The user support programme and the training infrastructure of the EGI Federated Cloud

The EGI Federated Cloud is a standards-based, open cloud system as well as its enabling technologies that federates institutional clouds to offer a scalable computing platform for data and/or compute driven applications and services. The EGI Federated Cloud is based on open standards and open source Cloud Management Frameworks and offers to its users IaaS, PaaS and SaaS capabilities and interfaces tuned towards the needs of users in research and education. The federation enables scientific data, workloads, simulations and services to span across multiple administrative locations, allowing researchers and educators to access and exploit the distributed resources as an integrated system. The EGI Federated Cloud collaboration established a user support model and a training infrastructure to raise visibility of this service within European scientific communities with the overarching goal to increase adoption and, ultimately increase the usage of e-infrastructures for the benefit of the whole European Research Area. The paper describes this scalable user support and training infrastructure models. The training infrastructure is built on top of the production sites to reduce costs and increase its sustainability. Appropriate design solutions were implemented to reduce the security risks due to the cohabitation of production and training resources on the same sites. The EGI Federated Cloud educational program foresees different kind of training events from basic tutorials to spread the knowledge of this new infrastructure to events devoted to specific scientific disciplines teaching how to use tools already integrated in the infrastructure with the assistance of experts identified in the EGI community. The main success metric of this educational program is the number of researchers willing to try the Federated Cloud, which are steered into the EGI world by the EGI Federated Cloud Support Team through a formal process that brings them from the initial tests to fully exploit the production resources. © 2015 IEEE

Automatic deployment of interoperable legacy code services

The Grid Execution Management for Legacy Code Architecture (GEMLCA) enables exposing legacy applications as Grid services without re-engineering the code, or even requiring access to the source files. The integration of current GT3 and GT4 based GEMLCA implementations with the P-GRADE Grid portal allows the creation, execution and visualisation of complex Grid workflows composed of legacy and nonlegacy components. However, the deployment of legacy codes and mapping their execution to Grid resources is currently done manually. This paper outlines how GEMLCA can be extended with automatic service deployment, brokering, and information system support. A conceptual architecture for an Automatic Deployment Service (ADS) and for an x-Service Interoperability Layer (XSILA) are introduced explaining how these mechanisms support desired features in future releases of GEMLCA

Orbital textures and charge density waves in transition metal dichalcogenides

Low-dimensional electron systems, as realized naturally in graphene or created artificially at the interfaces of heterostructures, exhibit a variety of fascinating quantum phenomena with great prospects for future applications. Once electrons are confined to low dimensions, they also tend to spontaneously break the symmetry of the underlying nuclear lattice by forming so-called density waves; a state of matter that currently attracts enormous attention because of its relation to various unconventional electronic properties. In this study we reveal a remarkable and surprising feature of charge density waves (CDWs), namely their intimate relation to orbital order. For the prototypical material 1T-TaS2 we not only show that the CDW within the two-dimensional TaS2-layers involves previously unidentified orbital textures of great complexity. We also demonstrate that two metastable stackings of the orbitally ordered layers allow to manipulate salient features of the electronic structure. Indeed, these orbital effects enable to switch the properties of 1T-TaS2 nanostructures from metallic to semiconducting with technologically pertinent gaps of the order of 200 meV. This new type of orbitronics is especially relevant for the ongoing development of novel, miniaturized and ultra-fast devices based on layered transition metal dichalcogenides

EX Lupi in quiescence

EX Lup is the prototype of EXors, a subclass of low-mass pre-main sequence stars whose episodic eruptions are attributed to temporarily increased accretion. In quiescence the optical and near-infrared properties of EX Lup cannot be distinguished from those of normal T Tau stars. Here we investigate whether it is the circumstellar disk structure which makes EX Lup an atypical Class II object. During outburst the disk might undergo structural changes. Our characterization of the quiescent disk is intended to serve as a reference to study the physical changes related to one of EX Lupi's strongest known eruptions in 2008 Jan-Sep. We searched the literature for photometric and spectroscopic observations including ground-based, IRAS, ISO and Spitzer data. After constructing the optical-infrared spectral energy distribution (SED), we compared it with the typical SEDs of other young stellar objects and modeled it using the Monte Carlo radiative transfer code RADMC. A mineralogical decomposition of the 10 micron silicate emission feature and also the description of the optical and near-infrared spectra were performed. The SED is in general similar to that of a typical T Tauri star, though above 7 micron EX Lup emits higher flux. The quiescent phase data suggest low level variability in the optical-mid-infrared domain. Integrating the optical and infrared fluxes we derived a bolometric luminosity of 0.7 L_Sun. The 10 micron silicate profile could be fitted by a mixture consisting of amorphous silicates, no crystalline silicates were found. A modestly flaring disk model with a total mass of 0.025 M_Sun and an outer radius of 150 AU was able to reproduce the observed SED. The derived inner radius of 0.2 AU is larger than the sublimation radius, and this inner gap sets EX Lup aside from typical T Tauri stars.Comment: Accepted for publication in Astronomy and Astrophysics, 10 pages, 6 figure

