NCCC170: Research Advances in Agricultural Statistics

(Multistate Research Coordinating Committee and Information Exchange Group)

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SAES-422 Reports

08/26/2022

A total of 123 scientific publications were authored or co-authors by NCCC-170 members during the reporting period. Publication venues spanned a wide range of scientific domains and included the Proceedings of the National Academy of Sciences, the PloS and BMC series, Journal of Dairy Science, Journal of Animal Science, Frontiers in Genetics, Frontiers in Veterinary Medicine, Frontiers in Agronomy, Crop Science, HortScience, Journal of Ecology, Evolutionary Applications, Stat, Biometrical Journal, Journal of Food Protection, Food Packaging and Shelf, Journal of Apicultural Research, G3 Genes|Genomes|Genetics, Journal of Animal Breeding and Genetics, Theoretical and Applied Genetics, and Agrosystems, Geosciences & Environment, to name a few. A selected subset of publications is listed below for illustrative purposes. Member co/authors are highlighted in bold.


 



  1. Ribeiro, L. A. C., Bresolin, T., Rosa, G. J. M., Casagrande, D. M., Danes, M. A. C. and Dórea, J. R. R. Disentangling data dependency using cross-validation strategies to evaluate prediction quality of cattle grazing activities using machine learning algorithms and wearable sensor data. Journal of Animal Science 99(9): 1-8, 2021.

  2. Tepedino VJ, Parker FD, and Durham SL (2022) Mixed diapause duration in cohorts of four species of Osmia bees (Megachilidae) along an elevation and temperature gradient in Northern Utah (USA). Journal of Apicultural Research. DOI: 10.1080/00218839.2022.2042049

  3. Griffith, E. H., Sharp, J. L., Bridges, W. C., Craig, B. A., Hanford, K. J., and Stevens, J. R. “The academic collaborative statistician: research, training, and evaluation,” Stat 2022 https://doi.org/10.1002/sta4.483.

  4. Lewis, M, Stock, M., Black, B., Drost, D., and Dai, X. (2021). Improving Snapdragon Cut Flower Production through High Tunnel Season Extension, Transplant Timing, and Cultivar Selection. HORTSCIENCE 56(10):1206–1212.

  5. Taghouti, M.; García, J.; Ibáñez, M.A.; Macchiavelli, R.E.; Nicodemus, N. (2021) Relationship between Body Chemical Composition and Reproductive Traits in Rabbit Does. Animals 2021, 11, 2299. https://doi.org/10.3390/ani11082299

  6. Poudel, P., M. Bello, D. Marburger, B. F Carver, Y. Liang and P. D. Alderman*. 2022. “Ecophysiological modeling of yield and yield components in winter wheat using hierarchical Bayesian analysis”. Crop Science 62(1): 358-373. https://doi.org/10.1002/csc2.20652

  7. Brethauer, D. K., Sharma, A., Vogel, J. G., Miller, D. L., & Santen, E. v. (2021). Longleaf pine seedling growth and survival: effects of season and intensity of simulated prescribed burning. Forest Ecology and Management, 502. doi:10.1016/j.foreco.2021.119719

  8. Dogan, O., Stratton, J., Arciniega, A., Clarke, J., Tamplin, M., Bianchini, A., and Wang, B. Quantitative modeling of the survival of Listeria monocytogenes in soy sauce-based acidified food products. International Journal of Food Microbiology, 370: 109635. June 2022

  9. Lawrence-Dill, C., Allscheid, R., Boaitey, A., Bauman, T., Buckler, E., Clarke, J., Cullis, C., Dekkers, J., Dorius, C., Dorius, S., Ertl, D., Homann, M., Hu, G., Losch, M., Lyons, E., Murdoch, B., Navabi, Z.-K., Punnuri, S., Rafiq, F., Reecy, J., Schnable, P., Scott, N., Sheehan, M., Sirault, X., Staton, M., Tuggle, C., Van Eenennaam, A., and Voas, R. Ten Simple Rules to Ruin a Collaborative Environment. PLoS Computational Biology, 18(4): e1009957. https://doi.org/10.1371/journal.pcbi.1009957

