Digital Commons Network^™

Ibd Configuration Transition Matrices And Linkage Score Tests For Unilineal Relative Pairs, Sandrine Dudoit

U.C. Berkeley Division of Biostatistics Working Paper Series

Properties of transition matrices between IBD configurations are derived for four general classes of unilineal relative pairs obtained from the grand-parent/ grand-child, half-sib, avuncular, and cousin relationships. In this setting, IBD configurations are defined as orbits of groups acting on a set of inheritance vectors. Properties of the transition matrix between IBD configurations at two linked loci are derived by relating its infinitesimal generator to the adjacency matrix of a quotient graph. The second largest eigenvalue of the infinitesimal generator and its multiplicity are key in determining the form of the transition matrix and of likelihood-based linkage tests such as …

Rank Regression In Stability Analysis, Ying Qing Chen, Annpey Pong, Biao Xing

U.C. Berkeley Division of Biostatistics Working Paper Series

Stability data are often collected to determine the shelf-life of certain characteristics of a pharmaceutical product, for example, a drug's potency over time. Statistical approaches such as the linear regression models are considered as appropriate to analyze the stability data. However, most of these regression models in both theory and practice rely heavily on their underlying parametric assumptions, such as normality of the continuous characteristics or their transformations. In this article, we propose and study some rank-based regression procedures for the stability data when the linear regression models are semiparametric with unspecified error structure. Numerical studies including Monte Carlo simulations …

Asymptotic Optimality Of Likelihood Based Cross-Validation, Mark J. Van Der Laan, Sandrine Dudoit, Sunduz Keles

U.C. Berkeley Division of Biostatistics Working Paper Series

Likelihood-based cross-validation is a statistical tool for selecting a density estimate based on n i.i.d. observations from the true density among a collection of candidate density estimators. General examples are the selection of a model indexing a maximum likelihood estimator, and the selection of a bandwidth indexing a nonparametric (e.g. kernel) density estimator. In this article, we establish asymptotic optimality of a general class of likelihood based cross-validation procedures (as indexed by the type of sample splitting used, e.g. V-fold cross-validation), in the sense that the cross-validation selector performs asymptotically as well (w.r.t. to the Kullback-Leibler distance to the true …

Asymptotics Of Cross-Validated Risk Estimation In Estimator Selection And Performance Assessment, Sandrine Dudoit, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Risk estimation is an important statistical question for the purposes of selecting a good estimator (i.e., model selection) and assessing its performance (i.e., estimating generalization error). This article introduces a general framework for cross-validation and derives distributional properties of cross-validated risk estimators in the context of estimator selection and performance assessment. Arbitrary classes of estimators are considered, including density estimators and predictors for both continuous and polychotomous outcomes. Results are provided for general full data loss functions (e.g., absolute and squared error, indicator, negative log density). A broad definition of cross-validation is used in order to cover leave-one-out cross-validation, V-fold …

Modern Spectral Climate Patterns In Rhythmically Deposited Argillites Of The Gowganda Formation (Early Proterozoic), Southern Ontario, Canada, Gary B. Hughes, Robert Giegengack, Haralambos N. Kritikos

Statistics

Rhythmically deposited argillites of the Gowganda Formation (ca. 2.0–2.5 Ga) probably formed in a glacial setting. Drop stones and layered sedimentary couplets in the rock presumably indicate formation in a lacustrine environment with repeating freeze–thaw cycles. It is plausible that temporal variations in the thickness of sedimentary layers are related to interannual climatic variability, e.g. average seasonal temperature could have influenced melting and the amount of sediment source material carried to the lake. A sequence of layer couplet thickness measurements was made from high-resolution digitized photographs taken at an outcrop in southern Ontario, Canada. The frequency spectrum of thickness measurements …

Analysis Of Gene Expression Data Using Expressionist 3.1 And Genespring 4.2, Indu Shrivastava

Theses

The purpose of this study was to determine the differences in the gene expression analysis methods of two data mining tools, Expressionistic^TM 3.1 and GeneSpring^TM 4.2 with focus on basic statistical analysis and clustering algorithms. The data for this analysis was derived from the hybridization of Rattus norvegicus RNA to the Affymetrix RG34A GeneChip. This analysis was derived from experiments designed to identify changes in gene expression patterns that were induced in vivo by an experimental treatment.

The tools were found to be comparable with respect to the list of statistically significant genes that were up-regulated by more …

A Method For Developing In-Silico Protein Homologs, Susan Mcclatchy

Theses

Computational methods for identifying and screening the most promising drug receptor candidates in the human genome are of great interest to drug discovery researchers. Successful methods will accurately identify and narrow the field of potential drug receptor candidates. This study details one such method.

