Performance portability of Earth system models with user-controlled GGDML code translation

The increasing need for performance of earth system modeling and other scientific domains pushes the computing technologies in diverse architectural directions. The development of models needs technical expertise and skills of using tools that are able to exploit the hardware capabilities. The heterogeneity of architectures complicates the development and the maintainability of the models. To improve the software development process of earth system models, we provide an approach that simplifies the code maintainability by fostering separation of concerns while providing performance portability. We propose the use of high-level language extensions that reflect scientific concepts. The scientists can use the programming language of their own choice to develop models, however, they can use the language extensions optionally wherever they need. The code translation is driven by configurations that are separated from the model source code. These configurations are prepared by scientific programmers to optimally use the machine’s features. The main contribution of this paper is the demonstration of a user-controlled source-to-source translation technique of earth system models that are written with higher-level semantics. We discuss a flexible code translation technique that is driven by the users through a configuration input that is prepared especially to transform the code, and we use this technique to produce OpenMP or OpenACC enabled codes besides MPI to support multi-node configurations

A new method to quantify and compare the multiple components of fitness-A study case with kelp niche partition by divergent microstage adaptations to Temperature

Point 1 Management of crops, commercialized or protected species, plagues or life-cycle evolution are subjects requiring comparisons among different demographic strategies. The simpler methods fail in relating changes in vital rates with changes in population viability whereas more complex methods lack accuracy by neglecting interactions among vital rates. Point 2 The difference between the fitness (evaluated by the population growth rate.) of two alternative demographies is decomposed into the contributions of the differences between the pair-wised vital rates and their interactions. This is achieved through a full Taylor expansion (i.e. remainder = 0) of the demographic model. The significance of each term is determined by permutation tests under the null hypothesis that all demographies come from the same pool. Point 3 An example is given with periodic demographic matrices of the microscopic haploid phase of two kelp cryptic species observed to partition their niche occupation along the Chilean coast. The method provided clear and synthetic results showing conditional differentiation of reproduction is an important driver for their differences in fitness along the latitudinal temperature gradient. But it also demonstrated that interactions among vital rates cannot be neglected as they compose a significant part of the differences between demographies. Point 4 This method allows researchers to access the effects of multiple effective changes in a life-cycle from only two experiments. Evolutionists can determine with confidence the effective causes for changes in fitness whereas population managers can determine best strategies from simpler experimental designs.CONICYT-FRENCH EMBASSADY Ph.D. gran

Monitoring health-related quality of life in paediatric practice: development of an innovative web-based application

<p>Abstract</p> <p>Background</p> <p>Health Related Quality of Life (HRQOL) questionnaires are increasingly used in clinical practice. These Patient Reported Outcomes (PROs) are provided to the paediatrician to facilitate communication with patients during a consultation. The aim of the current article is to describe the development and introduction of a new web-based application for the use of PROs in daily paediatric clinical practice.</p> <p>Methods</p> <p>Currently, the use of PROs in daily clinical practice is very time consuming and often has logistical problems. The use of a web-based programme can overcome these problems and contributes to an improved use of PROs in clinical practice. We therefore developed an easily accessible website (KLIK) for outpatient treatment and a training programme for paediatricians to maximize the effectiveness and the practical use of PROs (KLIK PROfile).</p> <p>Results</p> <p>The KLIK study was launched in August 2008 to evaluate the use of the KLIK PROfile in daily clinical practice. The KLIK study evaluates whether feedback from HRQOL data could influence patient satisfaction with the consultation, the advice given, the type of referrals and topics discussed. In this multicentre study, a control group (without the use of the KLIK PROfile) is compared to an intervention group (with the use of the KLIK PROfile). A sequential cohort design is chosen to avoid contamination between the study groups.</p> <p>Conclusions</p> <p>Based on the positive experiences with the use of the KLIK PROfile acquired during the study we conclude that the KLIK PROfile may contribute to systematically monitor and discuss HRQOL issues during consultations. The next steps will be a comprehensive evaluation of the KLIK study data and the implementation of the KLIK PROfile in daily clinical practice in different patient groups.</p

Impact of sex-specific target dose in chronic heart failure patients with reduced ejection fraction

