Life Sciences Commons^™

Proc Report In Style, Wendy Boberg

Conference on Applied Statistics in Agriculture

I would like to demonstrate how you can create colorful PDF files using ODS (Output Delivery System) with different predefined style templates for the layout and color scheme of both tables and graphs. There are a few different ways you can customize your reports in the Report Procedure. Traffic lighting is a very popular technique and can be achieved by changing the font and/or the background colors. I prefer to customize my reports by adding background color to highlight a row, column, and/or cell in a table.

I will share my favorite styles and show you how to look at …

Using Time Series To Study Effect Of Air Temperature On Body Temperature Of Cows In Puerto Rico, Y. Zeng, A. M. Parkhurst, J. Pantoja

Conference on Applied Statistics in Agriculture

Body temperature is an important measure for monitoring the health status of cows. The objective of this study is to (1) determine if a cow’s body temperature is related to ambient temperature, relative humidity, and/or temperature humidity index (THI); (2) look for signs of heat stress. The data are collected at five minute intervals during the summer months (December through February) in Puerto Rico. Regression analysis and a succession of time series analyses are conducted in time domains. Nonparametric spectral estimation and cross-spectra analysis are also performed in the frequency domain. A search for indications of heat stress is performed …

Comparing Experimental Designs For A Bi-Logistical Model Used To Estimate Heat Stress When Moving Feedlot Cattle, X. Li, A. M. Parkhurst, T. L. Mader

Conference on Applied Statistics in Agriculture

Processing and handling cattle requires expenditure of energy causing an elevation of body temperature, depending on the ambient conditions. Therefore, caution should be exercised in moving cattle, especially during summer. More knowledge of the dynamics of body temperature, (Tb), could lead to specific recommendations on how far and under what conditions cattle can be moved before becoming thermally challenged. Data comes from feedlot trials conducted over four days. A bi-logistic mixed model of Tb is used to describe the effects of moving and handling on Tb. This model provides estimates for several important biological parameters describing the thermal challenge and …

Using Time Series To Study Dynamics Of Sweat Rates Of Holstein Cows Exposed To Initial And Prolonged Solar Heat Stress, B. Liang, A. M. Parkhurst, K. G. Gebremedhin, C. N. Lee, R. J. Collier, P. E. Hillman

Conference on Applied Statistics in Agriculture

Sweating is a very important way for cows to cope with heat stress. We are interested in the ability of Holstein cows to sustain high sweat or evaporation rates when exposed to solar radiation. There were two solar heat stress treatments: onset and prolonged. The onset data provided an opportunity to examine the impact of sudden exposure to a solar thermal load. The prolonged data allowed us to examine the impact of exposure to solar heat stress for an expended period (5 hr). Two questions of interest were: Do cows sweat at a constant or cyclic rate? Is there a …

Sequential Bayesian Classification: Dna Barcodes, Michael P. Anderson, Suzanne Dubnicka

Conference on Applied Statistics in Agriculture

DNA barcodes are short strands of nucleotide bases taken from the cytochrome c oxidase subunit 1 (COI) of the mitochondrial DNA (mtDNA). A single barcode may have the form C C G G C A T A G T A G G C A C T G and typically ranges in length from 255 to around 700 nucleotide bases. Unlike nuclear DNA (nDNA), mtDNA remains largely unchanged as it is passed from mother to o spring. It has been proposed that these barcodes may be used as a method of di erentiating between biological species (Hebert, Ratnasingham, and deWaard 2003). …

A Stem Profile Model Calibrated By Nonlinear Mixed-Effects Modeling, Yuqing Yang, Shongming Huang, Shawn X. Meng

Conference on Applied Statistics in Agriculture

A stem profile model was developed for black spruce (Picea mariana (Mill.) B.S.P.) trees in Alberta, Canada using a nonlinear mixed model approach. The model included two random parameters to capture between-subject variation and a general covariance structure to model within-subject residual autocorrelation. After evaluating various covariance structures, the 4-banded toeplitz and the spatial power structures were chosen for further evaluation. The 4-banded toeplitz structure provided a better fit. The model was further evaluated using an independent data set to examine its validation accuracy. Model validation results showed that the model was able to accurately predict stem diameters at the …

Mapping Qtl With Covariates, Cherie A. Ochsenfeld, Kristofer Jennings, R. W. Doerge

Conference on Applied Statistics in Agriculture

Quantitative trait loci (QTL) analysis is an effective tool for locating regions of the genome associated with a trait. Quantitative trait data are complex, and when statistically testing for the location of a QTL, the distribution of the test statistic is typically unknown. Historically, asymptotic thresholds have been difficult to derive for QTL analysis. Permutation testing has successfully provided significance thresholds for QTL analysis, but the need for exchangeability among the observations limits these empirically derived thresholds to simple linear models and does not permit the inclusion of important covariates in the model. We address the limitation of permutation theory …

