Digital Commons Network^™

A Compartmentalized Approach To The Assembly Of Physical Maps, Serdar Bozdag, Timothy J. Close, Stefano Lonardi

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background: Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint data. Results: We propose a novel compartmentalized method for the assembly of high quality physical maps from fingerprinted clones. The knowledge of genetic markers enables us to group clones into clusters so that clones in the same cluster are more likely to overlap. For each cluster of clones, a local physical map is first …

Modeling Peer Influence And Peer Selection As Processes, Bob Edward Vasquez

Legacy Theses & Dissertations (2009 - 2024)

Behavioral scientists are aware of the strong and persistent correlation between peer and individual behavior. Evidence suggests selection and socialization effects explain the correlation, but the processes, or the details of the ways in which these effects operate in an empirical model, remain relatively unexamined.

Variance-Mean Relationships To Analyze Large Survey Data With Application To Health Expenditure Data, Wenli Luo

Legacy Theses & Dissertations (2009 - 2024)

A great deal of work has been done in cost analysis in the last several decades. However, relatively little has been done to learn how efficiently to address the relationship between the variance and mean of the response distribution and how this will affect the choice of an appropriate generalized linear model.

Barriers Encountered During Enrollment In An Internet-Mediated Randomized Controlled Trial, Lorraine R. Buis, Adrienne W. Janney, Michael L. Hess, Silas A. Culver, Caroline R. Richardson

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Online technology is a promising resource for conducting clinical research. While the internet may improve a study's reach, as well as the efficiency of data collection, it may also introduce a number of challenges for participants and investigators. The objective of this research was to determine the challenges that potential participants faced during the enrollment phase of a randomized controlled intervention trial of Stepping Up to Health, an internet-mediated walking program that utilized a multi-step online enrollment process.

Methods

We conducted a quantitative content analysis of 623 help tickets logged in a participant management database during the enrollment …

Policy Relevant Heterogeneity In The Value Of Statistical Life: New Evidence From Panel Data Quantile Regressions, Thomas J. Kniesner, W. Kip Viscusi

Center for Policy Research

We examine differences in the value of statistical life (VSL) across potential wage levels in panel data using quantile regressions with intercept heterogeneity. Latent heterogeneity is econometrically important and affects the estimated VSL. Our findings indicate that a reasonable average cost per expected life saved cut-off for health and safety regulations is $7 million to $8 million per life saved, but the VSL varies considerably cross the labor force. Our results reconcile the previous discrepancies between hedonic VSL estimates and the values implied by theories linked to the coefficient of relative risk aversion. Because the VSL varies elastically with income, …

The Value Of Statistical Life: Pursuing The Deadliest Catch, Kurt E. Schnier, William C. Horrace, Ronald G. Felthoven

Center for Policy Research

Observed tradeoffs between monetary returns and fatality risk identify estimates of the value of a statistical life (VSL), inform public policy and quantity preferences for environmental quality, health and safety. To date, few investigations have estimated the VSL associated with tradeoffs between returns from natural resource extraction activities and the fatality risks they involve. Furthermore researchers have been unable to determine whether or not one's VSL is stable across multiple decision environments using revealed preference methods. Understanding these tradeoffs (and the VSL that they imply) may be used to inform resource management policy and safety regulations, as well as our …

Extending The Skill Test For Disease Diagnosis, Shu-Chuan Lin, Paul H. Kvam, Jye-Chyi Lu

Department of Math & Statistics Faculty Publications

For diagnostic tests, we present an extension to the skill plot introduced by Briggs and Zaretski (Biometrics 2008; 64:250–261). The method is motivated by diagnostic measures for osteopetrosis in a study summarized by Hans et al. (The Lancet 1996; 348:511–514). Diagnostic test accuracy is typically defined using the area (or partial area) under the receiver operator characteristic (ROC) curve. If partial area is used, the resulting statistic can be highly subjective because the focus region of the ROC curve corresponds to a set of low false‐positive rates that are chosen by the experimenter. This paper introduces a more …

