L., D. S. Hodgson and N. M. Bello. 2018. On accuracy and precision of oxygen therapy flowmeters in a veterinary teaching hospital. Veterinary Anaesthesia and Analgesia 45(1): 41-47.  Goncalves, M. A. D., M. D. Tokach, S. S. Dritz, N. M. Bello, K. J. Touchette, R. D. Goodband, J. M. DeRouchey and J. C. Woodworth. 2018. Standardized ileal digestible valine:lysine dose-response effects in 25- to 45- kg pigs under commercial conditions. Journal of Animal Science 96(2): 591-599.  Cha, E., M. Sanderson, D. Renter, N. Cernicchiaro, A. Jager and N. M. Bello. 2017. Implementing structural equation models to observational data from feedlot production systems. Preventive Veterinary Medicine 147: 163-171.  Ekong, P.S., N. M. Bello, L. W. Noll, N. Cernicchiaro, D. G. Renter, J. Bai, T. G. Nagaraja and M. W. Sanderson. 2017. Bayesian estimation of true prevalence, sensitivity and specificity of three diagnostic tests for detection of Escherichia coli O157 in cattle feces. Preventive Veterinary Medicine 148: 21-27.  Goncalves, M. A. D., M. D. Tokach, N. M. Bello, K. J. Touchette, R. D. Goodband, J. M. DeRouchey, J. C. Woodworth and S. S. Dritz. 2017. Dose-response evaluation of the standardized ileal digestible tryptophan:lysine ratio to maximize growth performance of growing-finishing gilts under commercial conditions. Animal. doi:10.1017/S1751731117002968.  Clark, A. B., M. D. Tokach, J. M. DeRouchey, S. S. Dritz, R. D. Goodband, J. C. Woodworth, K. J. Touchette and N. M. Bello. 2017. Modeling the effects of standardized ileal digestible isoleucine to lysine ratio on growth performance of nursery pigs. Translational Animal Science doi:10.2527/tas2017.0048.  Clark, A. B., M. D. Tokach, J. M. DeRouchey, S. S. Dritz, R. D. Goodband, J. C. Woodworth, K. J. Touchette and N. M. Bello. 2017. Modeling the effects of standardized ileal digestible valine to lysine ratio on growth performance of nursery pigs. Translational Animal Science. doi:10.2527/tas2017.0049  Fissekis, S., D. S. Hodgson and N. M. Bello. 2017. Effect of cleaning on accuracy and precision of oxygen flow meters on anesthetic machines of various ages. Veterinary Anaesthesia and Analgesia. http://dx.doi.org/10.1016/j.vaa.2016.10.002.  Delph, K., E. G. Davis, N. M. Bello, K. Hankins, M. J. Wilkerson, C. Ewen. 2017. Comparison of immunologic responses following intranasal and oral administration of a USDA-approved, live-attenuated Streptococcus equi vaccine. Journal of Equine Veterinary Science. doi: 10.1016/j.jevs.2016.08.015  Hardie, L.C., M. J. Vandehaar, R.J. Tempelman, K.A. Weigel, L.E. Armentano, G. Wiggans, R.F. Veerkamp, Y. deHaas, M. Coffey, E.E. Connor, M.D. Hanigan, C.R. Staples, Z. Wang, J.C.M Dekkers, and D.M. Spurlock.  2017.  The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows.  Journal of Dairy Science 100:9061-9075.  de Souza, R.A, R.J. Tempelman, M.S. Allen, W.P. Weiss, J.K. Bernard, and M.J. Vandehaar. 2018. Predicting nutrient digestibility in high producing lactating dairy cows. Journal of Dairy Science 101: 1123-1135.  Toledo-Alvarado, H., A.I. Vazquez, G. de los Campos, R.J. Tempelman, G. Bittante, and A. Cecchinato. 2018.  Diagnosing pregnancy status using infrared spectra and milk composition in dairy cows. Journal of Dairy Science 101:2496-2505.  Lu, Y., M.J. Vandehaar, D.M. Spurlock, K.A. Weigel, L.E. Armentano, E.E. Connor, M. Coffey,R.F. Veerkamp, Y. de Haas, C.R. Staples, Z. Wang, M.D. Hanigan, and R.J. Tempelman. 2018.  Genome wide association analyses based on a multiple trait approach for modeling feed efficiency.  Journal of Dairy Science 101:3140-3154.  Zhou, Y., E.E. Connor, G.R. Wiggans, Y. Lu, R.J. Tempelman, S.G. Schroeder, H. Chen, and G.F. Liu. 2018. Genome-wide copy number variant analysis reveals variants associated with 10 diverse production traits in Holstein cattle.  BMC Genomics 19:314.  Regmi, P., C.I. Robison, D.R. Jones, R.K. Gast, R.J. Tempelman, and D.M. Karcher. 2018.  Effects of different litter substrates and induced molt on production performance and welfare quality parameters of white Leghorn hens housed in multi-tiered aviary system.  Poultry Science. doi.org/10.3382/ps/pey211.  Vanous A, Gardner C, Blanco M, Martin-Schwarze A, Lipka AE, Flint-Garcia S, Bohn M,  Edwards J, and Lübberstedt T. 2018. Association Mapping of Flowering and Height Traits in Germplasm Enhancement of Maize Doubled Haploid (GEM-DH) Lines. The Plant Genome.  Fenton ME, Owens BF, Lipka AE, Ortiz D, Tiede T, Mateos-Hernandez M, Ferruzzi MG, and Rocheford T. 2018. High-density linkage mapping of vitamin E content in maize grain. Molecular Breeding 38(3):31.  Diepenbrock CH, Kandianis CB, Lipka AE, Magallanes-Lundback M, Vaillancourt B, Góngora-Castillo E, Wallace JG, Cepela J, Mesberg A, Bradbury P, Ilut DC, Mateos-Hernandez M, Hamilton J, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, and DellaPenna D. 2017. Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain. The Plant Cell Online: tpc-00475.  Ding Yezhang, Huffaker A, Köllner TG, Weckwerth P, Robert CAM, Spencer JL, Lipka AE, and Schmelz EA. 2017. Selinene volatiles are essential precursors for maize defense promoting fungal pathogen resistance. Plant Physiology: pp-00879.  Dong H, Liu S, Clark LV, Sharma S, Gifford JM, Juvik JA, Lipka AE, and Sacks EJ. 2017. Genetic mapping of biomass yield in three interconnected Miscanthus populations. GCB Bioenergy.  Hu S, Sanchez DL, Wang C, Lipka AE, Yin Y, Gardner CA and Lübberstedt T. 2017. Brassinosteroid and Gibberellin control of seedling traits in maize (Zea mays L.). Plant Science.  Feldman MJ, Paul RE, Banan D, Barrett JF, Sebastian J, Yee MC, Jiang H, Lipka AE, Brutnell TP, Dinneny JR, Leakey AD. 2017. Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria. PLoS Genetics 13(6):e1006841.  Hu S, Wang C, Sanchez  DL, Lipka AE, Liu P, Yin Y, M Blanco, and Lübberstedt T. 2017. Gibberellins promote brassinosteroids action and both increase heterosis for plant height in maize (Zea mays L.). Frontiers in Plant Science 8:1039.  Dórea, J. R. R., Rosa, G. J. M., Weld, K. A. and Armentano, L. E. 2018. Mining data from milk infrared spectroscopy to improve feed intake predictions in lactating dairy cows. Journal of Dairy Science 101(7): 5878-5889.  Wang, Y., Mi, X., Rosa, G. J. M., Chen, Z., Lin, P., Wang, S. and Bao, Z. 2018. Technical note: an R package for fitting sparse neural networks with application in animal breeding. Journal of Animal Science 96: 2016-2026.  Lopes, F. B., Wu, X.-L., Li, H., Xu, J., Perkins, T., Genho, J., Ferretti, R., Tait Jr. R. G., Bauck, S. and Rosa, G. J. M. 2018. Improving accuracy of genomic prediction in Brangus cattle by adding animals with imputed low-density SNP genotypes. Journal of Animal Breeding and Genetics 135:14-27.  Ramos, S. B., Caetano, S. L., Rosa, G. J. M., Savegnago, R. P., Kern, E. L., Bernardes, P. A., Lôbo, R. B. and Munari, D. P. 2018. Estimation of genetic parameters for cow age at last calving under different censorship criteria. Livestock Science 208: 40-43.  Amiri Roudbar, M., Abdollahi-Arpanahi, R., Ayatollahi Mehrgardi, A., Mohammadabadi, M., Taheri Yeganeh, A. and Rosa, G. J. M. 2018. Estimation of the variance due to parent-of-origin effects for productive and reproductive traits in Lori-Bakhtiari sheep. Small Ruminant Research 160: 95-102.  Huang, X., Elston, R. C., Rosa, G. J. M., Mayer, J., Ye, Z., Kitchner, T., Brilliant, M. H., Page, D. and Hebbring, S. J. 2018. Applying family analyses to electronic health records to facilitate genetic research. Bioinformatics 34(4): 635-642.  Dadousis, C., Pegolo, S., Rosa, G. J. M., Bittante, G., Cecchinato, A. 2017. Genome-wide association and pathway-based analysis using latent variables related to milk protein composition and cheesemaking traits in dairy cattle. Journal of Dairy Science 100: 9085-9102.  Ferreira, V. C., Thomas, D. L., Valente, B. D. and Rosa, G. J. M. 2017. Causal effect of prolificacy on milk yield in dairy sheep using propensity score. Journal of Dairy Science 100: 8443–8450.  Töpner, K., Rosa, G. J. M., Gianola, D. and Schön, C.-C. 2017. Bayesian networks illustrate genomic and residual trait connections in maize (Zea mays L.). G3-Genes Genomes Genetics 7:2779-2789.  Caetano, S. L., Rosa, G. J. M., Savegnago, R. P., Ramos, S. B., Bernardes, P. A., Bezerra, L. A. F., Lôbo, R. B., Paz, C. C. P. and Munari, D. P. 2017. Estimation of genetic parameters for longevity considering the cow’s age at last calving. Journal of Genetics 58:103-109.  