  10. Wilson, H., V. Bremer, G. Erickson, T. Carr, K. Hanford, A. Watson, T. Klopfenstein, J. MacDonald. Digestion characteristics and prediction of digestible energy and total digestible nutrients in beef cattle finishing diets containing traditional and by-product lipid sources. Applied Animal Science. 2021. 7:377–387. https://doi.org/10.15232/aas.2020-02131

  11. Estee Y Cramer, Evan L Ray, Velma K Lopez, Johannes Bracher, Andrea Brennen, Alvaro J Castro Ri- vadeneira, Aaron Gerding, Tilmann Gneiting, Katie H House, Yuxin Huang, Dasuni Jayawardena, Abdul H Kanji, Ayush Khandelwal, Khoa Le, Anja Muhlemann, Jarad Niemi, [256 other authors], Nicholas G Reich. (2022) “Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US” Proceedings of the National Academy of Sciences, 119(15), e2113561119. https://doi.org/10.1073/pnas.2113561119

  12. Adam Martin-Schwarze*, Jarad Niemi, and Philip Dixon. (2021) “Joint modeling of distances and times in point-count surveys.” Journal of Agricultural, Biological, and Environmental Statistics. 26, 289-305. https://doi.org/10.1007/s13253-021-00437-3

  13. Hensley, C., K.R. Brye, M.C. Savin, L.S. Wood and E. Gbur (2021). Earthworm density differences among tallgrass prairies over time in the Ozark Highlands. Agrosystems, Geosciences & Environment. 4:e20136.

  14. Fernandes SB, Zhang KS, Jamann TM and Lipka AE (2021). “How Well Can Multivariate and Univariate GWAS Distinguish Between True and Spurious Pleiotropy?” Frontiers in Genetics: 11:1747 doi: 10.3389/fgene.2020.602526.

  15. Piepho, H.P., Boer, M., Williams, E.R. (2022): Two-dimensional P-spline smoothing for spatial analysis of field trials. Biometrical Journal 64, 835-857.

  16. Piepho, H.-P., and Madden, L. V. How to observe the principle of concurrent control in an arm-based meta-analysis using SAS procedures GLIMMIX and BGLIMM. Research Synthesis Methods. 1-8. doi:10.1002/jrsm.1576 .

  17. Larson, K.J., Bundy, A.N., Kuntz, T., Hur, J., Yeater, K.M., Casperson, S., Brunelle, D.C. and Roemmich, J.N., 2022. Effect of a maternal high fat diet with vegetable substitution on fetal brain transcriptome. The Journal of Nutritional Biochemistry, p.109088. https://doi.org/10.1016/j.jnutbio.2022.109088

  18. Runcie, D.E., Qu, J., Cheng, H., and L. Crawford. (2021). MegaLMM: Mega-scale linear mixed mod- els for genomic predictions with thousands of traits. Genome Biology 22(1), 1-25.

  19. Dunn, Bruce L., Stephen Stanphill, and Carla Goad (2021). Branching Response of Poinsettia ‘Orange Spice’ to a Combination of Pinching, No Pinching, and Atrimmec, HortScience, 56(10). https://doi.org/10.21273/HORTSCI16105-21  

  20. Perttu RK, Ventura BA, Rendahl AK and Endres MI. Public Views of Dairy Calf Welfare and Dairy Consumption Habits of American Youth and Adults. Front Vet Sci. 8:693173 (August 2021). doi:10.3389/fvets.2021.693173

  21. Khanal, P., and J. Tempelman. 2022. The use of milk Fourier transform mid-infrared spectroscopy to diagnose pregnancy and determine spectral regional associations with pregnancy in US dairy cows.  Journal of Dairy Science 105(4):3209-3221.


 


 

09/01/2023

A total of 86 scientific publications were authored or co-authors by NCCC170 members during the reporting period. Publication venues spanned a wide range of scientific domains and included Nature Communications Earth & Environment, Plos One, Journal of Dairy Science, Journal of Animal Science, Translational Animal Sciences, Applied Animal Behavior, Journal of Animal Breeding and Genetics, Agronomy Journal, Crop Science, HortScience, Communications in Soil Science and Plant Analysis, Frontiers in Sustainable Food Systems, G3 Genes|Genomes|Genetics, Frontiers in Genetics, Journal of Apicultural Research, Vaccine, Computational Statistics, Stat, Research Synthesis Methods, Computers and Electronics in Agriculture, to name a few.