Preferential Utilization Of Nadph As The Endogenous Electron Donor For Nad(P)H:Quinone Oxidoreductase 1 (Nqo1) In Intact Pulmonary Arterial Endothelial Cells, Robert D. Bongard, Brian J. Lindemer, Gary S. Krenz, Marilyn P. Merker

Mathematics, Statistics and Computer Science Faculty Research and Publications

The goal was to determine whether endogenous cytosolic NAD(P)H:quinone oxidoreductase 1 (NQO1) preferentially uses NADPH or NADH in intact pulmonary arterial endothelial cells in culture. The approach was to manipulate the redox status of the NADH/NAD⁺ and NADPH/NADP⁺ redox pairs in the cytosolic compartment using treatment conditions targeting glycolysis and the pentose phosphate pathway alone or with lactate, and to evaluate the impact on the intact cell NQO1 activity. Cells were treated with 2-deoxyglucose, iodoacetate, or epiandrosterone in the absence or presence of lactate, NQO1 activity was measured in intact cells using duroquinone as the electron acceptor, and …

Dendrites, Topological Graphs, And 2-Dominance, Paul Bankston

Mathematics, Statistics and Computer Science Faculty Research and Publications

For each positive ordinal α, the reflexive and transitive binary relation of α-dominance between compacta was first defined in our paper [Mapping properties of co-existentially closed continua, Houston J. Math., 31 (2005), 1047-1063] using the ultracopower construction. Here we consider the important special case α =2, and show that any Peano compactum 2-dominated by a dendrite is itself a dendrite (with the same being true for topological graphs and trees). We also characterize the topological graphs that 2-dominate arcs (resp., simple closed curves) as those that have cut points of order 2 (resp., those that are not trees).

Development And Implementation Of High-Throughput Snp Genotyping In Barley, Timothy J. Close, Prasanna R. Bhat, Stefano Lonardi, Yonghui Wu, Nils Rostoks, Luke Ramsay, Arnis Druka, Nils Stein, Jan T. Svensson, Steve Wanamaker, Serdar Bozdag, Mikeal L. Roose, Matthew J. Moscou, Shiaoman Chao, Rajeev K. Varshney, Peter Szucs, Kazuhiro Sato, Patrick M. Hayes, David E. Matthews, Andris Kleinhofs, Gary J. Muehlbauer, Joseph Deyoung, David F. Marshall, Kavitha Madishetty, Raymond D. Fenton, Pascal Condamine, Andreas Graner, Robbie Waugh

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background

High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of …

The Deterrent Effect Of Death Penalty Eligibility: Evidence From The Adoption Of Child Murder Eligibility Factors, Michael D. Frakes, Matthew Harding

Faculty Scholarship

We draw on within-state variations in the reach of capital punishment statutes between 1977 and 2004 to identify the deterrent effects associated with capital eligibility. Focusing on the most prevalent eligibility expansion, we estimate that the adoption of a child murder factor is associated with an approximately 20% reduction in the homicide rate of youth victims. Eligibility expansions may enhance deterrence by (1) paving the way for more executions and (2) providing prosecutors with greater leverage to secure enhanced non-capital sentences. While executions themselves are rare, this latter channel is likely to be triggered fairly regularly, providing a reasonable basis …

A Semiparametric Approach To A Nonlinear Acd Model, Pipat Wongsaart, Jiti Gao, David E. Allen

Research outputs pre 2011

We introduce in this paper a new semiparametric approach to a nonlinear ACD model, namely the Semiparametric ACD (SEMI-ACD) model. This new model is more flexible in the sense that the data are allowed to speak for themselves, without a hypothetical assumption being imposed arbitrarily on its key component. Moreover, it enables a much more thorough examination of the intertemporal importance of the conditional duration on the ACD process. Our experimental analysis suggests that the new model possesses a sound asymptotic character, while its performance is also robust across data generating processes and assumptions about the conditional distribution of the …

