Physical Sciences and Mathematics Commons^™

A Bayesian Hierarchical Approach To Multirater Correlated Roc Analysis, Tim Johnson, Valen Johnson

The University of Michigan Department of Biostatistics Working Paper Series

In a common ROC study design, several readers are asked to rate diagnostics of the same cases processed under different modalities. We describe a Bayesian hierarchical model that facilitates the analysis of this study design by explicitly modeling the three sources of variation inherent to it. In so doing, we achieve substantial reductions in the posterior uncertainty associated with estimates of the differences in areas under the estimated ROC curves and corresponding reductions in the mean squared error (MSE) of these estimates. Based on simulation studies, both the widths of confidence intervals and MSE of estimates of differences in the …

A Bayesian Chi-Squared Test For Goodness Of Fit, Valen Johnson

The University of Michigan Department of Biostatistics Working Paper Series

This article describes an extension of classical x 2 goodness-of-fit tests to Bayesian model assessment. The extension, which essentially involvesevaluating Pearson's goodness-of-fit statistic at a parameter value drawn from its posterior distribution, has the important property that it is asymptoti-cally distributed as a x2 random variable on K-1 degrees of freedom, indepen-dently of the dimension of the underlying parameter vector. By averaging over the posterior distribution of this statistic, a global goodness-of-fit diagnostic is obtained. Advantages of this diagnostic{which may be interpreted as the area under an ROC curve{include ease of interpretation, computational conve-nience, and favorable power properties. The proposed …

Individualized Predictions Of Disease Progression Following Radiation Therapy For Prostate Cancer., Jeremy Taylor, Menggang Yu, Howard M. Sandler

The University of Michigan Department of Biostatistics Working Paper Series

Background: Following treatment for localized prostate cancer, men are monitored with serial PSA measurements. Refining the predictive value of post-treatment PSA determinations may add to clinical management and we have developed a model that predicts for an individual patient future PSA values and estimates the time to future clinical recurrence.

Methods: Data from 934 patients treated for prostate cancer between 1987 and 2000 were used to develop a comprehensive statistical model to fit the clinical recurrence events and pattern of PSA data. A logistic regression model was used for the probability of cure, non-linear hierarchical mixed models were used for …

Piecewise Constant Cross-Ratio Estimation For Association In Bivariate Survival Data With Application To Studying Markers Of Menopausal Transition, Bin Nan, Xihong Lin, Lynda D. Lisabet, Sioban Harlow

The University of Michigan Department of Biostatistics Working Paper Series

A question of significant interest in female reproductive aging is to identify bleeding criteria for the menopausal transition. Although various bleeding criteria, or markers, have been proposed for the menopausal transition, their validity has not been adequately examined. The Tremin Trust data are collected from a long-term cohort study that followed a group of women throughout their whole reproductive life, and provide a unique opportunity for assessing the association between age at onset of a bleeding marker and age onset of menopause. Formal statistical analysis of this dependence is challenging give the fact that both the marker event and menopause …

Individual Prediction In Prostate Cancer Studies Using A Joint Longitudinal-Survival-Cure Model, Menggang Yu, Jeremy Taylor, Howard M. Sandler

The University of Michigan Department of Biostatistics Working Paper Series

For monitoring patients treated for prostate cancer, Prostate Specific Antigen (PSA) is measured periodically after they receive treatment. Increases in PSA are suggestive of recurrence of the cancer and are used in making decisions about possible new treatments. The data from studies of such patients typically consist of longitudinal PSA measurements, censored event times and baseline covariates. Methods for the combined analysis of both longitudinal and survival data have been developed in recent years, with the main emphasis being on modeling and estimation. We analyze data from a prostate cancer study that has been extended by adding a mixture structure …

Incorporating Death Into Health-Related Variables In Longitudinal Studies, Paula Diehr, Laura Lee Johnson, Donald L. Patrick, Bruce Psaty

UW Biostatistics Working Paper Series

Background: The aging process can be described as the change in health-related variables over time. Unfortunately, simple graphs of available data may be misleading if some people die, since they may confuse patterns of mortality with patterns of change in health. Methods have been proposed to incorporate death into self-rated health (excellent to poor) and the SF-36 profile scores, but not for other variables.