 


A selected subset of publications is listed below for illustrative purposes. Member co/authors are highlighted in bold.


 



  1. Griffith E.H., Sharp J.L., Bridges W.C., Craig B.A., Hanford K.J., and Stevens J.R. (2022) The Academic Collaborative Statistician: Research, Training, and Evaluation. Stat 11(1):e483. doi:10.1002/sta4.483

  2. Rafael Della Coletta, Sharon E Liese, Samuel B Fernandes, Mark A Mikel, Martin O Bohn, Alexander E Lipka, Candice N Hirsc, Linking genetic and environmental factors through marker effect networks to understand trait plasticity, Genetics, 2023;, iyad103, https://doi.org/10.1093/genetics/iyad103

  3. Christie H. Guetling CH, Jones LC, Strand EK, Morishita DW, Piaskowski J and TS Prather. 2023 Susceptibility models and habitat typing of two invasive Hieracium species in the Greater Yellowstone Ecosystem. Biological Invasions. DOI: https://link.springer.com/article/10.1007/s10530-023-03037-z

  4. Hayes, H. A., Wallau, M. O., Caram, N., Sollenberger, L. E., Kenworthy, K. E., & van Santen, E. (2023). Early-stage evaluation of grazed tetraploid bahiagrass experimental entries. Crop Science, n/a(n/a). doi:https://doi.org/10.1002/csc2.20930

  5. Crookston B.S., Yost M.A., Bowman M., Veum K., and Stevens J.R. (2023) Microbial respiration gives early indication of soil health improvement following cover crops. The Journal of Soil and Water Conservation 78(3):1-10. doi:10.2489/jswc.2023.00015

  6. Coppock DL, Crowley L, Durham SL, Groves D, Jamison JC, Karlan D, Norton BE, and Ramsey RD (2022) Community-based rangeland management in Namibia improves resource governance but not environmental and economic outcomes. Nature Communications Earth & Environment 3:32. doi.org/10.1038/s43247-022-00361-5

  7. Rosario, C.M.A., R.J. Miller, G.M. Klafke, C. Coates, W.E. Grant, G. Samenuk, K. Yeater, J. Tidwell, S. Bach, A.A.P. de León, and P.D. Teel. 2022. Interaction between anti-tick vaccine and a macrocyclic lactone improves acaricidal efficacy against Rhipicephalus (Boophilus) microplus (Canestrini)(Acari: Ixodidae) in experimentally infested cattle. Vaccine, 40(47), 6795-6801.

  8. Odell, Sarah G, Hudson, Asher I, Praud, Sébastien, Dubreuil, Pierre, Tixier, Marie-Hélène, Ross-Ibarra, Jeffrey, Runcie, Daniel E. Modeling allelic diversity of multiparent mapping populations affects detection of quantitative trait loci . G3 Genes|Genomes|Genetics, 12(3).

  9. Dustin, D., Clarke, B., and Clarke, J. Predictive Criteria for Prior Selection Using Shrinkage in Linear Models. Computational Statistics, online ahead of print, March 2023 https://doi.org/10.1007/s00180-023-01342-8

  10. Khanal, P., K.L. Parker Gaddis, M.J. Vandehaar, K.A. Weigel, H.M. White, F. Peñagaricano, J.E. Koltes, J.E.P. Santos, R.L. Baldwin, J.F. Burchard, J.W. Dürr and R.J. Tempelman. 2022.  Multiple trait random regression modeling of feed efficiency in US Holsteins. Journal of Dairy Science 105(7):5954-5971.

  11. Matt Nowatzke, Luis Damiano, Fernando Miguez, Gabe McNunn, Jarad Niemi, Lisa Schulte-Moore, Emily Heaton, Andy VanLoocke. (2022) Augmenting agroecosystem models with remote sensing data and machine learning changes overall estimates of nitrate-nitrogen leaching. Environmental Research Letters, 17:11, 114010.

