European rodent on the edge: status and distribution of the Vojvodina blind mole rat

Recent research of blind mole rats of the species complex Nannospalax (superspecies leucodon) identified a small and fragmented population of these rodents on both sides of the Hungarian-Serbian border. Cytogenetic investigations proved that this population karyologically identical with the Vojvodina blind mole rat described earlier as Nannospalax (leucodon) montanosyrmiensis. Based on cytochrome b gene sequences obtained from three specimens originating from separate locations, these blind mole rats form a discrete phylogenetic clade which, with a difference of about 10%, is well separated from other blind mole rat taxa inhabiting the Carpathian Basin. The taxon has only two extant populations that are 150 km apart from each other. The combined occupied area is estimated to be less than 10 km(2), and the total estimated number of individuals is less than 300. These two remaining populations are heavily fragmented and under imminent threat by the establishment of tree plantations, small-scale and agro-industrial farms and land development. The situation is further aggravated by the fact that 80% of the individuals inhabit unprotected areas. A study of the landscape history of the wider area surrounding one of the populations - based on military maps spanning over the last 200 years - has shown a drastic decrease in the extent and quality of potential habitats. Based on our present knowledge, the Vojvodina blind mole rat is one of the most seriously threatened, rarest mammal in Europe, the remaining population of which can be wiped out within years unless immediate conservation action is taken. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/2193-1801-2-2) contains supplementary material, which is available to authorized users

Structured Sparsity: Discrete and Convex approaches

Compressive sensing (CS) exploits sparsity to recover sparse or compressible signals from dimensionality reducing, non-adaptive sensing mechanisms. Sparsity is also used to enhance interpretability in machine learning and statistics applications: While the ambient dimension is vast in modern data analysis problems, the relevant information therein typically resides in a much lower dimensional space. However, many solutions proposed nowadays do not leverage the true underlying structure. Recent results in CS extend the simple sparsity idea to more sophisticated {\em structured} sparsity models, which describe the interdependency between the nonzero components of a signal, allowing to increase the interpretability of the results and lead to better recovery performance. In order to better understand the impact of structured sparsity, in this chapter we analyze the connections between the discrete models and their convex relaxations, highlighting their relative advantages. We start with the general group sparse model and then elaborate on two important special cases: the dispersive and the hierarchical models. For each, we present the models in their discrete nature, discuss how to solve the ensuing discrete problems and then describe convex relaxations. We also consider more general structures as defined by set functions and present their convex proxies. Further, we discuss efficient optimization solutions for structured sparsity problems and illustrate structured sparsity in action via three applications.Comment: 30 pages, 18 figure

Mechanisms of Endothelial Dysfunction in Resistance Arteries from Patients with End-Stage Renal Disease

The study focuses on the mechanisms of endothelial dysfunction in the uremic milieu. Subcutaneous resistance arteries from 35 end-stage renal disease (ESRD) patients and 28 matched controls were studied ex-vivo. Basal and receptor-dependent effects of endothelium-derived factors, expression of endothelial NO synthase (eNOS), prerequisites for myoendothelial gap junctions (MEGJ), and associations between endothelium-dependent responses and plasma levels of endothelial dysfunction markers were assessed. The contribution of endothelium-derived hyperpolarizing factor (EDHF) to endothelium-dependent relaxation was impaired in uremic arteries after stimulation with bradykinin, but not acetylcholine, reflecting the agonist-specific differences. Diminished vasodilator influences of the endothelium on basal tone and enhanced plasma levels of asymmetrical dimethyl L-arginine (ADMA) suggest impairment in NO-mediated regulation of uremic arteries. eNOS expression and contribution of MEGJs to EDHF type responses were unaltered. Plasma levels of ADMA were negatively associated with endothelium-dependent responses in uremic arteries. Preserved responses of smooth muscle to pinacidil and NO-donor indicate alterations within the endothelium and tolerance of vasodilator mechanisms to the uremic retention products at the level of smooth muscle. We conclude that both EDHF and NO pathways that control resistance artery tone are impaired in the uremic milieu. For the first time, we validate the alterations in EDHF type responses linked to kinin receptors in ESRD patients. The association between plasma ADMA concentrations and endothelial function in uremic resistance vasculature may have diagnostic and future therapeutic implications