Statistical Methods For Affymetrix Tiling Array Data, Gayla Olbricht, Nagesh Sardesai, Stanton B. Gelvin, Bruce A. Craig, R. W. Doerge

Conference on Applied Statistics in Agriculture

Tiling arrays are a microarray technology currently being used for a variety of genomic and epigenomic applications, such as the mapping of transcription, DNA methylation, and histone modifications. Tiling arrays provide high-density coverage of a genome, or a genomic region, through the systematic and sequential placement of probes without regard to genome annotation. In this paper we compare the Affymetrix tiling array to the Affymetrix GeneChip® 3’ expression array and propose methods that address statistical and bioinformatic issues that accompany gene expression data that are generated from Affymetrix tiling arrays. Real data from the model organism Arabidopsis thaliana motivate this …

Application Of The Dya Method To Compare Wheat Cultivar Yields, Arlin Feyerherm, Allan Fritz

Conference on Applied Statistics in Agriculture

At the 1998 conference, we proposed use of the DYA (differential yielding ability) method to compare the yielding ability of wheat cultivars. In this paper we review the method: its models and assumptions, and then show computation of sample statistics. An example will exhibit the output from performance trial yields when the method is applied in one of the nine ecogeographic areas of fall-planted wheat in the Midwest. Results of comparable outputs over years forecasted which cultivars would become popular with growers in Kansas

Comparative Study Of Time Series And Multiple Regression For Modeling Dependence Of Cattle Body Temperature On Environmental Variables During Heat Stress, M. Pathak, A. M. Parkhurst, R. A. Arias, T. L. Mader

Conference on Applied Statistics in Agriculture

During the summer, a challenging thermal environment is known to cause a significant reduction in food intake, growth, milk production, reproduction and even death in cattle. In this study, we attempt to characterize the relationship of cattle body temperature with several environmental variables, such as air temperature, soil surface temperature, relative humidity, solar radiation, wind speed, incoming and outgoing short and long wave radiation. For these variables, the measurements taken over time are correlated. This places severe restrictions on the applicability of many conventional statistical methods that depend on the assumption of independent and identically distributed errors. In addition to …

Statistical Issues In Next-Generation Sequencing, Paul L. Auer, R. W. Doerge

Conference on Applied Statistics in Agriculture

High throughput deep-sequencing or next-generation sequencing has emerged as an exciting new tool in a great number of applications (e.g., variant discovery, profiling of histone modifications, identifying transcription factor binding sites, resequencing, and transcriptome characterization). Even though this technology has generated unprecedented amounts of data in the scientific community few studies have looked carefully at its inherent variability. Recent studies of mRNA expression levels found little appreciable technical variation in Illumina’s Solexa sequencing platform (a next-generation sequencing device). Although these results are encouraging, they are limited to a specific platform and application, and have been made without any attention to …

Hierarchical Bayesian Methods To Model Heterogeneity In Cow- And Herd-Level Relationships Between Milk Production And Reproduction In Dairy Cows, Nora M. Bello, Juan P. Steibel, Robert J. Tempelman

Conference on Applied Statistics in Agriculture

Two of the most important broad classifications of phenotypes for successful dairy production are milk yield and fertility. The nature of the relationship between milk production and reproductive performance of dairy cows is uncertain due to conflicting results reported in many studies. A common deficiency in many such studies is an underappreciation of the dual dimension of the production-reproduction relationship, as defined by herd (random or u) level and cow (residual or e) level sources of (co)variation. Our overall hypothesis is that the e- and u- level relationships between milk production and reproduction in dairy cows are heterogeneous and depend …

Relative Potency Estimation In Direct Bioassay With Measurement Errors*, Weixing Song

Conference on Applied Statistics in Agriculture

The dosage levels measured in direct bioassays are often contaminated with measurement errors, which are usually neglected in the statistical inference. This paper proposes several estimation procedures for the relative potencies in direct bioassays taking the measurement errors into account. Asymptotic theories are developed for constructing the confidence intervals. Numerical simulations are also included to compare different estimation procedures.