Spatial Clustering Using The Likelihood Function, April Kerby

Department of Statistics: Dissertations, Theses, and Student Research

Researchers have been using clustering algorithms for many years to group similar observations based on a set of recorded characteristics. The majority of these algorithms maximize the similarity of the observations within a cluster, while at the same time maximize the dissimilarity with observations in other clusters. However, nearly all of the current clustering algorithms do not take into account the actual geographic location of the observation during the clustering process. This dissertation consists of three papers which propose a method to incorporate the geographical location of an observation into the clustering algorithm, known as spatial clustering. The first paper …

Detecting Differentially Expressed Genes While Controlling The False Discovery Rate For Microarray Data, Shuo Jiao

Department of Statistics: Dissertations, Theses, and Student Research

Microarray is an important technology which enables people to investigate the expression levels of thousands of genes at the same time. One common goal of microarray data analysis is to detect differentially expressed genes while controlling the false discovery rate. This dissertation consists with four papers written to address this goal. The dissertation is organized as follows: In Chapter 1, a brief introduction of the Affymetrix GeneChip microarray technology is provided. The concept of differentially expressed genes and the definition of the false discovery rate are also introduced. In Chapter 2, a literature review of the related works on this …

Statistical Approaches For Adding Or Switching Hypotheses In Multi-Armed Clinical Trials, Jordan Jaskwhich Elm

MUSC Theses and Dissertations

As treatments become ready for testing at staggered times, it is desirable to have clinical trials that can accommodate different entry and exit times without prematurely discarding potentially efficacious treatments. In a group sequential multi-armed clinical trial, one treatment arm could be found to be superior or inferior at an interim analysis while the remaining arm is inconclusive. Existing methods address dropping an inferior arm from further study, , but do not fully address the handling of an early finding of overwhelming superiority of one arm (scenario 1). We consider an approach to transition from a multi-armed superiority trial to …

In Step With Hiv Vaccines? A Content Analysis Of Local Recruitment Campaigns For An International Hiv Vaccine Study, Paula M. Frew, Wendy Macias, Kayshin Chan, Ashley Harding

Environmental & Global Health Faculty Research

During the past two decades of the HIV/AIDS pandemic, several recruitment campaigns were designed to generate community involvement in preventive HIV vaccine clinical trials. These efforts utilized a blend of advertising and marketing strategies mixed with public relations and community education approaches to attract potential study participants to clinical trials (integrated marketing communications). Although more than 30,000 persons worldwide have participated in preventive HIV vaccine studies, no systematic analysis of recruitment campaigns exists. This content analysis study was conducted to examine several United States and Canadian recruitment campaigns for one of the largest-scale HIV vaccine trials to date (the “Step …

Law, Statistics, And The Reference Class Problem, Edward K. Cheng

Vanderbilt Law School Faculty Publications

Statistical data are powerful, if not crucial, pieces of evidence in the courtroom. Whether one is trying to demonstrate the rarity of a DNA profile, estimate the value of damaged property, or determine the likelihood that a criminal defendant will recidivate, statistics often have an important role to play. Statistics, however, raise a number of serious challenges for the legal system, including concerns that they are difficult to understand, are given too much deference from juries, or are easily manipulated by the parties' experts. In this preview piece, I address one of these challenges, known as the "reference class problem," …

Compartmentalized Approach To The Assembly Of Physical Maps, Serdar Bozdag, Timothy J. Close, Stefano Lonardi

Mathematics, Statistics and Computer Science Faculty Research and Publications

Background

Physical maps have been historically one of the cornerstones of genome sequencing and map-based cloning strategies. They also support marker assisted breeding and EST mapping. The problem of building a high quality physical map is computationally challenging due to unavoidable noise in the input fingerprint data.