Cieniewicz, E. J., Pethybridge, S. J., Gorny, A., Madden, L. V., McLane H., Perry, K. L., and Fuchs, M. 2017. Spatiotemporal spread of grapevine red blotch-associated virus in a California vineyard. Virus Research 241: 156-162.  Cordova, L. G., Madden, L. V., Amiri, A., Schnabel, G., and Peres, N. A. 2017. Meta-analysis of a web-based disease forecast system for control of anthracnose and Botrytis fruit rots of strawberry in southeastern United States. Plant Disease 101: 1910-1917.  Ojiambo, P.S., Yuen, J., van den Bosch, F., and Madden, L.V. 2017. Epidemiology: Past, present, and future impacts on understanding disease dynamics and improving plant disease management—a summary of Focus Issues articles. Phytopathology 107: 1092-1094.  Savary, S., Djurle, A., Yuen, J., Ficke, A., Rossi, V., Esker, P.D., Fernandes, M. C., Del Ponte, E. M., Kumar, J., Madden, L. V., Paul, P., McRoberts, N., Singh, P. K., Huber, L., Pope de Vallavielle, C., Saint-Jean, S., and Willocquet, L. 2017. A white paper on global wheat health based on scenario development and analysis. Phytopathology 107:  1109-1122.  Conrad, A. O., McPherson, B. A., Wood, D. L., Madden, L. V., and Bonello, P. 2017. Constitutive phenolic biomarkers identify naïve Quercus agrifolia resistant to Phytophthora ramorum, the causal agent of sudden oak death. Tree Physiology 37: 1686-1696.  Jeger, M. J., Madden, L. V., and van den Bosch, F. 2018. Plant virus epidemiology: Applications and prospects for mathematical modeling and analysis to improve understanding and disease control. Plant Disease 102: 837-854.  Madden, L. V., Hughes, G., Bucker Moraes, W., Xu, X.-M., and Turechek, W. W. 2018. Twenty-five years of the binary power law for characterizing heterogeneity of disease incidence. Phytopathology 108: 656-680.  Piepho, H.-P., Madden, L. V., Roger, J., Payne, R., and Williams, E. R. 2018. Estimating the variance for heterogeneity in arm-based network meta-analysis. Pharmaceutical Statistics 17: 264-277.  Thomason, J.E., M.C. Savin, K.R. Brye and E.E. Gbur 2017. Native earthworm population dominance after seven years of tillage, burning, and residue level management in a wheat-soybean double crop system. Applied Soil Ecology, 120, 211-218.  Brye, K.R., C.W. Rogers, A.D. Smartt, R.J. Norman, J.T. Hardke and E.E. Gbur 2017. Methane emissions as affected by crop rotation and rice cultivar in the Lower Mississippi River Valley, USA. Geodermal Regional, 11, 8-17.  Sharpley, A.N., B.E. Haggard, L. Berry, J. Burke, K. Brye, M.D. Daniels, E. Gbur, T. Glover, T. Kresse, P. Hays and K.W. VanDevender 2017. Nutrient concentrations in Big Creek correlate to regional watershed land use. Agricultural & Environmental Letters. doi: 10.2134/ael2017.08.0027.  Fournier, A.M.V., D.C. Mengel, E.E. Gbur and D.G. Krementz 2017. The timing of Autumn Sora (Porzana carolina) migration in Missouri. The Wilson Journal of Ornithology, 129, 765-770.  Adams, T.C., K.R. Brye, M.C. Savin, J.A. Lee and E.E. Gbur 2017. Microbial carbon substrate utilization differences among high and average yield soybean areas. Agriculture, 7(6), 48. doi: 10.3390/agriculture760048.  Bourland, F.M. and E.E. Gbur 2017. Relationships of plant trichomes to yield and fiber quality parameters in upland cotton. Journal of Cotton Science 21, 296-305.  Xing, X.Y., M. Popp, P. Chen, P. Manjarrez-Sandoval and E. Gbur 2018. Evaluation of high oil and high protein soybean using component pricing. Journal of Crop Improvement. doi: 10.1080/15427528.2017.1414722 .  Martin, S.M., J.K. Norsworthy, R.C. Scott, J. Hardke, G.M. Lorenz and E.Gbur 2018. Effect of thiamethoxam on injurious herbicides in rice. Advances in Crop Science and Technology, 6(2). doi:10.4172/2329-8863.1000351.  Adams, T.C., K.R. Brye, L.C. Purcell, J. Ross, E.E. Gbur  and M.C. Savin 2018. Physiological plant response differences among high and average yield soybean areas in Arkansas. Crop, Forage, and Turf Management. doi:10.2134/cfm2017.07.0047.  Nayduch, D., K. Zurek, J.L. Thomson, and K.M. Yeater.  2018. Effects of bacterial dose and fly sex on persistence and excretion of Salmonella enterica serovar Typhimiurium from adult house flies (Musca domestica L.; Diptera: Muscidae).  J. Medical Entomology, tjy055, doi.org/10.1093/jme/tjy055  Brabec, D., M. Perez-Fajardo, H. Dogan, K. Yeater, and E. Maghirang.  2018.  Effectiveness of modified 1-hour air-oven moisture methods for determining popcorn moisture.  Applied Engineering in Agriculture. 34(3):617-621. doi: 10.13031/aea.12621.  Funk, P., C. Armijo, D. Whitelock, M., Pelletier, J. Wanjura, G. Holt, R. Hardin IV, C. Delhom, and K. Yeater.  2018.  Accuracy of alternate oven drying procedures. In Proceedings of the National Cotton Council Beltwide Cotton Conference.  San Antonio, TX.  Parsa, S, V Ortiz, MI Gómez-Jiménez, M Kramer, FE Vega.  2018.  Root environment is a key determinant of fungal entomopathogen endophytism following seed treatment in the common bean, Phaseolus vulgaris.  Biological Control 116: 74–81.  Wright, BN, Bailey, RL, Craig, BA, Mattes, RD, McCormack, L, Stluka, S, Franzen-Castle, L, Henne, B, Mehrle, D, Remley, D, and Eicher-Miller, HA. 2018.  Daily Dietary Intake Patterns Improve after Visiting a Food Pantry among Food-Insecure Rural Midwestern Adults, Nutrients, 10(5), 583.  Adelsperger, AR, Phillips, EH, Ibriga, HS, Craig, BA, Green, LA, Murphy, MP, and Goergen, CJ. 2018.  Development and growth trends in angiotensin II-induced murine dissecting abdominal aortic aneurysms, Physiological Reports, 6(8), e13668.  DePalma, G and Craig, BA. 2018. Bayesian monotonic errors-in-variables models with applications to pathogen susceptibility testing, Statistics in Medicine, 37(3), 487.  Mischler, RA, Armah, SM, Craig, BA, Rosen, AD, Banerjee, A, Selzer, DJ, Choi, JN, and Gletsu-Miller, N. 2018.  Comparison of Oral Iron Supplement Formulations for Normalization of Iron Status Following Roux-EN-y Gastric Bypass Surgery: A Randomized Trial, Obesity Surgery, 28(2), 369  Torres, Norma, Xue Yu, Ingrid Y. Padilla, Raul E. Macchiavelli, Reza Ghasemizadeh, David Kaeli, Jose F. Cordero, John D. Meeker, Akram N. Alshawabkeh 2018. The influence of hydrogeological and anthropogenic variables on phthalate contamination in eogenetic karst groundwater systems. Environmental Pollution 237:298-307.  Bishop, M.O., Stevens, J.R., and Isom, S.C. Statistical methods for assessing individual oocyte viability through gene expression profiles.  Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture, 2017.  Saunders, G., Fu, G. and Stevens, J.R. 2017. A Bivariate Hypothesis Testing Approach for Mapping the Trait-Influential Gene. Scientific Reports 7: 12798.  Pillai, S.M., Hoffman, M.L., Jones, A.K., McFadden, K.K., Stevens, J.R., Zinn, S.A., Reed, S.A., and Govoni, K.E. 2017. Poor maternal nutrition during gestation alters muscle gene expression in fetal offspring.  Journal of Animal Science 95(suppl4): 150-150.  Stevens, J.R., Jones, T.R., Lefevre, M., Ganesan, B., and Weimer, B.C. 2017. SigTree: a microbial community analysis tool to identify and visualize significantly responsive branches in a phylogenetic tree. Computational and Structural Biotechnology Journal 15: 372-378.  Buckland KR, Reeve JR, Creech JE, and Durham SL. 2018. Managing soil fertility and health for quinoa production and weed control in organic systems. Soil & Tillage Research 184: 52-61. doi.org/10.1016/j.still.2018.07.001  Heroy KY, St. Clair SB, Burritt EA, Durham SL, and Villalba JJ. 2018. Nutritional state and secondary compounds influence trembling aspen (Populus tremuloides) intake by lambs. Applied Animal Behaviour Science.  doi.org/10.1016/j.applanim.2018.05.031  Ryan MP, Neuman-Lee LA, Durham SL, Smith GD, and French SS. 2018. A sex-dependent change in behavioral temperature regulation in African house snakes (Lamprophis fuliginosus) challenged with different pathogens. Journal of Thermal Biology 73: 8-13. doi:10.1016/j.jtherbio.2018.02.001  Portman ZM, Tepedino VJ, Tripodi AD, Szalanski AL, and Durham SL. 2018. Local extinction of a rare plant pollinator in Southern Utah (USA) associated with invasion by Africanized honey bees. Biological Invasions 20(3): 593-606. doi:10.1007/s10530-017-1559-1  Other project related activities: Larry Madden maintains a website with statistical software code (SAS) and PowerPoint presentations on a range of data-analytic subjects. The material is based heavily on previously presented workshops. The address is https://u.osu.edu/agstatworkshops/

