bluuebunny/crossref_metadata_2025_split huggingface dataset:
Value of information analysis for a new technology: Computer-assisted total knee replacement
Authors: Dong Hengjin , Coyle Doug , Buxton Martin 
Published: June 2007

Objectives: The aim of this study was to demonstrate how value of information analysis can measure the upper limit on returns to future research and identify the research priorities for computer-assisted total knee replacement (CAS-TKR).Methods: Using a previous economic analysis of CAS-TKR compared with conventional TKR, the population expected value of perfect information (EVPI) was calculated using Monte Carlo simulation to provide an estimate of the upper limit on returns to future research. The population expected value of partial perfect information (EVPPI) for both individual parameters and groups of parameters was estimated to inform specific future research priorities.Results: The UK individual EVPI would be £21.4 if the willingness to pay for one QALY (quality-adjusted life-year) were £30,000. The population EVPPI would be £8.3 million, assuming a 10-year time horizon for CAS-TKR. In this instance, the expected value of information is positively related to willingness to pay for one QALY for the range of £0 to £50,000. Although each individual parameter had an EVPPI of £0, groups of utility parameters had positive EVPPI. Population EVPPI was £5.6 million for utility parameters, £20,000 for transition probabilities relating to CAS-TKR, and £5,000 for transition probabilities related to conventional TKR.Conclusions: The study provides evidence on which parameters further information may be of most value. Focusing research on the utility values associated with health states relating to TKR would be of greatest value.
Cost-effectiveness analysis of two management strategies for dyspepsia
Authors: Kjeldsen Hans C. , Bech Mickael , Christensen Bo 
Published: June 2007

Objectives:To compare the cost-effectiveness of endoscopy and empirical proton pump inhibition (PPI) therapy for management of dyspepsia in primary care.Methods:A randomized controlled trial, including prospective collection of economic resource data, was conducted in general practice from June 2000 to August 2002, Aarhus County, Denmark. We randomly assigned 368 dyspeptic patients from thirty-two general practices to treatment with omeprazol 40 mg for 2 weeks (n=184) or endoscopy (n=184). The study adopted a societal perspective, and the year of costing was 2006. Outcome measures: days free of dyspeptic symptoms and proportion of patients with dyspepsia after 1 year based on patients' and general practitioners' (GPs) assessment. Costs were estimated from patient and GP questionnaires and from medical records.Results:The incremental cost-effectiveness (CE) ratio for 1 day free of dyspeptic symptoms using the endoscopy strategy was €/day 154 compared with the PPI strategy. The incremental CE ratio for one person free of dyspeptic symptoms after 1 year using the endoscopy strategy was €13,905 based on the patients' evaluation, and the incremental CE ratio for one person free of predominant symptoms after 1 year was €5,990 according to the GPs' evaluation. The PPI strategy was both cheaper and more effective than the endoscopy strategy when reflux was the predominant symptom.Conclusions:A strategy using empirical antisecretory PPI therapy should be recommended if the alternative is an endoscopy strategy for managing dyspeptic patients in general practice, especially if reflux was the predominant symptom.
Health economic evaluations alongside clinical trials: A review of study protocols at the Swedish Medical Products Agency
Authors: Lindfors Anne , Feltelius Nils , Lundkvist Jonas 
Published: June 2007

