bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum random walks on the set of contingency tables
Authors: Sawae Ryuichi , Sakata Toshio , Takarabe Kenichi , Tei Minaru , Mizuno Youichi , Mori Yoshiyuki , Manmoto Yoshinori 
Published: November 2002

AbstractIn this article, we define the quantum version of this classic Metropolis walks on the set of contingency tables and get several theoretical conclusions with computer simulation for two‐way contingency tables with fixed‐row sums and column sums. Also, quantum random walks for three‐way contingency tables will be defined. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
Comparing proportional hazards and accelerated failure time models for survival analysis
Authors: Orbe Jesus , Ferreira Eva , Núñez‐Antón Vicente 
Published: October 2002

AbstractThis paper describes a method proposed for a censored linear regression model that can be used in the context of survival analysis. The method has the important characteristic of allowing estimation and inference without knowing the distribution of the duration variable. Moreover, it does not need the assumption of proportional hazards. Therefore, it can be an interesting alternative to the Cox proportional hazards models when this assumption does not hold. In addition, implementation and interpretation of the results is simple. In order to analyse the performance of this methodology, we apply it to two real examples and we carry out a simulation study. We present its results together with those obtained with the traditional Cox model and AFT parametric models. The new proposal seems to lead to more precise results. Copyright © 2002 John Wiley & Sons, Ltd.
Assessing intrarater, interrater and test–retest reliability of continuous measurements
Authors: Rousson Valentin , Gasser Theo , Seifert Burkhardt 
Published: October 2002

AbstractIn this paper we review the problem of defining and estimating intrarater, interrater and test–retest reliability of continuous measurements. We argue that the usual notion of product‐moment correlation is well adapted in a test–retest situation, whereas the concept of intraclass correlation should be used for intrarater and interrater reliability. The key difference between these two approaches is the treatment of systematic error, which is often due to a learning effect for test–retest data. We also consider the reliability of a sum and a difference of variables and illustrate the effects on components. Further, we compare these approaches of reliability with the concept of limits of agreement proposed by Bland and Altman (for evaluating the agreement between two methods of clinical measurements) and show how product‐moment correlation is related to it. We then propose new kinds of limits of agreement which are related to intraclass correlation. A test battery to study the development of neuro‐motor functions in children and adolescents illustrates our purpose throughout the paper. Copyright 2002 John Wiley & Sons, Ltd.
Block principal component analysis with application to gene microarray data classification
Authors: Liu Aiyi , Zhang Ying , Gehan Edmund , Clarke Robert 
Published: October 2002

AbstractWe propose a block principal component analysis method for extracting information from a database with a large number of variables and a relatively small number of subjects, such as a microarray gene expression database. This new procedure has the advantage of computational simplicity, and theory and numerical results demonstrate it to be as efficient as the ordinary principal component analysis when used for dimension reduction, variable selection and data visualization and classification. The method is illustrated with the well‐known National Cancer Institute database of 60 human cancer cell lines data (NCI60) of gene microarray expressions, in the context of classification of cancer cell lines. Copyright © 2002 John Wiley & Sons, Ltd.
Binary partitioning for continuous longitudinal data: categorizing a prognostic variable
Authors: Abdolell M. , LeBlanc M. , Stephens D. , Harrison R. V. 
Published: October 2002

AbstractWe investigate a binary partitioning algorithm in the case of a continuous repeated measures outcome. The procedure is based on the use of the likelihood ratio statistic to evaluate the performance of individual splits. The procedure partitions a set of longitudinal data into two mutually exclusive groups based on an optimal split of a continuous prognostic variable. A permutation test is used to assess the level of significance associated with the optimal split, and a bootstrap confidence interval is obtained for the optimal split. Copyright © 2002 John Wiley & Sons, Ltd.
Use of statistical models for evaluating antibody response as a correlate of protection against varicella
Authors: Chan Ivan S. F. , Li Shu , Matthews Holly , Chan Christina , Vessey Rupert , Sadoff Jerald , Heyse Joseph 
Published: October 2002

