Statistics and Probability Commons^™

The Strength Of Statistical Evidence For Composite Hypotheses With An Application To Multiple Comparisons, David R. Bickel

COBRA Preprint Series

The strength of the statistical evidence in a sample of data that favors one composite hypothesis over another may be quantified by the likelihood ratio using the parameter value consistent with each hypothesis that maximizes the likelihood function. Unlike the p-value and the Bayes factor, this measure of evidence is coherent in the sense that it cannot support a hypothesis over any hypothesis that it entails. Further, when comparing the hypothesis that the parameter lies outside a non-trivial interval to the hypotheses that it lies within the interval, the proposed measure of evidence almost always asymptotically favors the correct hypothesis …

An Assessment Of The Role Of Chimpanzees In Aids Vaccine Research, Jarrod Bailey

Laboratory Experiments Collection

Prior to Simian Immunodeficiency Virus (SIV)-infected macaques becoming the ‘model of choice’ in the 1990s, chimpanzees were widely used in AIDS vaccine research and testing. Faced with the continued failure to develop an effective human vaccine, some scientists are calling for a return to their widespread use. To assess the past and potential future contribution of chimpanzees to AIDS vaccine development, databases and published literature were systematically searched to compare the results of AIDS vaccine trials in chimpanzees with those of human clinical trials, and to determine whether the chimpanzee trials were predictive of the human response. Protective and/or therapeutic …

The Comparative Radiopacity Between Primary And Permanent Teeth, Robert C. Lee

Loma Linda University Electronic Theses, Dissertations & Projects

Purpose: This in vitro study compared the radiopacity between human primary and permanent enamel and dentin. It also compared the radiopacity between human anterior and posterior teeth.

Methods: Extracted primary and permanent teeth were used in this study. One mm enamel and one mm dentin slices were cut from each extracted tooth. Radiographs were taken of each enamel and dentin specimen 1 mm in thickness along with an aluminum step-wedge using procedures specified in International Standards Organization (ISO) 4049:2000. A densitometer was used to measure the Optical Density (OD) of the radiographs of the specimen and the accompanying aluminum step-wedge. …

Simultaneous Confidence Bands For The Coefficient Function In Functional Regression, Philip T. Reiss

Philip T. Reiss

No abstract provided.

Volunteer Studies In Pain Research — Opportunities And Challenges To Replace Animal Experiments: The Report And Recommendations Of A Focus On Alternatives Workshop, C. K. Langley, Q. Aziz, C. Bountra, N. Gordon, P. Hawkins, A. Jones, G. Langley, T. Nurmikko, I. Tracey

Experimentation Collection

Despite considerable research, effective and safe treatments for human pain disorders remain elusive. Understanding the biology of different human pain conditions and researching effective treatments continue to be dominated by animal models, some of which are of limited value. British and European legislation demands that non-animal approaches should be considered before embarking on research using experimental animals. Recent scientific and technical developments, particularly in human neuroimaging, offer the potential to replace some animal procedures in the study of human pain. A group of pain research experts from academia and industry met with the aim of exploring creatively the tools, strategies …

Inferring Group Differences In Brain Connectivity From Functional Magnetic Resonance Images, Philip T. Reiss

Philip T. Reiss

No abstract provided.

Reliability Of Functional Connectivity Networks: How Can We Assess It?, Philip T. Reiss

Philip T. Reiss

No abstract provided.

Estimation And Testing For The Effect Of A Genetic Pathway On A Disease Outcome Using Logistic Kernel Machine Regression Via Logistic Mixed Models, Dawei Liu, Debashis Ghosh, Xihong Lin

Harvard University Biostatistics Working Paper Series

No abstract provided.

A Powerful And Flexible Multilocus Association Test For Quantitative Traits, Lydia Coulter Kwee, Dawei Liu, Xihong Lin, Debashis Ghosh, Michael P. Epstein

Harvard University Biostatistics Working Paper Series

No abstract provided.

Model-Based Clustering Of Methylation Array Data: A Recursive-Partitioning Algorithm For High-Dimensional Data Arising As A Mixture Of Beta Distributions, E. Andres Houseman, Brock C. Christensen, Ru-Fang Yeh, Carmen J. Marsit, Margaret R. Karagas, Margaret Wrensch, Heather H. Nelson, Joseph Wiemels, Shichun Zheng, John K. Wiencke, Karl T. Kelsey

Harvard University Biostatistics Working Paper Series

No abstract provided.