Impact Statements

(3) Members continuing to offer workshops and, where appropriate, alternative means of continuing education and support for subject matter scientists, reviewers, and technical editors on valid design and statistical analysis of studies.

Date of Annual Report: 08/09/2019

Report Information

Annual Meeting Dates: 06/20/2019 - 06/21/2019
Period the Report Covers: 10/01/2018 - 09/30/2019

Participants

Nora Bello (KS), Deborah Boykin (USDA-ARS), Bruce Craig (IN, Admin.), Xin Dai (UT), Philip Dixon (IA), Sara Duke (USDA-ARS), Susan Durham (UT), Ed Gbur (AR), Carla Goad (OK), Kathryn Goode (IA), Kathy Hanford (NE), Nick Keuler (WI), Matt Kramer (USDA-ARS), Alex Lipka (IL), Larry Madden (OH), Neil Paton (Cargill), Guilherme Rosa (WI), John Stevens (UT), Rob Tempelman (MI), Edzard van Santen (FL), Kathy Yeater (USDA-ARS), Linda Young (USDA-NASS), Bruce Mackey (USDA-ARS), Debra Palmquist (USDA-ARS), Bryan Vinyard (USDA-ARS), Matthew Murphy (IL), Brian Rice (IL), Marcus Olatoye (IL)

Brief Summary of Minutes

Minutes Attachment:

NCCC-170_2019_Meeting_Minutes.pdf

Accomplishments

Workshops: Nora Bello, Bruce Craig and Rob Tempelman co-led a one and a half day short course on general and generalized linear mixed models in conjunction with the American Dairy Science Association. Cincinnati, Ohio. June 26-27, 2019. Nora Bello presented a short course entitled “Modern Statistics for Agricultural Research” at the College of Agriculture, Royal University of Agriculture, Phnom Penh, Cambodia. August 11-15, 2019. Nora Bello presented a short course entitled “Hierarchical Structural Equation Models” as part of the Graduate Program in Applied Statistics at National University of Cordoba (Universidad Nacional de Cordoba), Argentina. December 19, 2018. Nora Bello presented a short course entitled on “Applied Bayesian Modeling” for the Association of Veterinary Epidemiology and Preventive Veterinary Medicine (AVEPM) at the 2018 Conference of Research Workers in Animal Disease (CRWAD). December 1-2, 2018. Nora Bello presented a short course on generalized linear mixed models at the XXIII Meeting of the International Biometrics Society Argentinean Chapter (Grupo Argentino de Biometria) and the II Argentinean-Chilean Biometrical Meeting. Neuquen, Argentina. October 10-12, 2018. Nora Bello presented a two day workshop entitled “Summer Workshop on Mixed Models” sponsored by Shell, Inc. US at Kansas State University in Manhattan, Kansas. 2018. Larry Madden taught a workshop on “Mixed models in plant pathology” at the annual meeting of the American Phytopathological Society (APS). Cleveland, Ohio. August 3, 2019. Larry Madden taught a series of six lectures on “Plant disease prediction: Concepts, examples, model development and testing, cost functions, and Bayesian decisions” in a plant pathology short course in Honne, Norway. May 6-11, 2019. Kathy Yeater taught a training seminar on survival analysis methods to the USDA Biosciences Research Laboratory, Insect Genetics and Biochemistry Research Unit, Fargo, ND.  June 12, 2019. Raul Macchiavelli and A. Pimentel taught a short course entitled “Mixed Models for Data Analysis” at the Universidad Autónoma de Santo Domingo, May 20-24, 2019. Raul Macchiavelli and E. Jiménez Cabán taught a workshop entitled “Introduction to SAS University Edition” organized by CEP, Mayaguez, PR, March 12, 2019. Raul Macchiavelli taught a short course entitled “Spatial and Spatio-temporal Models with R-INLA” at the Congreso Escuela de Estadística Espacial, Córdoba, Argentina. December 10-14, 2018. Di Rienzo and Raul Macchiavelli taught a short course entitled “Linear Mixed Models” at the at Universidad Nacional del Comahue during the Reunión Científica Anual Grupo Argentino de Biometría, Neuquén, Argentina. October 2018 J Di Rienzo, Raul Macchiavelli and F. Casanoves, taught a short cousre entitled “Advanced Linear Mixed Models” at CATIE (Tropical Agronomic Center for Research and Teaching), Turrialba, Costa Rica, August-September 2018. Raul Macchiavelli and P. Torres taught a short course entitled “Advanced Statistical Models Applied in Health and Environmental Sciences” at CELFI (National University of Buenos Aires. August 6-15, 2018. Guilherme Rosa taught a short on “Graphical Models and the Analysis of Observational Data” at the 64th Annual Meeting of the Brazilian Region of the International Biometric Society (RBRAS - IBS), Cuiaba - Brazil. July 29 - Aug 2, 2019. Guilherme Rosa taught a short course on “Quantitative Genetics” (co-taught with Dr. Bruce Walsh) at the 24th Summer Institute in Statistical Genetics, University of Washington, Seattle, WA. July 15-17, 2019. Guilherme Rosa taught a short course on “Mixed Models in Quantitative Genetics” (co-taught with Dr. Bruce Walsh) at the 24th Summer Institute in Statistical Genetics, University of Washington, Seattle - WA. July 17-19, 2019. Bruce Walsh and Guilherme Rosa taught a short course on “Selection and Breeding” at the Technical University of Munich, Herrsching, Germany. June 24 - July 2, 2019. Guilherme Rosa taught a short course on “Introduction to Graphical Models with Applications to Quantitative Genetics and Genomics” (co-taught with Francisco Penagaricano) at the University of Padova, Padova, Italy. June 3-7, 2019. Guilherme Rosa taught a short course on “Introduction to Graphical Models with Applications to Quantitative Genetics and Genomics” (co-taught with Francisco Penagaricano) at the University of New England, Armidale, Australia. January 28-February 1, 2019. Guilherme Rosa taught a short course on Statistical Modeling in Animal Breeding and Genetics at the Sao Paulo State University (UNESP), Jaboticabal, Brazil. November 10-14, 2018. Alex Lipka presented workshop at the II International Meeting on Plant Breeding, University of Sao Paulo, ESALQ, Piracicaba, Brazil entitled “Statistical mechanisms and practical applications of genome-wide association studies, genomic selection, and related analyses.” October 5, 2018. Alex Lipka presented workshop at the 10th Congresso Brasileiro de Melhoramento de Plantas, Aguas de Lindoia, Brazil entitled “Implementing genomic selection and comparing it to marker-assisted selection.” July 28, 2019. Edzard van Santen taught a one-day workshop at the 2018 International Meetings of the Tri-Societies (ASA-CSSA-SSA) in Baltimore, MD on basic data handling techniques in SAS. (November 4, 2018). Presentations: Bello, N.M. Dynamic crop modeling: A hierarchical Bayesian specification and extensions for genomic prediction. AgMiP Global Workshop. Oklahoma State University. May 29, 2019 (Invited). Bello, N.M. Systems modeling: Interdisciplinary opportunities in animal agriculture. Department of Pathobiology, College of Veterinary Medicine, University of Illinois. March 29, 2019 (Invited). Bello, N.M. Systems modeling: a case study in animal production agriculture. Department of Pathobiology, College of Veterinary Medicine, University of Illinois, March 28, 2019 (Invited). Bello, N.M. Causality networks and experimental data: a swine application. XXIII Meeting of the International Biometric Society Argentinean-Chilean Chapter (Grupo Argentino de Biometria). Neuquen, Argentina. October 13, 2018 (Invited). Lipka, A.E. Quantification of the genomic contribution towards food and energy-related crop traits. Hokkaido University, Sapporo, Japan. August 22, 2018 (Invited). Lipka, A.E. Quantification of the genomic contribution towards food and energy-related crop traits. Chinese Academy of Sciences, Beijing, China. August 27, 2018 (Invited). Lipka, A.E. Quantification of the genomic contribution towards food and energy-related crop traits. Tokyo University, Tokyo, Japan. August 30, 2018 (Invited). Lipka, A.E. Quantification of the genomic contribution towards food and energy-related crop traits. II International Meeting on Plant Breeding, University of Sao Paulo, ESALQ, Piracicaba, Brazil. October 3, 2018 (Invited). Lipka, A.E. Exploration of the performance of GWAS models quantifying epistasis and genomic selection models that include peak-associated markers as fixed-effect covariates. Plant and Animal Genome (PAG) Genomic Selection and Genome-wide Association Studies Workshop, San Diego, CA. January 12, 2019 (Invited). Lipka, A.E. Quantification of the genomic contribution towards food and energy-related crop traits. Georg-August-Universität Göttingen, Göttingen, Germany. February 7, 2019 (Invited). Lipka, A.E. Quantification of the genomic contribution towards food and energy-related crop traits. KWS SAAT SE Company Headquarters, Einbeck, Germany. February 8, 2019 (Invited). Lipka, A.E. Exploration of the impact of genetic architecture on the performance of GWAS and GS models. National Association of Plant Breeders Webinar Series (Online). May 29, 2019 (Invited). Lipka, A.E. Exploration of the Impact of Genetic Architecture on the Performance of GWAS Models Quantifying Epistasis and Genomic Selection Models that Include Peak-Associated Markers as Fixed-Effect Covariates. 10th Congresso Brasileiro de Melhoramento de Plantas. Aguas de Lindoia, Brazil. July 31, 2019 (Invited). Johnson, L., M. Galliart, N.M. Bello, S. Baer, B. Maricle, J. Poland. Experimental selection of big bluestem grass ecotypes across the Great Plains climate gradient. Joint Annual Conference of the American Society of Naturalists, the Society for the Study of Evolution and the Society of Systematic Biologists. Providence, RI. June 21-25, 2019 (Invited). Renter, D.G., N.M. Bello, N. Cernicchiaro, R.L. Larson, M.W. Sanderson, T.C. Schroeder, B.J. White. Risk management strategies to reduce the impacts of bovine respiratory disease complex I commercial feedlot cattle. Conference of Research Workers in Animal Disease (CRWAD). Chicago, IL. December 1-4, 2018 (Invited). Albin, N., P. Alderman, N.M. Bello, C. Chen, L. Duke, D. Flippo, F. Fondjo-Fotou, A. Fritz, G. Hettiarachchi, C. Howard, K. Jagadish, J. Poland, E. Santos, J. Snow, S. Welch, L. Yan. Building field-based ecophysiological genome-to-phenome prediction. Kansas State University Global Food Systems Focus Day. Manhattan, KS. March 7, 2019. Welch, S. M., P.D. Alderman, F. Fondjo, C. Leuschen, A. Lamsal, D. Gomez-Garcia, M. Guttieri, A. Fritz, A. Asebedo, N.M. Bello, S. Kulesza, B. Washburn, E. Santos, K. Corwin. Co-design of Gene-Based Ecophysiological Crop Models for Breeding and Management. 2018 International Annual Meeting of the American Society of Agronomy, the Crop Science Society of America and the Canadian Society of Agronomy. Baltimore, MD. November 4-7, 2018. Johnson, L., S. Sharpe, N.M. Bello, M. Galliart and O. Parrish. Rapid adaptation in a contaminated environment: Evolutionary adaptive response of old field grass Andropogon virginicus to heavy metals in an abandoned mine site. Annual meeting of the Botanical Society of America. Rochester, MN. July 21-25, 2018. Chitakasempornkul, K., A. Jager, N.M. Bello. Hierarchical Bayesian structural equation modeling of heterogeneous relationships between performance outcomes in animal production systems.  International Biometrics Conference. Barcelona, Spain. July 8-13, 2018. De Jesús, A., R. Macchiavelli. Application of meta-analysis in nitrogen fertilizer studies in Puerto Rico.  XVII Conferencia Española de Biometría y VII Encuentro Iberoamericano de Biometría. Valencia, Spain. June 21-23, 2019. Di Rienzo, J., R. Macchiavelli,  Casanoves, F., Balzarini, M. Non-linear mixed model implementation in InfoStat and Interface with the nmle and lme4 Libraries in R. XVII Conferencia Española de Biometría y VII Encuentro Iberoamericano de Biometría. Valencia, Spain. June 21-23, 2019. Madden, L.V. Meta-analysis for the synthesis of evidence in plant pathology. Ohio State University. August 2018. Madden, L.V. The cost of plant disease prediction: A case study with Fusarium head blight of wheat.  Colorado State University. September 2018. Other project related activities: Nora Bello is an Associate Editor for the Journal of Agricultural, Biological and Environmental Statistics (JABES). Nora Bello is a reviewer for Federal Grant Review Panels in the USDA–AFRI–NIFA Exploratory Research Program. Larry Madden maintains a website with statistical software code (SAS) and PowerPoint presentations on a range of data-analytic subjects. Material based heavily on previously presented workshops. https://u.osu.edu/agstatworkshops/