AbstractIn vaccine clinical trials, humoral antibody responses are often used to measure the effect of a vaccine because they correlate with a vaccine's protective efficacy against the target disease. While the concept of a correlate of protection usually refers to establishing a protective level of antibody titre, identifying a clear‐cut value is often impossible because vaccine efficacy is not related solely to the antibody titre. We propose examining the relationship between disease protection and the whole distribution of antibody responses rather than a single cut‐off level. In particular, we use failure‐time models to estimate the relationship between long‐term disease breakthroughs and primary antibody responses after vaccination. We apply these models to show that the varicella antibody response measured by glycoprotein enzyme‐linked immunosorbent assay 6 weeks after vaccination strongly correlate with protection against varicella (chickenpox); we used 7‐year follow‐up data from children who received one dose of a live attenuated varicella (Oka/Merck) vaccine. In addition, we explore the potential use of these models to predict long‐term disease breakthrough rates and to estimate the predicted vaccine efficacy of a similar varicella vaccine made with a modified manufacturing process. Copyright © 2002 John Wiley & Sons, Ltd.
Two approaches to mutation detection based on functional data
Authors: Pfeiffer Ruth M. , Bura Efstathia , Smith Amelia , Rutter Joni L. 
Published: October 2002

AbstractA new technique, denaturing high‐performance liquid chromatography (dHPLC), allows for detection of any heterozygous sequence variation in a gene without prior knowledge of the precise location of the sequence change. The results of a dHPLC analysis are recorded in real‐time in the form of a chromatogram that is sequence‐specific. In this paper we present methods to classify an individual, based on the observed chromatogram, as a homozygous wild‐type or a carrier of a specific variant for the given DNA segment by comparison to representative chromatograms that are obtained from the training set of individuals with known variant status. The first approach consists of finding a parsimonious parametric model and then classifying each newly observed curve based on comparing the most discriminating characteristic, the main mode, to the main mode of the training curves. The second approach consists of finding empirical estimates of the modes of each chromatogram and using a bootstrap test for equality with the corresponding estimates of the training curves. We apply both methods to data on the breast cancer susceptibility geneBRCA1and test the performance of the methods on independent samples. Published in 2002 by John Wiley & Sons, Ltd.
Dealing with competing risks: testing covariates and calculating sample size
Authors: Pintilie Melania 
Published: October 2002

AbstractIt is universally agreed that Kaplan–Meier estimates overestimate the probability of the event of interest in the presence of competing risks. Kalbfleisch and Prentice recommend using the cumulative incidence as an estimate of the probability of an event of interest. However, there is no consensus on how to test the effect of a covariate in the presence of competing risks. Using simulations, this paper illustrates that the Cox proportional hazards model gives valid results when employed in testing the effect of a covariate on the hazard rate and when estimating the hazard ratio. A method to calculate the sample size for testing the effect of a covariate on outcome in the presence of competing risks is also provided. Copyright © 2002 John Wiley & Sons, Ltd.
Regression analysis based on pairwise ordering of patients' clinical histories
Authors: Follmann Dean A. 
Published: October 2002

AbstractWhen a medical treatment influences a variety of outcomes, describing the global effect of treatment can be difficult. Traditional approaches specify how treatment affects each separate outcome. This can be done with separate models for each outcome, or by using a combined multivariate model. Describing the overall effect of a treatment thus requires combining these separate effects in some fashion and can be difficult to explain. In this paper, I specify a regression model for use with multiple outcomes where the outcome histories for each pair of patients are ranked. Pairs of patients with different lengths of follow‐up are evaluated solely over the common follow‐up interval. The logit of the probability that the outcome for patient i is better than that of patient j is assumed to depend on a linear function of the difference of the covariate vectors (for example, treatment indicators) for persons i and j. Thus covariates directly affect the entire clinical history, rather than directly affecting specific outcomes that comprise the history. The idea is that ranking outcomes is more relevant and interpretable than statistically combining separate effects. An estimating equations approach for estimation is described and an example of a clinical trial involving patients with heart failure is provided. Published in 2002 by John Wiley & Sons, Ltd.
Local likelihood analysis of the latency distribution with interval censored intermediate events
Authors: Bebchuk Judith D. , Betensky Rebecca A. 
Published: October 2002

