Statistics and Probability Commons^™

A Graph Theoretic Approach To Testing Associations Between Disparate Sources Of Functional Genomic Data, Raji Balasubramanian, Thomas Laframboise, Denise Scholtens, Robert Gentleman

Bioconductor Project Working Papers

The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data sources, or lack thereof, can shed light on the mechanisms that govern cellular function. A central challenge for bioinformatics research is to develop a unified framework for combining the multiple sources of functional genomics information and testing associations between them, thus obtaining a robust and integrated view of the underlying biology.

We present a graph theoretic approach to test the significance of the association between multiple disparate sources of functional genomics …

Animal Model Research: The Apples And Oranges Quandary, Kenneth J. Shapiro

Experimentation Collection

In this paper, I explore the premises underlying the problem of the evaluation of animal models. I argue that the presence of similarities and differences between the model and the modelled, although historically and currently a dominant antinomy framing evaluation, is not a bottom-line consideration. What is critical is 1) whether we learn and 2) whether we improve treatment through the animal model research. Similarity between model and modelled and the closely related concept of validity are not coterminus with these critical evaluative measures. In fact, differences between the model and modelled also can provide impetus to new understanding and …

Familial And Psychosocial Factors Affecting Adolescents' Academic Achievement, Isa Abdulnasir Ribadu

Loma Linda University Electronic Theses, Dissertations & Projects

This study examined the influence of family cohesion, family adaptability, self-image, and locus-of-control on two measures of academic achievement among male and female adolescents. Using a self-administered questionnaire, data were gathered from a convenient sample of 230 students from five high schools in San Bernardino County in southern California. The survey included the Offer Self-image Questionnaire, Family Adaptability and Cohesion Evaluation Scale III, the Nowick-Strickland Locus-of-Control Scale, academic achievement measures, and demographic measures that assessed individual and family characteristics. Family cohesion, family adaptability, self-image, and locus-of-control were significant predictors of both measures of academic achievement. Also, family cohesion and family …

The Association Of Blood Type On The Five Factors Of Personality In Chinese Adolescents, Kunher Wu

Loma Linda University Electronic Theses, Dissertations & Projects

The purpose of this study was to identify the number of personality factors in Chinese adolescents using the Chinese Revised NEO Personality Inventory (NEO-PI-R) and to determine whether blood type is associated with personality. It is widely accepted by psychologists that the five-factor model can provide an adequate representation of adult personality dimensions, but there is less agreement on the number of factors observable in adolescence. A total of 3,396 11^th graders from the city of Kaohsiung, Taiwan completed the Chinese NEO-PI-R. Principle component analysis with varimax rotation showed five factors of personality in these Taiwanese adolescents, which clearly …

Relative Validity Of A Food Frequency Questionnaire Used To Assess Food And Nutrient Intake In A Dietary Intervention Study, Gina Segovia Siapco

Loma Linda University Electronic Theses, Dissertations & Projects

Food frequency questionnaire is a cost effective alternative for measuring dietary intake when conducting large scale surveys. We investigated the validity of a 171-item semi-quantitative food frequency questionnaire in assessing food and nutrient intakes and the prescribed intervention measure during a randomized field trial. Eighty-seven free-living adults (48 females and 39 males) aged 30-72 years provided dietary information by self-administering the Walnut Study Dietary Assessment Questionnaire (WSDAQ), which assessed intake over the past six months, and through seven unannounced non-consecutive 24-hour dietary recalls by telephone. Participants were randomly assigned to either a walnut or habitual diet at baseline. For six …

On Similarity Measures For Cluster Analysis, Ahmed Najeeb Khalaf Albatineh

Dissertations

This study discusses the relationship between measures of similarity which quantify the agreement between two clusterings of the same set of data. This study identifies a family [Special characters omitted.] of similarity measures which are of a special form and attain a maximum value of 1 and becomes identical when corrected for chance agreement. In particular, this study proves that the similarity measures of Rand (R), Hubert (H), and Czekanowski (CZ) are identical when corrected for chance agreement. It also proves that the measures of McConnaughey (MC) and Kulczynski (K) are identical when corrected for chance agreement. Moreover, if the …