Objectives: (1) To incorporate death into the following variables: ADLs, IADLs, mini-mental state examination, depressive symptoms, body mass index (BMI), blocks walked per week, bed days, hospitalization, systolic blood pressure, and the timed walk. (2) To …

Overlap Bias In The Case-Crossover Design, With Application To Air Pollution Exposures, Holly Janes, Lianne Sheppard, Thomas Lumley

UW Biostatistics Working Paper Series

The case-crossover design uses cases only, and compares exposures just prior to the event times to exposures at comparable control, or “referent” times, in order to assess the effect of short-term exposure on the risk of a rare event. It has commonly been used to study the effect of air pollution on the risk of various adverse health events. Proper selection of referents is crucial, especially with air pollution exposures, which are shared, highly seasonal, and often have a long term time trend. Hence, careful referent selection is important to control for time-varying confounders, and in order to ensure that …

Incremental Genetic K-Means Algorithm And Its Application In Gene Expression Data Analysis, Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng, Susan J. Brown

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

In recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM, etc, genes are partitioned into groups based on the similarity between their expression profiles. In this way, functionally related genes are identified. As the amount of laboratory data in molecular biology grows exponentially each year due to advanced technologies such as Microarray, new efficient and effective methods for clustering must be developed to process this growing amount of biological data.

Results

In this paper, we propose a new clustering …

A Hidden Markov Model Capable Of Predicting And Discriminating Β-Barrel Outer Membrane Proteins, Pantelis G. Bagos, Theodore D. Liakopoulos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas

Pantelis Bagos

BACKGROUND: Integral membrane proteins constitute about 20-30% of all proteins in the fully sequenced genomes. They come in two structural classes, the alpha-helical and the beta-barrel membrane proteins, demonstrating different physicochemical characteristics, structure and localization. While transmembrane segment prediction for the alpha-helical integral membrane proteins appears to be an easy task nowadays, the same is much more difficult for the beta-barrel membrane proteins. We developed a method, based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the outer membrane proteins of gram-negative bacteria, and discriminating those from water-soluble proteins in large datasets. The model is trained …

Santa Clara Magazine, Volume 46 Number 3, Winter 2004, Santa Clara University

Santa Clara Magazine

8 - AN ARTIST WITH A MISSION By Elizabeth Kelley Gillogly '93. In his latest series, Howard Anderson '71 created paintings of the 21 California missions.

10 - THE SPIRITUALITY OF GIFT GIVING By Tom Beaudoin. Is it possible to turn our gift giving into a spiritual exercise?

14 - RAISING ARIZONA By Susan Shea. Arizona Governor Janet Napolitano '79, a rising political star, uses the lessons learned at SCU to serve her state.

20 - LEAVING COMMUNISM BEHIND By Jane Curry. An SCU professor and Fulbright Scholar researches forgiveness and justice in post-communist Poland.

Response Of Dark-Adapted Retinal Rod Photoreceptors, H. Khanal, V. Alexiades, E. Dibenedetto

Publications

The process of phototransduction, whereby light is converted into an electrical response, in rod and cone photoreceptors in the retina, involves as a key setp, the diffusion of the cytoplasmic, signaling molecules cGMP (cyclic guanosime monophosphate) and Ca²+ diffuse in the cytoplasm (the fluid surrounding the discs). the complex geometry of the rod creates computational difficulties. We present spatio-temporal compuational models for interacctions and diffusion of cGMP and Ca²+ in the cytoplasm of vertebrate rod photoreceptors, as well as numerical simulations fo the response to light of dark-adapted Salamander rods.

President's Message, David J. Stroup

Journal of the South Carolina Academy of Science

No abstract provided.

Building New Culture Media For Assisted Reproductive Technology., Mary N. Egbuniwe, H. Lee Higdon Iii, William R. Boone

Journal of the South Carolina Academy of Science

No abstract provided.

Bioinformatics: An Undergraduate Research/Teaching Tool., Abhishek Agrawal, Valgene L. Dunham

Journal of the South Carolina Academy of Science

No abstract provided.

Estimation Of Standardized Mortality Ratio In Geographic Epidemiology, Anna Kettermann

Electronic Theses and Dissertations

The analysis of geographic variation of disease and its representation on a map form an important topic of research in epidemiology and in public health in general. Identification of spatial heterogeneity of relative risk using morbidity and mortality data is required. The usual technique of disease atlas generation consists of data collection (observed number of disease cases). These data are collected during a continuous period of time (5 to 10 years). The second aspect of atlas creation relates to the analysis of these data. A traditional measure of the spatial variation is usually taken as a ratio of the number …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

I Don't Care If I Ever Get Back: Marathons Lasting 20 Or More Innings, Phil Lowry, Darren B. Glass

