A Non-Parametric Empirical Bayes Approach For Estimating Transcript Abundance In Un-Replicated Next-Generation Sequencing Data,
2010
Kansas State University Libraries
A Non-Parametric Empirical Bayes Approach For Estimating Transcript Abundance In Un-Replicated Next-Generation Sequencing Data, Sanvesh Srivastava, R. W. Doerge
Conference on Applied Statistics in Agriculture
Empirical Bayes approaches have been widely used to analyze data from high throughput sequencing devices. These approaches rely on borrowing information available for all the genes across samples to get better estimates of gene level expression. To date, transcript abundance in data from next generation sequencing (NGS) technologies has been estimated using parametric approaches for analyzing count data, namely – gamma-Poisson model, negative binomial model, and over-dispersed logistic model. One serious limitation of these approaches is they cannot be applied in absence of replication. The high cost of NGS technologies imposes a serious restriction on the number of biological replicates …
Nonlinear Regression Parameters As Outcomes: Simple Vs. Sophisticated Analyses,
2010
Kansas State University Libraries
Nonlinear Regression Parameters As Outcomes: Simple Vs. Sophisticated Analyses, Reid D. Landes
Conference on Applied Statistics in Agriculture
Sometimes a nonlinear regression parameter for an individual is the outcome of interest. But due to variability among individuals, the individuals’ regression parameters cannot be estimated with the same amount of precision. This problem of heterogeneous variance complicates the ultimate goal of estimating population-level regression parameters with two usual methods: (i) the simple arithmetic mean of individually estimated regression parameters and (ii) random coefficients regression (RCR). Weights are proposed for each method to account for the heterogeneity problem. The methods are illustrated with chick weights collected over time. Monte Carlo simulation allows comparison of statistical properties of the four estimators …
Approximate Bayesian Approaches For Reverse Engineering Biological Networks,
2010
Kansas State University Libraries
Approximate Bayesian Approaches For Reverse Engineering Biological Networks, Andrea Rau, Florence Jaffr´Ezic, Jean-Louis Foulley, R. W. Doerge
Conference on Applied Statistics in Agriculture
Genes are known to interact with one another through proteins by regulating the rate at which gene transcription takes place. As such, identifying these gene-to-gene interactions is essential to improving our knowledge of how complex biological systems work. In recent years, a growing body of work has focused on methods for reverse-engineering these so-called gene regulatory networks from time-course gene expression data. However, reconstruction of these networks is often complicated by the large number of genes potentially involved in a given network and the limited number of time points and biological replicates typically measured. Bayesian methods are particularly well-suited for …
On Testing For Significant Quantitative Trait Loci (Qtl) Effects When Variances Are Unequal,
2010
Kansas State University Libraries
On Testing For Significant Quantitative Trait Loci (Qtl) Effects When Variances Are Unequal, Pradeep Singh, Shesh N. Rai
Conference on Applied Statistics in Agriculture
The basic theory of QTL (Quantitative Trait Loci) mapping is to score a population for a quantitative trait according to the marker genotype, and then to use statistics to identify differences associated with the markers and the quantitative trait of interest. Permutation based methods have been used to estimate threshold values for quantitative mapping. The permutation test based on the Student t-test for equality of means does not control Type I error rate to its nominal value when variances are unequal. In this study we propose a modification of the Student t-test based on the jackknife estimator of population variance. …
Functional Divergence Of Duplicated Genes In The Soybean Genome,
2010
Kansas State University Libraries
Functional Divergence Of Duplicated Genes In The Soybean Genome, Paul L. Auer, R. W. Doerge
Conference on Applied Statistics in Agriculture