  12. Annear, A.R., Simonson, M.A., Dixon, P.M. and Weber, M.J. 2023.  Intra-annual variability of common carp and bigmouth buffalo electrofishing data in shallow lakes.  North American Journal of Fisheries Management 43(2):556-568.

  13. Holder, Amanda, Megan A. Gross, Alexandra n. Moehlenpah, Carla Goad, Megan Rolf, Ryon Walker, James K. Rogers, David Lalman (2022) Effects of Diet on Feed Intake, Weight Change, and Gas Emissions in Beef Cows, Journal of Animal Science 100(10). DOI: 10.1093/jas/skac257

  14. DeVetter, L.W., S. Chabert, M.O. Milbrath, R.E. Mallinger, J. Walters, R. Isaacs, S.P Galinato, C. Kogan, K. Brouwer, A. Melathopoulos, and M. Eeraerts. (2022). Towards evidence-based decision support systems to optimize pollination and yields in highbush blueberry. Front. Sustain. Food Syst. https://doi.org/10.3389/fsufs.2022.1006201

  15. Piepho, H.-P., and Madden, L. V. 2022. How to observe the principle of concurrent control in an arm-based meta-analysis using SAS procedures GLIMMIX and BGLIMM. Research Synthesis Methods 13: 821-828.

  16. Rauter S, Stock M, Black B, Drost D, Dai X, Ward R. (2022). Overwintering Improves Ranunculus Cut Flower Production in the US Intermountain West. Horticulturae. 2022; 8(12):1128.  

  17. Brewer, G., M. Kentaro, and K. Hanford. (2023). Measuring bee effect on seed traits of hybrid sunflower. Plants. https://doi.org/10.3390/plants12142662.



  1. Ferreira, R. E. P., Bresolin, T., Rosa, G. J. M. and Dórea, J. R. R. (2022) Using dorsal surface for individual identification of dairy calves through 3D deep learning algorithms. Computers and Electronics in Agriculture 201: 107272.

  2. Mosimann, S., K. Ouk, N. M. Bello, M. Chhoeun, J. Vipham, L. Hok and P. Ebner. 2023. “Describing capability, opportunity, and motivation for food safety practices among actors in Cambodian informal vegetable market”. Frontiers in Sustainable Food Systems. Volume 7, 2023:  https://doi.org/10.3389/fsufs.2023.1060876.

08/13/2024

A total of 86 scientific publications were authored or co-authors by NCCC170 members during the reporting period. Publication venues spanned a wide range of scientific domains and included Scientific Reports, PLoS One and PLoS Computational Biology, The Plant Genome, Genetics, G3 Genes Genomes Genetics,  Frontiers in Genetics, Journal of Animal Breeding and Genetics, Theoretical and Applied Genetics, BMC Bioinformatics, Genome Biology, Databases, Research Synthesis Methods, Spatial Statistics, Statistical Analysis and Data Mining, Frontiers in Sustainable Food Systems, Journal of Agriculture and Food Research, International Journal of Food Science, Journal of Stored Products Research, Cereal Chemistry, Agronomy Journal, HortTechnology, Frontiers in Horticulture, Phytopathology, Pest Management Science, Agricultural Water Management, Nematology, Journal of Plant Interactions, Crop Science, International Journal of Vegetable Science, Frontiers in Agronomy, Biocontrol Science and Technology, Journal of experimental botany, Journal of Experimental Botany, Phytopathology, HortScience, Field Crops Research, Computers and Electronics in Agriculture, Journal of Animal Science, Journal of Dairy Science, Translational Animal Science, Journal of Animal Science and Biotechnology, Poultry Science, Animal Feed Science and Technology, Preventive Veterinary Medicine, Research in Veterinary Science, Applied Animal Behaviour, Animals, Tropical Animal Health and Production, Journal of Mammary Gland Biology and Neoplasia, Cryobiology, Microorganisms, Ecosphere, Journal of Soil and Water Conservation, Journal of Environmental Quality, North American Journal of Fisheries Management, Forest Ecology and Management, amongst others.


A selected subset of publications is listed below for illustrative purposes. Member co/authors are highlighted in bold.



