bluuebunny/crossref_metadata_2025_split huggingface dataset:
ToF‐SIMS for the characterization of hyperbranched aliphatic polyesters: probing their molecular weight on surfaces based on principal component analysis (PCA)
Authors: Coullerez Géraldine , Lundmark Stefan , Malmström Eva , Hult Anders , Mathieu Hans Jörg 
Published: August 2003

AbstractA series of 2,2‐bis(hydroxymethyl)propionic acid (Bis‐MPA) hyperbranched aliphatic polyesters with different molecular weights (generations) is analysed for the first time by time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS). The main negative and positive low‐mass fragments are identified in the fingerprint part of the spectra (m/z < 400) and are principally assigned to fragmentation of the Bis‐MPA repeating units. In addition, it is shown that the fragmentation pattern is highly affected by the functional end‐groups. This is illustrated for a phthalic acid end‐capped hyperbranched polymer and for an acetonide‐terminated dendrimer analog. Also, typical fragments assigned to the ethoxylated pentaerythritol core molecule are detected. These ions show decreasing intensities with increasing molecular weight. This intensity dependency on the generation is used to calibrate the molecular weight of hyperbranched polyesters on the surface. To obtain quantitative information, a principal component analysis (PCA) multivariate statistical method is applied to the ToF‐SIMS data. The influence of different normalization procedures prior to PCA calculation is tested, e.g. normalization to the total intensity, to the intensities of ions assigned to the Bis‐MPA repeating unit or to intensities of fragments due to the core molecule. It is shown that only one principal component (PC1) is needed to describe most of the variance between the samples. In addition, PC1 takes into account the generation effect. However, different relationships between the PC1 scores and the hyperbranched mass average molecular weights are observed depending on the normalization procedure used. Normalization of data set ion intensities by ion intensities from the core molecule allows linearization of the SIMS intensities versus the molecular weight and allows the hyperbranched polymers to be discriminated up to the highest generations. In addition, PCA applied to ToF‐SIMS data provides an extended interpretation of the spectra leading to further identification of the correlated mass peaks, such as those of the Bis‐MPA repeating unit (terminal, dendritic and linear) and those of the core molecule. Finally, the work presented demonstrates the extreme potential of the static ToF‐SIMS and PCA techniques in the analysis of dendritic molecules on solid surfaces. Copyright © 2003 John Wiley & Sons, Ltd.
Relation between adsorption of some anionic surfactants on barite and solution/air interfaces
Authors: Omar A. M. A. , Azzam E. M. S. 
Published: August 2003

AbstractThe adsorption behaviour of synthesized anionic surfactants with chemical structure RO–Ph–NN–Ph–X, where R is octyl, dodecyl or cetyl and X is SO3Na, was analysed. Analysis of the behaviour of the surfactants was made using a modified version of the Frumkin adsorption isotherm. The values of thermodynamic parameters were calculated at the solution/air interface. The relation between adsorption of the surfactants at the solution/air interface and solid/liquid interface was investigated. The surface properties of these synthetic surfactants were studied. The results show that the length of the hydrocarbon chain of these surfactants plays a major role in determining the surface and thermodynamic properties. The results also indicate that there is a good relationship between effectiveness of adsorption of the surfactant and its efficiency as a collector. Copyright © 2003 John Wiley & Sons, Ltd.
A comparison of several regression models for analysing cost of CABG surgery
Authors: Austin Peter C. , Ghali William A. , Tu Jack V. 
Published: August 2003

AbstractInvestigators in clinical research are often interested in determining the association between patient characteristics and cost of medical or surgical treatment. However, there is no uniformly agreed upon regression model with which to analyse cost data. The objective of the current study was to compare the performance of linear regression, linear regression with log‐transformed cost, generalized linear models with Poisson, negative binomial and gamma distributions, median regression, and proportional hazards models for analysing costs in a cohort of patients undergoing CABG surgery. The study was performed on data comprising 1959 patients who underwent CABG surgery in Calgary, Alberta, between June 1994 and March 1998. Ten of 21 patient characteristics were significantly associated with cost of surgery in all seven models. Eight variables were not significantly associated with cost of surgery in all seven models. Using mean squared prediction error as a loss function, proportional hazards regression and the three generalized linear models were best able to predict cost in independent validation data. Using mean absolute error, linear regression with log‐transformed cost, proportional hazards regression, and median regression to predict median cost, were best able to predict cost in independent validation data. Since the models demonstrated good consistency in identifying factors associated with increased cost of CABG surgery, any of the seven models can be used for identifying factors associated with increased cost of surgery. However, the magnitude of, and the interpretation of, the coefficients vary across models. Researchers are encouraged to consider a variety of candidate models, including those better known in the econometrics literature, rather than begin data analysis with one regression model selected a priori. The final choice of regression model should be made after a careful assessment of how best to assess predictive ability and should be tailored to the particular data in question. Copyright © 2003 John Wiley & Sons, Ltd.
Confidence intervals for the mean of a variable taking the values 0,1 and 2
Authors: Newcombe Robert G. 
Published: August 2003

