Clinical Epidemiology Commons^™

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 …

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 …

The Analysis Of Placement Values For Evaluating Discriminatory Measures, Margaret S. Pepe, Tianxi Cai

UW Biostatistics Working Paper Series

The idea of using measurements such as biomarkers, clinical data, or molecular biology assays for classification and prediction is popular in modern medicine. The scientific evaluation of such measures includes assessing the accuracy with which they predict the outcome of interest. Receiver operating characteristic curves are commonly used for evaluating the accuracy of diagnostic tests. They can be applied more broadly, indeed to any problem involving classification to two states or populations (D = 0 or D = 1). We show that the ROC curve can be interpreted as a cumulative distribution function for the discriminatory measure Y in the …

Clinical And Epidemiological Correlates Of Genotypes Within The Mycobacterium Avium Complex Defined By Restriction And Sequence Analysis Of Hsp65, Sandra C. Smole, Fionnuala Mcaleese, Jutamas Ngampasutadol, C. Fordham Von Reyn, Robert D. Arbeit

Dartmouth Scholarship

Species identification of isolates of the Mycobacterium avium complex (MAC) remains a difficult task. Although M. avium and Mycobacterium intracellulare can be identified with expensive, commercially available probes, many MAC isolates remain unresolved, including those representing Mycobacterium lentiflavum as well as other potentially undefined species. PCR restriction analysis (PRA) of the hsp65 gene has been proposed as a rapid and inexpensive approach. We applied PRA to 278 MAC isolates, including 126 from blood of human immunodeficiency virus (HIV)-infected patients, 59 from sputum of HIV-negative patients with chronic obstructive pulmonary disease, 88 from environmental sources, and 5 pulmonary isolates from …

Trends. Controlling Aids Through Control, Ibpp Editor

International Bulletin of Political Psychology

This article discusses the concept of political control and public health in the context of the HIV/AIDS epidemic.

The Association Of Fluid Intake With Total Natural-Cause Mortality, Coronary Heart Disease And Fatal Stroke, Jacqueline Chung Lun Chan

Loma Linda University Electronic Theses, Dissertations & Projects

Hypohydration may be more widespread than realized since it does not always arouse a sense of thirst. When thirst is felt, it is often ignored, or satisfied before euhydration is achieved. There is growing evidence indicating that hypohydration contributes to acute and chronic illnesses, and to rheological factors associated with coronary heart disease (CHD) and stroke. Therefore the relationship of fluid intake with risk of total natural-cause mortality, CHD and stroke death was examined using data on 34,192 white, non-Hispanic participants in the Adventist Health Study.

Among the 27,342 reporting no CHD, stroke or diabetes at baseline, during six years …

Assessing The Accuracy Of A New Diagnostic Test When A Gold Standard Does Not Exist, Todd A. Alonzo, Margaret S. Pepe

UW Biostatistics Working Paper Series

Often the accuracy of a new diagnostic test must be assessed when a perfect gold standard does not exist. Use of an imperfect test biases the accuracy estimates of the new test. This paper reviews existing approaches to this problem including discrepant resolution and latent class analysis. Deficiencies with these approaches are identified. A new approach is proposed that combines the results of several imperfect reference tests to define a better reference standard. We call this the composite reference standard (CRS). Using the CRS, accuracy can be assessed using multistage sampling designs. Maximum likelihood estimates of accuracy and expressions for …

Condom Availability In New York City Public High Schools: Relationships To Condom Use And Sexual Behavior, Sally Guttmacher, Lisa D. Lieberman, David Ward, Nick Freudenberg, Alice Radosh, Don Des Jarlais

Department of Public Health Scholarship and Creative Works

OBJECTIVES: This study examines the impact of the condom availability program in New York City public high schools by comparing rates of sexual activity and condom use for New York students and similar students in Chicago. METHODS: A total of 7119 students from 12 randomly selected New York schools and 5738 students from 10 Chicago schools participated in a cross-sectional survey. RESULTS: New York students, compared with Chicago students, reported equal rates of sexual activity but higher rates of condom use at last intercourse (odds ratio [OR] = 1.36). For higher-risk students (those with three or more sexual partners in …

Assessing Stress In Teachers: Depressive Symptoms Scales And Neutral Self-Reports Of The Work Environment, Irvin Sam Schonfeld

Publications and Research

The focal interest of this chapter on teacher stress is methodologic. The chapter enumerates a number of defects in existing measures of job stress in teachers and, concomitantly, other helping professionals. Alternative ways of measuring stress in teachers are suggested and evaluated. The use of depressive symptom scales in concert with more 'objective' measures of the work environment is discussed. An application of the proposed alternative measurement strategy is described. The wider utility of the measurement strategy is briefly described.

The Effect Of Electroshock On The Passage Of Bacteria From A Contaminated Transducer Past A Protective Membrane Into A Disposable Chamber Dome, Patricia K. Taylor Pothier

Loma Linda University Electronic Theses, Dissertations & Projects

Infection related to use of Intra-arterial Hemodynamic Monitoring Devices is a serious complication. In an attempt to decrease the risk of infection presterilized chamber domes were developed to isolate the patient vascular system from the pressure transducer. Users were informed by manufacturers of the domes that routine decontamination of transducer heads was not necessary. Since the development of these disposable chamber domes infection outbreaks have continued to occur. Epidemiological investigation has implicated contact transmission of bacteria due to poor handling techniques in some outbreaks. However, in other outbreaks the source of the epidemic was found to be contaminated transducer heads …

Contamination Of Stuffed Cloth Toys On A Pediatric Unit, Virginia Lois Fowler, Dynnette Nelson Hart

Loma Linda University Electronic Theses, Dissertations & Projects

The purpose of the study was to determine if cloth stuffed toys used by children in the pediatric unit of Loma Linda University Hospital carry microbacterial pathogens that are the same type as those pathogens found in the throat of the child using the toy. A second purpose was to determine how long the selected pathogens, Staphylococcus aureus, Streptococcus pyogenes, and Diplococcus pneumonia, survive on the same cloth toys as used in the selected hospital. Throat cultures were taken of twenty-four patients and each patient was given a cloth stuffed toy selected to be studied. Cultures of the toys were …

A Study Of Door Pulls On Isolation Carts In A General Hospital For Evidence Of Contamination, Mary Alice Harper

Loma Linda University Electronic Theses, Dissertations & Projects

The purpose of the study was to find out if isolation carts were serving as a means of cross infection. Literature pertaining to sources of possible contamination on hospital units written in the past five years were reviewed.

Using the descriptive survey as the method of study, effort was made to find out if isolation carts were a means of cross infection on the hospital unit. Two laboratory cultures were obtained from both door pulls on all isolation carts used by nursing units. This was done over a three month period from December 12, 1963 to March 11, 1964. The …