  1. Clarke, J., Cooper, L., Poelchau, M., Berardini, T, Elser, J., Farmer, A., Ficklin, S., Kumari, S., Laporte, M.-A., Nelson, R., Sadohara, R., Selby, S., Thessen, A., Whitehead, B., and Sen, T. Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the AgBioData consortium. Databases, November 2023. https://doi.org/10.1093/database/baad076

  2. Wisnieski, L., M. W. Sanderson, D. G. Renter and M. Bello. 2023. Inferential implications of normalizing binomial proportions in a structural equation model: A simulation study motivated by feedlot data”. Preventive Veterinary Medicine 2023 Aug; 217:105963. doi: 10.1016/j.prevetmed.2023.105963.

  3. Martínez-Rodríguez, G. A., Vázquez-Cartagena, M. A., Perdomo-García, C. R., Macchiavelli, R. E., Sotomayor-Ramírez, D., & Rosa, J. R. 2024. Water quality trends of streams in Puerto Rico: Evaluating 50 years of the Clean Water Act. Journal of Environmental Quality, 53, 253–264.https://doi.org/10.1002/jeq2.20550

  4. Madden, L.V., and Ojiambo, P.S. 2024. The value of generalized linear mixed models (GLMMs) for data analysis in the plant sciences. Frontiers in Horticulture 3: 1423462. doi:10.3389/fhort.2024.1423462

  5. Koebernick, J., A. Gillen, R. Fett, S. Patel, B. Fallen, V. Pantalone, G. Shannon, Z. Li, A. Scaboo, W. Schapaugh, R. Mian, and Q. D. Read. 2024. Soybean test weight in relation to genotype, environment, and genotype × environment interaction in the southern USA. Agronomy Journal. DOI: 10.1002/agj2.21551 

  6. Mathews, J., Y. Sun, P. Harris, Dai, S. Price, D. McAvoy, M. Farrell, & K. Kopp (2024). Sap Yield and Sugar Content of Boxelder and Norway Maple Trees in Northern Utah. HortTechnology, 34(1), 52-59. https://doi.org/10.21273/HORTTECH05304-23.

  7. Mota, L. F. M., Arikawa, L. M., Santos, S. W. B., Junior, G. A. F., Alves, A. A. C., Rosa, G. J. M., Mercadante, M. E. Z., Cyrillo, J. N. S. G., Carvalheiro, R. and Albuquerque, L. G. Benchmarking machine learning and parametric methods for genomic prediction of feed efficiency‑related traits in Nellore cattle. Scientific Reports 14: 6404, 2024.

  8. Annear, A.R., Simonson, M.A., Dixon, P.M. and Weber, M.J. 2023. Intra-annual variability of common carp and bigmouth buffalo electrofishing data in shallow lakes.  North American Journal of Fisheries Management 43(2):556-568.

  9. Buczkowski, G, Wang, SH and Craig, BA (2023) Behavioral assays reveal mechanisms of supercolony formation in odorous house ants, Scientific Reports, 13(1): Article #9013

  10. Brabec, D., S. Grothe, M. Perez-Fajardo, L. Pordesimo, and Yeater. 2024. Potential of a flatbed scanner for evaluation of flour samples for dark specks and flour color. Cereal Chemistry, 101(3), pp.508-517. https://doi.org/10.1002/cche.10758

  11. Deer, C, Dunn BL, Hu B, Goad C, Shoup DE (2023), Grafted and Nongrafted ‘Cherokee Purple’ Tomato Performance in Aquaponic and Hydroponic Greenhouse Production in Oklahoma, 1 Nov 2023, HortScience 58(11): 1332-1340. https://doi.org/10.21273/HORTSCI17248-23

  12. Kogan, C., DeVetter, L. W., & Hoheisel, G.-A. (2023). Modeling Northern Highbush Blueberry Cold Hardiness for the Pacific Northwest. HortScience, 58(11), 1314-1320. https://doi.org/10.21273/HORTSCI17320-23

  13. Vechia Jaqueline F. Della, Andrade Daniel J., Tassi Aline D., Roda Amy, van Santen Edzard, Carrillo Daniel. 2023. Can predatory mites aid in the management of the citrus leprosis mite? Frontiers in Agronomy 5. DOI=10.3389/fagro.2023.1304656