AbstractThe problem of setting a confidence interval for the mean of a variable on {0, 1,2} arises in three contexts: paired organ procedure rates; estimation of gene frequency, and three‐point Likert scales. An effective approach to its estimation may be based on a good interval for a paired difference of proportions. Four good methods due to Newcombe and Tango are shown to have much better performance than more naive methods over regions of the parameter space corresponding to the above applications. Copyright © 2003 John Wiley & Sons, Ltd.
Prediction of cancer incidence in the Nordic countries: empirical comparison of different approaches
Authors: Møller Bjørn , Fekjær Harald , Hakulinen Timo , Sigvaldason Helgi , Storm Hans H. , Talbäck Mats , Haldorsen Tor 
Published: August 2003

AbstractPrediction of the future number of cancer cases is of great interest to society. The classical approach is to use the age‐period‐cohort model for making cancer incidence predictions. We made an empirical comparison of different versions of this model, using data from cancer registries in the Nordic countries for the period 1958–1997. We have applied 15 different methods to 20 sites for each sex in Denmark, Finland, Norway and Sweden. Median absolute value of the relative difference between observed and predicted numbers of cases for these 160 combinations of site, sex and country was calculated. The medians varied between 10.4 per cent and 15.3 per cent in predictions 10 years ahead, and between 15.1 per cent and 32.0 per cent for 20 year predictions. We have four main conclusions: (i) projecting current trends worked better than assuming that future rates are equal to present rates; (ii) the method based on the multiplicative APC model often overestimated the number of cancer cases due to its exponential growth over time, but using a power function to level off this growth improved the predictions; (iii) projecting only half of the trend after the first 10 years also gave better long‐term predictions; (iv) methods that emphasize trends in the last decade seem to perform better than those that include earlier time trends. Copyright © 2003 John Wiley & Sons, Ltd.
Improved tests for a random effects meta‐regression with a single covariate
Authors: Knapp Guido , Hartung Joachim 
Published: August 2003

AbstractThe explanation of heterogeneity plays an important role in meta‐analysis. The random effects meta‐regression model allows the inclusion of trial‐specific covariates which may explain a part of the heterogeneity. We examine the commonly used tests on the parameters in the random effects meta‐regression with one covariate and propose some new test statistics based on an improved estimator of the variance of the parameter estimates. The approximation of the distribution of the newly proposed tests is based on some theoretical considerations. Moreover, the newly proposed tests can easily be extended to the case of more than one covariate. In a simulation study, we compare the tests with regard to their actual significance level and we consider the log relative risk as the parameter of interest. Our simulation study reflects the meta‐analysis of the efficacy of a vaccine for the prevention of tuberculosis originally discussed in Berkey et al. The simulation study shows that the newly proposed tests are superior to the commonly used test in holding the nominal significance level. Copyright © 2003 John Wiley & Sons, Ltd.
Baseline adjustments for binary data in repeated cross‐sectional cluster randomized trials
Authors: Nixon R. M. , Thompson S. G. 
Published: August 2003

AbstractAnalysis of covariance models, which adjust for a baseline covariate, are often used to compare treatment groups in a controlled trial in which individuals are randomized. Such analysis adjusts for any baseline imbalance and usually increases the precision of the treatment effect estimate. We assess the value of such adjustments in the context of a cluster randomized trial with repeated cross‐sectional design and a binary outcome. In such a design, a new sample of individuals is taken from the clusters at each measurement occasion, so that baseline adjustment has to be at the cluster level. Logistic regression models are used to analyse the data, with cluster level random effects to allow for different outcome probabilities in each cluster. We compare the estimated treatment effect and its precision in models that incorporate a covariate measuring the cluster level probabilities at baseline and those that do not. In two data sets, taken from a cluster randomized trial in the treatment of menorrhagia, the value of baseline adjustment is only evident when the number of subjects per cluster is large. We assess the generalizability of these findings by undertaking a simulation study, and find that increased precision of the treatment effect requires both large cluster sizes and substantial heterogeneity between clusters at baseline, but baseline imbalance arising by chance in a randomized study can always be effectively adjusted for. Copyright © 2003 John Wiley & Sons, Ltd.
A relative survival regression model using B‐spline functions to model non‐proportional hazards
Authors: Giorgi Roch , Abrahamowicz Michal , Quantin Catherine , Bolard Philippe , Esteve Jacques , Gouvernet Joanny , Faivre Jean 
Published: August 2003

