On the effects of turbulence on a screw dynamo

In an experiment in the Institute of Continuous Media Mechanics in Perm (Russia) an non--stationary screw dynamo is intended to be realized with a helical flow of liquid sodium in a torus. The flow is necessarily turbulent, that is, may be considered as a mean flow and a superimposed turbulence. In this paper the induction processes of the turbulence are investigated within the framework of mean--field electrodynamics. They imply of course a part which leads to an enhanced dissipation of the mean magnetic field. As a consequence of the helical mean flow there are also helical structures in the turbulence. They lead to some kind of $\alpha$--effect, which might basically support the screw dynamo. The peculiarity of this $\alpha$--effect explains measurements made at a smaller version of the device envisaged for the dynamo experiment. The helical structures of the turbulence lead also to other effects, which in combination with a rotational shear are potentially capable of dynamo action. A part of them can basically support the screw dynamo. Under the conditions of the experiment all induction effects of the turbulence prove to be rather weak in comparison to that of the main flow. Numerical solutions of the mean--field induction equation show that all the induction effects of the turbulence together let the screw dynamo threshold slightly, at most by one per cent, rise. The numerical results give also some insights into the action of the individual induction effects of the turbulence.Comment: 15 pages, 7 figures, in GAFD prin

Mean-field diffusivities in passive scalar and magnetic transport in irrotational flows

Certain aspects of the mean-field theory of turbulent passive scalar transport and of mean-field electrodynamics are considered with particular emphasis on aspects of compressible fluids. It is demonstrated that the total mean-field diffusivity for passive scalar transport in a compressible flow may well be smaller than the molecular diffusivity. This is in full analogy to an old finding regarding the magnetic mean-field diffusivity in an electrically conducting turbulently moving compressible fluid. These phenomena occur if the irrotational part of the motion dominates the vortical part, the P\`eclet or magnetic Reynolds number is not too large, and, in addition, the variation of the flow pattern is slow. For both the passive scalar and the magnetic cases several further analytical results on mean-field diffusivities and related quantities found within the second-order correlation approximation are presented, as well as numerical results obtained by the test-field method, which applies independently of this approximation. Particular attention is paid to non-local and non-instantaneous connections between the turbulence-caused terms and the mean fields. Two examples of irrotational flows, in which interesting phenomena in the above sense occur, are investigated in detail. In particular, it is demonstrated that the decay of a mean scalar in a compressible fluid under the influence of these flows can be much slower than without any flow, and can be strongly influenced by the so-called memory effect, that is, the fact that the relevant mean-field coefficients depend on the decay rates themselves.Comment: 13 pages, 10 figures, published on PR

The mean electromotive force due to turbulence of a conducting fluid in the presence of mean flow

The mean electromotive force caused by turbulence of an electrically conducting fluid, which plays a central part in mean--field electrodynamics, is calculated for a rotating fluid. Going beyond most of the investigations on this topic, an additional mean motion in the rotating frame is taken into account. One motivation for our investigation originates from a planned laboratory experiment with a Ponomarenko-like dynamo. In view of this application the second--order correlation approximation is used. The investigation is of high interest in astrophysical context, too. Some contributions to the mean electromotive are revealed which have not been considered so far, in particular contributions to the $\alpha$--effect and related effects due to the gradient of the mean velocity. Their relevance for dynamo processes is discussed. In a forthcoming paper the results reported here will be specified to the situation in the laboratory and partially compared with experimental findings.Comment: 16 pages, 2 figures, in PRE pres

Alpha-effect dynamos with zero kinetic helicity

A simple explicit example of a Roberts-type dynamo is given in which the alpha-effect of mean-field electrodynamics exists in spite of point-wise vanishing kinetic helicity of the fluid flow. In this way it is shown that alpha-effect dynamos do not necessarily require non-zero kinetic helicity. A mean-field theory of Roberts-type dynamos is established within the framework of the second-order correlation approximation. In addition numerical solutions of the original dynamo equations are given, that are independent of any approximation of that kind. Both theory and numerical results demonstrate the possibility of dynamo action in the absence of kinetic helicity.Comment: 6 pages, 3 figures, accepted for PR

Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation

The Changing Landscape for Stroke\ua0Prevention in AF: Findings From the GLORIA-AF Registry Phase 2