AbstractThe distribution of time between an intermediate event and a terminal event is frequently of interest both in studying the behaviour of populations and in predicting outcomes for individuals. Current methods for estimating this latency distribution have either imposed assumptions on the hazard for the terminal event following the occurrence of the intermediate event or on the parametric form of the hazards. Here, local likelihood estimation is applied to the underlying hazard functions of a three‐state process in which the time of the intermediate event may be interval censored and the time of the terminal event is either observed or right censored. Smooth non‐parametric estimates of the latency distribution, along with bootstrap confidence intervals, are calculated, and tests for the comparison of two latency distributions are presented. The method is applied to two studies: a cohort of haemophiliacs who were infected with HIV by contaminated blood factor and followed for AIDS onset, and an AIDS clinical trial in which the intermediate event is the time to 50 per cent drop in CD4 count and the terminal event is AIDS or death. Simulations are presented to assess the performance of the estimation procedure. Copyright © 2002 John Wiley & Sons, Ltd.
Assessing chronic disease progression using non‐homogeneous exponential regression Markov models: an illustration using a selective breast cancer screening in Taiwan
Authors: Hsieh Hsin‐Ju , Chen Tony Hsiu‐Hsi , Chang Shu‐Hui 
Published: October 2002

AbstractPrevious research on estimation of the progression of chronic disease, from the normal preclinical screen‐detectable phase (PCDP) to the final clinical phase, has usually assumed constant transition rates and has rarely addressed how relevant covariates affect multi‐state transitions. The present study proposes two non‐homogeneous models using the Weibull distribution and piecewise exponential model, together with covariate functions of the proportional hazard form, to tackle these problems. We illustrate the models by application to a selective breast cancer screening programme. The results of the Weibull model yield estimates of scale and shape parameters for annual preclinical incidence rate as 0.0000058 (SE=0.0000019) and 2.4755 (SE=0.1153), the latter being significantly higher than 1. Annual transition rate was estimated as 0.3153 (SE=0.1385). Relative risks for the effects of late age at first pregnancy (AP) and high body mass index (BMI) on preclinical incidence rate were 1.98 and 2.59, respectively. The corresponding figures on the transition from the PCDP to clinical phase were 1.56 and 1.99, respectively. Non‐homogeneous Markov models proposed in this study can be easily applied to rates of progression of chronic disease with increasing or decreasing rates with time and to model the effect of relevant covariates on multi‐state transition rates. Copyright © 2002 John Wiley & Sons, Ltd.
An adaptive test of significance for a subset of regression coefficients
Authors: O'Gorman Thomas W. 
Published: October 2002

AbstractAn F‐test for a subset of regression coefficients is often used in order to compare two nested linear models. An adaptive test is proposed that has higher power than this F‐test for many non‐normal distributions of error terms. The adaptive test uses a weighted least squares procedure with weights determined from the Studentized deleted residuals from a linear model. A permutation method is then used so that the resulting test maintains its size near the nominal value. Results from several simulation studies are used to compare the power of the adaptive test to the F‐test. The adaptive test is recommended as a way of increasing the power of many common tests when used with models that have few parameters whenever the distribution of errors is non‐normal and the number of observations exceeds 20. Copyright © 2002 John Wiley & Sons, Ltd.
Choice of stratification in Poisson process analysis of recurrent event data with environmental covariates
Authors: Dewanji Anup , Moolgavkar Suresh H. 
Published: October 2002