Bayesian Nonparametric Bioassay Estimation, Bahman Shafii, William J. Price

Conference on Applied Statistics in Agriculture

Estimation of unknown pesticide levels in experimental samples is an important aspect of many agricultural and environmental studies. Such measurements are often made utilizing a “standard” dose response curve. This methodology compares the biological response of a target organism at known dosages to the response of the same organism exposed to an unknown sample. These “bioassays” are typically more efficient in time and resources than direct chemical assessment of the unknown sample. The form and choice of the standard curve, however, is subjective and can influence the estimation of the unknown dose. Problems may also arise when incomplete or preliminary …

Associating Snps With Binary Traits, Alexander E. Lipka, George P. Mccabe, R. W. Doerge

Conference on Applied Statistics in Agriculture

Association mapping uses statistical analyses to test for relationships between genomic markers called single nucleotide polymorphisms (SNPs) and traits. This research focuses on the use of logistic regression to assess the additive, dominance, and epistatic effects when investigating associations between SNPs and binary traits, such as disease status. A very specific phenomenon that results in infinite maximum likelihood estimates (MLEs) of logistic regression parameters, called quasi-separation of points (QSP), is investigated. We provide a solution that relies on the use of Firth’s MLE to estimate logistic regression parameters. Simulated and real data are utilized to investigate the use of Firth’s …

Editor's Preface And Table Of Contents, Gary L. Gadbury

Conference on Applied Statistics in Agriculture

These proceedings contain papers presented in the twenty-first annual Kansas State University Conference on Applied Statistics in Agriculture, held in Manhattan, Kansas, April 19 - April 21, 2009.

Director's Report Of Research In Kansas 2008, Kansas State University. Agricultural Experiment Station

Kansas Agricultural Experiment Station Research Reports

The 2008 Director's Report of Research in Kansas provides a list of journal articles, station publications, and other published manuscripts from scientists in our departments, centers, fields, and associated programs. On cover: July 1, 2003 to June 30, 2008

2009 Agricultural Research Southeast Agricultural Research Center, Kansas State University. Agricultural Experiment Station And Cooperative Extension Service

Kansas Agricultural Experiment Station Research Reports

No abstract provided.

Dried Corn Germ In Natural Finishing Programs Reduces Incidence Of Liver Abscess, J.O. Wallace, James S. Drouillard, Christopher D. Reinhardt

Kansas Agricultural Experiment Station Research Reports

Changes in consumer preference for beef produced without growth promotants, ionophores, or antibiotics and consumers' willingness to pay price premiums for such products have led some producers to begin raising beef under "natural" feeding regimens. Some natural programs prohibit use of injectable antibiotics, feed additive drugs, or growth promoting implants throughout the life of the animal. This creates challenges for maintaining efficient growth and preventing disease or metabolic disorders. A key problem facing producers who feed cattle under a natural regimen, without use of antibiotics such as tylosin and ionophores, is ruminal acidosis, which is commonly linked with liver abscesses. …

Southwest Research-Extension Center, Field Day 2009

Kansas Agricultural Experiment Station Research Reports

Report of agricultural research from Southwest Research-Extension Center of Kansas State University.

Determination Of Amino Acid Digestibility And Calculated Energy Values In High-Protein Sorghum Dried Distillers Grains With Solubles In Growing Pigs (2009), H L. Frobose, J Y. Jacela, Joel M. Derouchey, Michael D. Tokach, Jim L. Nelssen, Robert D. Goodband, Steven S. Dritz

Kansas Agricultural Experiment Station Research Reports

An experiment was conducted to determine the digestibility of amino acids (AA) and energy in high-protein sorghum dried distillers grain with solubles (DDGS). Six growing barrows (initially 50 lb) surgically fitted with T-cannulas were randomly assigned to 1 of 2 dietary treatments in a 2-period crossover design. The treatments were a diet with the high-protein sorghum DDGS (50% of the diet) as the only protein source and an N-free diet for determining basal endogenous AA loss. Both diets contained 0.25% chromic oxide as an indigestible marker. Fecal and ileal digesta samples were collected during each period for energy and AA …

K-State Turfgrass Research 2009, Kansas State University. Agricultural Experiment Station And Cooperative Extension Service

Kansas Agricultural Experiment Station Research Reports

Turfgrass Research 2009 contains results of projects conducted by K-State faculty and graduate students. Some of these results will be presented at the Kansas Turfgrass Field Day on August 6, 2009, at the John C. Pair Horticultural Center in Wichita, KS. Articles in this Report of Progress summarize research projects that were completed recently or will be completed in the next year or two. Specifically, this year's report presents summaries of research on environmental stresses and the environment, disease control, and cultivar evaluations.

Efficacy Of Different Commercial Phytase Sources And Development Of A Phosphorus Release Curve (2009), C K. Jones, B W. Ratliff, N L. Horn, Michael D. Tokach, Robert D. Goodband, Joel M. Derouchey, Jim L. Nelssen, Steven S. Dritz

Kansas Agricultural Experiment Station Research Reports

Two experiments used 184 pigs (PIC, 22.7 and 21.3 lb BW, respectively) to develop an available P (aP) release curve for commercial phytase products. In Exp. 1 and 2, pigs were fed a basal diet (0.06% aP) and 2 levels of added aP from inorganic P (monocalcium P) to develop a standard curve. In Exp. 1, 100, 175, 250, or 500 phytase units (FTU)/kg OptiPhos (Enzyvia LLC, Sheridan, IN) or 200, 350, 500 or 1,000 FTU/kg Phyzyme XP (Danisco Animal Nutrition, Marlborough, UK) was added to the basal diet. In Exp. 2, 250, 500, 750, or 1,000 FTU/kg OptiPhos; 500, …

Field Research 2008, Kansas State University. Agricultural Experiment Station And Cooperative Extension Service

Kansas Agricultural Experiment Station Research Reports

Includes research reports from these locations: Harvey County Experiment Field, South Central Kansas Experiment Field, Irrigation and North Central Kansas Experiment Fields, Kansas River Valley Experiment Field, East Central Kansas Experiment Field, and Harvey County Experiment Field.