The soybean genome has undergone many different evolutionary changes that are observable with modern technologies. Of particular interest to scientists and plant breeders is the fact that the soybean genome exhibits features of genome duplication from millions of years ago. Genes that were copied during the duplication event have since diverged functionally. Identifying functionally divergent duplicate genes may provide insight into the evolution of soybean. To investigate functional divergence, transcripts from seven different tissue samples of pooled soybean messenger RNA were sequenced using the Solexa next-generation sequencer and analyzed for gene expression. We tested differential expression of duplicated genes within …
Generalized Linear Mixed Model Estimation Using Proc Glimmix: Results From Simulations When The Data And Model Match, And
When The Model Is Misspecified,
2010
Kansas State University Libraries
Generalized Linear Mixed Model Estimation Using Proc Glimmix: Results From Simulations When The Data And Model Match, And When The Model Is Misspecified, Debbie Boykin, Mary J. Camp, Luann Johnson, Matthew Kramer, David Meek, Debra Palmquist, Bryan Vinyard, Mark West
Conference on Applied Statistics in Agriculture
A simulation study was conducted to determine how well SAS® PROC GLIMMIX (SAS Institute, Cary, NC), statistical software to fit generalized linear mixed models (GLMMs), performed for a simple GLMM, using its default settings, as a naïve user would do. Data were generated from a wide variety of distributions with the same sets of linear predictors, and under several conditions. Then, the data sets were analyzed by using the correct model (the generating model and estimating model were the same) and, subsequently, by misspecifying the estimating model, all using default settings. The data generation model was a randomized complete block …
Using Time-Series Intervention Analysis To Model Cow Heart Rate Affected By Programmed Audio And Environmental/Physiological Cues,
2010
Kansas State University Libraries
Using Time-Series Intervention Analysis To Model Cow Heart Rate Affected By Programmed Audio And Environmental/Physiological Cues, Dean M. Anderson, Norbert Remenyi, Leigh W. Murray
Conference on Applied Statistics in Agriculture
This research is the first use of Box-Jenkins time-series models to describe changes in heart rate (HR) of free-ranging crossbred cows (Bos taurus) receiving both programmed audio cues from directional virtual fencing (DVFTM) devices and non-programmed environmental/physiological cues. The DVFTM device is designed to control the animal's location on the landscape. Polar Accurex® devices were used to capture HR every minute between 19 and 24 March 2003, when three mature free-ranging beef cows, previously habituated to the DVFTM device, were confined to a brush-infested area of an arid rangeland paddock. Global positioning system (GPS) electronics were used to record each …
A Generalized Approach And Computer Tool For Quantitative Genetics Study,
2010
Kansas State University Libraries
A Generalized Approach And Computer Tool For Quantitative Genetics Study, Jixiang Wu, Johnie N. Jenkins, Jack C. Mccarty
Conference on Applied Statistics in Agriculture
Quantitative genetics is one of the most important components to provide valuable genetic information for improving production and quality of plants and animals. The research history of quantitative genetics study could be traced back more than one hundred years. Since the Analysis of Variance (ANOVA) methods were proposed by Fisher in 1925, several useful genetic models have been proposed and have been widely applied in both plant and animal quantitative genetics studies. Useful examples included various North Carolina (NC) and diallel cross mating designs. However, many genetic models derived from these mating designs are ANOVA method based, so there are …
Modeling Dna Methylation Tiling Array Data,
2010
Missouri University of Science and Technology
Modeling Dna Methylation Tiling Array Data, Gayla Olbricht, Bruce A. Craig, R. W. Doerge
Conference on Applied Statistics in Agriculture
Epigenetics is the study of heritable changes in gene function that occur without a change in DNA sequence. It has quickly emerged as an essential area for understanding inheritance and variation that cannot be explained by the DNA sequence alone. Epigenetic modifications have the potential to regulate gene expression and may play a role in diseases such as cancer. DNA methylation is a type of epigenetic modification that occurs when a methyl chemical group attaches to a cytosine base on the DNA molecule. To better understand this epigenetic mechanism, DNA methylation profiles can be constructed by identifying all locations of …