The method described here begins with the assumption that novel drug receptors have high sequence similarity to established drug receptors. The similarity search program FASTA3 aligns translated sequences of the human genome to known drug receptor sequences and ranks these alignments by measuring their statistical significance. Query results returned by FASTA3 are assembled into "in-silico proteins" …

Selecting Differentially Expressed Genes From Microarray Experiments, Margaret S. Pepe, Gary M. Longton, Garnet L. Anderson, Michel Schummer

UW Biostatistics Working Paper Series

High throughput technologies, such as gene expression arrays and protein mass spectrometry, allow one to simultaneously evaluate thousands of potential biomarkers that distinguish different tissue types. Of particular interest here is cancer versus normal organ tissues. We consider statistical methods to rank genes (or proteins) in regards to differential expression between tissues. Various statistical measures are considered and we argue that two measures related to the Receiver Operating Characteristic Curve are particularly suitable for this purpose. We also propose that sampling variability in the gene rankings be quantified and suggest using the “selection probability function”, the probability distribution of rankings …

Semiparametric Receiver Operating Characteristic Analysis To Evaluate Biomarkers For Disease, Tianxi Cai, Margaret S. Pepe

UW Biostatistics Working Paper Series

The receiver operating characteristic (ROC) curve is a popular method for characterizing the accuracy of diagnostic tests when test results are not binary. Various methodologies for estimating and comparing ROC curves have been developed. One approach, due to Pepe, uses a parametric regression model with the baseline function specified up to a finite-dimensional parameter. In this article we extend the regression models by allowing arbitrary nonparametric baseline functions. We also provide asymptotic distribution theory and procedures for making statistical inference. We illustrate our approach with dataset from a prostate cancer biomarker study. Simulation studies suggest that the extra flexibility inherent …

Semi-Parametric Regression For The Area Under The Receiver Operating Characteristic Curve, Lori E. Dodd, Margaret S. Pepe

UW Biostatistics Working Paper Series

Medical advances continue to provide new and potentially better means for detecting disease. Such is true in cancer, for example, where biomarkers are sought for early detection and where improvements in imaging methods may pick up the initial functional and molecular changes associated with cancer development. In other binary classification tasks, computational algorithms such as Neural Networks, Support Vector Machines and Evolutionary Algorithms have been applied to areas as diverse as credit scoring, object recognition, and peptide-binding prediction. Before a classifier becomes an accepted technology, it must undergo rigorous evaluation to determine its ability to discriminate between states. Characterization of …

Selective Multiple Imputation Of Keys For Statistical Disclosure Control In Microdata, Rod Little, Fang Liu

The University of Michigan Department of Biostatistics Working Paper Series

The fundamental tension in statistical disclosure control (SDC) of microdata is the trade-off between the protection of individual respondents and the release of enough information for statistical inferences. We consider microdata that include key variables that contain identifying information and target variables that include sensitive information. Releasing the original data may expose some individuals in the sample to high risk of disclosure; deleting key variables is a common approach, but this loses information for some statistical analysis. This paper proposes selective multiple imputation of key variables (SMIKe) as an alternative SDC technique between those two extremes, and applies SMIKe to …

Estimating Disease Prevalence In Two-Phase Studies, Todd A. Alonzo, Margaret S. Pepe

UW Biostatistics Working Paper Series

Disease prevalence is ideally estimated using a “gold standard” to ascertain true disease status on all subjects in a population of interest. In practice, however, the gold standard may be too costly or invasive to be applied to all subjects, in which case a two-phase design is often employed. Phase 1 data consisting of inexpensive and non-invasive screening tests on all study subjects are used to determine the subjects that receive the gold standard in the second phase. Naïve estimates of prevalence in two-phase studies can be biased (verification bias). Imputation and re-weighting estimators are often used to avoid this …

Checking Assumptions In Latent Class Regression Models Via A Markov Chain Monte Carlo Estimation Approach: An Application To Depression And Socio-Economic Status, Elizabeth Garrett, Richard Miech, Pamela Owens, William W. Eaton, Scott L. Zeger

Johns Hopkins University, Dept. of Biostatistics Working Papers

Latent class regression models are useful tools for assessing associations between covariates and latent variables. However, evaluation of key model assumptions cannot be performed using methods from standard regression models due to the unobserved nature of latent outcome variables. This paper presents graphical diagnostic tools to evaluate whether or not latent class regression models adhere to standard assumptions of the model: conditional independence and non-differential measurement. An integral part of these methods is the use of a Markov Chain Monte Carlo estimation procedure. Unlike standard maximum likelihood implementations for latent class regression model estimation, the MCMC approach allows us to …