National records of 3000 European bee and hoverfly species: A contribution to pollinator conservation

Pollinators play a crucial role in ecosystems globally, ensuring the seed production of most flowering plants. They are threatened by global changes and knowledge of their distribution at the national and continental levels is needed to implement efficient conservation actions, but this knowledge is still fragmented and/or difficult to access. As a step forward, we provide an updated list of around 3000 European bee and hoverfly species, reflecting their current distributional status at the national level (in the form of present, absent, regionally extinct, possibly extinct or non-native). This work was attainable by incorporating both published and unpublished data, as well as knowledge from a large set of taxonomists and ecologists in both groups. After providing the first National species lists for bees and hoverflies for many countries, we examine the current distributional patterns of these species and designate the countries with highest levels of species richness. We also show that many species are recorded in a single European country, highlighting the importance of articulating European and national conservation strategies. Finally, we discuss how the data provided here can be combined with future trait and Red List data to implement research that will further advance pollinator conservation

OSIRIS-SR: a safety ring for self-healing distributed composite service execution

The advent of service-oriented architectures has strongly facilitated the development and deployment of large-scale distributed applications. The middleware for orchestrating applications that consist of several distributed services has to be inherently distributed as well, in order to provide a high degree of scalability and to avoid any single point of failure. Self-healing execution of composite services requires replicated control metadata and instance data in a way that does not affect adaptivity and elasticity of the middleware. In this paper, we present OSIRIS-SR, a decentralized approach to self-healing composite service execution in a distributed environment. OSIRIS-SR exploits dedicated node monitors, organized in a self-organizing Safety Ring, for the replication of control data. Moreover, OSIRIS-SR leverages virtual stable storage for managing composite service instance data in a robust way. We present the architecture of OSIRIS-SR's Safety Ring and discuss how it provides self-healing composite service execution. The performance evaluation shows that the additional gain in robustness has only marginal effects on the scalability characteristics of the system

A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL.

Regulation of transcription is fundamental to development and physiology, and occurs through binding of transcription factors to specific DNA sequences in the genome. CSL (CBF1/Suppressor of Hairless/LAG-1), a core component of the Notch signaling pathway, is one such transcription factor that acts in concert with co-activators or co-repressors to control the activity of associated target genes. One fundamental question is how CSL can recognize and select among different DNA sequences available in vivo and whether variations between selected sequences can influence its function. We have therefore investigated CSL-DNA recognition using computational approaches to analyze the energetics of CSL bound to different DNAs and tested the in silico predictions with in vitro and in vivo assays. Our results reveal novel aspects of CSL binding that may help explain the range of binding observed in vivo. In addition, using molecular dynamics simulations, we show that domain-domain correlations within CSL differ significantly depending on the DNA sequence bound, suggesting that different DNA sequences may directly influence CSL function. Taken together, our results, based on computational chemistry approaches, provide valuable insights into transcription factor-DNA binding, in this particular case increasing our understanding of CSL-DNA interactions and how these may impact on its transcriptional control.BBSRC [BB/J008842/1 to S.J.B., B.A., Dr Steve Russell.]; National Institutes of Health (NIH) [CA178974 to R.A.K.] and a Leukemia and Lymphoma Society Scholar Award (to R.A.K.); Unilever (to R.T. and R.G.). China Scholarship Council Cambridge (to J.L.); BBSRC Studentship (to R.A.F.); NIH training [5T32ES007250 to A.N.C.]. Funding for open access charge: University RCUK Open Access Fund.This is the final published version, originally published by Oxford Journals and available at http://nar.oxfordjournals.org/content/early/2014/08/11/nar.gku730.abstract

Towards self-organizing service-oriented architectures

Service-oriented architectures (SOAs) provide a successful model for structuring complex distributed software systems, as they reduce the cost of ownership and ease the creation of new applications by composing existing services. However, currently, the development of service-oriented applications requires many manual tasks and prevailing infrastructure is often based on centralized components that are central points of failure and easily become bottlenecks. In this paper, we promote self-organizing SOA as a new approach to overcome these limitations. Self-organizing SOA integrates research results in the areas of autonomic and service-oriented computing. We consider self-organizing features for the whole life-cycle of a service-oriented application, from the creation to the execution, optimization, and monitoring