Affine Equivariant Multivariate Rank-Based And Generalized Rank Regression, Majeda Salman

Dissertations

Affine equivariant estimates for the regression coefficient matrix of the multivariate linear model are proposed. These estimates are based on a transformation and retransformation technique that uses Tyler's (1987) M -estimator of scatter. The proposed estimates are obtained by retransforming the componentwiserank-based estimate due to Davis and McKean (1993) and a componentwise generalized rank estimate. Asymptotic properties of the estimates are established under some regularity conditions. It is shown that both estimates have a multivariate normal limiting distribution. The influence function of the retransformed generalized rank estimate has a bounded influence in both factor and response spaces. It is shown …

Analysis Of Auf1 Targeted Mrna Sequences, Jiebo Lu

Theses

AUF 1, an A+U rich element (ARE) binding protein, plays an important role in mRNA decay. To identify the mRNAs that interact with AUF 1, mRNA derived from a human cardiac cDNA expression library was purified by AUF 1 affinity chromatography and cloned following RT-PCR. 261 sequences were obtained. The sequences were searched against two protein databases and four nucleic acid databases, and the sequence information and database search results were input into a local Microsoft Access database, BLAST-AUF 1, by Java applets for parsing document. Analysis of protein information by querying BLAST-AUF 1 identified 194 function-known proteins, which were …

Analysis Of Molecular Conformations Using Relative Planes, Deepa S. Pai

Theses

Ring substructures of a drug usually participate actively in binding to the receptor. It is necessary to study the spatial relationship of these molecular recognition features in order to determine the pharmacophore of the drug. This is a particularly difficult problem when the drug is a flexible molecule with many energetically accessible conformations.

In this research an innovative approach to calculate the relative displacement and orientation of every possible pair of rings in a given molecule was designed, tested, and implemented in the "Planes" program. Planes were defined from each of the ring substructures and the displacement and rotation of …

Random Search Conformational Analysis Of Piperazine And Piperadine Analogs Of Gbr12909 : Implicit Aqueous Solvation Effects, William A. Roosma

Theses

The object of this work was to study the effect of solvent on the conformational potential energy surface (PES) of GBR12909 analogs. Local minima on the PES's were found by the Random Search algorithm using the Sybyl molecular modeling package from Tripos, Inc., and an implicit solvent model. Two force-field/charge models were employed in the analysis: the Tripos force field with Gasteiger-Huckel charges and the MMFF94 force field with MMFF94 charges.

The effect of solvent on the location of minima in multi-dimensional torsional angle space was studied by comparison to the vacuum phase results. Minima were plotted in torsional angle …

A Model Based Background Adjustment For Oligonucleotide Expression Arrays, Zhijin Wu, Rafael A. Irizarry, Robert Gentleman, Francisco Martinez Murillo, Forrest Spencer

Johns Hopkins University, Dept. of Biostatistics Working Papers

High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of further pre-processing and data reduction occurs following the image processing step. Statistical procedures developed by academic groups have been successful at improving the default algorithms provided by the Affymetrix system. In this paper we present a solution to one of the pre-processing steps, background adjustment, based on a formal statistical framework. Our solution greatly improves the performance of the technology in various practical applications.