Characterizing Thermal Hysteresis In Body Temperature For A Heat Stressed Steer,
2010
Kansas State University Libraries
Characterizing Thermal Hysteresis In Body Temperature For A Heat Stressed Steer, F. Yang, A. M. Parkhurst, D. A. Spiers, J. B. Gaughan, T. L. Mader, G. L. Hahn
Conference on Applied Statistics in Agriculture
Studies have shown that exposure of animals to a high ambient temperature environment poses serious threats to their health, performance and productivity. Above a certain threshold an animal's body temperature (Tb) appears to be driven by the hot ambient temperature (Ta). For steers challenged by heat stress, the Tb-Ta relationship shows a dramatic increase in Tb per unit change of Ta and the dynamics of the Tb-Ta relationship follow a pattern which depends on whether Ta is increasing or decreasing. A delay becomes noticeable in a steer’s thermo-regulatory response to Ta when Ta is controlled to be sinusoidal in the …
Evaluating Pen-Day Interactions In Body Temperature Bilogistic Mixed Model For Handling Of Feedlot Heifers During Heat Stress,
2010
Kansas State University Libraries
Evaluating Pen-Day Interactions In Body Temperature Bilogistic Mixed Model For Handling Of Feedlot Heifers During Heat Stress, F. Yang, A. M. Parkhurst, T. M. Brown-Brandl, R. A. Eigenberg, J. A. Nienaber
Conference on Applied Statistics in Agriculture
Daily activities consume the energy of heifers, subsequently causing an elevation of body temperature, depending on the ambient conditions. A better understanding of the dynamics of body temperature (Tb) would be helpful when deciding how to process and handle heifers. It would also lead to specific recommendations on moving heifers under different ambient conditions, especially during the summer. In this study, a bilogistic mixed model is used to describe the dynamics of Tb during the moving event. Data was taken from heifers in pens located at different distances from the heifer work station on four separate summer days under hot …
Characterizing Foraging Patterns Among Cattle And Bonded And Non-Bonded Small Ruminants Using Spatial Point Process Techniques,
2010
Kansas State University Libraries
Characterizing Foraging Patterns Among Cattle And Bonded And Non-Bonded Small Ruminants Using Spatial Point Process Techniques, D. M. Anderson, L. W. Murray, P. Sun, E. L. Fredrickson, R. E. Estell, V. B. Nakamatsu
Conference on Applied Statistics in Agriculture
This paper uses the technique of spatial point processes to describe the spatial patterns of freeranging cattle and small ruminants. Two mixed-species livestock groups were monitored while foraging on 410 ha of brush-infested Southern New Mexico rangeland during July and August 1988. The groups consisted of crossbred Bos taurus and Bos indicus beef cattle with white-faced sheep (Ovis aries) and mohair goats (Capra hircus). The bonded group consisted of small ruminants that had their behaviours modified through socialization with cattle to form a ‘flerd’ in which small ruminants consistently remained near cattle. Small ruminants in the non-bonded group had not …
Modeling Fish Length Distribution Using A Mixture Technique,
2010
Kansas State University Libraries
Modeling Fish Length Distribution Using A Mixture Technique, Bahman Shafii, William J. Price, Charlie Holderman, Cathy Gidley, Paul J. Anders
Conference on Applied Statistics in Agriculture
In fisheries science, length and age are important aspects of fish life history. Length is a function of growth, which provides an integrated measure of the environmental and endogenous conditions, e.g. genetics, affecting individuals and populations. Length at age data can be used to assess quality and quantity of habitat, food availability, or the need for and influence of management activities. Statistical mixture techniques may be used as a means to effectively model fish length distribution. A three-component mixture model, based on normal variates, was employed to describe length distribution in mountain whitefish species. The resulting model provided parameter estimates …
Editor's Preface And Table Of Contents,
2010
Kansas State University Libraries
Editor's Preface And Table Of Contents, Weixing Song
Conference on Applied Statistics in Agriculture
These proceedings contain papers presented in the twenty-second annual Kansas State University Conference on Applied Statistics in Agriculture, held in Manhattan, Kansas, April 25 - April 27, 2010.