Publications

Chitakasempornku, K., M.B. Menegat, G.J.M. Rosa, F.B. Lopes, A. Jager, M.A.D. Goncalves, S.S. Dritz, M.D. Tokach, R.D. Goodband, N.M. Bello (2019). Investigating causal biological relationships between reproductive traits in high-performing gilts and sows. Journal of Animal Science 97(6): 2385-2401. DOI: 10.1093/jas/skz1 Li, Y., R.A. Cloyd and N.M. Bello (2019). Effect of integrating the entomopathogenic fungus, Beauveria bassiana and the rove beetle Dalotia coriaria in suppressing western flower thrips, Frankliniella occidentalis populations under greenhouse conditions. Journal of Economic Entomology.  doi.org/10.1093/jee/toz132 Li, Y., R.A. Cloyd and N.M. Bello (2019). Effect of insecticide drench applications on western flower thrips, Frankliniella occidentalis, pupae in the growing medium. HortScience 54(5): 890-895. doi.org/10.21273/HORTSCI13892-19 Passafaro, T., D. Van de Stroet, N.M. Bello and G.J.M. Rosa (2019). Generalized additive mixed modeling of total transport losses of market-weight pigs. Journal of Animal Science 97(5): 2025-2034. doi.org/10.1093/jas/skz087 Oliveira, R.C., K.J. Sailer, H.T. Holdorf, C.R. Seely, R.S. Pralle, M.B. Hall, N.M. Bello and H.M.White  (2019). The effect of fermented ammoniated condensed whey supplementation on lactation performance and metabolic health in transition dairy cows. Journal of Dairy Science 102(3): 2283-2297. doi.org/10.3168/jds.2018-15519. ***Selected as Editor’s choice for the March Issue of the Journal of Dairy Science Wu, F., M.D. Tokach, J.M. DeRouchey, S.S. Dritz, J.C. Woodworth, R.D. Goodband, K. Capps, S. Remfry, K. Chitakasempornkul, N.M. Bello, T.G. Nagaraja and R.G. Amachawadi (2019). Effects of tylosin administration routes on the prevalence of antimicrobial resistance among fecal enterococci of finishing swine. Foodborne Pathogens and Disease. doi.org/10.1089/fpd.2018.2551 Galliart, M., N.M. Bello, M. Knapp, J. Poland, P. St. Amand, S. Baer, B. Maricle, A.B. Smith and L. Johnson. (2019). Local adaptation, genetic divergence, and experimental selection in a foundation grass across the US Great Plains’ climate gradient. Global Change Biology 25: 850-868. doi.org/10.1111/gcb.14534 Chen, R.; N.M. Bello; M.W. Becker and L. Bix. (2018). Chasing red herrings: Can visual distracters extend the time children take to open child resistant vials? PLOS ONE 13(12): e0207738. doi.org/10.1371/journal.pone.0207738 Chitakasempornkul, K., E. Cha, D. Renter, M. Sanderson, A. Jager, and N.M. Bello (2018). Accounting for data architecture in structural equation modeling of feedlot performance outcomes. Journal of Agricultural, Biological and Environmental Statistics 23(4): 529-549. doi.org/10.1007/s13253-018-0336-7. Ekong, P.S., M.W. Sanderson, P.B. Shridhar, N. Cernicchiaro, D.G. Renter, N.M. Bello, J. Bai and T.G. Nagaraja (2018). Bayesian estimation of sensitivity and specificity of culture- and PCR-based methods for the detection of the six major non-O157 Escherichia coli serogroups in cattle feces. Preventive Veterinary Medicine 161: 90-99. doi: 10.1016/j.prevetmed.2018.10.012 Bello, N.M., V.C. Ferreira, D. Gianola and G. J. M. Rosa (2018). Invited review: Conceptual framework for investigating causal effects from observational data in livestock. Journal of Animal Science 96(10): 4045-4062. doi: 10.1093/jas/sky277. Bello, N.M. and D. Renter (2018). Invited review: Reproducible research from noisy data - revisiting key statistical principles for the animal sciences. Journal of Dairy Science 101(7):1-23. doi: 10.3168/jds.2017-13978 Lamsal, A., S. Welch, J. White, K. Thorp and N.M. Bello (2018). Estimating Parametric Phenotypes that Determine Anthesis Date in Zea mays: Challenges in Combining Ecophysiological Models with Genetics. PLoS One 13(4): e0195841. Murphy, M.L., D.S. Hodgson and N.M. Bello (2018). On accuracy and precision of oxygen therapy flowmeters in a veterinary teaching hospital. Veterinary Anaesthesia and Analgesia 45(1): 41-47. Goncalves, M.A.D., M.D. Tokach, S.S. Dritz, N.M. Bello, K. J. Touchette, R. D. Goodband, J. M. DeRouchey and J. C. Woodworth (2018). Standardized ideal digestible valine:lysine dose-response effects in 25- to 45- kg pigs under commercial conditions. Journal of Animal Science 96(2): 591-599. doi: 10.1093/jas/skx059. Williams, H.E., M.D. Tokach, S.S. Dritz, J.C. Woodworth, J.M. DeRouchey, T.G. Nagaraja, R.D. Goodband, K. Chitakasempornkul, N.M. Bello and R.G. Amachawadi (2018). Effects of chlortetracycline alone or in combination with probiotics on nursery pig growth performance and antimicrobial susceptibility of fecal Escherichia coli. Journal of Animal Science doi: 10.1093/jas/sky370. Goncalves, M.A.D., M.D. Tokach, N.M. Bello, K.J. Touchette, R.D. Goodband, J.M. DeRouchey, J.C. Woodworth and S.S. Dritz (2018). Dose-response evaluation of the standardized ideal digestible tryptophan:lysine ratio to maximize growth performance of growing-finishing gilts under commercial conditions. Animal 12(7):1380-1387. doi: 10.1017/S1751731117002968. Delph, K., E.G. Davis, N.M. Bello, K. Hankins, M.J. Wilkerson, C. Ewen (2018). Comparison of immunologic responses following intranasal and oral administration of a USDA-approved, live-attenuated Streptococcus equi vaccine. Journal of Equine Veterinary Science 60:29-34. doi: 10.1016/j.jevs.2016.08.015 Lalman, D. L., C. E. Andresen, C. L. Goad, L. Kriese-Anderson, M. E. King, K. G. Odde (2019). Weaning weight trends in the US beef cattle industry. Applied Animal Science 35(1): 57-65. Akehi K, BC Long, C Goad, and A Cody (2018). Pulsed shortwave diathermy and moist heat pack application on musculotendinous stiffness and hysteresis during passive ankle motion. Athl Train Sports Health Care 10(1):31-40. Cobb, Adam B., Gail W. T. Wilson, Carla Goad, Michael A. Grusak (2018). Influence of alternative soil amendments on mycorrhizal fungi and cowpea production. Heliyon 4(7):e00704. DOI: 10.1016/j.heliyon.2018.e00704. Dunn, Bruce, Hardeep Singh, Carla Goad, (2018). Relationship between chlorophyll meter readings and nitrogen in poinsettia leaves, Journal of Plant Nutrition 41(12): 1-10. DOI: 10.1080/01904167.2018.1459697. Haviland, C. L., Chris J. Richards, J. A. Reed, M. E. Youngers, S. T. Quanz, C. G. Lockard, M. A. Woolsoncroft, T. C. Husz, Carla Goad, T. A. Jackson, D. L. Step, M. Corbin, Clint R. Krehbiel (2018). Growth, performance, and carcass characteristics of feedlot Holstein steers fed ractopamine hydrochloride. Journal of Animal Science 96 (suppl_2): 80-81. Swearengin, Lance, Bruce Dunn, Hardeep Singh, Carla Goad (2018). Evaluation of a mobile phone plant nitrogen recommendation application in the greenhouse, Journal of Plant Nutrition, DOI: 10.1080/01904167.2018.1510519. Panthi, R., Kelly, A., McMahon, D.J., Dai, X., Vollmer, A., and Sheehan, J. (2019). Response surface methodology modeling of protein concentration, coagulum cut size, and set temperature on curd moisture loss kinetics during curd stirring. Journal of Dairy Science, 102 (6): 4989-5004.   Wang, Y. X., Li, L. Q., Sun, Y. P., and Dai, X. (2019). Relative salt tolerance of Seven Japanese Spirea cultivars. HortTechnology, 29 (3): 367–373. Stewart, E. K., Beauchemin, K. A., Dai, X., MacAdam, J.W., and Villalba, J. J. (2019). Effect of tannin-containing hays on enteric methane emissions and nitrogen partitioning in beef cattle. Journal of Animal Science, 97(8): 3286-3299. Krombeen, S. K., Shankar, V., Noorai, R. E., Saski, C. A., Sharp, J. L., Wilson, M. E. (2019).  The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestations. BMC Genomics, 20 (1): 254-269. Gredell, D., Schroeder, A. R., Belk, K., Broeckling, C., Heuberger, A., Kim, S.Y., King, D. A., Shackelford, S. D., Sharp, J. L., Wheeler, T. L., Woerner, D. R., and Prenni, J. (2019).  Comparison of machine learning algorithms for predictive modeling of beef attributes using Rapid Evaporative Ionization Mass Spectrometry (REIMS) data. Scientific Reports, 9: 5721. Krombeen, S. K., Shankar, V., Noorai, R. E., Saski, C. A., Sharp, J. L., Wilson, M. E. (2019). The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestations. BMC Genomics, 20 (1): 254-269. Funk, P.A., A.A. Terrazas, K.M. Yeater, R.G. Hardin IV, C.B. Armijo, D.Pl. Whitelock, M.G. Pelletier, J.D. Wanjura, G.A. Holt, and C.D. Delhom  (2018). Procedures for Moisture Analytical Tests Used in Cotton Ginning Research. Transactions of the ASABE. 61(6): 1985-1995.  https://doi.org/10.13031/trans.12980 Halvorson, J.J., D.W. Archer, M.A. Liebig, K.M. Yeater, and D.L. Tanaka (2019). 