Aims: A recent study suggested that women with heart failure and heart failure reduced ejection fraction might hypothetically need lower doses of angiotensin-converting enzyme inhibitors or angiotensin II receptor blockers (= renin-angiotensin-system inhibitors) and β-blockers than men to achieve the best outcome. We assessed the current medical treatment of heart failure reduced ejection fraction in men and women in a large contemporary cohort and address the hypothetical impact of changing treatment levels in women. Methods: This analysis is part of a large contemporary quality of heart failure care project which includes 5320 (64%) men and 3003 (36%) women with heart failure reduced ejection fraction. Detailed information on heart failure therapy prescription and dosage were collected. Results: Women less often received renin-angiotensin-system inhibitors (79% vs 83%, p 100% of the new hypothetical target dose would be 24% for β-blockers and 52% for renin-angiotensin-system inhibitors, which can be considered as relatively overdosed. Conclusion: In this large contemporary heart failure registry, there were significant but relatively small differences in drug dose between men and women with heart failure reduced ejection fraction. Implementation of the hypothetical sex-specific target dosing schedule would lead to considerably more women adequately treated. In contrast, we identified a group of women who might have been relatively overdosed with increased risk of side-effects and intolerance

Temperature Effects on Gametophyte Life-History Traits and Geographic Distribution of Two Cryptic Kelp Species

A major determinant of the geographic distribution of a species is expected to be its physiological response to changing abiotic variables over its range. The range of a species often corresponds to the geographic extent of temperature regimes the organism can physiologically tolerate. Many species have very distinct life history stages that may exhibit different responses to environmental factors. In this study we emphasized the critical role of the haploid microscopic stage (gametophyte) of the life cycle to explain the difference of edge distribution of two related kelp species. Lessonia nigrescens was recently identified as two cryptic species occurring in parapatry along the Chilean coast: one located north and the other south of a biogeographic boundary at latitude 29–30°S. Six life history traits from microscopic stages were identified and estimated under five treatments of temperature in eight locations distributed along the Chilean coast in order to (1) estimate the role of temperature in the present distribution of the two cryptic L. nigrescens species, (2) compare marginal populations to central populations of the two cryptic species. In addition, we created a periodic matrix model to estimate the population growth rate (λ) at the five temperature treatments. Differential tolerance to temperature was demonstrated between the two species, with the gametophytes of the Northern species being more tolerant to higher temperatures than gametophytes from the south. Second, the two species exhibited different life history strategies with a shorter haploid phase in the Northern species contrasted with considerable vegetative growth in the Southern species haploid stage. These results provide strong ecological evidence for the differentiation process of the two cryptic species and show local adaptation of the life cycle at the range limits of the distribution. Ecological and evolutionary implications of these findings are discussed

Effects of shared medical appointments on quality of life and cost-effectiveness for patients with a chronic neuromuscular disease. Study protocol of a randomized controlled trial

Contains fulltext : 96862.pdf (publisher's version ) (Open Access)BACKGROUND: Shared medical appointments are a series of one-to-one doctor-patient contacts, in presence of a group of 6-10 fellow patients. This group visits substitute the annual control visits of patients with the neurologist. The same items attended to in a one-to-one appointment are addressed. The possible advantages of a shared medical appointment could be an added value to the present management of neuromuscular patients. The currently problem-focused one-to-one out-patient visits often leave little time for the patient's psychosocial needs, patient education, and patient empowerment. METHODS/DESIGN: A randomized, prospective controlled study (RCT) with a follow up of 6 months will be conducted to evaluate the clinical and cost-effectiveness of shared medical appointments compared to usual care for 300 neuromuscular patients and their partners at the Radboud University Nijmegen Medical Center. Every included patient will be randomly allocated to one of the two study arms. This study has been reviewed and approved by the medical ethics committee of the region Arnhem-Nijmegen, The Netherlands. The primary outcome measure is quality of life as measured by the EQ-5D, SF-36 and the Individualized neuromuscular Quality of Life Questionnaire. The primary analysis will be an intention-to-treat analysis on the area under the curve of the quality of life scores. A linear mixed model will be used with random factor group and fixed factors treatment, baseline score and type of neuromuscular disease. For the economic evaluation an incremental cost-effectiveness analysis will be conducted from a societal perspective, relating differences in costs to difference in health outcome. Results are expected in 2012. DISCUSSION: This study will be the first randomized controlled trial which evaluates the effect of shared medical appointments versus usual care for neuromuscular patients. This will enable to determine if there is additional value of shared medical appointments to the current therapeutical spectrum. When this study shows that group visits produce the alleged benefits, this may help to increase the acceptance of this innovative and creative way of using one of the most precious resources in health care more efficiently: time. TRIAL REGISTRATION: DutchTrial Register http://www.trialregister.nlNTR1412

COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia

Background: Microarrays are the main technology for large-scale transcriptional gene expression profiling, but the large bodies of data available in public databases are not useful due to the large heterogeneity. There are several initiatives that attempt to bundle these data into expression compendia, but such resources for bacterial organisms are scarce and limited to integration of experiments from the same platform or to indirect integration of per experiment analysis results. Methodology/Principal Findings: We have constructed comprehensive organism-specific cross-platform expression compendia for three bacterial model organisms (Escherichia coli, Bacillus subtilis, and Salmonella enterica serovar Typhimurium) together with an access portal, dubbed COLOMBOS, that not only provides easy access to the compendia, but also includes a suite of tools for exploring, analyzing, and visualizing the data within these compendia. It is freely available at http://bioi.biw.kuleuven.be/colombos. The compendia are unique in directly combining expression information from different microarray platforms and experiments, and we illustrate the potential benefits of this direct integration with a case study: extending the known regulon of the Fur transcription factor of E. coli. The compendia also incorporate extensive annotations for both genes and experimental conditions; these heterogeneous data are functionally integrated in the COLOMBOS analysis tools to interactively browse and query the compendia not only for specific genes or experiments, but also metabolic pathways, transcriptional regulation mechanisms, experimental conditions, biological processes, etc. Conclusions/Significance: We have created cross-platform expression compendia for several bacterial organisms and developed a complementary access port COLOMBOS, that also serves as a convenient expression analysis tool to extract useful biological information. This work is relevant to a large community of microbiologists by facilitating the use of publicly available microarray experiments to support their research

Competency-based (CanMEDS) residency training programme in radiology: systematic design procedure, curriculum and success factors

Based on the CanMEDS framework and the European Training Charter for Clinical Radiology a new radiology curriculum was designed in the Netherlands. Both the development process and the resulting new curriculum are presented in this paper. The new curriculum was developed according to four systematic design principles: discursiveness, hierarchical decomposition, systematic variation and satisficing (satisficing is different from satisfying; in this context, satisficing means searching for an acceptable solution instead of searching for an optimal solution). The new curriculum is organ based with integration of radiological diagnostic techniques, comprises a uniform national common trunk followed by a 2-year subspecialisation, is competency outcome based with appropriate assessment tools and techniques, and is based on regional collaboration among radiology departments. The application of the systematic design principles proved successful in producing a new curriculum approved by all authorities. The principles led to a structured, yet flexible, development process in which creative solutions could be generated and adopters (programme directors, supervisors and residents) were highly involved. Further research is needed to empirically test the components of the new curriculum

Angular and Current-Target Correlations in Deep Inelastic Scattering at HERA

Correlations between charged particles in deep inelastic ep scattering have been studied in the Breit frame with the ZEUS detector at HERA using an integrated luminosity of 6.4 pb-1. Short-range correlations are analysed in terms of the angular separation between current-region particles within a cone centred around the virtual photon axis. Long-range correlations between the current and target regions have also been measured. The data support predictions for the scaling behaviour of the angular correlations at high Q2 and for anti-correlations between the current and target regions over a large range in Q2 and in the Bjorken scaling variable x. Analytic QCD calculations and Monte Carlo models correctly describe the trends of the data at high Q2, but show quantitative discrepancies. The data show differences between the correlations in deep inelastic scattering and e+e- annihilation.Comment: 26 pages including 10 figures (submitted to Eur. J. Phys. C

Plastisol Foaming Process. Decomposition of the Foaming Agent, Polymer Behavior in the Corresponding Temperature Range and Resulting Foam Properties

The decomposition of azodicarbonamide, used as foaming agent in PVC - plasticizer (1/1) plastisols was studied by DSC. Nineteen different plasticizers, all belonging to the ester family, two being polymeric (polyadipates), were compared. The temperature of maximum decomposition rate (in anisothermal regime at 5 K min-1 scanning rate), ranges between 434 and 452 K. The heat of decomposition ranges between 8.7 and 12.5 J g -1. Some trends of variation of these parameters appear significant and are discussed in terms of solvent (matrix) and viscosity effects on the decomposition reactions. The shear modulus at 1 Hz frequency was determined at the temperature of maximum rate of foaming agent decomposition, and differs significantly from a sample to another. The foam density was determined at ambient temperature and the volume fraction of bubbles was used as criterion to judge the efficiency of the foaming process. The results reveal the existence of an optimal shear modulus of the order of 2 kPa that corresponds roughly to plasticizer molar masses of the order of 450 ± 50 g mol-1. Heavier plasticizers, especially polymeric ones are too difficult to deform. Lighter plasticizers such as diethyl phthalate (DEP) deform too easily and presumably facilitate bubble collapse