Micro-CernVM: Slashing the Cost of Building and Deploying Virtual Machines

The traditional virtual machine building and and deployment process is centered around the virtual machine hard disk image. The packages comprising the VM operating system are carefully selected, hard disk images are built for a variety of different hypervisors, and images have to be distributed and decompressed in order to instantiate a virtual machine. Within the HEP community, the CernVM File System has been established in order to decouple the distribution from the experiment software from the building and distribution of the VM hard disk images. We show how to get rid of such pre-built hard disk images altogether. Due to the high requirements on POSIX compliance imposed by HEP application software, CernVM-FS can also be used to host and boot a Linux operating system. This allows the use of a tiny bootable CD image that comprises only a Linux kernel while the rest of the operating system is provided on demand by CernVM-FS. This approach speeds up the initial instantiation time and reduces virtual machine image sizes by an order of magnitude. Furthermore, security updates can be distributed instantaneously through CernVM-FS. By leveraging the fact that CernVM-FS is a versioning file system, a historic analysis environment can be easily re-spawned by selecting the corresponding CernVM-FS file system snapshot.Comment: Conference paper at the 2013 Computing in High Energy Physics (CHEP) Conference, Amsterda

CernVM Online and Cloud Gateway: a uniform interface for CernVM contextualization and deployment

In a virtualized environment, contextualization is the process of configuring a VM instance for the needs of various deployment use cases. Contextualization in CernVM can be done by passing a handwritten context to the user data field of cloud APIs, when running CernVM on the cloud, or by using CernVM web interface when running the VM locally. CernVM Online is a publicly accessible web interface that unifies these two procedures. A user is able to define, store and share CernVM contexts using CernVM Online and then apply them either in a cloud by using CernVM Cloud Gateway or on a local VM with the single-step pairing mechanism. CernVM Cloud Gateway is a distributed system that provides a single interface to use multiple and different clouds (by location or type, private or public). Cloud gateway has been so far integrated with OpenNebula, CloudStack and EC2 tools interfaces. A user, with access to a number of clouds, can run CernVM cloud agents that will communicate with these clouds using their interfaces, and then use one single interface to deploy and scale CernVM clusters. CernVM clusters are defined in CernVM Online and consist of a set of CernVM instances that are contextualized and can communicate with each other.Comment: Conference paper at the 2013 Computing in High Energy Physics (CHEP) Conference, Amsterda

Priority setting in the German healthcare system: results from a discrete choice experiment

Worldwide, social healthcare systems must face the challenges of a growing scarcity of resources and of its inevitable distributional effects. Explicit criteria are needed to define the boundaries of public reimbursement decisions. As Germany stands at the beginning of such a discussion, more formalised priority setting procedures seem in order. Recent research identified multi-criteria decision analysis (MCDA) as a promising approach to inform and to guide decision-making in healthcare systems. In that regard, this paper aims to analyse the relative weight assigned to various criteria in setting priority interventions in Germany. A discrete choice experiment (DCE) was employed in 2015 to elicit equity and efficiency preferences of 263 decision makers, through six attributes. The experiment allowed us to rate different policy interventions based on their features in a composite league table (CLT). As number of potential beneficiaries, severity of disease, individual health benefits and cost-effectiveness are the most relevant criteria for German decision makers within the sample population, the results display an overall higher preference towards efficiency criteria. Specific high priority interventions are mental disorders and cardiovascular diseases

Incidence of intracranial bleeding in anticoagulated patients with minor head injury: a systematic review and meta-analysis of prospective studies.

Guidelines advise performing a computed tomography head scan for all anticoagulated head injured patients, but the risk of intracranial haemorrhage (ICH) after a minor head injury is unclear. We conducted a systematic review and meta-analysis to determine the incidence of ICH in anticoagulated patients presenting with a minor head injury and a Glasgow Coma Score (GCS) of 15. We followed Meta-Analyses and Systematic Reviews of Observational Studies guidelines. We included all prospective studies recruiting consecutive anticoagulated emergency patients presenting with a head injury. Anticoagulation included vitamin-K antagonists (warfarin, fluindione), direct oral anticoagulants (apixaban, rivaroxaban, dabigatran and edoxaban) and low molecular weight heparin. A total of five studies (including 4080 anticoagulated patients with a GCS of 15) were included in the analysis. The majority of patients took vitamin K antagonists (98·3%). There was significant heterogeneity between studies with regards to mechanism of injury and methods. The random effects pooled incidence of ICH was 8·9% (95% confidence interval 5·0-13·8%). In conclusion, around 9% of patients on vitamin K antagonists with a minor head injury develop ICH. There is little data on the risk of traumatic intracranial bleeding in patients who have a GSC 15 post-head injury and are prescribed a direct oral anticoagulant