Objectives: Conducting economic evaluation in the context of clinical studies is common but has been the subject of extensive discussion due to its limitations. Various standard approaches and guidelines how such studies should be conducted have been proposed, but there is very limited information available about how common these studies are, what type of data that is collected, and how the quality of the protocols compares to the suggested standards. This study examines the prevalence and study design of health economic evaluations conducted alongside clinical trials in Sweden between 1995 and 2005.Methods: A systematic assessment of clinical trial protocols that had arrived as applications to the Medical Products Agency between 1995 and 2005 was performed. Only protocols arriving during the first half of odd years within the time period were included.Results: A total number of 680 protocols from 1995 to 2005 were examined, and among them, 14.4 percent included a health economic part. With the exception of year 2001, a trend toward an increased prevalence of economic evaluations next to clinical trials can be seen.Conclusions: This study shows that economic evaluations alongside clinical trials are becoming more common, although most trials still lack a health economic part of the protocol. The information about the economic evaluation provided in the protocols is in many cases scarce, possibly due to the fact that there currently are no generally accepted and applied guidelines for economic evaluations in clinical trial protocols. Introducing requirements for detailed study plans also for the economic evaluation should improve the quality of economic evaluations alongside clinical trials.
Effective early warning systems for new and emerging health technologies: Developing an evaluation framework and an assessment of current systems
Authors: Murphy Kieran , Packer Claire , Stevens Andrew , Simpson Sue 
Published: June 2007

Objectives: The aim of this study was to define an effective early warning system, to identify and rank the characteristics of an effective early warning system for emerging health technologies, and to evaluate current early warning systems against these characteristics.Methods: An iterative Delphi-type process with the thirteen members of the International Information Network on New and Changing Health Technologies (EuroScan). We synthesized key characteristics that network members had graded. Members were then asked whether these characteristics were present or fulfilled in their system.Results: The definition of an effective early warning system developed was the following: a system that identifies innovations in the field of health technology likely to have a significant impact; and disseminates information relevant to the needs of the customer which is timely, so as to enable appropriate decision making (such as resource allocation), facilitate appropriate adoption, and identify further research requirements. Five primary and eleven secondary components of effective early warning systems were identified. The five primary characteristics concerned relevance, independence, resourcing, a clear pathway for the outputs to reach decision makers, and defined customers. Although the primary characteristics were present or fulfilled to some extent in the majority of evaluated early warning systems, there was considerable variability in the presence of the secondary characteristics in the evaluated systems.Conclusions: Our study provides a definition for an effective early warning system and a shared understanding of the important characteristics and components of such systems. This work should provide guidance to those setting up new early warning systems as well as for those managing and reviewing current systems.
Determinants of adolescents’ soft drink consumption
Authors: Bere Elling , Sørli Glomnes Elin , te Velde Saskia J , Klepp Knut-Inge 
Published: June 2007

AbstractObjectiveTo identify determinants of adolescents’ consumption of carbonated
soft drinks (regular and diet), both of total consumption and of consumption
at school.Design/Setting/SubjectsRegular and diet soft drink consumption was measured by food frequency
questions that were dichotomised. Several potential environmental and
personal determinants of consumption were measured. A total of 2870
(participation rate: 85%) 9th and 10th graders, within 33 Norwegian schools,
participated in the study. Multilevel logistic regression analyses were
preformed for total soft drink consumption (twice a week or more vs. less)
and for consumption at school (once a week or more vs. less).ResultsA total of 63% and 27% of the participants reported to drink respectively
regular and diet soft drinks twice a week or more, and 24% and 8%,
respectively, reported to drink soft drinks once a week or more at school.
Preferences, accessibility, modelling and attitudes were the strongest
determinants of both regular and diet soft drink consumption. In addition,
gender, educational plans and dieting were related to both total soft drink
consumption and consumption at school. Pupils with longer distance from
school to shop and those in schools with rules concerning soft drink
consumption tended to have lower odds of drinking both regular and diet soft
drinks at school.ConclusionThis study shows that gender, educational plans, dieting, accessibility,
modelling, attitudes and preferences all seem to be strong determinants of
adolescents’ soft drink consumption. Parents and the home
environment appear as great potential intervention targets.
Development and validation of a short questionnaire to assess sodium intake
Authors: Charlton Karen E , Steyn Krisela , Levitt Naomi S , Jonathan Deborah , Zulu Jabulisiwe V , Nel Johanna H 
Published: June 2007