Partial Auc Estimation And Regression, Lori E. Dodd, Margaret S. Pepe

UW Biostatistics Working Paper Series

Accurate disease diagnosis is critical for health care. New diagnostic and screening tests must be evaluated for their abilities to discriminate disease from non-diseased states. The partial area under the ROC curve (partial AUC) is a measure of diagnostic test accuracy. We present an interpretation of the partial AUC that gives rise to a new non-parametric estimator. This estimator is more robust than existing estimators, which make parametric assumptions. We show that the robustness is gained with only a moderate loss in efficiency. We describe a regression modelling framework for making inference about covariate effects on the partial AUC. Such …

An Oscillation Theorem For Discrete Eigenvalue Problems, Martin Bohner, Ondřej Došlý, Werner Kratz

Mathematics and Statistics Faculty Research & Creative Works

In this paper we consider problems that consist of symplectic difference systems depending on an eigenvalue parameter, together with self-adjoint boundary conditions. Such symplectic difference systems contain as important cases linear Hamiltonian difference systems and also Sturm-Liouville difference equations of second and of higher order. The main result of this paper is an oscillation theorem that relates the number of eigenvalues to the number of generalized zeros of solutions.

Nuclear Genes That Encode Mitochondrial Proteins For Dna And Rna Metabolism Are Clustered In The Arabidopsis Genome, Annakaisa Elo, Anna Lyznik, Delkin O. Gonzalez, Stephen D. Kachman, Sally A. Mackenzie

Department of Statistics: Faculty Publications

The plant mitochondrial genome is complex in structure, owing to a high degree of recombination activity that subdivides the genome and increases genetic variation. The replication activity of various portions of the mitochondrial genome appears to be nonuniform, providing the plant with an ability to modulate its mitochondrial genotype during development. These and other interesting features of the plant mitochondrial genome suggest that adaptive changes have occurred in DNA maintenance and transmission that will provide insight into unique aspects of plant mitochondrial biology and mitochondrial- chloroplast coevolution. A search in the Arabidopsis genome for genes involved in the regulation of …

Conjugated Linoleic Acid Does Not Improve Insulin Tolerance In Mice, Kimberly M Hargrave, Michael J. Azain, Stephen D. Kachman, Jess Miner

Department of Statistics: Faculty Publications

Objective: To determine if the addition or removal of dietary conjugated linoleic acid (CLA) would alter insulin tolerances in mice from two genetic lines.

Research Methods and Procedures: High metabolic rate (MH) and low metabolic rate (ML) mice were assigned to consume 1) a control diet ad libitum, 2) a control diet at a restricted intake, or 3) a diet containing 1% CLA ad libitum. After 9 weeks, an insulin tolerance test was conducted, and a portion of the mice were killed. All remaining mice consumed the control diet ad libitum. Insulin tolerance tests were conducted 11 and 32 days …

Comparing Bayes Model Averaging And Stacking When Model Approximation Error Cannot Be Ignored, Bertrand S. Clarke

Department of Statistics: Faculty Publications

We compare Bayes Model Averaging, BMA, to a non-Bayes form of model averaging called stacking. In stacking, the weights are no longer posterior probabilities of models; they are obtained by a technique based on cross-validation. When the correct data generating model (DGM) is on the list of models under consideration BMA is never worse than stacking and often is demonstrably better, provided that the noise level is of order commensurate with the coefficients and explanatory variables. Here, however, we focus on the case that the correct DGM is not on the model list and may not be well approximated by …

Pain And Distress Associated With Polyclonal Antibody Production: Discussion And Recommendations, The Humane Society Of The United States

ANIMAL RESEARCH

The Humane Society of the United States (HSUS) held a workshop in August 2002 in order to develop recommendations for minimizing pain and distress associated with polyclonal antibody (Pab) production. A small group of experts in the fields of antibody production, animal welfare, in vitro alternatives, and/or regulatory compliance participated in the roundtable discussion. The workshop was a scientifically based meeting, and recommendations were based on the extensive experience of the workshop participants as well as published literature regarding the relevant issues.

Participants recognized that insufficient attention has been paid to animal welfare aspects of Pab production, in part because …

Ua56/1 Fact Book, Wku Institutional Research

WKU Administration Documents

Statistical and demographic profile of WKU.

Perturbation Of Global Solution Curves For Semilinear Problems, Philip Korman, Yi Li, Tiancheng Ouyang

Mathematics and Statistics Faculty Publications

We revisit the question of exact multiplicity of positive solutions for a class of Dirichlet problems for cubic-like nonlinearities, which we studied in 161. Instead of computing the direction of bifurcation as we did in [6], we use an indirect approach, and study the evolution of turning points. We give conditions under which the critical (turning) points continue on smooth curves, which allows us to reduce the problem to the easier case of f (0) = 0. We show that the smallest root of f (u) does not have to be restricted.