Math Faculty Publications

This article looks at marathon games of baseball. For purposes of this article, a marathon is defined as a game lasting 20 or more innings. In my research I have discovered 341 marathons. These games are hard to find. Leagues either keep no records, or keep track only of their longest game; only the Texas League keeps records on all marathons. Nobody has ever before explored such questions as: What is the probability a game will go x number of innings? How often should we expect a marathon of 20 or more innings, or 40 or more innings? What is …

Development Of Dose Coefficients For Radionuclides Produced In Spallation Targets, Phillip W. Patton, Mark Rudin

Transmutation Sciences Physics (TRP)

Dose coefficients permit simple determination of radiation dose associated with various exposure scenarios, and ultimately permit radiation safety personnel to assess the health risks to workers in a nuclear facility. Specifically, radiation safety personnel use dose coefficients to determine the radiation dose incurred to a tissue or organ system from a given exposure. These parameters are often expressed in terms of Annual Limits on Intake (ALIs) and Derived Air Concentrations (DACs).

Results from this study will be used to produce ALIs and DACs for these rare radionuclides created by spallation target systems that are not included in Federal Guidance Report …

Pathobiology Of Mycobacteria In Striped Bass (Morone Saxatilis), David T. Gauthier

Dissertations, Theses, and Masters Projects

Striped bass (Morone saxatilis) in Chesapeake Bay, USA, are experiencing an epizootic of mycobacteriosis. This disease, caused by bacteria in the genus Mycobacterium, causes granulomatous lesions of the skin and viscera. Diseased fish are often emaciated, and fish with skin lesions may be significantly disfigured. The overall goal of this work was to examine aspects of the pathobiology of mycobacteria in striped bass via laboratory exposure studies and cellular assays. Striped bass were injected intraperitoneally with a sublethal dose of Mycobacterium marinum, M. shottsii, or M. gordonae and sampled for histology and bacteriology at regular intervals to 45 weeks post-injection …

Phytoplankton Composition Within The Tidal Freshwater-Oligohaline Regions Of The Rappahannock And Pamunkey Rivers In Virginia, Harold G. Marshall, Lubomira Burchardt

Biological Sciences Faculty Publications

The Rappahannock River is a major river system across north central Virginia prior to entering the Chesapeake Bay. In contrast, the Pamunkey River is smaller in size and joins the Mattoponi River to form the York River, which flows parallel to the Rappahannock before it also flows into Chesapeake Bay. A unique mixing area for both flora and environmental conditions exists in the tidal freshwater-oligohaline region of both rivers. This is a dynamic mixing section where freshwater and estuarine species are subject to the interaction of river flow and daily tidal rhythms. The phytoplankton composition in this region of the …

Scas Officers And Council Members 2004 - 2005

Journal of the South Carolina Academy of Science

No abstract provided.

Advances And Applications Of Dezert-Smarandache Theory (Dsmt), Vol. 1, Florentin Smarandache, Jean Dezert

Branch Mathematics and Statistics Faculty and Staff Publications

The Dezert-Smarandache Theory (DSmT) of plausible and paradoxical reasoning is a natural extension of the classical Dempster-Shafer Theory (DST) but includes fundamental differences with the DST. DSmT allows to formally combine any types of independent sources of information represented in term of belief functions, but is mainly focused on the fusion of uncertain, highly conflicting and imprecise quantitative or qualitative sources of evidence. DSmT is able to solve complex, static or dynamic fusion problems beyond the limits of the DST framework, especially when conflicts between sources become large and when the refinement of the frame of the problem under consideration …

Dual Energy Scanning Beam X -Radiography, Randolph Frank Wojcik

Dissertations, Theses, and Masters Projects

Dual energy X-radiography is a method first developed in the mid-1970's by which one uses the information contained in the energy spectrum of the transmitted X-ray flux through an object. With this information one can distinguish the types of materials present in a radiograph and thus allow a computer to subtract them from the image enhancing the contrast of the remaining materials. Using this method, one can see details, which would have been hidden by overlying structures of other materials such as seen in radiographs of parts, made up of mixtures of metals and composites. There is also great interest …

A Study Of The Eastern Oyster, Crassostrea Virginica: (1) Dermo Tolerance, Survival, Growth, Condition And Hsp70 Expression In Different Geographic Stocks; (2) Heat Tolerance And Effects Of Sublethal Heat Shock On Survival And Hsp70 Expression Of Infected And Uninfected Oysters, Vincent G. Encomio