AbstractObjectivesTo develop and validate a short food-frequency questionnaire to assess habitual dietary salt intake in South Africans and to allow classification of individuals according to intakes above or below the maximum recommended intake of 6 g salt day−1.DesignCross-sectional validation study in 324 conveniently sampled men and women.MethodsRepeated 24-hour urinary Na values and 24-hour dietary recalls were obtained on three occasions. Food items consumed by >5% of the sample and which contributed ≥50 mg Na serving−1were included in the questionnaire in 42 categories. A scoring system was devised, based on Na content of one index food per category and frequency of consumption.ResultsPositive correlations were found between Na content of 35 of the 42 food categories in the questionnaire and total Na intake, calculated from 24-hour recall data. Total Na content of the questionnaire was associated with Na estimations from 24-hour recall data (r= 0.750;P< 0.0001;n= 328) and urinary Na (r= 0.152;P= 0.0105;n= 284). Urinary Na was higher for subjects in tertile 3 than tertile 1 of questionnaire Na content (P< 0.05). Questionnaire Na content of <2400 and ≥2400 mg day−1equated to a reference cut-off score of 48 and corresponded to mean (standard deviation) urinary Na values of 145 (68) and 176 (99) mmol day−1, respectively (P< 0.05). Sensitivity and specificity against urinary Na ≥100 and <100 mmol day−1was 12.4% and 93.9%, respectively.ConclusionA 42-item food-frequency questionnaire has been shown to have content-, construct- and criterion-related validity, as well as internal consistency, with regard to categorising individuals according to their habitual salt intake; however, the devised scoring system needs to show improved sensitivity.
Experimenting with recursive queries in database and logic programming systems
Authors: TERRACINA G. , LEONE N. , LIO V. , PANETTA C. 
Published: June 2007

AbstractThis article considers the problem of reasoning on massive amounts of (possibly distributed) data. Presently, existing proposals show some limitations: (i) the quantity of data that can be handled contemporarily is limited, because reasoning is generally carried out in main-memory; (ii) the interaction with external (and independent) Database Management Systems is not trivial and, in several cases, not allowed at all; and (iii) the efficiency of present implementations is still not sufficient for their utilization in complex reasoning tasks involving massive amounts of data. This article provides a contribution in this setting; it presents a new system, called DLVDB, which aims to solve these problems. Moreover, it reports the results of a thorough experimental analysis we have carried out for comparing our system with several state-of-the-art systems (both logic and databases) on some classical deductive problems; the other tested systems are LDL++, XSB, Smodels, and three top-level commercial Database Management Systems. DLVDB significantly outperforms even the commercial database systems on recursive queries.
Phyloclimatic Modelling: Phylogenies, Palaeo-climate and Environmental Preferences
Authors: Yesson Chris , Culham Alastair 
Published: June 2007

AbstractA new technique is demonstrated for the interpretation of the role played by climate in plant diversity through the optimisation of climate variables on phylogenetic trees. This is achieved by calculating climate preferences for individual species based on established bioclimatic modelling techniques using pointdistribution data from distributed sources. We demonstrate a new technique for optimising the component parameters on phylogenetic trees. These parameters can be re-combined intobioclimatic models for ancestral nodes throughout the phylogenetic tree. The combination of DNA-sequence data and the fossil record is used to establish time-calibrated phylogenies. Using these chronograms, bioclimatic models can in turn can be projected into the relevant palaeo-climate scenario to establish possible areas of palaeo-distribution. This technique is demonstrated using exemplar plant groups from Mediterranean-type winter-wet climate zones.
Extreme ultraviolet spectroscopy of highly charged argon ions at the Berlin EBIT
Authors: Biedermann C , Radtke R , Fussmann G , Allen F I 
Published: June 2007

AbstractExtreme ultraviolet radiation from highly charged argon was investigated at the Berlin Electron Beam Ion Trap with a 2 m grazing incidence spectrometer. Lines in the wavelength range 150 to 660 Å originating from C-like Ar12+to Li-like Ar15+ions have been identified and are compared with database information from solar line lists and predictions. Line ratios for the observed resonance, intercombination and forbidden lines offer important diagnostic capabilities for low density, hot plasmas.
Stochastic simulation GUI for biochemical networks
Authors: Vallabhajosyula Ravishankar Rao , Sauro Herbert M. 
Published: June 2007

