bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using observational data to estimate prognosis: an example using a coronary artery disease registry
Authors: DeLong Elizabeth R. , Nelson Charlotte L. , Wong John B. , Pryor David B. , Peterson Eric D. , Lee Kerry L. , Mark Daniel B. , Califf Robert M. , Pauker Stephen G. 
Published: January 2005

AbstractWith the proliferation of clinical data registries and the rising expense of clinical trials, observational data sources are increasingly providing evidence for clinical decision making. These data are viewed as complementary to randomized clinical trials (RCT). While not as rigorous a methodological design, observational studies yield important information about effectiveness of treatment, as compared with the efficacy results of RCTs. In addition, these studies often have the advantage of providing longer‐term follow‐up, beyond that of clinical trials. Hence, they are useful for assessing and comparing patients' long‐term prognosis under different treatment strategies. For patients with coronary artery disease, many observational comparisons have focused on medical therapy versus interventional procedures. In addition to the well‐studied problem of treatment selection bias (which is not the focus of the present study), three significant methodological problems must be addressed in the analysis of these data: (i) designation of the therapeutic arms in the presence of early deaths, withdrawals, and treatment cross‐overs; (ii) identification of an equitable starting point for attributing survival time; (iii) site to site variability in short‐term mortality. This paper discusses these issues and suggests strategies to deal with them. A proposed methodology is developed, applied and evaluated on a large observational database that has long‐term follow‐up on nearly 10 000 patients. Copyright © 2001 John Wiley & Sons, Ltd.
Planning a reproducibility study: how many subjects and how many replicates per subject for an expected width of the 95 per cent confidence interval of the intraclass correlation coefficient
Authors: Giraudeau B. , Mary J. Y. 
Published: January 2005

AbstractReproducibility of a quantitative outcome is usually assessed by means of the intraclass correlation coefficient (ICC). When we are interested in assessing reproducibility from only one sample, we suggest that the study be planned with regards to the expected width of the 95 per cent confidence interval of the ICC. An approximation of this latter width is derived, which allows appraisal of the influence of n the number of subjects and p the number of replicates. Through simulation studies, the approximation is shown to be of good accuracy and can therefore be used reliably. Optimal designs are also discussed such as the optimal distribution between the number of subjects and the number of replicates per subject for a fixed total number of measures. Copyright © 2001 John Wiley & Sons, Ltd.
Variable selection and Bayesian model averaging in case‐control studies
Authors: Viallefont Valerie , Raftery Adrian E. , Richardson Sylvia 
Published: January 2005

AbstractCovariate and confounder selection in case‐control studies is often carried out using a statistical variable selection method, such as a two‐step method or a stepwise method in logistic regression. Inference is then carried out conditionally on the selected model, but this ignores the model uncertainty implicit in the variable selection process, and so may underestimate uncertainty about relative risks. We report on a simulation study designed to be similar to actual case‐control studies. This shows that p‐values computed after variable selection can greatly overstate the strength of conclusions. For example, for our simulated case‐control studies with 1000 subjects, of variables declared to be ‘significant’ with p‐values between 0.01 and 0.05, only 49 per cent actually were risk factors when stepwise variable selection was used. We propose Bayesian model averaging as a formal way of taking account of model uncertainty in case‐control studies. This yields an easily interpreted summary, the posterior probability that a variable is a risk factor, and our simulation study indicates this to be reasonably well calibrated in the situations simulated. The methods are applied and compared in the context of a case‐control study of cervical cancer. Copyright © 2001 John Wiley & Sons, Ltd.
A method to assess the proportion of treatment effect explained by a surrogate endpoint
Authors: Li Zhengqing , Meredith Michael P. , Hoseyni Mohammad S. 
Published: January 2005