Data Integration for Open Data on the Web

In this lecture we will discuss and introduce challenges of integrating openly available Web data and how to solve them. Firstly, while we will address this topic from the viewpoint of Semantic Web research, not all data is readily available as RDF or Linked Data, so we will give an introduction to different data formats prevalent on the Web, namely, standard formats for publishing and exchanging tabular, tree-shaped, and graph data. Secondly, not all Open Data is really completely open, so we will discuss and address issues around licences, terms of usage associated with Open Data, as well as documentation of data provenance. Thirdly, we will discuss issues connected with (meta-)data quality issues associated with Open Data on the Web and how Semantic Web techniques and vocabularies can be used to describe and remedy them. Fourth, we will address issues about searchability and integration of Open Data and discuss in how far semantic search can help to overcome these. We close with briefly summarizing further issues not covered explicitly herein, such as multi-linguality, temporal aspects (archiving, evolution, temporal querying), as well as how/whether OWL and RDFS reasoning on top of integrated open data could be help

Small tumor necrosis factor receptor biologics inhibit the tumor necrosis factor-p38 signalling axis and inflammation

Anti-TNF therapy has improved the treatment of inflammatory disease but can predispose to infection and malignancy. Here the authors show an anti-TNF biologic peptide that functionally and selectively targets the TNF-p38 pathway in multiple models of inflammation

Testing macroecological abundance patterns: The relationship between local abundance and range size, range position and climatic suitability among European vascular plants

Aim: A fundamental question in macroecology centres around understanding the relationship between species' local abundance and their distribution in geographical and climatic space (i.e. the multi‐dimensional climatic space or climatic niche). Here, we tested three macroecological hypotheses that link local abundance to the following range properties: (a) the abundance-range size relationship, (b) the abundance-range centre relationship and (c) the abundance-suitability relationship. Location: Europe. Taxon: Vascular plants. Methods: Distribution range maps were extracted from the Chorological Database Halle to derive information on the range and niche sizes of 517 European vascular plant species. To estimate local abundance, we assessed samples from 744,513 vegetation plots in the European Vegetation Archive, where local species' abundance is available as plant cover per plot. We then calculated the 'centrality', that is, the distance between the location of the abundance observation and each species' range centre in geographical and climatic space. The climatic suitability of plot locations was estimated using coarse‐grain species distribution models (SDMs). The relationships between centrality or climatic suitability with abundance was tested using linear models and quantile regression. We summarized the overall trend across species' regression slopes from linear models and quantile regression using a meta‐analytical approach. Results: We did not detect any positive relationships between a species' mean local abundance and the size of its geographical range or climatic niche. Contrasting yet significant correlations were detected between abundance and centrality or climatic suitability among species. Main conclusions: Our results do not provide unequivocal support for any of the relationships tested, demonstrating that determining properties of species' distributions at large grains and extents might be of limited use for predicting local abundance, including current SDM approaches. We conclude that environmental factors influencing individual performance and local abundance are likely to differ from those factors driving plant species' distribution at coarse resolution and broad geographical extents

Physicochemical uptake and release of volatile organic compounds by soil in coated-wall flow tube experiments with ambient air

Volatile organic compounds (VOCs) play a key role in atmospheric chemistry. Emission and deposition on soil have been suggested as important sources and sinks of atmospheric trace gases. The exchange characteristics and heterogeneous chemistry of VOCs on soil, however, are not well understood. We used a newly designed differential coated-wall flow tube system to investigate the long-term variability of bidirectional air–soil exchange of 13 VOCs under ambient air conditions of an urban background site in Beijing. Sterilized soil was investigated to address physicochemical processes and heterogeneous/multiphase reactions independently from biological activity. Most VOCs revealed net deposition with average uptake coefficients (γ) in the range of 10−7–10−6 (referring to the geometric soil surface area), corresponding to deposition velocities (Vd) of 0.0013–0.01&thinsp;cm&thinsp;s−1 and soil surface resistances (Rc) of 98–745&thinsp;s&thinsp;cm−1, respectively. Formic acid, however, was emitted at a long-term average rate of ∼6×10-3&thinsp;nmol&thinsp;m−2&thinsp;s−1, suggesting that it was formed and released upon heterogeneous oxidation of other VOCs. The soil–atmosphere exchange of one individual VOC species can be affected by both its surface degradation/depletion caused by surface reactions and by competitive uptake or heterogeneous formation/accommodation of other VOC species. Overall, the results show that physicochemical processing and heterogeneous oxidation on soil and soil-derived dust can act as a sink or as a source of atmospheric VOCs, depending on molecular properties and environmental conditions.</p

Evidence for Paternal Leakage in Hybrid Periodical Cicadas (Hemiptera: Magicicada spp.)

Mitochondrial inheritance is generally assumed to be maternal. However, there is increasing evidence of exceptions to this rule, especially in hybrid crosses. In these cases, mitochondria are also inherited paternally, so “paternal leakage” of mitochondria occurs. It is important to understand these exceptions better, since they potentially complicate or invalidate studies that make use of mitochondrial markers. We surveyed F1 offspring of experimental hybrid crosses of the 17-year periodical cicadas Magicicada septendecim, M. septendecula, and M. cassini for the presence of paternal mitochondrial markers at various times during development (1-day eggs; 3-, 6-, 9-week eggs; 16-month old 1st and 2nd instar nymphs). We found evidence of paternal leakage in both reciprocal hybrid crosses in all of these samples. The relative difficulty of detecting paternal mtDNA in the youngest eggs and ease of detecting leakage in older eggs and in nymphs suggests that paternal mitochondria proliferate as the eggs develop. Our data support recent theoretical predictions that paternal leakage may be more common than previously estimated