AbstractThe Poisson process approach for studying the association between environmental covariates and recurrent events depends on the stratification of study period into intervals within which the baseline intensities are assumed constant. In this work we investigate the problem of bias and variance due to misspecification of this stratification. We suggest a cross‐validation approach to choosing a stratification model to balance the trade‐off between bias and variance. We also establish a connection between the Poisson process approach and case cross‐over studies. Copyright © 2002 John Wiley & Sons, Ltd.
Aggregate data meta‐analysis with time‐to‐event outcomes
Authors: Williamson Paula R. , Smith Catrin Tudur , Hutton Jane L. , Marson Anthony G. 
Published: October 2002

AbstractIn a meta‐analysis of randomized controlled trials with time‐to‐event outcomes, an aggregate data approach may be required for some or all included studies. Variation in the reporting of survival analyses in journals suggests that no single method for extracting the log(hazard ratio) estimate will suffice. Methods are described which improve upon a previously proposed method for estimating the log(HR) from survival curves. These methods extend to life‐tables. In the situation where the treatment effect varies over time and the trials in the meta‐analysis have different lengths of follow‐up, heterogeneity may be evident. In order to assess whether the hazard ratio changes with time, several tests are proposed and compared. A cohort study comparing life expectancy of males and females with cerebral palsy and a systematic review of five trials comparing two anti‐epileptic drugs, carbamazepine and sodium valproate, are used for illustration. Copyright © 2002 John Wiley & Sons, Ltd.
Estimation and projections of cancer prevalence from cancer registry data
Authors: Verdecchia Arduino , Angelis Giovanni De , Capocaccia Riccardo 
Published: October 2002

AbstractA method, PIAMOD (Prevalence, Incidence, Analysis MODel), which allows the estimation and projection of cancer prevalence patterns by using cancer registry incidence and survival data is presented. As a first step the method involves the fit of incidence data by an age, period and cohort model to derive incidence projections. Prevalence is then estimated from modelled incidence and survival estimates. Cancer mortality is derived as a third step from modelled incidence, prevalence and survival. An application to female breast cancer is given for the Connecticut State by using data from the Connecticut Tumor Registry (CTR), 1973–1993. The age, period and cohort model fitted incidence quite well and allowed us to derive long‐term projections up to 2030. Patients' survival was also projected to future years according to a scenario approach based on two extreme hypotheses: steady, that is, no more improvements after 1993 (conservative), and continuously improving at the same rate as during the observation period. Age‐standardized estimated incidence shows a changing trend around the year 2005, when it starts decreasing. Age‐standardized prevalence is expected to increase and change trend at a later date. Breast cancer mortality is projected as decreasing, as the combined result of no further increase in incidence and improving cancer patients' survival. An easy‐to‐use PIAMOD software package, on which work is in progress, will be made available to individual cancer registries and/or health planning institutions or authorities once it is developed. The use of the PIAMOD method for cancer registries will allow them to provide results of paramount importance for the whole community involved in the assessment of future disease burden scenarios in an evolving society. Copyright © 2002 John Wiley & Sons, Ltd.
Detecting dose–response using contrasts: asymptotic power and sample size determination for binomial data
Authors: Bretz Frank , Hothorn Ludwig A. 
Published: October 2002

AbstractRecently, Stewart and Ruberg proposed the use of contrast tests for detecting dose–response relationships. They considered in particular bivariate contrasts for healing rates and gave several possibilities of defining adequate sets of coefficients. This paper extends their work in several directions. First, asymptotic power expressions for both single and multiple contrast tests are derived. Secondly, well known trend tests are rewritten as multiple contrast tests, thus alleviating the inherent problem of choosing adequate contrast coefficients. Thirdly, recent results on the efficient calculation of multivariate normal probabilities overcome the traditional simulation‐based methods for the numerical computations. Modifications of the power formulae allow the calculation of sample sizes for given type I and II errors, the spontaneous rate, and the dose–response shape. Some numerical results of a power study for small to moderate sample sizes show that the nominal power is a reasonably good approximation to the actual power. An example from a clinical trial illustrates the practical use of the results. Copyright © 2002 John Wiley & Sons, Ltd.
OUT OF AFRICA
Authors: FEINBERG HARVEY M. , SOLODOW JOSEPH B. 
Published: October 2002