AbstractRandomized clinical trials are the standard for evaluating new drugs, devices and procedures. Traditional clinical trials entail not only considerable expense, but require considerable time to complete. The use of surrogate endpoints constitutes an effort to control cost and completion time for clinical trials. We propose a method to quantify the proportion of treatment effect explained by a surrogate endpoint based on a general model setting which includes the commonly used linear, logistic and Cox regression models. The interpretation of this quantitative measure is facilitated by graphical displays. To reduce the variability associated with the estimate, a meta‐analytic approach is proposed based on random effects models. An example using real clinical trial data is given to illustrate the proposed procedures. Copyright © 2001 John Wiley & Sons, Ltd.
Determinants of transnational new product development capability: testing the influence of transferring and deploying tacit overseas knowledge
Authors: Subramaniam Mohan , Venkatraman N. 
Published: January 2005

AbstractBased on a survey of 90 transnational product introductions, we find that the transnational product development capabilities of organizations significantly depend upon their ability to transfer and deploy tacit knowledge concerning overseas markets. Specifically, we find that organizations which use cross‐national teams, teams with members who have prior overseas experience, or teams whose members communicate frequently with overseas managers in order to acquire information about tacit differences among countries have greater transnational product development capabilities. This study contributes to our understanding of how organizations transfer and deploy knowledge across borders for competitive advantage and makes an important contribution to the literature on global strategy. Copyright © 2001 John Wiley & Sons, Ltd.
An approach to the measurement of software evolution
Authors: Nikora Allen P. , Munson John C. 
Published: January 2005

AbstractOur current work involves developing methods of measuring changes to evolving software systems. We study a system's change characteristics over a large number of builds using the distinct sources of variation in the software metrics used to measure the system.We have been collaborating with a flight software technology development effort at the Jet Propulsion Laboratory (JPL) and have progressed in resolving the limitations of our earlier work in two distinct steps. First, we have developed a repeatable and consistent fault enumeration methodology, allowing them to be precisely and accurately measured. Second, we have developed a practical framework for automating fault measurement, which we applied to the JPL software system during its development. Every change to the system was measured and every identified fault was tracked to a specific code module.Our analysis indicates that measures of the evolving system's structure are strongly related to the number of faults inserted during its development, and that some types of change are more likely to result in the insertion of faults than others. The fault enumeration methodology ensures that the resulting fault model has greater predictive validity; it also provides a higher quality model than other popular definitions of a fault. Copyright © 2005 John Wiley & Sons, Ltd.
Automating regression testing for evolving GUI software
Authors: Memon Atif , Nagarajan Adithya , Xie Qing 
Published: January 2005

AbstractWith the widespread deployment of broadband connections worldwide, software development and maintenance are increasingly being performed by multiple engineers, often working around‐the‐clock to maximize code churn rates. To ensure rapid quality assurance of such software, techniques such as ‘nightly/daily building and smoke testing’ have become widespread since they often reveal bugs early in the software development process. During these builds, a development version of the software is checked out from the source code repository tree, compiled, linked, and (re)tested with the goal of (re)validating its basic functionality. Although successful for conventional software, smoke tests are difficult to develop and automatically re‐run for software that has a graphical user interface (GUI). In this paper, we describe a framework called DART (Daily Automated Regression Tester) that addresses the needs of frequent and automated re‐testing of GUI software. The key to our success is automation: DART automates everything from structural GUI analysis, smoke‐test‐case generation, test‐oracle creation, to code instrumentation, test execution, coverage evaluation, regeneration of test cases, and their re‐execution. Together with the operating system's task scheduler, DART can execute frequently with little input from the developer/tester to re‐test the GUI software. We provide results of experiments showing the time taken and memory required for GUI analysis, test case and test oracle generation, and test execution. We empirically compare the relative costs of employing different levels of detail in the GUI test oracle. We also show the events and statements covered by the smoke test cases. Copyright © 2005 John Wiley & Sons, Ltd.
An analysis of some ‘core studies’ of software process improvement
Authors: Rainer Austen , Hall Tracy 
Published: January 2005