Needle-Free Injection Enhancement Of Beef Improves Tenderness But Slightly Increases Microbial Translocation, A. Sutterfield, B.A. Crow, J.P. Grobbel, Randall K. Phebus, Michael E. Dikeman, Larry C. Hollis

Kansas Agricultural Experiment Station Research Reports

Blade tenderization has been used for decades to increase tenderness in beef cuts that are highly variable in tenderness or predicted to be "tough." Injection enhancement also is commonly used in industry to increase tenderness, juiciness, and flavor of some beef muscles. These processes have the potential to translocate microbial organisms on the exterior to interior portions of whole muscles. One research study reported that 3 to 4% of surface bacteria are transferred into the interior of muscles but only penetrate an average of ¼ inch deep into the surface. Even though the frequency of subprimal surfaces being contaminated with …

Thermal Process With Additional Drying Provides Proper Lethality For Controlling Pathogens During Jerky Production, Kelly J.K. Getty, N.M. Harper, Elizabeth A.E. Boyle

Kansas Agricultural Experiment Station Research Reports

The New Mexico Department of Health linked salmonellosis to beef jerky in 2003 after 26 individuals became ill; this prompted a recall of nearly 21,600 lb of product. Following this incident, the USDA's Food Safety and Inspection Service instituted the Compliance Guideline for Meat and Poultry Jerky Produced by Small and Very Small Plants in 2004 and updated this document in 2007 with the Quick Guide on Jerky Processing. The Quick Guide states that water activity for jerky products should be ≤ 0.85 for safety and a moisture-to-protein ratio (MPR) must be ≤ 0.75:1 for product to be labeled as …

Field Research 2009, Kansas State University. Agricultural Experiment Station And Cooperative Extension Service

Kansas Agricultural Experiment Station Research Reports

Includes research reports from these locations: East Central Kansas Experiment Field, Kansas River Valley Experiment Field, Harvey County Experiment Field, Irrigation and North Central Kansas Experiment Fields, South Central Kansas Experiment Field, and Western Kansas Agricultural Research Centers.

Influences Of Heat Stress On Serological Response And Performance Of Dairy Calves (2009), Larry C. Hollis, Michael J. Brouk

Kansas Agricultural Experiment Station Research Reports

Objectives of this study were to investigate the possible effects of heat stress on calf growth and the development of active immunity. Eighteen heifer calves born between July 21 and August 24, 2008, were housed in individual hutches, and half of the calves were provided supplemental shade from birth to 8 weeks of age. During this time, milk replacer intake, dry feed intake, and fecal scores were recorded daily. Calf weight and hip and shoulder heights were measured and recorded weekly. The bovine viral diarrhea portion of the vaccine given at 5 weeks of age was used as an indicator …

Effect Of Acidulant Addition On Yogurt Fermentation (2009), Karen A. Schmidt

Kansas Agricultural Experiment Station Research Reports

Yogurt was manufactured by pre-acidifying the yogurt mix with citric acid, lactic acid, or concentrated lemon juice either before or after pasteurization to a target pH of 6.2, and then the traditional manufacturing process was continued. Adding citric acid or lemon juice to the yogurt mix after pasteurization resulted in a 13% reduction in fermentation time compared with the control. This reduction in fermentation time may result in greater efficiency for yogurt manufacturers, allowing for a more sustainable manufacturing process.; Dairy Day, 2009, Kansas State University, Manhattan, KS, 2009; Dairy Research, 2009 is known as Dairy Day, 2009

Differences Among High, Medium, And Low Profitdairy Operations: An Analysis Of 2004-2008 Kansasfarm Management Association Dairy Enterprises (2009), K.M. Schulte, Kevin C. Dhuyvetter

Kansas Agricultural Experiment Station Research Reports

The financial bottom line, or net income, is a key factor in determining how successful a dairy has been historically as well as an indicator of the financial ease or struggles the dairy might have in the future. What causes net income to vary from one operation to another is a key question for dairy farmers. For example, does milk price received, feed cost, total cost, or milk production have the greatest impact on net return variability? In this study, we evaluated Kansas Farm Management Dairy Enterprise data from the past 5 years to determine correlation of revenue, production, and …