AbstractMotivation: This article describes the development of a useful graphical user interface for stochastic simulation of biochemical networks which allows model builders to run stochastic simulations of their models and perform statistical analysis on the results. These include the construction of correlations, power-spectral densities and transfer functions between selected inputs and outputs.Availability: The software is licensed under the BSD open source license and is available at http://sourceforge.net/projects/jdesigner. In addition, a more detailed account of the algorithms employed in the tool can be found at the Wiki at http://www.sys-bio.org/sbwWiki.Contact: rrao@kgi.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Visualization-based cancer microarray data classification analysis
Authors: Mramor Minca , Leban Gregor , Demšar Janez , Zupan Blaž 
Published: June 2007

Abstract
Motivation: Methods for analyzing cancer microarray data often face two distinct challenges: the models they infer need to perform well when classifying new tissue samples while at the same time providing an insight into the patterns and gene interactions hidden in the data. State-of-the-art supervised data mining methods often cover well only one of these aspects, motivating the development of methods where predictive models with a solid classification performance would be easily communicated to the domain expert.
Results: Data visualization may provide for an excellent approach to knowledge discovery and analysis of class-labeled data. We have previously developed an approach called VizRank that can score and rank point-based visualizations according to degree of separation of data instances of different class. We here extend VizRank with techniques to uncover outliers, score features (genes) and perform classification, as well as to demonstrate that the proposed approach is well suited for cancer microarray analysis. Using VizRank and radviz visualization on a set of previously published cancer microarray data sets, we were able to find simple, interpretable data projections that include only a small subset of genes yet do clearly differentiate among different cancer types. We also report that our approach to classification through visualization achieves performance that is comparable to state-of-the-art supervised data mining techniques.
Availability: VizRank and radviz are implemented as part of the Orange data mining suite (http://www.ailab.si/orange).
Contact: blaz.zupan@fri.uni-lj.si
Supplementary information: Supplementary data are available from http://www.ailab.si/supp/bi-cancer.
PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets
Authors: Kim Kyu-Won , Chung Hun-Ki , Cho Gyu-Taek , Ma Kyung-Ho , Chandrabalan Dorothy , Gwag Jae-Gyun , Kim Tae-San , Cho Eun-Gi , Park Yong-Jin 
Published: June 2007

Abstract
Motivation: Core sets are necessary to ensure that access to useful alleles or characteristics retained in genebanks is guaranteed. We have successfully developed a computational tool named ‘PowerCore’ that aims to support the development of core sets by reducing the redundancy of useful alleles and thus enhancing their richness.
Results: The program, using a new approach completely different from any other previous methodologies, selects entries of core sets by the advanced M (maximization) strategy implemented through a modified heuristic algorithm. The developed core set has been validated to retain all characteristics for qualitative traits and all classes for quantitative ones. PowerCore effectively selected the accessions with higher diversity representing the entire coverage of variables and gave a 100% reproducible list of entries whenever repeated.
Availability: PowerCore software uses the .NET Framework Version 1.1 environment which is freely available for the MS Windows platform. The files can be downloaded from http://genebank.rda.go.kr/powercore/. The distribution of the package includes executable programs, sample data and a user manual.
Contact: yjpark@rda.go.kr
MareyMap: an R-based tool with graphical interface for estimating recombination rates
Authors: Rezvoy Clément , Charif Delphine , Guéguen Laurent , Marais Gabriel A.B. 
Published: June 2007