AbstractIn this paper we analyse 39 publications that have reported issues relating to software process improvement. Together, the 39 publications refer to 14 sites in 11 organizations. The 11 organizations include all five of the organizations that have been awarded the IEEE Computer Society Award for Process Achievement. Twelve of the 14 sites have been assessed at CMM level 3 or higher. Two main issues, and a number of more specific issues, emerge from our analysis. The two main issues are organizational stability and process expertise. We further distinguish between inter‐ and intra‐organizational stability. Several other specific issues are identified and discussed. We direct attention at how the specific issues relate to each other, how the two main issues relate to each other, and how all these issues relate to software process improvement. We speculate that organizational stability provides a stable environment within which to perform the process and to develop expertise. In addition to the 39 publications, the paper provides cross‐references to survey studies and other case studies on process improvement, and studies into process understanding. Copyright © 2001 John Wiley & Sons, Ltd.
Managing instructional software acquisition
Authors: Demirors Onur , Demirors Elif , Tarhan Ayca 
Published: January 2005

AbstractManaging acquisition and development efforts of contracted software is hard work for many organisations which require high‐quality products to be produced. Mature supplier processes best work with mature acquisition processes which are able to appropriately plan, track and evaluate the work of the supplier. However, acquirer organisations might not always be that mature, so selecting and managing the best‐fit suppliers becomes rather difficult. This paper introduces a study performed to overcome this difficulty for the Ministry of National Education (MONE) of Turkey. The first phase of the study includes defining the evaluation criteria for pre‐qualification of software development companies, and the second phase includes defining the basic instructional software development process as well as the standards for the deliverables of the process. The paper also identifies the effort required by the Ministry for evaluating and managing the pre‐qualification and development work in practice. Copyright © 2001 John Wiley & Sons, Ltd.
Serotonin modulation of cerebral blood flow measured with positron emission tomography (PET) in humans
Authors: Geday Jacob , Hermansen Flemming , Rosenberg Raben , Smith Donald F. 
Published: January 2005

AbstractTo develop a method to measure the dynamic response of the serotonin system in vivo, the effects of intravenously administered citalopram (the most selective of the serotonin reuptake inhibitors) or clomipramine on cerebral blood flow (CBF) were evaluated. CBF was measured with positron emission tomography (PET) in 27 normal subjects scanned under baseline conditions and, on the same day, after an intravenous (IV) infusion of placebo, citalopram, or clomipramine using a randomized, double‐blind design. The main effects of the drugs on blood flow occurred in the thalamus, hypothalamus, and cingulate cortex. Compared to placebo, clomipramine reduced blood flow in the mediodorsal and ventral lateral nuclei of the thalamus, whereas citalopram reduced blood flow in the pulvinar nucleus and the hypothalamus. Compared to clomipramine, citalopram decreased blood flow in the cingulate cortex. The findings support previous reports showing acute central effects of citalopram and clomipramine on regional serotonergic functions measured by PET. Acute side effects may, however, require that care is taken in the selection of experimental designs for future PET studies using IV administration of these antidepressants. Synapse 55:224–229, 2005. © 2005 Wiley‐Liss, Inc.
Optimization of experimental conditions of thin‐window EPMA for light‐element analysis of individual environmental particles
Authors: Szalóki I. , Osán J. , Worobiec A. , de Hoog J. , Van Grieken R. 
Published: January 2005

AbstractDifferent metallic substrates such as beryllium, aluminium, silicon and silver were rigorously tested in all aspects of energy‐dispersive electron probe x‐ray microanalysis of single particles, including the semi‐quantitative determination of low‐Z elements. The effect of the collecting substrate on the capability to locate, to analyse and to classify particles automatically was extensively studied by the analysis of particulate standards and aerosol particles collected at the Belgian coast. Beam‐sensitive particles such as ammonium sulphate and ammonium nitrate were analysed using a liquid nitrogen‐cooled sample stage. The dependence of the beam‐damage effect on the type of collecting substrate was also studied using standard aerosol particles. The results obtained show that the use of beryllium as a collecting surface offers some advantages: (i) detailed spectral information can be obtained in a broad elemental range (6 ≤ Z ≤ 92) without overlap with x‐ray lines of the substrate and (ii) complete chemical classification can be done with one set of analyses. Copyright © 2001 John Wiley & Sons, Ltd.
Rapid method for EDXRF analysis of clayey and sandy soil
Authors: Laursen Jens , Vestergaard Brian Tang , Pind Niels , Karlsen Kresten , Bruun Hansen Hans Christian 
Published: January 2005