AbstractRelative survival, a method for assessing prognostic factors for disease‐specific mortality in unselected populations, is frequently used in population‐based studies. However, most relative survival models assume that the effects of covariates on disease‐specific mortality conform with the proportional hazards hypothesis, which may not hold in some long‐term studies. To accommodate variation over time of a predictor's effect on disease‐specific mortality, we developed a new relative survival regression model using B‐splines to model the hazard ratio as a flexible function of time, without having to specify a particular functional form. Our method also allows for testing the hypotheses of hazards proportionality and no association on disease‐specific hazard. Accuracy of estimation and inference were evaluated in simulations. The method is illustrated by an analysis of a population‐based study of colon cancer. Copyright © 2003 John Wiley & Sons, Ltd.
Non‐parametric methods to predict HIV drug susceptibility phenotype from genotype
Authors: Gregory DiRienzo A. , DeGruttola Victor , Larder Brendan , Hertogs Kurt 
Published: August 2003

AbstractMedical management of HIV infection requires an understanding of the relationship between viral genetic sequences and viral susceptibility to antiretroviral drugs. Because of the high dimensionality of the data on viral genotype, traditional statistical methods are not well suited for investigating this relationship. We develop non‐parametric methods specifically for the setting where high‐dimensional data provides a basis for predicting a low‐dimensional response variable. Our non‐recursive methods proceed in three stages: (i) build models, in a forward‐stepwise manner, that predict phenotype response from genotype sequence; (ii) identify specific patterns of amino acid sequence that are most influential in predicting phenotype, and (iii) identify combinations of codons that have either a concordant or a discordant association in the occurrence of a mutation. The methods are applied to a data set provided by the Virco Group that contains protease genome sequences and IC50 measurements on a drug from the protease inhibitor class, amprenavir, for 2747 patient samples. From these methods, we were able to identify eight codons from the protease region of the HIV genome that predict resistance to amprenavir, and to determine pairs of codons that tend either to occur together or to preclude the occurrence of the other member of the pair. Copyright © 2003 John Wiley & Sons, Ltd.
A global sensitivity analysis of performance of a medical diagnostic test when verification bias is present
Authors: Kosinski Andrzej S. , Barnhart Huiman X. 
Published: August 2003

AbstractCurrent advances in technology provide less invasive or less expensive diagnostic tests for identifying disease status. When a diagnostic test is evaluated against an invasive or expensive gold standard test, one often finds that not all patients undergo the gold standard test. The sensitivity and specificity estimates based only on the patients with verified disease are often biased. This bias is called verification bias. Many authors have examined the consequences of verification bias and have proposed bias correction methods based on the assumption of independence between disease status and election for verification conditionally on the test result, or equivalently on the assumption that the disease status is missing at random using missing data terminology. This assumption may not be valid and one may need to consider adjustment for a possible non‐ignorable verification bias resulting from the non‐ignorable missing data mechanism. Such an adjustment involves ultimately uncheckable assumptions and requires sensitivity analysis. The sensitivity analysis is most often accomplished by perturbing parameters in the chosen model for the missing data mechanism, and it has a local flavour because perturbations are around the fitted model. In this paper we propose a global sensitivity analysis for assessing performance of a diagnostic test in the presence of verification bias. We derive a region of all sensitivity and specificity values consistent with the observed data and call this region a test ignorance region (TIR). The term ‘ignorance’ refers to the lack of knowledge due to the missing disease status for the not verified patients. The methodology is illustrated with two clinical examples. Copyright © 2003 John Wiley & Sons, Ltd.
Estimate of standard deviation for a log‐transformed variable using arithmetic means and standard deviations
Authors: Quan Hui , Zhang Ji 
Published: August 2003

AbstractAnalyses of study variables are frequently based on log transformations. To calculate the power for detecting the between‐treatment difference in the log scale, we need an estimate of the standard deviation of the log‐transformed variable. However, in many situations a literature search only provides the arithmetic means and the corresponding standard deviations. Without individual log‐transformed data to directly calculate the sample standard deviation, we need alternative methods to estimate it. This paper presents methods for estimating and constructing confidence intervals for the standard deviation of a log‐transformed variable given the mean and standard deviation of the untransformed variable. It also presents methods for estimating the standard deviation of change from baseline in the log scale given the means and standard deviations of the untransformed baseline value, on‐treatment value and change from baseline. Simulations and examples are provided to assess the performance of these estimates. Copyright 2003 John Wiley & Sons, Ltd.
Experimental evaluation and improvements to linear scan register allocation
Authors: Sagonas Konstantinos , Stenman Erik 
Published: August 2003