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Pereira, R.E. Mason, J.R. Rupe, B.H. Bluhm, L. Wood, L.A. Mozzoni and P. Chen (2019). QTL mapping of charcoal rot resistance in PI 567562A soybean accession. Crop Science, 59(2). doi:10.2135/cropsci2018.02.0145. Desrochers, J., K.R. Brye, E. Gbur, and E. Mason (2019). Long term residue and water management effects on infiltration in a wheat-soybean system on a loessial soil in eastern Arkansas. Geoderma Regional, doi.org/10.1016/j.geodrs.2019.e00203. da Silva, M., A. Pereira, J. Rupe, B. Bluhm, E. Gbur, L. Wood, L. Mazzoni, and P. Chen (2019). Effectiveness of a seed plate assay for evaluating charcoal rot resistance in soybean and relationship to field performance. Plant Disease. doi.org/10.1094/PDIS-10-18-19-RE. Fournier, A.M.V., D.C. Mengel, E. Gbur, A. Raedeke and D.G. Krementz (2019). Evaluating tradeoffs in the response of Sora (Porzana carolina) and waterfowl to the timing of early autumn wetland inundation. Waterbirds, 42, 168-178. Folgelman, M., J.K. Norsworthy, T. Barber and E. Gbur (2019). Influence of formulation and rate on rice tolerance to early season applications of Acethlor. Weed Technology, 33, 239-245. Jones, G.T., J.K. Norsworthy, T. Barber, E. Gbur and G.R. Kruger (2019). Off-target movement of DGA and BAPMA dicamba to sensitive soybean. Weed Technology, 33, 51-65. Jones, G.T., J.K. Norsworthy, T. Barber, E. Gbur and G.R. Kruger (2019). Effect of low doses of dicamb alone and in combination with glyphosate on parent soybean and offspring. Weed Technology, 33, 17-23. Norsworthy, J.K., M. Fogelman, T. Barber and E. Gbur (2019). Evaluation of acetochlor-containing herbicide programs in imidazolinone- and quizalofol-resistant rece. Crop Protection, 122, 98-105. Duree, T.J., K.R. Brye, L.S. Wood, D.M. Miller and E.E. Gbur (2019). Soil moisture regime and mound position effects on soil profile properties in a native tallgrass prairie in northwest Arkansas, USA. Geoderma, 352, 49-60. Cordova L.G., Ellis, M.A., Wilson, L.L., Madden, L.V., and Peres, N.A. (2018). Evaluation of the Florida strawberry advisory system for control of Botrytis and anthracnose fruit rots in Ohio. Plant Health Progress 19: 182-187. Paul, P.A., Bradley, C.A., Madden, L.V., Dalla Lana, F., Bergstrom, G.C, Dill-Macky, R., Esker, P.D., Wise, K.A., McMullen, M., Grybauskas, A., Kirk, W.W., Milus, E., and Ruden, K. (2018). Meta-analysis of the effects of QoI and DMI fungicide combinations on Fusarium head blight and deoxynivalenol in wheat. Plant Disease 102: 2602-2615. Paul, P.A., Bradley, C.A., Madden, L.V., Dalla Lana, F., Bergstrom, G.C, Dill-Macky, R., Wise, K.A., Esker, P.D., McMullen, M., Grybauskas, A., Kirk, W.W., Milus, E., and Ruden, K. (2018). Effects of pre- and post-anthesis applications of demethylation inhibitor fungicides on Fusarium head blight and deoxynivalenol in spring and winter wheat. Plant Disease 102: 2500-2510. Piepho, H.-P., Madden, L.V., and Williams, E.R. (2018). Contribution to the discussion of the paper by Jackson and White: Using general-purpose GLMM software for meta-analysis. Biometrical Journal 60: 1059-1061. Shah, D.A., De Wolf, E.D., Paul, P.A., and Madden, L.V. (2019). Functional data analysis of weather variables linked to Fusarium head blight epidemics in the United States. Phytopathology 109: 96-110. Paul, P.A., Salgado, J.D., Bergstrom, G.C., Bradley, C., Byamukama, E., Byrne, A.M., Chapara, V., Cummings, J.A., Chilvers, M.I., Dill-Macky, R., Friskop, A.J. Kleczewski, N.M., Madden, L.V., Nagelkirk, M., Stevens, J., Smith, M., Wegulo, S.N., Wise, K.A., Yabwalo, D. (2019). Integrated effects of genetic resistance and prothioconazole + tebuconazole application timing on Fusarium head blight in wheat. Plant Disease 103: 223-237. Shah, D.A., Paul, P.A., De Wolf, E.D., and Madden, L.V. (2018). Predicting plant disease epidemics from functionally-represented weather series. Philosophical Transactions of the Royal Society B 374: 20180273. Kramer M. (2019).  Stats: How useful is the treatment?  Nature 569, 192. Kesoju S.R., Greene S.L., Martin R.C., Kramer M., Walsh D.B. and Boydston R.A. (2019). Isolation distances for transgenic alfalfa seed production in the Pacific Northwest. Crop Science 59: 1701-1708. Kramer, M.  (2018). Using the posterior predictive distribution as a diagnostic tool for mixed models.  Proceedings from Joint Statistics Meeting, Biometrics Section 448-466. Ebbets, A., Lane, D., Dixon, P.M., Hollweg, T., Huisenga, M., and Gurevitch, J. (2019).  Using meta-analysis to develop evidence-based recovery trajectories of vegetation and soils in restored wetlands in the Northern Gulf of Mexico.  Estuaries and Coasts. doi.org/10.1007/s12237-019-00536-y Griebel, S., Webb, M.W., Campaneela, O.H., Craig, B.A., Weil, C.F., and Tuinstra, M.R. (2019). The alkali spreading phenotype in Sorghum bicolor and its relationship to starch gelatinization, Journal of Cereal Science, 86, 41–47. Aiken, V, C.F., Dórea, J.R.R., Acedo, J.S., Sousa, F.G., Dias, F.G. and Rosa, G.J.M. (2019). Record linkage for farm-level data analytics: Comparison of deterministic, stochastic and machine learning methods. Computers and Electronics in Agriculture 163: 104857. Goto, T., Fernandes, A.F.A., Tsudzuki, M., Rosa, G.J.M. (2019). Causal phenotypic networks for egg traits in an F2 chicken population. Molecular Genetics and Genomics. doi.org/10.1007/s00438-019-01588-2 Fernandes, A.F.A., Dorea, J.R.R., Fitzgerald, R., Herring, W. and Rosa, G.J.M. (2019). A novel automated system to acquire biometric and morphological measurements, and predict body weight of pigs via 3D computer vision. Journal of Animal Science 97: 496-508. Abdalla, E.A., Lopes, F.B., Byrem, T.M., Weigel, K.A. and Rosa, G.J.M. (2019). Genomic prediction of bovine leukosis incidence in a US Holstein population. Livestock Science 225: 73–77. Bresolin, T., Rosa, G.J.M., Valente, B.D., Espigolan, R., Gordo, D.G.M., Braz, C.U., Fernandes, G.A., Magalhães, A.F.B., Garcia, D.A., Frezarim, G.B., Leão, G.F.C., Carvalheiro, R., Baldi, F., Oliveira H.N. and Albuquerque, L.G. (2019). Effect of quality control, density and allele frequency of markers on the accuracy of genomic prediction for complex traits in Nellore cattle. Animal Production Science 59(1): 48-54. Momen, M., Mehrgardi, A.A., Sheikhi, A., Kranis, A., Tusell, L., Morota, G., Rosa, G.J.M. and Gianola, D. (2018). Predictive ability of genome-assisted statistical models under various forms of gene action. Scientific Reports 8:12309. Baker, L.A., Rosa, G.J.M., Hao, Z., Piazza, A., Hoffman, C., Binversie, E.E., Sample, S.J. and Muir, P. (2018). Multivariate genome-wide association analysis identifies novel and relevant variants associated with anterior cruciate ligament rupture risk in the dog model. BMC Genetics 19:39. Momen, M., Mehrgardi, A.A., Amiri Roudbar, M., Kranis, A., Pinto, R.M., Valente, B.D., Morota, G., Rosa, G.J.M. and Gianola, D. (2018). Including phenotypic causal networks in genome-wide association studies using mixed effects structural equation models. Frontiers in Genetics, 9:455. Diers, B.W., Specht, J., Rainey, K.M., Cregan, P., Song, Q., Ramasubramanian, V., Graef, G., Nelson, R., Schapaugh, W., Wang, D., Shannon, G., McHale, L., Kantartzi. S., Xavier, A., Mian, R., Stupar, R.M., Michno, J.M., An, Y.Q.C., Goettel, W., Ward, R., Fox, C., Lipka, A.E., Hyten, H., Cary, T. and Beavis, W.D. (2018). Genetic architecture of soybean yield and agronomic traits. G3: Genes, Genomes, Genetics 8: 3367-3375. Shenstone, E., Cooper, J., Rice, B., Bohn, M., Jamann, T.M., and Lipka, A.E. (2018). An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels. PLoS ONE 13: e0207752. Dong, H., Liu. S., Clark, L.V., Sharma, S., Gifford, J.M., Juvik,.J.A., Lipka, A.E., and Sacks, E.J. (2018). Winter hardiness of miscanthus (II): genetic mapping for overwintering ability and adaptation traits in three interconnected Miscanthus populations. GCB Bioenergy. DOI: 10.1111/gcbb.12587. Mastrodomenico, A.T., Bohn, M.O., Lipka, A.E., and Below, F.E (2019). Genomic selection using maize ex-plant variety protection germplasm for the prediction of nitrogen-use traits. Crop Science 58: 1-19. Chen, A.H., Ge, W., Metcalf, W., Jakobsson, E., Mainzer, L.S., and Lipka, A.E. (2019). An assessment of true and false positive detection rates of stepwise epistatic model selection as a function of sample size and number of markers. Heredity 122: 660-671. Clark, L.V., Lipka, A.E., and Sacks, E.J. (2019). polyRAD: genotype calling with uncertainty from sequencing data in polyploids and diploids. G3: Genes, Genomes, Genetics 9: 663-673. Rice, B., and Lipka, A.E. (2019). Evaluation of RR-BLUP genomic selection models that   incorporate peak genome-wide association study signals in maize and sorghum. The Plant Genome 12. Cooper, J., Rice, B., Shenstone, E., Lipka, A.E., and Jamann, T.M. (2019). Genome-wide analysis and prediction of resistance to Goss’ wilt in maize. The Plant Genome. DOI: 10.3835/plantgenome2018.06.0045. Clark, L.V., Dwiyanti, M.S., Anzoua, K.G., Brummer, J.E., Ghimire, B.K., Głowacka, K., Hall, M., Heo, K., Jin, X., Lipka, A.E., Peng, J., Yamada, T., Yoo, J.H., Yu, Cy, Zhao, H., Long, S.P., and Sacks, E.J. (2019). Biomass yield in a genetically diverse Miscanthus sinensis germplasm panel evaluated at five locations revealed individuals with exceptional potential. GCB Bioenergy. DOI: 10.1111/gcbb.12606. 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Impact Statements