The Beginning Of The End For Chimpanzee Experiments?, Andrew Knight

Experimentation Collection

The advanced sensory, psychological and social abilities of chimpanzees confer upon them a profound ability to suffer when born into unnatural captive environments, or captured from the wild – as many older research chimpanzees once were – and when subsequently subjected to confinement, social disruption, and involuntary participation in potentially harmful biomedical research. Justifications for such research depend primarily on the important contributions advocates claim it has made toward medical advancements. However, a recent large-scale systematic review indicates that invasive chimpanzee experiments rarely provide benefits in excess of their profound animal welfare, bioethical and financial costs. The approval of large …

Comparison Of Microleakage In Three Sealant Placement Protocols Vs. The Enamel Loc System, Audrey T. Sheu

Loma Linda University Electronic Theses, Dissertations & Projects

PURPOSE: To evaluate sealant microleakage using four different application techniques.

METHODS: The four application techniques evaluated were acid etch only, Adper L-Pop bonding, Optibond bonding, and Enamel Loc One-Step Sealant. Sixty-four extracted third molar teeth were assigned on one of four application techniques (n=16) and Clinpro sealants applied according to the manufacturer's instructions. The teeth were thermocycled for 500 cycles, dyed, and embedded in resin. The samples were then sectioned and evaluated for microleakage on the buccal and lingual surfaces. Statistical methods employed to analyze the data were the Kruskal-Willis rank test and the Mann-Whitney U test.

RESULTS: No significant …

An Improved String Composition Method For Sequence Comparison, Guoquing Lu, Shunpu Zhang, Xiang Fang

Biology Faculty Publications

Background: Historically, two categories of computational algorithms (alignment-based and alignment-free) have been applied to sequence comparison–one of the most fundamental issues in bioinformatics. Multiple sequence alignment, although dominantly used by biologists, possesses both fundamental as well as computational limitations. Consequently, alignment-free methods have been explored as important alternatives in estimating sequence similarity. Of the alignment-free methods, the string composition vector (CV) methods, which use the frequencies of nucleotide or amino acid strings to represent sequence information, show promising results in genome sequence comparison of prokaryotes. The existing CV-based methods, however, suffer certain statistical problems, thereby underestimating the amount of evolutionary …

Systematic Reviews Of Animal Experiments Demonstrate Poor Contributions To Human Healthcare, Andrew Knight

Experimentation Collection

Widespread reliance on animal models during preclinical research and toxicity testing assumes their reasonable predictivity for human outcomes. However, of 20 published systematic reviews examining human clinical utility located during a comprehensive literature search, animal models demonstrated significant potential to contribute toward clinical interventions in only two cases, one of which was contentious. Included were experiments expected by ethics committees to lead to medical advances, highly-cited experiments published in major journals, and chimpanzee experiments—the species most generally predictive of human outcomes. Seven additional reviews failed to demonstrate utility in reliably predicting human toxicological outcomes such as carcinogenicity and teratogenicity. Results …

Developing Accurate Spatial Maps Of Cotton Fiber Quality Parameters, Gretchen F. Sassenrath

Conference on Applied Statistics in Agriculture

Awareness of the importance of cotton fiber quality (Gossypium, L. sps.) has increased as advances in spinning technology require better quality cotton fiber. Recent advances in geospatial information sciences allow an improved ability to study the extent and causes of spatial variability in fiber parameters. However, these studies are often harvested by hand and ginned on small research gins. Fiber quality from cotton lint harvested and ginned in this manner is different from that machine-harvested and ginned on production-scale equipment. The objective of this study was to develop a method of correcting for error introduced into cotton fiber quality parameters …

Nonlinear Mixed Models To Evaluate Effects Of Environment Conditions, Hair Coat, And Anchor Length On Body Temperature During Afternoon Milking Of Holstein Cows In Hawaii, N Aitha, A. M. Parkhurst, C. N. Lee, P. E. Hillman

Conference on Applied Statistics in Agriculture

A hot thermal environment is one factor that causes loss of activity, productivity and even death in cows. One reason may be the effect of hair coat (black or white) on body temperature during different activities and environment conditions. In this study, we attempt to characterize the relationship between body temperature over time using activity, physiological and environmental effects with a nonlinear regression model. The fixed and mixed versions of models are examined. We also examine the effect of the measuring device, anchor length (long or short). Environmental effects, such as, air temperature, thermal heat index (THI), relative humidity, solar …

A Two-Stage Approach For Estimating The Effect Of Dna Methylation On Differential Expression Using Tiling Array Technology, Suk-Young Yoo, R. W. Doerge

Conference on Applied Statistics in Agriculture

Epigenetics is the study of heritable alterations in gene function without changing the DNA sequence itself. It is known that epigenetic modifications such as DNA methylation and histone modifications are highly correlated with the regulation of gene expression. A twostage analysis is proposed that employs a hidden Markov model and a linear model to evaluate differential expression as related to DNA methylation for the purpose of examining the effects of DNA methylation on gene regulation using tiling array technology. In the first stage, a hidden Markov model (HMM) is employed to estimate the methylation status per tile by utilizing information …