Results

We propose a novel compartmentalized method for the assembly of high quality physical maps from fingerprinted clones. The knowledge of genetic markers enables us to group clones into clusters so that clones in the same cluster are more likely to overlap. For each cluster of clones, a local physical map is first …

Complete Identification Of Permissible Sampling Rates For First-Order Sampling Of Multi-Band Bandpass Signals, Yan Wu, Daniel F. Linder

Biostatistics: Faculty Publications

The first-order sampling of multi-band bandpass signals with arbitrary band positions is considered in this paper. Gaps between the spectral sub-bands are utilized to achieve lower sampling rates than the Nyquist. The lowest possible sampling rate along with other permissible sampling rates is identified via a unique partition of the frequency axis. With the complete identification of all the permissible sampling rates, a necessary and sufficient sampling theorem for multi-band bandpass signals is presented in terms of a series of csinc-interpolators.

Applications Of Modern Classification Methods To Predict Occurrences Of Rare And Invasive Plant Species, Stacey Reynolds

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Statistical classification methods are among the most widely used statistical procedures in ecology. Applications include vegetation mapping by remote sensing (Steele 2000), discrimination of subspecies using morphological measurements (Fisher 1936, 1938; Conner and Schenk 2003), and species distribution modelling (Guisan and Zimmerman 2000). Examples of the last application abound in the ecological literature and include predicting the distribution or characteristics of plant species (see, e.g., Austin et al. 1990), predicting presence and absence aquatic biota in streams (Hawkins et al. 2000), and habit at relationships of terrestrial animal species (Welch and MacMahon 2005). Over the last 20 years two mainstays …

The Statistical Evaluation Of Collective Risk Models With Various Distributional Assumptions, Chang Li

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Our thesis includes 2 sections. In section 1, we mainly discuss the distribution function and the empirical simulation of the total claims amount for a portfolio with multiple distributional assumptions, under the collective risk model for a single period.

In section 2, we discuss the collective risk model for an extended period, which mainly deals with the amount of surplus over several periods of time. Let Un denote the surplus at time n, then we interested in the probability of ruin, that is, the probability that there exists an n such that Un< O. In this section, we put forward an algorithm for the probability of ruin (both theoretical and empirical) using this model, with various distributional assumptions, and compare the theoretical and empirical results.

The reference of this project is Actuarial …

Research Design And Statistical Applications, Grayson Holmbeck, Kathy Zebracki, Katie Mcgoron

Psychology: Faculty Publications and Other Works

What is the role of research in the field of pediatric psychology? To answer this question, it is useful to imagine what clinical practice would be like if we had no research foundation for our work. Without such a foundation, practitioners would have no basis for suggesting specific interventions or understanding why some interventions are successful and why others fail. Similarly, without a research foundation, assessments conducted with children would be based on unstandardized assessment methods, and no normative data would be available. Clearly, most of us would agree that scientific research is the foundation of pediatric psychology, including all …

Multiple Imputation To Correct For Measurement Error In Admixture Estimates In Genetic Structured Association Testing, Miguel A. Padilla, Jamin Divers, Laura K. Vaughan, David B. Allison, Hemant K. Tiwari

Psychology Faculty Publications

Objectives: Structured association tests ( SAT), like any statistical model, assumes that all variables are measured without error. Measurement error can bias parameter estimates and confound residual variance in linear models. It has been shown that admixture estimates can be contaminated with measurement error causing SAT models to suffer from the same afflictions. Multiple imputation (MI) is presented as a viable tool for correcting measurement error problems in SAT linear models with emphasis on correcting measurement error contaminated admixture estimates. Methods: Several MI methods are presented and compared, via simulation, in terms of controlling Type I error rates for both …

Fact Sheet, Yale University Office Of Institutional Research

Fact Sheets

No abstract provided.