Affymetrix GeneChip arrays use short oligonucleotides to …

Seasonal Analyses Of Air Pollution And Mortality In 100 U.S. Cities, Roger D. Peng, Francesca Dominici, Roberto Pastor-Barriuso, Scott L. Zeger, Jonathan M. Samet

Johns Hopkins University, Dept. of Biostatistics Working Papers

Time series models relating short-term changes in air pollution levels to daily mortality counts typically assume that the effects of air pollution on the log relative rate of mortality do not vary with time. However, these short-term effects might plausibly vary by season. Changes in the sources of air pollution and meteorology can result in changes in characteristics of the air pollution mixture across seasons. The authors develop Bayesian semi-parametric hierarchical models for estimating time-varying effects of pollution on mortality in multi-site time series studies. The methods are applied to the updated National Morbidity and Mortality Air Pollution Study database …

Semiparametric Regression Analysis Of Mean Residual Life With Censored Survival Data, Ying Qing Chen, Su-Chun Cheng

U.C. Berkeley Division of Biostatistics Working Paper Series

As a function of time t, mean residual life is the remaining life expectancy of a subject given survival up to t. The proportional mean residual life model, proposed by Oakes & Dasu (1990), provides an alternative to the Cox proportional hazards model to study the association between survival times and covariates. In the presence of censoring, we develop semiparametric inference procedures for the regression coefficients of the Oakes-Dasu model using martingale theory for counting processes. We also present simulation studies and an application to the Veterans' Administration lung cancer data.

Nonparametric And Semiparametric Inference For Models Of Tumor Size And Metastasis, Debashis Ghosh

The University of Michigan Department of Biostatistics Working Paper Series

There has been some recent work in the statistical literature for modelling the relationship between the size of primary cancers and the occurrences of metastases. While nonparametric methods have been proposed for estimation of the tumor size distribution at which metastatic transition occurs, their asymptotic properties have not been studied. In addition, no testing or regression methods are available so that potential confounders and prognostic factors can be adjusted for. We develop a unified approach to nonparametric and semiparametric analysis of modelling tumor size-metastasis data in this article. An equivalence between the models considered by previous authors with survival data …

Model Checking Techniques For Regression Models In Cancer Screening, Debashis Ghosh

The University of Michigan Department of Biostatistics Working Paper Series

There has been much work on developing statistical procedures for associating tumor size with the probability of detecting a metastasis. Recently, Ghosh (2004) developed a unified statistical framework in which equivalences with censored data structures and models for tumor size and metastasis were examined. Based on this framework, we consider model checking techniques for semiparametric regression models in this paper. The procedures are for checking the additive hazards model. Goodness of fit methods are described for assessing functional form of covariates as well as the additive hazards assumption. The finite-sample properties of the methods are assessed using simulation studies.

Binary Isotonic Regression Procedures, With Application To Cancer Biomarkers, Debashis Ghosh, Moulinath Banerjee, Pinaki Biswas

The University of Michigan Department of Biostatistics Working Paper Series

There is a lot of interest in the development and characterization of new biomarkers for screening large populations for disease. In much of the literature on diagnostic testing, increased levels of a biomarker correlate with increased disease risk. However, parametric forms are typically used to associate these quantities. In this article, we specify a monotonic relationship between biomarker levels with disease risk. This leads to consideration of a nonparametric regression model for a single biomarker. Estimation results using isotonic regression-type estimators and asymptotic results are given. We also discuss confidence set estimation in this setting and propose three procedures for …

Semiparametic Models And Estimation Procedures For Binormal Roc Curves With Multiple Biomarkers, Debashis Ghosh

The University of Michigan Department of Biostatistics Working Paper Series

In diagnostic medicine, there is great interest in developing strategies for combining biomarkers in order to optimize classification accuracy. A popular model that has been used for receiver operating characteristic (ROC) curve modelling when one biomarker is available is the binormal model. Extension of the model to accommodate multiple biomarkers has not been considered in this literature. Here, we consider a multivariate binormal framework for combining biomarkers using copula functions that leads to a natural multivariate extension of the binormal model. Estimation in this model will be done using rank-based procedures. We show that the Van der Waerden rank score …

Performance Of The Kenward-Project When The Covariance Structure Is Selected Using Aic And Bic, Elisa Valderas Gomez