Spatial Clustering Using The Likelihood Function, April Kerby, David Marx, Ashok Samal, Viacheslav Adamchuk

Conference on Applied Statistics in Agriculture

Clustering has been widely used as a tool to group multivariate observations that have similar characteristics. However, most attempts at formulating a method to group similar multivariate observations while taking into account their spatial location are relatively ad hoc and do not account for the underlying spatial structure of the variables measured [12, 13, 14]. This paper proposes a method to spatially cluster similar observations based on the likelihood function. The geographic or spatial location of the observations can be incorporated into the likelihood of the multivariate normal distribution through the variance-covariance matrix. The variance-covariance matrix can be computed using …

Statistical Issues In Efficacy Evaluation For Companion Animal Drug Development, Zhanglin Lin Cui, Wherly Hoffman

Conference on Applied Statistics in Agriculture

Companion animals, commonly called pets, are animals such as dogs, cats, and horses. The companion animal drug market has expanded rapidly in recent years. Two major points of focus in companion animal drug development are therapeutics and parasiticides. From a statistics point of view, experimental design, experimental unit determination, sample size estimation and reestimation, treatment design, data transformation, multiple testing, and proper modeling are major statistical issues when efficacy evaluation in a companion animal study is conducted. These major statistical issues are addressed using two clinical studies as examples: Reconcile® (Fluoxetine) for the treatment of separation anxiety in dogs and …

Modeling Seasonal Wine Grape Development Using A Mixture Technique, William J. Price, Bahman Shafii, Paul E. Blom, Julie M. Tarara, Nick Dokoozlian, Luis J. Sanchez

Conference on Applied Statistics in Agriculture

Biological growth data typically display an increasing sigmoidal pattern over time. Grape development is no exception and shows a similar general trend. A detailed examination of the growth process in grapes, however, reveals a few systematic deviations from this pattern. Specifically, grape development is often characterized by localized areas of growth plateaus leading to an overall growth pattern referred to as a double sigmoidal curve. Capturing and characterizing these local changes in growth is important as they represent important phases in grape development such as veraison. This paper utilizes a model adapted from the technique of mixture models to estimate …

Comparisons Of Two Symmetric Density Function Solutions Of Aphid Population Growth Models, J. H. Matis, T. R. Kiffey, W. Van Der Werf, A. C. Costamagna, T. I. Matis, G. J. Michels Jr

Conference on Applied Statistics in Agriculture

Aphids are among the world's most devastating crop pests, and their population trajectories in field crops are characterized by rapid boom and bust, under the influence of bottom up (host plant) and top down (natural enemy) forces. Theoretical development in aphid growth trajectory modeling has recently advanced quite significantly, and the logistic and normal probability density functions have been found to provide analytical solutions to mechanistic models of the aphid population growth dynamics. The logistic or hyperbolic secant squared model captures a growth trajectory shaped by negative feedback of the aphid population on itself, due to the accumulation of adverse …

Statistical Issues In The Normalizationof Multi-Species Microarray Data, John R. Stevens, Balasubramanian Ganesan, Prerak Desai, Sweta Rajan, Bart C. Weimer

Conference on Applied Statistics in Agriculture

Several species of bacteria are involved in the production of cheese, including Lactobacillus brevis and Lactococcus lactis. A custom-designed Affymetrix microarray was recently developed to study gene expression in three organisms on a single chip. This array contains only perfect match features for the coding and non-coding regions in the genomes of all three sequences. The multi-species nature of this array version raises interesting questions regarding the preprocessing or normalization strategies for the analysis of gene expression data. We present and evaluate several possible strategies using both cDNA dilution data and experimental expression data from a repeated measures design. The …

Multi-Trait Qtl Mapping Using A Structural Equation Model, Xiaojuan Mi, Kent M. Eskridge, Dong Wang

Conference on Applied Statistics in Agriculture

Research on mapping quantitative trait loci (QTL) often results in data on a number of traits that have well established causal relationships. Many multi-trait QTL mapping methods, taking into account the correlation among the multiple traits, have been developed to improve the statistical power of the test for QTL and the precision of parameter estimation. However none of these methods are capable of incorporating the causal structure among the traits with the consequence that genetic functions of the QTL may not be fully understood. Structural equation modeling (SEM) allows researchers to explicitly characterize the causal structure among the variables and …