Members continuing to offer workshops and, where appropriate, alternative means of continuing education and support for subject matter scientists, reviewers, and technical editors on valid design and statistical analysis of studies. Specific examples may be found in the Outputs section of this report under the Workshops and Presentations subsections.

Date of Annual Report: 08/23/2020

Report Information

Annual Meeting Dates: 06/26/2020 - 06/26/2020
Period the Report Covers: 09/01/2019 - 08/31/2020

Participants

Nora Bello (KS), Bruce Craig (IN, Admin.), Xin Dai (UT), Philip Dixon (IA), Sara Duke (USDA-ARS), Susan Durham (UT), Ed Gbur (AR), Carla Goad (OK), Kathy Hanford (NE), Xuelin Lao (GA), Alex Lipka (IL), Larry Madden (OH), Raul Macchiavelli (PR), Dan Nettleton (IA), Bill Price (ID), Guilherme Rosa (WI), Walt Stroup (NE), Kathy Yeater (USDA-ARS), Jun Zhu (WI) William Bridges (SC), Nick Keuler (WI), Julia Piaskowski (ID), John Stevens (UT), Linda Young (USDA-NASS)

Brief Summary of Minutes

Minutes Attachment:

Minutes-NCCC-170_2020_Report.docx

Accomplishments

Publications

Impact Statements

(3) Members continuing to offer workshops and, where appropriate, alternative means of continuing education and support for subject matter scientists, reviewers, and technical editors on valid design and statistical analysis of studies. Specific examples may be found in the Outputs section of this report under the Workshops and Presentations subsections.

Date of Annual Report: 08/16/2021

Report Information

Annual Meeting Dates: 06/24/2021 - 06/25/2021
Period the Report Covers: 09/01/2020 - 08/16/2021

Participants

Members Present: Nora Bello (KS), Bruce Craig (IN, Admin.), Xin Dai (UT), Philip Dixon (IA), Sara Duke (USDA-ARS), Susan Durham (UT), Ed Gbur (AR), Carla Goad (OK), Kathy Hanford (NE), Clark Kogan (WA), Matt Kramer (USDA-ARS), Xuelin Luo (GA), Raul Macchiavelli (PR), Larry Madden (OH), Gayla Olbricht (MO), Julia Piaskowski (ID), Bill Price (ID), Guilherme Rosa (WI), Daniel Runcie (CA), Julia Sharp (CO), Rob Tempelman (MI)

Others Present: Arianna Bunnell (UT), Nick Keuler (WI), Neil Paton (Cargill), Hannah Phillips (MN), Hans-Peter Piepho (Germany), Aaron Rendahl (MN), John Stevens (UT), Walt Stroup (NE emeritus), Edzard van Santen (FL)

2021 Officers: Nora Bello, chair; Susan Durham, secretary (minutes); Nora Bello, program chair; Nora Bello, “local” arrangements (virtual); Ed Gbur, report preparation.

Participants Attachment:

NCCC-170_2021_Minutes and Report 081621 - Submitted.pdf

Brief Summary of Minutes

Meeting minutes attached

Minutes Attachment:

NCCC-170_2021_Minutes and Report 081621 - Submitted.pdf

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 / Short Courses: Nora Bello, Bruce Craig, Robert Tempelman. Invited Short Course on Mixed Models (July 2021). Workshop delivered in conjunction with the Annual Meetings of the American Dairy Science Association. Nora Bello (July 2020). Invited Short Course on Mixed Models. National University of Litoral, Corrientes, Argentina. Postponed due to COVID-19 shut-down. Nora Bello (July 2020) Invited Short Course entitled: At the frontier of Mixed Models: Scope, limitations and challenges. National University of Buenos Aires, Buenos Aires, Argentina. Postponed due to COVID-19 shut-down. Macchiavelli, R. Strategies for the Statistical Analysis of Spatial Correlated Data. Short course (20 hours) Special Topics Course in the Master’s Program in Applied Statistics. National University of Córdoba (Argentina). August-September, 2021 (remote course). Guilherme J. M. Rosa. Statistical Modeling in Animal Breeding and Genetics. Sao Paulo State University (UNESP) - Jaboticabal, Brazil. August 10-14, 2020. (remote course)  Guilherme J. M. Rosa. Quantitative Genetics. 25th Summer Institute in Statistical Genetics, University of Washington, Seattle - WA. July 20-22, 2020. (remote course) Guilherme J. M. Rosa. Mixed Models in Quantitative Genetics. 25th Summer Institute in Statistical Genetics, University of Washington, Seattle - WA. July 22-24, 2020. (remote course) Walter W Stroup. 2021 Bayesian Analysis of GLMMs Using PROC BGLIMM SAS Global Forum 2021: Tutorial.   Presentations:  Nora Bello “Statistics for Reproducible Research in Companion Animal Nutrition”. Invited talk at the Companion Animal Symposium: Experimental Design and Statistics Applied to Companion Animal Nutrition, at the American Society of Animal Science (ASAS) and Canadian Society of Animal Science (CSAS) Annual Meeting and Trade Show. Virtual platform. July 15, 2021. Nora Bello “Thoughts on Modern Quantitative Literacy for the Agricultural Sciences”. Invited Seminar, Department of Animal Sciences, Ohio State University. Virtual platform. June 9, 2021. Nora Bello “Systems Modeling for Integrated Animal Production”. Invited Seminar, Department of Animal Sciences, Ohio State University. Virtual platform. June 8, 2021. Nora Bello “On Transdisciplinary Research and Education at K-State: A Personal Snapshot”. Department of Statistics Seminar Series, Kansas State University. Virtual platform. April 22, 2021. Nora Bello “Statistics for Reproducible Research: Transition Cows”. Invited talk at the 39th American Dairy Science Association (ADSA) Discover Conference on Food Animal Agriculture: The transition period – from physiology to management. Virtual platform. October 28, 2020. Nora Bello “Excellence in Engaged Scholarship: Thoughts for the Animal Sciences of the 21st Century”. Invited talk, Department of Animal Sciences, Purdue University. Virtual platform. October 16, 2020. P.M. Dixon. “Where do Bayesian methods fit in an applied statistician’s toolbox?” Conference on Applied Statistics in Agriculture and Natural Resources, May 2021 (virtual) P.M. Dixon “How and where does Bayesian inference fit in out statistical toolbox?”Agronomy Society of America annual meeting November 2020 (virtual) Bianchi-Santiago, J., D. Valdés, R. Macchiavelli . « KABCO Severity Cost Estimation by Cluster Analysis for Injury-Only Crashes in Puerto Rico”, Refereed Oral Presentation, Transportation Safety Board 100th Annual Meeting, January 24-28, 2021. Macchiavelli, R. “Seed Rain” in a Caribbean Forest: Generalized Linear Mixed Models for Count Data. XXV Jornadas de Investigaciones en la Facultad de Ciencias Económicas y Estadística de la Universidad Nacional de Rosario, April, 28, 2021. (Virtual Invited Talk) Macchiavelli, R. Modern Methods for Statistical Analysis in the Big Data Era. Jornadas de Aniversario, Escuela de Ingeniería Agronómica de la Universidad Autónoma de Santo Domingo. Santo Domingo (Dominican Republic), October 27, 2020 (Virtual Talk) Adjei, R. and Stevens J.R. Comparative Analysis of Statistical Methods for Single-Cell RNA Sequencing Data. Conference on Applied Statistics in Ag and Natural Resources, virtual via University of Florida. May 19, 2021. Madden, L. V. Purdue University Seminar: “The cost of plant disease prediction”. November 2020. Madden, L. V. Ohio State University invited Seminar: “Following my passions in plant disease epidemiology: The director’s cut”. Dept. of Plant Pathology, Fall 2020. Madden, L. V. Invited keynote presentation: “Model ensembles for plant disease prediction”. Plant Science Symposium 2021, The Ohio State University. March 26, 2021. Bruce Craig Invited speaker at American Statistical Association sponsored webinar: Advice for the Promotion of Collaborative Statisticians in Research and Teaching Institutions. May 26, 2021. Khanal, P. and R.J. Tempelman. 2021. Diagnosing the pregnancy status of dairy cows using milk spectral data. Presented (virtual) at the Conference on Applied Statistics in Agriculture and Natural Resources, May 20,2021. https://conference.ifas.ufl.edu/applied-stats/ Tempelman, R.J. 2021. Using genetic relationships to improve the design and analysis of animal science studies. Invited paper (virtual) given at the 56th Meeting of the Brazilian Society of Animal Science. August 19, 2021 56a Reunião SBZ Tempelman, R.J. 2020. Making the journey from frequentist to Bayesian analysis. Invited paper (virtual) presented at the American Society of Agronomy International Annual Meetings, November 11, 2020. Walter W Stroup. 2021 Bayesian Analysis of GLMMs Using PROC BGLIMM SAS Global Forum 2021: Paper 1146-2021 (presented virtually) Lipka, A.E. 2021. Using simulations to assess the performance of quantitative genetics models in crops. Soil and Crop Sciences and Ag Bio Seminar Series at Colorado State University (Presented virtually because of the COVID-19 pandemic). March 10, 2021. (Invited speaker) Lipka, A.E. 2020. The performance of genotype-to-phenotype models accounting for large-effect loci, epistasis, and pleiotropy. International Conference of the Genetics Society of Korea Asia Pacific Chromosome Colloquium 7, Busan, Korea (Presented virtually because of the COVID-19 pandemic). November 26, 2020. (Invited speaker) Lipka, A.E. 2020. Using simulations to assess the performance of genotype-to-phenotype models accounting for pleiotropy, epistasis, large-effect loci, and interspecific breeding material. 2020 ACES (Virtual) Global Academy Seminar Series, presented to partner universities in Brazil (Federal University of Lavras and Federal University of Viçosa).November 18, 2020. (Invited speaker)   Books and Book Chapters: Goad, Carla L., SAS Programming for Elementary Statistics: Getting Started, CRC Press, 2021. DOI:10.4324/9780429491900, ISBN: 9780429491900 (ebook), ISBN-13: 978-1138589094 (hardcover), ISBN-13: 978-1138589025 (paperback)  Duree, T., Brye, K., Wood, L. and E. Gbur (2020). Soil moisture regime and mound position effects on soil water and vegetation in a native tallgrass prairie in the mid-southern United States. In Grasses and Grassland. V.M. Kindomihou (ed). London, UK: IntechOpen.DOI:10.5772/intechopen.89043. 25 pp. Kidd, M.T., E,E, Gbur, J. Caldas, L.A. Mozzoni and C.W. Maynard (2021). Quantitative analysis of branched-chain amino acid independent data using an all possible subset regression meta-analysis. In: Branched-Chain Amino Acids: Metabolism, Benefits and Role in Disease. Ed. M.T. Kidd. Nova Scientific Publishers, New York, USA. Hutchins, J., Hueth, B. and Rosa, G. J. M. Quantifying Heterogeneous Returns to Genetic Selection: Evidence from Wisconsin Dairies. In: Economics of Research and Innovation in Agriculture, National Bureau of Economic Research, Inc., 2020.   Other project related activities: Nora Bello. Invited participation on the National Science Foundation Convergence Accelerator Workshop on Digital and Precision Agriculture. Virtual platform. May 10, 12, 14, 21, 2021.  Nora Bello. Invited discussion panel on: “The Changing Future of Data and Research: Cross-Disciplinary Problem Solving”. 2021 Conference of the Coalition for Advancing Digital Research and Education (CADRE) at Oklahoma State University. Virtual platform. April 14-16, 2021. Nora Bello. Invited Podcast: “Statistical Principles for Pig Research: Myths and Facts” <a href="https://www.swineit.com/blog/statistical-principles-in-pig-research-facts-and-myths-dr-nora-bello">https://www.swineit.com/blog/statistical-principles-in-pig-research-facts-and-myths-dr-nora-bello</a> Swine-it Podcast Show, hosted by Dr. Laura Greiner and Dr. Marcio Goncalves, June 21, 2021. Nora Bello (Co-PI) “Reducing foodborne pathogen contamination of vegetables in Cambodia: Innovative research, targeted interventions and impactful Cambodian-led engagement”. Lead investigators: Jessie Vipham, Animal Sciences and Industry, Kansas State University; and Paul Ebner, Department of Animal Sciences, Purdue University. 2020-2024. USAID Award #: 21-0968. Nora Bello (Co-PI). "RII Track-2 FEC: Building Field-based Ecophysiological Genome-to-Phenome Prediction”. Principal Investigator: Stephen Welch, Department of Agronomy, Kansas State University. 2018-2021.National Science Foundation – EPSCoR Research Infrastructure Improvement Program, Program Award #: 1826820. P.M. Dixon (Co-PI) Monitoring invasive Asian carp in Iowa  (PI, Michael Weber, ISU) USGS 2020-2021  Carla Goad. Validation and Delivery of Integrated Natural Enemy + Sugarcane Aphid Economic Thresholds and Monitoring Protocols in Grain Sorghum.  USDA 2021 (grant end date unknown) Bruce Craig, Robert Tempelman, Guilherme Rosa, Xin Dai, Linda Young, Edzard van Santen and Nora Bello served on the organizing committee for the 2021 Conference on Applied Statistics in Agriculture and Natural Resources held virtually on May 17-20, 2021. <a href="https://conference.ifas.ufl.edu/applied-stats/">https://conference.ifas.ufl.edu/applied-stats/</a> Bruce Craig began as a Senior Fellow, National Institute of Statistical Sciences collaborating with National Agricultural Statistics Service on July 1, 2020. Hans-Peter Piepho, Emlyn Williams and Robert Tempelman were guest editors for the special issue entitled "Recent Advances in Design and Analysis of Experiments and Observational Studies in Agriculture" in the Journal of Agricultural, Biological, and Environmental Statistics.

Publications

Impact Statements

(3) Members continuing to offer workshops and, where appropriate, alternative means of continuing education and support for subject matter scientists, reviewers, and technical editors on valid design and statistical analysis of studies.