Impulse Control Of Stochastic Navier-Stokes Equations, J. L. Menaldi, S. S. Sritharan

Mathematics Faculty Research Publications

In this paper we study stopping time and impulse control problems for stochastic Navier-Stokes equation. Exploiting a local monotonicity property of the nonlinearity, we establish existence and uniqueness of strong solutions in two dimensions which gives a Markov-Feller process. The variational inequality associated with the stopping time problem and the quasi-variational inequality associated with the impulse control problem are resolved in a weak sense, using semigroup approach with a convergence uniform over path.

An Algebraic Characterization Of Projective-Planar Graphs, Lowell Abrams, Dan Slilaty

Mathematics and Statistics Faculty Publications

We give a detailed algebraic characterization of when a graph G can be imbedded in the projective plane. The characterization is in terms of the existence of a dual graph G∗ on the same edge set as G which satisfies algebraic conditions inspired by homology groups and intersection products in homology groups.

Victim Characteristics And Victim Impact Evidence In South Carolina Capital Cases, Theodore Eisenberg, Stephen P. Garvey, Martin T. Wells

Cornell Law Faculty Publications

This article is available at:

http://scholarship.law.cornell.edu/facpub/290/.

The use of victim impact evidence (VIE) has been a standard feature of capital trials since 1991, when the Supreme Court lifted the previously existing constitutional bar to such evidence. Legal scholars have almost universally condemned the use of VIE, criticizing it on a variety of grounds.

Yet little empirical analysis exists that examines how VIE influences the course and outcome of capital trials. Moreover, the handful of empirical analyses that do exist rely on data gathered in simulation studies. Although valuable contributions have emerged from these experimental studies, such studies have often-rehearsed …

Victim Characteristics And Victim Impact Evidence In South Carolina Capital Cases, Theodore Eisenberg, Stephen P. Garvey, Martin T. Wells

Cornell Law Faculty Publications

The use of victim impact evidence (VIE) has been a standard feature of capital trials since 1991, when the Supreme Court lifted the previously existing constitutional bar to such evidence. Legal scholars have almost universally condemned the use of VIE, criticizing it on a variety of grounds. Yet little empirical analysis exists that examines how VIE influences the course and outcome of capital trials. We analyze the influence of VIE based on interviews with over two-hundred jurors who sat on capital trials in South Carolina between 1985 and 2001.

First, we describe the VIE introduced at sentencing trials, using a …

Nullification At Work? A Glimpse From The National Center For State Courts Study Of Hung Juries, Paula Hannaford-Agor, Valerie P. Hans

Cornell Law Faculty Publications

In recent years, the criminal justice community has become increasingly concerned about the possibility that jury nullification is the underlying motivation for increasing numbers of acquittals and mistrials due to jury deadlock in felony jury trials. In this Article, the authors discuss the inherent difficulty in defining jury nullification and identifying its occurrence in actual trials. They review the evolution in public and legal opinion about the legitimacy of jury nullification and contemporary judicial responses to perceived instances of jury nullification. Finally, the authors examine the possible presence of jury nullification through empirical analysis of data collected from 372 felony …

Census 2000 Demographic Profile Report Of The Older Adult Population In Cuyahoga, Lake, Geauga, Lorain And Medina Counties, Mark Salling, Sharon Bliss, Mcnamara, Brian

All Maxine Goodman Levin School of Urban Affairs Publications

No abstract provided.

Multiple Solutions For An Inhomogeneous Semilinear Elliptic Equation In Rn, Yinbin Deng, Yi Li, Xuejin Zhao

Mathematics and Statistics Faculty Publications

No abstract provided.

Identifying Minimum G Aberration Designs For Hadamard Matrices Of Order 28, Steffany Belcher-Novosad, Debra Ingram

Journal of the Arkansas Academy of Science

No abstract provided.

Effects Of Bank Funds Management Activities On The Disintermediation Of Bank Deposits, David E. Allen, Jerry T. Parwada

Research outputs pre 2011

This study investigates the alleged disintermediation of banks’ traditional deposit-taking in favour of investment management activities. Using data on Australian bank-affiliated funds and a nine-year record of the parent banks’ liability balances, this study finds that managed funds do not displace bank liabilities. Prudential capital adequacy requirements dissuade banks from using in-house managed investments as indirect conduits for raising funds in the same manner as deposit-taking.