AbstractThe success of quantitative full soil EDXRF analysis is strongly related to the ability establish a homogeneous and representative sample. When practicing thin‐film deposition techniques the soil particle size will furthermore have an influence on the quantification capability, especially when analyzing the light elements. Finally, the deposition of material on a substrate is coupled with the sedimentation mechanism, which again is influenced by the material grain size and uniformity. In the present investigation, an effective and simple micro‐milling technique for soil and sediment materials was tested. By light scattering it is demonstrated that a grain size of about 600 nm within a milling period of 15 min is obtained. The deposition of the crushed material on a polypropylene thin‐film support is carried out by adding a cationic detergent, thereby obtaining a homogeneous and geometrically well defined droplet. The detergent quality and strength together with its correlation with the soil cation‐exchange capacity are discussed. Clayey and sandy soil samples from different soil profiles containing a wide range of organic materials were investigated. Samples of 0.5–1 mg cm−2 were analyzed by use of a monochromatic Mo Kα irradiation technique. The utility of the data fitting and quantification software X‐Spec32 is discussed. A brief comment is made on the environmental aspects of soil analysis, especially in relation to metal and mineral transport and distribution through the different types of soil and soil profiles. Copyright © 2001 John Wiley & Sons, Ltd.
Human teeth elemental profiles measured by synchrotron x‐ray fluorescence: dietary habits and environmental influence
Authors: Carvalho M. L. , Casaca C. , Marques J. P. , Pinheiro T. , Cunha A. S. 
Published: January 2005

AbstractThis paper reports on the measurements of elemental profiles in teeth collected from two different populations, both living in isolated Portuguese islands of the Azores: S. Miguel and Terceira. Both populations are good producers of cattle, in spite of the proximity of the sea. The purpose of this work was to establish the influence of basic diet, based on meat, fish and dairy products, on teeth elemental content. Moreover, for a few elements, the differences between concentrations in corresponding regions of teeth was correlated with the proximity of the sea for the subjects of one of the islands. An x‐ray fluorescence set‐up with microprobe capabilities, installed at the LURE synchrotron (France), was used for elemental determination. The resolution of the synchrotron microprobe was 100 µm and the energy of the incident photons was 18 keV. Concentration profiles of Fe, Cu, Zn, Br, Sr and Pb in different parts of a tooth are discussed and correlated for both populations. The teeth collected for both populations show a similar behaviour with respect to the elemental distribution. Mn and Cu occur at low concentrations and they are almost constant in all the studied parts of teeth. The content of Sr is higher in the external enamel while the concentrations of Fe, Zn, Br and Pb increase in the inner part of the teeth. However, the contents of Br and Pb are different in the two populations. Higher levels of both elements were found in Terceira subjects. Moreover, the Sr concentration levels indicate that the diet of the studied individuals is richer in meat than in fish. Copyright © 2001 John Wiley & Sons, Ltd.
Overexpression of HUT1 gene stimulates in vivo galactosylation by enhancing UDP–galactose transport activity in Saccharomyces cerevisiae
Authors: Kainuma Mami , Chiba Yasunori , Takeuchi Makoto , Jigami Yoshifumi 
Published: January 2005

AbstractTransfer of activated sugar‐nucleotides from the cytoplasm to the lumen of the Golgi is an essential requirement for glycosylation of glycoproteins, proteoglycans and glycosphingolipids. Although mannosylation is the major modification in the yeast Saccharomyces cerevisiae, several reports suggest the presence of galactose residues on yeast proteins and sphingolipids. We have detected α‐galactosylated O‐linked chitinase by lectin blotting from cells that functionally express the gma12+ gene, encoding α1,2‐galactosyltransferase from Schizosaccharomyces pombe. This result implies the presence of a UDP–galactose transporter in S. cerevisiae. A conserved gene, HUT1, which encodes a putative multi‐transmembrane protein, was cloned and characterized for its possible involvement in galactosylation. The HUT1 gene is not essential and is expressed at a relatively low level under the physiological conditions we examined. The disruption of this gene did not show any apparent impairments in glycosylation. However, a temperature‐ and concentration‐dependent increase in UDP–galactose transport activity was detected from cells overexpressing HUT1 in the presence of gma12+. The surface of these cells was confirmed to carry galactose residues by staining with FITC‐conjugated α‐galactose‐specific lectin. These results suggest a role for Hut1p in the transport of UDP–galactose from the cytosol into the Golgi lumen in S. cerevisiae. Copyright © 2001 John Wiley & Sons, Ltd.
Co‐consumption of sugars or ethanol and glucose in a Saccharomyces cerevisiae strain deleted in the HXK2 gene
Authors: Raamsdonk Léonie M. , Diderich Jasper A. , Kuiper Arthur , van Gaalen Monique , Kruckberg Arthur L. , Berden Jan A. , Van Dam Karel 
Published: January 2005