Dissertations, Theses, and Masters Projects

The diseases Dermo and MSX have devastated Chesapeake Bay populations of the eastern oyster, Crassostrea virginica. The protozoan Perkinsus marinus, which causes Dermo, is particularly problematic since it persists over a wide range of salinities and temperatures. An objective of this dissertation was to determine whether specific wild oyster stocks had developed natural resistance to Dermo and if several parameters (survival, growth, condition and energy reserves) were associated with resistance. Another objective was to characterize heat shock protein (hsp70) expression in the eastern oyster. Heat shock proteins such as hsp70 protect organisms from thermal stress and other stressors, and this …

Natural Dermo Resistance And Related Defense Mechanisms In Eastern Oysters, Crassostrea Virginica, With Implications For Restoration, Shawn Michael Stickler

Dissertations, Theses, and Masters Projects

American oyster (Crassostrea virginica) stocks on the East Coast in general, and in Chesapeake Bay in particular, have been in decline over the past half-century in large part due to Dermo disease, caused by the protist parasite Perkinsus marinus. Efforts to restore oysters for their ecological and economic value have centered on the development and use of hatchery-based seed selectively bred for disease resistance. Selective breeding could benefit from the incorporation of oysters from wild stocks that have developed "natural Dermo resistance", but few such stocks have been identified and verified. This dissertation describes reciprocal common-garden experiments carried out at …

Ensuring The Comparability Of Comparison Groups: Is Randomization Enough?, Vance Berger, Sherri Rose

Sherri Rose

It is widely believed that baseline imbalances in randomized trials must necessarily be random. In fact, there is a type of selection bias that can cause substantial, systematic and reproducible baseline imbalances of prognostic covariates even in properly randomized trials. It is possible, given complete data, to quantify both the susceptibility of a given trial to this type of selection bias and the extent to which selection bias appears to have caused either observable or unobservable baseline imbalances. Yet, in articles reporting on randomized trials, it is uncommon to find either these assessments or the information that would enable a …

Fall Prevention Programs For The Elderly: A Bayesian Secondary Meta-Analysis, Joseph F. Lucke

Joseph Lucke

A secondary meta-analysis of programs to reduce falls in the elderly is undertaken to demonstrate a Bayesian analysis. The Bayesian statistical tradition is carefully distinguished from the standard Neyman-Pearson-Wald (NPW) statistical tradition. In the 12 studies, the logit effect size is used to compare treatment groups using a prevention program to control groups without a program. To contrast the Bayesian analysis, independent-effects and fixed-effect meta-analyses are first conducted in the NPW tradition. This is followed by Bayesian independent-effects and fixed-effect meta-analyses that numerically replicate the NPW results but have conceptually different interpretations. The final analyses comprise Bayesian random-effects and predictive …

Uncertainty And The Value Of Diagnostic Information With Application To Axillary Lymph Node Dissection In Breast Cancer, Giovanni Parmigiani

Johns Hopkins University, Dept. of Biostatistics Working Papers

In clinical decision making, it is common to ask whether, and how much, a diagnostic procedure is contributing to subsequent treatment decisions. Statistically, quantification of the value of the information provided by a diagnostic procedure can be carried out using decision trees with multiple decision points, representing both the diagnostic test and the subsequent treatments that may depend on the test's results. This article investigates probabilistic sensitivity analysis approaches for exploring and communicating parameter uncertainty in such decision trees. Complexities arise because uncertainty about a model's inputs determines uncertainty about optimal decisions at all decision nodes of a tree. We …

Survival Model Predictive Accuracy And Roc Curves, Patrick Heagerty, Yingye Zheng

UW Biostatistics Working Paper Series

The predictive accuracy of a survival model can be summarized using extensions of the proportion of variation explained by the model, or R^2, commonly used for continuous response models, or using extensions of sensitivity and specificity which are commonly used for binary response models.

In this manuscript we propose new time-dependent accuracy summaries based on time-specific versions of sensitivity and specificity calculated over risk sets. We connect the accuracy summaries to a previously proposed global concordance measure which is a variant of Kendall's tau. In addition, we show how standard Cox regression output can be used to obtain estimates of …

Semiparametric Estimation Of Time-Dependent: Roc Curves For Longitudinal Marker Data, Yingye Zheng, Patrick Heagerty

UW Biostatistics Working Paper Series

One approach to evaluating the strength of association between a longitudinal marker process and a key clinical event time is through predictive regression methods such as a time-dependent covariate hazard model. For example, a time-varying covariate Cox model specifies the instantaneous risk of the event as a function of the time-varying marker and additional covariates. In this manuscript we explore a second complementary approach which characterizes the distribution of the marker as a function of both the measurement time and the ultimate event time. Our goal is to flexibly extend the standard diagnostic accuracy concepts of sensitivity and specificity to …