Dynamic Clustering Of Cell-Cycle Microarray Data, Lingling An, R. W. Doerge

Conference on Applied Statistics in Agriculture

The cell cycle is a crucial series of events that are repeated over time, allowing the cell to grow, duplicate, and split. Cell-cycle systems play an important role in cancer and other biological processes. Using gene expression data gained from microarray technology it is possible to group or cluster genes that are involved in the cell-cycle for the purpose of exploring their functional co-regulation. Typically, the goal of clustering methods as applied to gene expression data is to place genes with similar expression patterns or profiles into the same group or cluster for the purpose of inferring the function of …

Testing Variance Components By Two Jackknife Methods, Jixiang Wu, Johnie N. Jenkins, Jack C. Mccarty

Conference on Applied Statistics in Agriculture

The jackknife method, a resampling technique, has been widely used for statistical tests for years. The pseudo value based jackknife method (defined as pseudo jackknife method) is commonly used to reduce the bias for an estimate; however, sometimes it could result in large variation for an estimate and thus reduce the power for parameters of interest. In this study, a non-pseudo value based jackknife method (defined as non-pseudo jackknife method) was used for testing variance components under mixed linear models. We compared this non-pseudo value based jackknife method and the pseudo value based method by simulation regarding their biases, Type …

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

Conference on Applied Statistics in Agriculture

These proceedings contain papers presented in the twentieth annual Kansas State University Conference on Applied Statistics in Agriculture, held in Manhattan, Kansas, April 27- April 29, 2008.

Mechanistic Home Range Models And Resource Selection Analysis: A Reconciliation And Unification, Paul R. Moorcroft, Alex Barnett

Dartmouth Scholarship

In the three decades since its introduction, resource selection analysis (RSA) has become a widespread method for analyzing spatial patterns of animal relocations obtained from telemetry studies. Recently, mechanistic home range models have been proposed as an alternative framework for studying patterns of animal space-use. In contrast to RSA models, mechanistic home range models are derived from underlying mechanistic descriptions of individual movement behavior and yield spatially explicit predictions for patterns of animal space-use. In addition, their mechanistic underpinning means that, unlike RSA, mechanistic home range models can also be used to predict changes in space-use following perturbation. In this …

Statistical Approach To The Characterization And Recognition Of Human Gaits, Derrick M. Chelliah

Theses and Dissertations

This thesis addresses the final portion of a complete process for human gait recognition. The thesis takes as input information that has been generated from videotaping walking individuals and converting their gaits into numerical data that measures the locations of various points on the body through time. Beginning with this data, this thesis uses a variety of mathematical and statistical methods to create identifying signatures for each individual and identify them on the basis of that signature. The end goal is to achieve under controlled laboratory conditions human gait recognition, an identification method which does not require contact or cooperation …

Empirical Null And False Discovery Rate Inference For Exponential Families, Armin Schwartzman

Harvard University Biostatistics Working Paper Series

No abstract provided.

Crop Updates 2008 - Cereals, Christine Zaicou, Shahajahan Miyan, Brenda Shackley, Steve Penny, Sarah Ellis, Darshan Sharma, Blakely Paynter, Jeff Russell, Andrea Hills, Glen Riethmuller, Bill Bowden, Paul Blackwell, Harmohinder Dhammu, Vince Lambert, Chris Roberts, David Cox, Sally Cox, Jeremy Lemon, Paul Damon, Zed Rengel, Geoff Thomas, Ciara Beard, Anne Smith, Kith Jayasena, Sean Kelly, Rob Loughman, Bill Macleod, Raj Malik, Ravjit Khangura, Vivien Vanstone, Colin Hanbury, Mehreteab Aberra, Gordon Masnish, Brenda Coutts, Geoff Strickland, Monica Kehoe, Dustin Severtson, Roger Jones, Dominie Wright, Megan Jordan, Xinhua He, Eli Manyol, Song-Ai Nio, Imran Malik, Tina Botwright-Acuña, Len Wade, Nigel Metz, Linda Price, Dean Diepeveen, Leisa Armstrong, Peter Clarke, Doug Abrecht, Rudi Appels, Matthew Bellgard

Crop Updates

This session covers twenty four papers from different authors:

WHEAT AGRONOMY

1. Wheat variety performance in the Northern Agricultural Region in 2007, Christine Zaicou, Department of Agriculture and Food

2. Wheat variety performance on the Central Agricultural Region in 2007, Shahajahan Miyan, Department of Agriculture and Food

3. Response of wheat varieties to sowing time in the Great Southern and Lakes Region in 2007, Brenda Shackley and Steve Penny, Department of Agriculture and Food

4. Wheat variety performance in the South Coastal Region in 2007, Sarah Ellis, Department of Agriculture and Food

5. Flowering dates of wheat varieties in Western …