This article traces the origins of the familiar quotation, ‘there is always something new coming out of Africa’. It demonstrates that the phrase was a proverb that originated in Greece no later than the fourth century BC. It charts the transmission of the phrase from Aristotle to the twentieth century, noting that Erasmus is the most important link in the Renaissance and that he may be responsible for the current form in which the phrase is used.The article also shows that the meaning of the phrase was very different in ancient times from what it is today. Whereas ‘something new’ to Aristotle meant strange hybrid animals, current writers use the phrase with a sense of admiration.
PCR detection of Tetramicra brevifilum (Microspora) infection in turbot (Scophthalmus maximus L.) musculature
Authors: LEIRO J. , IGLESIAS R. , PARAMÁ A. , ARAGORT W. , SANMARTÍN M. L. 
Published: October 2002

This study investigated the spatial distribution of Tetramicra brevifilum spores in the musculature of infected turbot Scophthalmus maximus, with the aim of identifying the most appropriate body locations for diagnostic assays. A PCR protocol optimized for the detection of T. brevifilum spores in turbot muscle is also described. In fish showing low- and moderate-intensity infection, the spatial distribution of spores was best fitted by a negative binomial distribution, indicating a clumped spatial pattern; the negative binomial coefficient k was lower for fish with low-intensity infection, indicating a more markedly clumped pattern in these fish. In fish with high-intensity infection, the spatial distribution of spores was best fitted by the Poisson distribution, indicating a random pattern. In both low- and moderate-intensity infection, spores were present at highest density in the musculature adjoining the dorsal fins. Samples for PCR were therefore obtained from this location. PCR amplification was of the small subunit ribosomal DNA (SSUrDNA), using a pair of species-specific primers that amplify the 1250 bp product. The PCR protocol developed showed better sensitivity than microscopical techniques (detection rate by microscopy 25%, versus 42% by PCR), suggesting that it may be useful for routine screening for Tetramicra brevifilum infection in cultured turbot.
Characterization and cytochemical localization of an ATP diphosphohydrolase from Leishmania amazonensis promastigotes
Authors: COIMBRA E. S. , GONÇALVES-DA-COSTA S. C. , CORTE-REAL S. , DE FREITAS F. G. R. , DURÃO A. C. , SOUZA C. S. F. , SILVA-SANTOS M. I. , VASCONCELOS E. G. 
Published: October 2002

An ATP diphosphohydrolase was identified in the plasma membranes isolated from promastigote forms of Leishmania amazonensis. Both ATP and ADP were hydrolysed at similar rates by the enzyme. Other nucleotides such as UTP, GTP and CTP were also degraded, revealing a broad substrate specificity. Adding ATP and ADP simultaneously, the amount of hydrolysis achieved was compatible with the presence of a single enzyme. ATPase activity was not affected by addition of vanadate, ouabain, thapsigargin, dicyclohexylcarbodiimide, oligomycin and bafilomycin A, thus excluding involvement of P-, F- and V-type ATPases. The effects of pH in the range 6·5–8·5 were examined using ATP or p-NPP as substrate. At pH 7·4, the phosphatase activity decreased, and did not show a significant contribution to ATP hydrolysis. In addition, the enzyme was not inhibited by levamisole and ammonium molybdate, excluding alkaline phosphatase and nucleotidase activities, respectively. Sodium azide (5–10 mM) caused inhibition of the ATP and ADP hydrolysis in a dose-dependent manner. Calcium was the best activating metal ion for both ATPase and ADPase activities. Ultrastructural cytochemical microscopy showed ATP diphosphohydrolase on the surface and flagellar pocket of the parasite. We have proposed that L. amazonensis ATP diphosphohydrolase may participate in the salvage pathway of nucleosides.