AbstractWe report our experience from implementing and experimentally evaluating the performance of various register allocation schemes, focusing on the recently proposed linear scan register allocator. In particular, we describe in detail our implementation of linear scan and report on its behavior both on register‐rich and on register‐poor computer architectures. We also extensively investigate how different options to the basic algorithm and to the compilation process as a whole affect compilation times and quality of the produced code.In a nutshell, our experience is that a well‐tuned linear scan register allocator is a good choice on register‐rich architectures. It performs competitively with graph coloring based allocation schemes and results in significantly lower compilation times. When compilation time is a concern, such as in just‐in‐time compilers, it can also be a viable option on register‐poor architectures. Copyright © 2003 John Wiley & Sons, Ltd.
Efficient implementation of lazy suffix trees
Authors: Giegerich R. , Kurtz S. , Stoye J. 
Published: August 2003

AbstractWe present an efficient implementation of a write‐only top‐down construction for suffix trees. Our implementation is based on a new, space‐efficient representation of suffix trees that requires only 12 bytes per input character in the worst case, and 8.5 bytes per input character on average for a collection of files of different type. We show how to efficiently implement the lazy evaluation of suffix trees such that a subtree is evaluated only when it is traversed for the first time. Our experiments show that for the problem of searching many exact patterns in a fixed input string, the lazy top‐down construction is often faster and more space efficient than other methods. Copyright © 2003 John Wiley & Sons, Ltd.
Adapting traditional software processes to virtual environments development
Authors: Sánchez‐Segura María I. , Cuadrado Juan J. , de Antonio Angelica , de Amescua Antonio , García Luis 
Published: August 2003

AbstractVirtual environments (VEs) are special kinds of interactive systems currently used in many fields such as education, training and medicine. However, as VE development is relatively recent, there is little experience in the area. Software engineering, the discipline which assures quality software, has not been successfully applied to date. In developing VEs, the object‐oriented software engineering paradigm is the most suitable even though principles and techniques are insufficient. In this paper, we will demonstrate this inadequacy through the development of two different VEs, identify the processes to be improved, offer a set of guidelines to improve them (coined SENDA), and present the results obtained with SENDA. Copyright © 2003 John Wiley & Sons, Ltd.
The directed Chinese Postman Problem
Authors: Thimbleby Harold 
Published: August 2003

AbstractThe Chinese Postman Problem has many applications, including robot exploration, and analysing interactive system and Web site usability. This paper reviews the wide range of applications of the problem and presents complete, executable code to solve it for the case of directed multigraphs. A variation called the ‘open Chinese Postman Problem’ is also introduced and solved. Although optimizations are possible, no substantially better algorithms are likely. Copyright © 2003 John Wiley & Sons, Ltd.
TNM: Evolution and relation to other prognostic factors
Authors: Sobin Leslie H. 
Published: August 2003

AbstractThe TNM Classification describes the anatomic extent of cancer. TNM's ability to separately classify the individual tumor (T), node (N), and metastasis (M) elements and then group them into stages differs from other cancer staging classifications (e.g., Dukes), which are only concerned with summarized groups. The objectives of the TNM Classification are to aid the clinician in the planning of treatment, give some indication of prognosis, assist in the evaluation of the results of treatment, and facilitate the exchange of information. During the past 50 years, the TNM system has evolved under the influence of advances in diagnosis and treatment. Radiographic imaging (e.g., endoscopic ultrasound for the depth of invasion of esophageal and rectal tumors) has improved the accuracy of the clinical T, N, and M classifications. Advances in treatment have necessitated more detail in some T4 categories. Developments in multimodality therapy have increased the importance of the “y” symbol and the R (residual tumor) classification. New surgical techniques have resulted in the elaboration of the sentinel node (sn) symbol. The use of immunohistochemistry has resulted in the classification of isolated tumor cells and their distinction from micrometastasis. The most important challenge facing users of the TNM Classification is how it should interface with the large number of non‐anatomic prognostic factors that are currently in use or under study. As non‐anatomic prognostic factors become widely used, the TNM system provides an inviting foundation upon which to build a prognostic classification; however, this carries a risk that the system will be overwhelmed by a variety of prognostic data. An anatomic extent‐of‐disease classification is needed to aid practitioners in selecting the initial therapeutic approach, stratifying patients for therapeutic studies, evaluating non‐anatomic prognostic factors at specific anatomic stages, comparing the weight of non‐anatomic factors with extent of disease, and communicating the extent of disease data in a uniform manner. Methods are needed to express the overall prognosis without losing the vital anatomic content of TNM. These methods should be able to integrate multiple prognostic factors, including TNM, while permitting the TNM system to remain intact and distinct. This article discusses examples of such approaches. Semin. Surg. Oncol. 21:3–7, 2003. Published 2003 Wiley‐Liss, Inc.