The semantic web ontology languages RDFS and OWL are widely used but limited in both their expressivity and their support for modularity and integrated documentation. Expressivity, modularity, and ...documentation of formal knowledge have always been important issues in the MKM community. Therefore, we try to improve these ontology languages by well-tried MKM techniques.
Concretely, we propose embedding the language concepts into OMDoc to make use of its modularity and documentation infrastructure. We show how OMDoc can be made compatible with semantic web ontology languages, focusing on knowledge representation, modular design, documentation, and metadata. We evaluate our technology by re-implementing the Friend-of-a-friend (FOAF) ontology and applying it in a novel metadata framework for technical documents (including ontologies).
Europe has the highest documented caseload and greatest increase in multidrug and extensively drug-resistant tuberculosis (M/XDR-TB) of all World Health Organization (WHO) regions. This survey ...examines how recommendations for M/XDR-TB management are being implemented.
TBNET is a pan-European clinical research collaboration for tuberculosis. An email survey of TBNET members collected data in relation to infection control, access to molecular tests and basic microbiology with drug sensitivity testing.
68/105 responses gave valid information and were from countries within the WHO European Region. Inpatient beds matched demand, but single rooms with negative pressure were only available in low incidence countries; ultraviolet decontamination was used in 5 sites, all with >10 patients with M/XDR-TB per year. Molecular tests for mutations associated with rifampicin resistance were widely available (88%), even in lower income and especially in high incidence countries. Molecular tests for other first line and second line drugs were less accessible (76 and 52% respectively). A third of physicians considered that drug susceptibility results were delayed by > 2 months.
Infection control for inpatients with M/XDR-TB remains a problem in high incidence countries. Rifampicin resistance is readily detected, but tests to plan regimens tailored to the drug susceptibilities of the strain of Mycobacterium tuberculosis are significantly delayed, allowing for further drug resistance to develop.
•M/XDR-TB poses a serious threat to TB control in Europe.•Isolation rooms are insufficient for safe diagnosis.•Drug susceptibility testing results are frequently delayed.•A positive test for rifampicin resistance should lead automatically to tests for other first- and second-line drug resistance.
For genome-wide association studies in family-based designs, we propose a powerful two-stage testing strategy that can be applied in situations in which parent-offspring trio data are available and ...all offspring are affected with the trait or disease under study. In the first step of the testing strategy, we construct estimators of genetic effect size in the completely ascertained sample of affected offspring and their parents that are statistically independent of the family-based association/transmission disequilibrium tests (FBATs/TDTs) that are calculated in the second step of the testing strategy. For each marker, the genetic effect is estimated (without requiring an estimate of the SNP allele frequency) and the conditional power of the corresponding FBAT/TDT is computed. Based on the power estimates, a weighted Bonferroni procedure assigns an individually adjusted significance level to each SNP. In the second stage, the SNPs are tested with the FBAT/TDT statistic at the individually adjusted significance levels. Using simulation studies for scenarios with up to 1,000,000 SNPs, varying allele frequencies and genetic effect sizes, the power of the strategy is compared with standard methodology (e.g., FBATs/TDTs with Bonferroni correction). In all considered situations, the proposed testing strategy demonstrates substantial power increases over the standard approach, even when the true genetic model is unknown and must be selected based on the conditional power estimates. The practical relevance of our methodology is illustrated by an application to a genome-wide association study for childhood asthma, in which we detect two markers meeting genome-wide significance that would not have been detected using standard methodology.
In this paper we propose a multivariate extension of family-based association tests based on generalized estimating equations. The test can be applied to multiple phenotypes and to phenotypic data ...obtained in longitudinal studies without making any distributional assumptions for the phenotypic observations. Methods for handling missing phenotypic information are discussed. Further, we compare the power of the multivariate test with permutation tests and with using separate tests for each outcome which are adjusted for multiple testing. Application of the proposed test to an asthma study illustrates the power of the approach.
A SNP upstream of the INSIG2 gene, rs7566605, was recently found to be associated with obesity as measured by body mass index (BMI) by Herbert and colleagues. The association between increased BMI ...and homozygosity for the minor allele was first observed in data from a genome-wide association scan of 86,604 SNPs in 923 related individuals from the Framingham Heart Study offspring cohort. The association was reproduced in four additional cohorts, but was not seen in a fifth cohort. To further assess the general reproducibility of this association, we genotyped rs7566605 in nine large cohorts from eight populations across multiple ethnicities (total n = 16,969). We tested this variant for association with BMI in each sample under a recessive model using family-based, population-based, and case-control designs. We observed a significant (p < 0.05) association in five cohorts but saw no association in three other cohorts. There was variability in the strength of association evidence across examination cycles in longitudinal data from unrelated individuals in the Framingham Heart Study Offspring cohort. A combined analysis revealed significant independent validation of this association in both unrelated (p = 0.046) and family-based (p = 0.004) samples. The estimated risk conferred by this allele is small, and could easily be masked by small sample size, population stratification, or other confounders. These validation studies suggest that the original association is less likely to be spurious, but the failure to observe an association in every data set suggests that the effect of SNP rs7566605 on BMI may be heterogeneous across population samples.
Based on a model of a typical operator network we have compared the power consumption of different broadband access technologies and architectures especially DSL, FTTN + VDSL and FTTH. Even though ...power management improves the performance there is still clear advantage of FTTH with respect to energy efficiency.
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