Abstract
Summary: Comparing genetic and physical maps (the so-called Marey map approach) is still the most widely used approach to estimate genome-wide recombination rates. Remarkably, there is no available bioinformatics tool specifically devoted to Marey map approach. Here, we developed such a tool called MareyMap based on GNU R and Tcl/Tk. MareyMap offers a user-friendly graphical interface and includes useful features, such as data cleaning process, sophisticated interpolation methods to estimate local rates, possibility of complex queries, various range of import–export files. Moreover, MareyMap comes with ready-to-use maps for human, Drosophila, Caenorhabditis elegans and Arabidopsis. MareyMap has been made so that it can be easily upgraded with new data and interpolation methods.
Availability: http://pbil.univ-lyon1.fr/software/mareymap/
Contact: marais@biomserv.univ-lyon1.fr
Evaporative cooling feature selection for genotypic data involving interactions
Authors: McKinney B.A. , Reif D.M. , White B.C. , Crowe J.E. , Moore J.H. 
Published: June 2007

Abstract
Motivation: The development of genome-wide capabilities for genotyping has led to the practical problem of identifying the minimum subset of genetic variants relevant to the classification of a phenotype. This challenge is especially difficult in the presence of attribute interactions, noise and small sample size.
Methods: Analogous to the physical mechanism of evaporation, we introduce an evaporative cooling (EC) feature selection algorithm that seeks to obtain a subset of attributes with the optimum information temperature (i.e. the least noise). EC uses an attribute quality measure analogous to thermodynamic free energy that combines Relief-F and mutual information to evaporate (i.e. remove) noise features, leaving behind a subset of attributes that contain DNA sequence variations associated with a given phenotype.
Results: EC is able to identify functional sequence variations that involve interactions (epistasis) between other sequence variations that influence their association with the phenotype. This ability is demonstrated on simulated genotypic data with attribute interactions and on real genotypic data from individuals who experienced adverse events following smallpox vaccination. The EC formalism allows us to combine information entropy, energy and temperature into a single information free energy attribute quality measure that balances interaction and main effects.
Availability: Open source software, written in Java, is freely available upon request.
Contact: brett.mckinney@gmail.com
Constraint-based functional similarity of metabolic genes: going beyond network topology
Authors: Rokhlenko Oleg , Shlomi Tomer , Sharan Roded , Ruppin Eytan , Pinter Ron Y. 
Published: June 2007

Abstract
Motivation: Several recent studies attempted to establish measures for the similarity between genes that are based on the topological properties of metabolic networks. However, these approaches offer only a static description of the properties of interest and offer moderate (albeit significant) correlations with pertinent experimental data.
Results: Using a constraint-based large-scale metabolic model, we present two effectively computable measures of functional gene similarity, one based on the response of the metabolic network to gene knockouts and the other based on the metabolic flux activity across a variety of growth media. We applied these measures to 750 genes comprising the metabolic network of the budding yeast. Comparing the in silico computed functional similarities to Gene Ontology (GO) annotations and gene expression data, we show that our computational method captures functional similarities between metabolic genes that go beyond those obtained by the topological analysis of metabolic networks alone, thus revealing dynamic characteristics of gene function. Interestingly, the measure based on the network response to different growth environments markedly outperforms the measure based on its response to gene knockouts, though both have some added synergistic value in depicting the functional relationships between metabolic genes.
Contact: olegro@cs.technion.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
MAnGO: an interactive R-based tool for two-colour microarray analysis
Authors: Marisa Laetitia , Ichanté Jean-Laurent , Reymond Nancie , Aggerbeck Lawrence , Delacroix Hervé , Mucchielli-Giorgi Marie-Hélène 
Published: June 2007

AbstractSummary: MAnGO (Microarray Analysis at the Gif/Orsay platform) is an interactive R-based tool for the analysis of two-colour microarray experiments. It is a compilation of various methods, which allows the user (1) to control data quality by detecting biases with a large number of visual representations, (2) to pre-process data (filtering and normalization) and (3) to carry out differential analyses. MAnGO is not only a ‘turn-key’ tool, oriented towards biologists but also a flexible and adaptable R script oriented towards bioinformaticians.Availability: http://bioinfome.cgm.cnrs-gif.fr/Contact: reymond@cgm.cnrs-gif.fr