Theses and Dissertations

Linear mixed models are frequently used to analyze data with random effects and/or repeated measures. A common approach to such analyses requires choosing a covariance structure. Information criteria, such as AIC and BIC, are often used by statisticians to help with this task. However, these criteria do not always point to the true covariance structure and therefore the wrong covariance structure is sometimes chosen. Once this step is complete, Wald statistics are used to test fixed effects. Degrees of freedom for these statistics are not known. However, there are approximation methods, such as Kenward and Roger (KR) and Satterthwaite (SW) …

The "Fair" Triathlon: Equating Standard Deviations Using Non-Linear Bayesian Models, Steven Mckay Curtis

Theses and Dissertations

The Ironman triathlon was created in 1978 by combining events with the longest distances for races then contested in Hawaii in swimming, cycling, and running. The Half Ironman triathlon was formed using half the distances of each of the events in the Ironman. The Olympic distance triathlon was created by combining events with the longest distances for races sanctioned by the major federations for swimming, cycling, and running. The relative importance of each event in overall race outcome was not given consideration when determining the distances of each of the races in modern triathlons. Thus, there is a general belief …

Validation Of Criteria Used To Predict Warfarin Dosing Decisions, Nicole Thomas

Theses and Dissertations

People at risk for blood clots are often treated with anticoagulants, warfarin is such an anticoagulant. The dose's effect is measured by comparing the time for blood to clot to a control time called an INR value. Previous anticoagulant studies have addressed agreement between fingerstick (POC) devices and the standard laboratory, however these studies rely on mathematical formulas as criteria for clinical evaluations, i.e. clinical evaluation vs. precision and bias. Fourteen such criteria were found in the literature. There exists little consistency among these criteria for assessing clinical agreement, furthermore whether these methods of assessing agreement are reasonable estimates of …

On Corrected Score Approach For Proportional Hazards Model With Covariate Measurement Error, Xiao Song, Yijian Huang

UW Biostatistics Working Paper Series

In the presence of covariate measurement error with the proportional hazards model, several functional modeling methods have been proposed. These include the conditional score estimator (Tsiatis and Davidian, 2001), the parametric correction estimator (Nakamura, 1992) and the nonparametric correction estimator (Huang and Wang, 2000, 2003) in the order of weaker assumptions on the error. Although they are all consistent, each suffers from potential difficulties with small samples and substantial measurement error. In this article, upon noting that the conditional score and parametric correction estimators are asymptotically equivalent in the case of normal error, we investigate their relative finite sample performance …

Fundamental Conditions For The Evolution Of Altruism: Towards A Unification Of Theories, Jeffrey Alan Fletcher

Dissertations and Theses

In evolutionary theory the existence of self-sacrificing cooperative traits poses a problem that has engendered decades of debate. The principal theories of the evolution of altruism are inclusive fitness, reciprocal altruism, and multilevel selection. To provide a framework for the unification of these apparently disparate theories, this dissertation identifies two fundamental conditions required for the evolution of altruism: 1) non-zero-sum fitness benefits for cooperation and 2) positive assortment among altruistic behaviors. I demonstrate the underlying similarities in these three theories in the following two ways.

First, I show that the game-theoretic model of the prisoner’s dilemma (PD) is inherent to …

Sub-Supersolution Method For Quasilinear Parabolic Variational Inequalities, Siegfried Carl, Vy Khoi Le

Mathematics and Statistics Faculty Research & Creative Works

This paper is about a systematic attempt to apply the sub-supersolution method to parabolic variational inequalities. We define appropriate concepts of sub-supersolutions and derive existence, comparison, and extremity results for such inequalities.