Memristics: Memristors, Again? – Part Ii, How To Transform Wired ‘Translations’ Between Crossbars Into Interactions?,
2010
ThinkArt Lab Glasgow
Memristics: Memristors, Again? – Part Ii, How To Transform Wired ‘Translations’ Between Crossbars Into Interactions?, Rudolf Kaehr
Rudolf Kaehr
The idea behind this patchwork of conceptual interventions is to show the possibility of a “buffer-free” modeling of the crossbar architecture for memristive systems on the base of a purely difference-theoretical approach. It is considered that on a nano-electronic level principles of interpretation appears as mechanisms of complementarity. The most basic conceptual approach to such a complementarity is introduced as an interchangeability of operators and operands of an operation. Therefore, the architecture of crossbars gets an interpretation as complementarity between crossbar functionality and “buffering” translation functionality. That is, the same matter functions as operator and at once, as operand – …
Experimental Manipulation Of Interfacial Molecular Assemblies,
2010
Kennesaw State University
Experimental Manipulation Of Interfacial Molecular Assemblies, Mark Anderson
Mark R. Anderson
No abstract currently available.
The Effect Of Ion-Pairing On The Open Circuit Potential Of 3-Mercaptoproprionic Acid Modified Gold Electrodes,
2010
Kennesaw State University
The Effect Of Ion-Pairing On The Open Circuit Potential Of 3-Mercaptoproprionic Acid Modified Gold Electrodes, Mark Anderson, Alice Harper
Mark R. Anderson
Open circuit potential (OCP) measurement is used to monitor the charge of a monolayer of 3-mercaptopropionic acid. OCP is determined by the concentrations of the reduced and oxidized forms of a redox couple in the solution adjacent to the modified interface. OCP values were monitored in the presence of the one-electron redox couple Fe(CN)63-/4- as a function of solution pH. The OCP measured at basic pHs was different from the acidic OCP due to differences in electrostatic interactions between the interface and the redox species as described by the Nernst equation. The influence of ion-pairing with the monolayer is studied …
Influence Of Canopy Cover, Nutrients, And Season On Stoichiometric Variation Of Epilithon In Neotropical Streams.,
2010
University of Nebraska at Lincoln
Influence Of Canopy Cover, Nutrients, And Season On Stoichiometric Variation Of Epilithon In Neotropical Streams., Tyler J. Kohler
Dissertations & Theses in Natural Resources
Light and nutrient availability are strong factors determining the nutrient composition of epilithon in temperate stream ecosystems. However, little work has been performed regarding this association in tropical streams. In our study, we investigated 1) how gradients of canopy cover and nutrients and 2) wet/dry seasonality influence epilithon standing stocks and nutrient quality. We surveyed 18 stream locations within six watersheds that varied in nutrient and light conditions during both the wet and dry seasons on the island of Trinidad to test these questions. Additionally, we sampled four stream reaches bimonthly for three years, thinning the canopy of two of …
2010 Sonia Kovalevsky Math For Girls Day Report,
2010
Lincoln University
2010 Sonia Kovalevsky Math For Girls Day Report, Association For Women In Mathematics, Lincoln University Of Missouri, Donna L. Stallings
Math for Girls Day Documents
Report for the Fifth Annual Lincoln University Sonia Kovalevsky Math for Girls Day that was held on April 23, 2010 from 8:00am to 2:00pm on the campus of Lincoln University in Jefferson City, MO.
A Numerical Method For Estimating The Variance Of Age At Maximum Growth Rate In Growth Models,
2010
Virginia Commonwealth University
A Numerical Method For Estimating The Variance Of Age At Maximum Growth Rate In Growth Models, Semhar Ogbagaber
Theses and Dissertations
Most studies on maturation and body composition using the Fels Longitudinal data mention peak height velocity (PHV) as an important outcome measure. The PHV is often derived from growth models such as the triple logistic model fitted to the stature (height) data. The age at PHV is sometimes ordinalized to designate an individual as an early, average or late maturer. In theory, age at PHV is the age at which the rate of growth reaches the maximum. Theoretically, for a well behaved growth function, this could be obtained by setting the second derivative of the growth function to zero and …