  14. Jiayi Qu, Daniel Runcie, Hao Cheng (2023). Mega-scale Bayesian regression methods for genome-wide prediction and association studies with thousands of traits, Genetics, Volume 223, Issue 3, March 2023, iyac183, https://doi.org/10.1093/genetics/iyac183

  15. Rafael Della Coletta, Sharon E Liese, Samuel B Fernandes, Mark A Mikel, Martin O Bohn, Alexander E Lipka, Candice N Hirsch. Linking genetic and environmental factors through marker effect networks to understand trait plasticity. Genetics, Volume 224, Issue 4, August 2023, iyad103, https://doi.org/10.1093/genetics/iyad103

  16. Nicolás Cafaro La Menza, Timothy J Arkebauer, John L Lindquist, Juan Pablo Monzon, Johannes MH Knops, George Graef, David Scoby, Réka Howard, Jennifer Rees, James E Specht, Patricio Grassini (2023). Decoupling between leaf nitrogen and radiation use efficiency in vegetative and early reproductive stages in high-yielding soybean. Journal of experimental botany. 74(1): 352-363

  17. Tepedino VJ, Griswold TL, and Durham SL (2023) Reproductive biology and flower visitors of two rare species of Sclerocactus (Cactaceae) in the southwestern United States. Western North American Naturalist 83(4): 445-453. DOI: 10.3398/064.083.0402

  18. Velma K. Lopez,Estee Y. Cramer,Robert Pagano,John M. Drake,Eamon B. O’Dea,Madeline Adee,Turgay Ayer,Jagpreet Chhatwal,Ozden O. Dalgic,Mary A. Ladd,Benjamin P. Linas,Peter P. Mueller,Jade Xiao,Johannes Bracher,Alvaro J. Castro Rivadeneira,Aaron Gerding,Tilmann Gneiting,Yuxin Huang,Dasuni Jayawardena,Abdul H. Kanji,Khoa Le,Anja Mühlemann,Jarad Niemi,Evan L. Ray,Ariane Stark,Yijin Wang,Nutcha Wattanachit,Martha W. Zorn,Sen Pei,Jeffrey Shaman,Teresa K. Yamana,Samuel R. Tarasewicz,Daniel J. Wilson,Sid Baccam,Heidi Gurung,Steve Stage,Brad Suchoski,Lei Gao,Zhiling Gu,Myungjin Kim,Xinyi Li,Guannan Wang,Lily Wang,Yueying Wang,Shan Yu,Lauren Gardner,Sonia Jindal,Maximilian Marshall,Kristen Nixon,Juan Dent,Alison L. Hill,Joshua Kaminsky,Elizabeth C. Lee,Joseph C. Lemaitre,Justin Lessler,Claire P. Smith,Shaun Truelove,Matt Kinsey,Luke C. Mullany,Kaitlin Rainwater-Lovett,Lauren Shin,Katharine Tallaksen,Shelby Wilson,Dean Karlen,Lauren Castro,Geoffrey Fairchild,Isaac Michaud,Dave Osthus,Jiang Bian,Wei Cao,Zhifeng Gao,Juan Lavista Ferres,Chaozhuo Li,Tie-Yan Liu,Xing Xie,Shun Zhang,Shun Zheng,Matteo Chinazzi,Jessica T. Davis,Kunpeng Mu,Ana Pastore y Piontti,Alessandro Vespignani,Xinyue Xiong,Robert Walraven,Jinghui Chen,Quanquan Gu,Lingxiao Wang,Pan Xu,Weitong Zhang,Difan Zou,Graham Casey Gibson,Daniel Sheldon,Ajitesh Srivastava,Aniruddha Adiga,Benjamin Hurt,Gursharn Kaur,Bryan Lewis,Madhav Marathe,Akhil Sai Peddireddy,Przemyslaw Porebski,Srinivasan Venkatramanan,Lijing Wang,Pragati V. Prasad,Jo W. Walker,Alexander E. Webber,Rachel B. Slayton,Matthew Biggerstaff,Nicholas G. Reich,Michael A. Johansson. (2024) Challenges of COVID-19 Case Forecasting in the US, 2020–2021. PLoS Computational Biology 20(5): e1011200. DOI: 10.1371/journal.pcbi.1011200


 

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