Classification Using Generalized Partial Least Squares, Beiying Ding, Robert Gentleman

Bioconductor Project Working Papers

The advances in computational biology have made simultaneous monitoring of thousands of features possible. The high throughput technologies not only bring about a much richer information context in which to study various aspects of gene functions but they also present challenge of analyzing data with large number of covariates and few samples. As an integral part of machine learning, classification of samples into two or more categories is almost always of interest to scientists. In this paper, we address the question of classification in this setting by extending partial least squares (PLS), a popular dimension reduction tool in chemometrics, in …

Beta-Normal Distribution: Bimodality Properties And Application, Felix Famoye, Carl Lee, Nicholas Eugene

Journal of Modern Applied Statistical Methods

The beta-normal distribution is characterized by four parameters that jointly describe the location, the scale and the shape properties. The beta-normal distribution can be unimodal or bimodal. This paper studies the bimodality properties of the beta-normal distribution. The region of bimodality in the parameter space is obtained. The beta-normal distribution is applied to fit a numerical bimodal data set. The beta-normal fits are compared with the fits of mixture-normal distribution through simulation.

Some Improvements In Kernel Estimation Using Line Transect Sampling, Omar M. Eidous

Journal of Modern Applied Statistical Methods

Kernel estimation provides a nonparametric estimate of the probability density function from which a set of data is drawn. This article proposes a method to choose a reference density in bandwidth calculation for kernel estimator using line transect sampling. The method based on testing the shoulder condition, if the shoulder condition seems to be valid using as reference the half normal density, while if the shoulder condition does not seem to be valid, we will use exponential reference density. Accordingly, the performances of the resultant estimator are studied under a wide range of underlying models using simulation techniques. The results …

A Visually Adaptive Bayesian Model In Wavelet Regression, Dongfeng Wu

Journal of Modern Applied Statistical Methods

The implementation of a Bayesian approach to wavelet regression that corresponds to the human visual system is examined. Most existing research in this area assumes non-informative priors, that is, a prior with mean zero. A new way is offered to implement prior information that mimics a visual inspection of noisy data, to obtain a first impression about the shape of the function that results in a prior with non-zero mean. This visually adaptive Bayesian (VAB) prior has a simple structure, intuitive interpretation, and is easy to implement. Skorohod topology is suggested as a more appropriate measure in signal recovering than …

Estimation Using Bivariate Extreme Ranked Set Sampling With Application To The Bivariate Normal Distribution, Mohammad Fraiwan Al-Saleh, Hani M. Samawi

Journal of Modern Applied Statistical Methods

In this article, the procedure of bivariate extreme ranked set sampling (BVERSS) is introduced and investigated as a procedure of obtaining more accurate samples for estimating the parameters of bivariate populations. This procedure takes its strength from the advantages of bivariate ranked set sampling (BVRSS) over the usual ranked set sampling in dealing with two characteristics simultaneously, and the advantages of extreme ranked set sampling (ERSS) over usual RSS in reducing the ranking errors and hence in being more applicable. The BVERSS procedure will be applied to the case of the parameters of the bivariate normal distributions. Illustration using real …

Kernel-Based Estimation Of P(X Less Than Y)With Paired Data, Omar M. Eidous, Ayman Baklizi

Journal of Modern Applied Statistical Methods

A point estimation of P(X < Y) was considered. A nonparametric estimator for P(X < Y) was developed using the kernel density estimator of the joint distribution of X and Y, may be dependent. The resulting estimator was found to be similar to the estimator based on the sign statistic, however it assigns smooth continuous scores to each pair of the observations rather than the zero or one scores of the sign statistic. The asymptotic equivalence of the sign statistic and the proposed estimator is shown and a simulation study is conducted to investigate the performance of the proposed estimator. Results indicate that …

Respondent-Generated Intervals (Rgi) For Recall In Sample Surveys, S. James Press

Journal of Modern Applied Statistical Methods

Respondents are asked for both a basic response to a recall-type question, their usage quantity, and are asked to provide lower and upper bounds for the (Respondent-Generated) interval in which their true values might possibly lie. A Bayesian hierarchical model for estimating the population mean and its variance is presented.. Telephone: (989) 774-