Background GLORIA-AF (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients with Atrial Fibrillation) is a prospective, global registry program describing antithrombotic treatment patterns in patients with newly diagnosed nonvalvular atrial fibrillation at risk of stroke. Phase 2 began when dabigatran, the first non\u2013vitamin K antagonist oral anticoagulant (NOAC), became available. Objectives This study sought to describe phase 2 baseline data and compare these with the pre-NOAC era collected during phase 1. Methods During phase 2, 15,641 consenting patients were enrolled (November 2011 to December 2014); 15,092 were eligible. This pre-specified cross-sectional analysis describes eligible patients\u2019 baseline characteristics. Atrial fibrillation disease characteristics, medical outcomes, and concomitant diseases and medications were collected. Data were analyzed using descriptive statistics. Results Of the total patients, 45.5% were female; median age was 71 (interquartile range: 64, 78) years. Patients were from Europe (47.1%), North America (22.5%), Asia (20.3%), Latin America (6.0%), and the Middle East/Africa (4.0%). Most had high stroke risk (CHA2DS2-VASc [Congestive heart failure, Hypertension, Age  6575 years, Diabetes mellitus, previous Stroke, Vascular disease, Age 65 to 74 years, Sex category] score  652; 86.1%); 13.9% had moderate risk (CHA2DS2-VASc = 1). Overall, 79.9% received oral anticoagulants, of whom 47.6% received NOAC and 32.3% vitamin K antagonists (VKA); 12.1% received antiplatelet agents; 7.8% received no antithrombotic treatment. For comparison, the proportion of phase 1 patients (of N = 1,063 all eligible) prescribed VKA was 32.8%, acetylsalicylic acid 41.7%, and no therapy 20.2%. In Europe in phase 2, treatment with NOAC was more common than VKA (52.3% and 37.8%, respectively); 6.0% of patients received antiplatelet treatment; and 3.8% received no antithrombotic treatment. In North America, 52.1%, 26.2%, and 14.0% of patients received NOAC, VKA, and antiplatelet drugs, respectively; 7.5% received no antithrombotic treatment. NOAC use was less common in Asia (27.7%), where 27.5% of patients received VKA, 25.0% antiplatelet drugs, and 19.8% no antithrombotic treatment. Conclusions The baseline data from GLORIA-AF phase 2 demonstrate that in newly diagnosed nonvalvular atrial fibrillation patients, NOAC have been highly adopted into practice, becoming more frequently prescribed than VKA in Europe and North America. Worldwide, however, a large proportion of patients remain undertreated, particularly in Asia and North America. (Global Registry on Long-Term Oral Antithrombotic Treatment in Patients With Atrial Fibrillation [GLORIA-AF]; NCT01468701

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture

Epilepsy is a highly heritable disorder affecting over 50 million people worldwide, of which about one-third are resistant to current treatments. Here we report a multi-ancestry genome-wide association study including 29,944 cases, stratified into three broad categories and seven subtypes of epilepsy, and 52,538 controls. We identify 26 genome-wide significant loci, 19 of which are specific to genetic generalized epilepsy (GGE). We implicate 29 likely causal genes underlying these 26 loci. SNP-based heritability analyses show that common variants explain between 39.6% and 90% of genetic risk for GGE and its subtypes. Subtype analysis revealed markedly different genetic architectures between focal and generalized epilepsies. Gene-set analyses of GGE signals implicate synaptic processes in both excitatory and inhibitory neurons in the brain. Prioritized candidate genes overlap with monogenic epilepsy genes and with targets of current antiseizure medications. Finally, we leverage our results to identify alternate drugs with predicted efficacy if repurposed for epilepsy treatment

Calreticulin is essential for cardiac development

Calreticulin is a ubiquitous Ca2+ binding protein, located in the endoplasmic reticulum lumen, which has been implicated in many diverse functions including: regulation of intracellular Ca2+ homeostasis, chaperone activity, steroid-mediated gene regulation, and cell adhesion. To understand the physiological function of calreticulin we used gene targeting to create a knockout mouse for calreticulin. Mice homozygous for the calreticulin gene disruption developed omphalocele (failure of absorption of the umbilical hernia) and showed a marked decrease in ventricular wall thickness and deep intertrabecular recesses in the ventricular walls. Transgenic mice expressing a green fluorescent protein reporter gene under the control of the calreticulin promoter were used to show that the calreticulin gene is highly activated in the cardiovascular system during the early stages of cardiac development. Calreticulin protein is also highly expressed in the developing heart, but it is only a minor component of the mature heart. Bradykinin-induced Ca2+ release by the InsP3-dependent pathway was inhibited in crt-/- cells, suggesting that calreticulin plays a role in Ca2+ homeostasis. Calreticulin-deficient cells also exhibited impaired nuclear import of nuclear factor of activated T cell (NF-AT3) transcription factor indicating that calreticulin plays a role in cardiac development as a component of the Ca2+/calcineurin/NF-AT/GATA-4 transcription pathway