A Comparison Of Methods For Generating Bivariate Non-Normally Distributed Random Variables, Jaimee E. Stewart

UNF Graduate Theses and Dissertations

Many distributions of multivariate data in the real world follow a non-normal model with distributions being skewed and/or heavy tailed. In studies in which multivariate non-normal distributions are needed, it is important for simulations of those variables to provide data that is close to the desired parameters while also being fast and easy to perform. Three algorithms for generating multivariate non-normal distributions are reviewed for accuracy, speed and simplicity. They are the Fleishman Power Method, the Fifth-Order Polynomial Transformation Method, and the Generalized Lambda Distribution Method. Simulations were run in order to compare the three methods by how well they …

Effect Of Dlk1 And Rtl1 But Not Meg3 Or Meg8 On Muscle Gene Expression In Callipyge Lambs, Jolena N. Fleming-Waddell, Gayla R. Olbricht, Tasia M. Taxis, Jason D. White, Tony Vuocolo, Bruce A. Craig, Ross L. Tellam, Mike K. Neary, Noelle E. Cockett, Christopher A. Bidwell

Mathematics and Statistics Faculty Research & Creative Works

Callipyge sheep exhibit extreme postnatal muscle hypertrophy in the loin and hindquarters as a result of a single nucleotide polymorphism (SNP) in the imprinted DLK1-DIO3 domain on ovine chromosome 18. The callipyge SNP up-regulates the expression of surrounding transcripts when inherited in cis without altering their allele-specific imprinting status. The callipyge phenotype exhibits polar overdominant inheritance since only paternal heterozygous animals have muscle hypertrophy. Two studies were conducted profiling gene expression in lamb muscles to determine the down-stream effects of over-expression of paternal allele-specific DLK1 and RTL1 as well as maternal allele-specific MEG3, RTL1AS and MEG8, using Affymetrix bovine expression …

Using Decision Analytic Modelling To Simulate Pregnancy, Jeffrey Cannon

Theses : Honours

Decision analytic modelling enables decision makers to assess the cost-effectiveness associated with a proposed change in a cunent system without physically implementing the changes. This can be achieved by formulating a mathematical model that represents all the major events occuning in the system through fmmulas and algorithms, and estimating the likely outcomes along with their costs. This type of modelling has been identified by the State Health Research Advisory Council (SHRAC) of the Western Australian Depmiment of Health as an asset for the plmming of health care investments in the future. One such area in which the Western Australian Department …

Using Paired Comparison Matrices To Estimate Parameters Of The Partial Credit Rasch Measurement Model For Rater-Mediated Assessments, Mary Garner, George Engelhard Jr.

Faculty Articles

The purpose of this paper is to describe a technique for estimating the parameters of a Rasch model that accommodates ordered categories and rater severity. The technique builds on the conditional pairwise algorithm described by Choppin (1968, 1985) and represents an extension of a conditional algorithm described by Garner and Engelhard (2000, 2002) in which parameters appear as the eigenvector of a matrix derived from paired comparisons. The algorithm is used successfully to recover parameters from a simulated data set. No one has previously described such an extension of the pairwise algorithm to a Rasch model that includes both ordered …

On The Estimation Of Averages Over Infinite Intervals With An Application To Average Persistence In Population Models, Sean F. Ellermeyer

Faculty Articles

We establish a general result for estimating the upper average of a continuous and bounded function over an infinite interval. As an application, we show that a previously studied model of microbial growth in a chemostat with time–varying nutrient input admits solutions (populations) that exhibit weak persistence but not weak average persistence.

An Investigation Of The Ends Of Finitely Generated Groups, Daniel T. Murphree

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Geometric group theory is a relatively new branch of mathematics, studied as a distinct area since the 1990's. It explores invariant properties of groups based on group actions defined on topological or geometrical spaces. One of the pioneering works in geometric group theory is the article "Topological Methods in Group Theory" by Peter Scott and Terry Wall, written in 1977. This article was an overview of revised notes from an advanced course give in Liverpool in the same year. This report is an attempt to make these notes more accessible to lower level graduate students in the fields of topology …