AbstractAn Erratum has been published for this article in Yeast 19(2) 2002, 183.
In previous studies it was shown that deletion of the HXK2 gene in Saccharomyces cerevisiae yields a strain that hardly produces ethanol and grows almost exclusively oxidatively in the presence of abundant glucose. This paper reports on physiological studies on the hxk2 deletion strain on mixtures of glucose/sucrose, glucose/galactose, glucose/maltose and glucose/ethanol in aerobic batch cultures. The hxk2 deletion strain co‐consumed galactose and sucrose, together with glucose. In addition, co‐consumption of glucose and ethanol was observed during the early exponential growth phase. In S.cerevisiae, co‐consumption of ethanol and glucose (in the presence of abundant glucose) has never been reported before. The specific respiration rate of the hxk2 deletion strain growing on the glucose/ethanol mixture was 900 µmol·min−1·(g protein)−1, which is four to five times higher than that of the hxk2 deletion strain growing oxidatively on glucose, three times higher than its parent growing on ethanol (when respiration is fully derepressed) and is almost 10 times higher than its parent growing on glucose (when respiration is repressed). This indicates that the hxk2 deletion strain has a strongly enhanced oxidative capacity when grown on a mixture of glucose and ethanol. Copyright © 2001 John Wiley & Sons, Ltd.
Extensive chromosome translocation in a clinical isolate showing the distinctive carbohydrate assimilation profile from a candidiasis patient
Authors: Iwaguchi Shin‐Ichi , Sato Mihoko , Magee Beatrice B. , Magee Paul T. , Makimura Koichi , Suzuki Takahito 
Published: January 2005

AbstractVariation of the electrophoretic karyotype is common among clinical strains of Candida albicans and chromosome translocation is considered one of the causes of karyotypic variation. Such chromosome translocations may be a mechanism to confer phenotypic diversity on the imperfect fungus C. albicans. A clinical strain, TCH23, from a vaginal candidiasis patient shows distinct carbohydrate assimilation profile, serotype B, no chlamydospore formation and an atypical karyotype (Asakura et al., 1991). To examine the taxonomic relationship among C. albicans, Candida dubliniensis and this strain, we sequenced the internal transcribed spacer 1 (ITS1) of nuclear ribosomal DNA. The ITS1 sequence of TCH23 was identical with that of C. albicans but not of C. dubliniensis. Thus, strain TCH23 was classified as a variant of C. albicans with an atypical phenotype. The chromosomal DNAs of this strain were resolved into 13 bands on pulse‐field gel electrophoresis (PFGE). Using DNA probes located at or near both ends of each chromosome of C. albicans, we investigated the chromosome organization of this strain. Referring to the SfiI map of C. albicans 1006 (Chu et al., 1993), we found that seven chromosomal DNA bands in strain TCH23 were reciprocal chromosome translocations. One homologue from chromosomes 1, 2 and 6 and both homologues from chromosomes 4 and 7 participated in these events. One translocation product was composed of three SfiI fragments, one each from chromosomes 2, 4 and 7. We deduced the breakpoints of chromosome translocation from the physical map of this strain; between 1J and 1J1, between 2A and 2U, both ends of 4F2, between 6C and 6O and both ends of 7F. Copyright © 2001 John Wiley & Sons, Ltd.