The rise of fully turbulent flow

Over a century of research into the origin of turbulence in wallbounded shear flows has resulted in a puzzling picture in which turbulence appears in a variety of different states competing with laminar background flow. At slightly higher speeds the situation changes distinctly and the entire flow is turbulent. Neither the origin of the different states encountered during transition, nor their front dynamics, let alone the transformation to full turbulence could be explained to date. Combining experiments, theory and computer simulations here we uncover the bifurcation scenario organising the route to fully turbulent pipe flow and explain the front dynamics of the different states encountered in the process. Key to resolving this problem is the interpretation of the flow as a bistable system with nonlinear propagation (advection) of turbulent fronts. These findings bridge the gap between our understanding of the onset of turbulence and fully turbulent flows.Comment: 31 pages, 9 figure

Comparative Network Analysis of Preterm vs. Full-Term Infant-Mother Interactions

Several studies have reported that interactions of mothers with preterm infants show differential characteristics compared to that of mothers with full-term infants. Interaction of preterm dyads is often reported as less harmonious. However, observations and explanations concerning the underlying mechanisms are inconsistent. In this work 30 preterm and 42 full-term mother-infant dyads were observed at one year of age. Free play interactions were videotaped and coded using a micro-analytic coding system. The video records were coded at one second resolution and studied by a novel approach using network analysis tools. The advantage of our approach is that it reveals the patterns of behavioral transitions in the interactions. We found that the most frequent behavioral transitions are the same in the two groups. However, we have identified several high and lower frequency transitions which occur significantly more often in the preterm or full-term group. Our analysis also suggests that the variability of behavioral transitions is significantly higher in the preterm group. This higher variability is mostly resulted from the diversity of transitions involving non-harmonious behaviors. We have identified a maladaptive pattern in the maternal behavior in the preterm group, involving intrusiveness and disengagement. Application of the approach reported in this paper to longitudinal data could elucidate whether these maladaptive maternal behavioral changes place the infant at risk for later emotional, cognitive and behavioral disturbance

Oscillatory surface rheotaxis of swimming E. coli bacteria

Bacterial contamination of biological conducts, catheters or water resources is a major threat to public health and can be amplified by the ability of bacteria to swim upstream. The mechanisms of this rheotaxis, the reorientation with respect to flow gradients, often in complex and confined environments, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow with two complementary experimental assays, based on 3D Lagrangian tracking and fluorescent flagellar labelling and we develop a theoretical model for their rheotactic motion. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A full theoretical analysis explains these regimes and predicts the corresponding critical shear rates. The predicted transitions as well as the oscillation dynamics are in good agreement with experimental observations. Our results shed new light on bacterial transport and reveal new strategies for contamination prevention.Comment: 12 pages, 5 figure

Comprehensive DNA Methylation Analysis Reveals a Common Ten-Gene Methylation Signature in Colorectal Adenomas and Carcinomas

Microarray analysis of promoter hypermethylation provides insight into the role and extent of DNA methylation in the development of colorectal cancer (CRC) and may be co-monitored with the appearance of driver mutations. Colonic biopsy samples were obtained endoscopically from 10 normal, 23 adenoma (17 low-grade (LGD) and 6 high-grade dysplasia (HGD)), and 8 ulcerative colitis (UC) patients (4 active and 4 inactive). CRC samples were obtained from 24 patients (17 primary, 7 metastatic (MCRC)), 7 of them with synchronous LGD. Field effects were analyzed in tissues 1 cm (n = 5) and 10 cm (n = 5) from the margin of CRC. Tissue materials were studied for DNA methylation status using a 96 gene panel and for KRAS and BRAF mutations. Expression levels were assayed using whole genomic mRNA arrays. SFRP1 was further examined by immunohistochemistry. HT29 cells were treated with 5-aza-2' deoxycytidine to analyze the reversal possibility of DNA methylation. More than 85% of tumor samples showed hypermethylation in 10 genes (SFRP1, SST, BNC1, MAL, SLIT2, SFRP2, SLIT3, ALDH1A3, TMEFF2, WIF1), whereas the frequency of examined mutations were below 25%. These genes distinguished precancerous and cancerous lesions from inflamed and healthy tissue. The mRNA alterations that might be caused by systematic methylation could be partly reversed by demethylation treatment. Systematic changes in methylation patterns were observed early in CRC carcinogenesis, occuring in precursor lesions and CRC. Thus we conclude that DNA hypermethylation is an early and systematic event in colorectal carcinogenesis, and it could be potentially reversed by systematic demethylation therapy, but it would need more in vitro and in vivo experiments to support this theory

The influence of long-term treadmill exercise on bone mass and articular cartilage in ovariectomized rats

<p>Abstract</p> <p>Background</p> <p>Loss of bone quality and deterioration of articular cartilage are commonly seen after menopause. While exercise may protect against tissue degeneration, a clear link has yet to be established. The aim of the present study is to investigate the influence of long-term treadmill exercise on changes in bone mass and articular cartilage in ovariectomized rats.</p> <p>Methods</p> <p>Sixty female Sprague-Dawley rats were randomly assigned to 4 groups: ovariectomized (OVX), ovariectomized plus treadmill exercise (OVX-RUN), treadmill exercise alone (RUN), and control (CON) groups. After 36 weeks, the following variables were compared among the 4 groups. Bone mass was evaluated by trabecular bone volume and bone mineral density (BMD). Articular cartilage in the knee joints was evaluated by histology analysis and a modified Mankin score.</p> <p>Results</p> <p>Rats in the ovariectomized groups (OVX and OVX-RUN) had significantly lower BMD and bone mass than the non-ovariectomized rats (CON and RUN), indicating that exercise did little to preserve bone mass. However, the sedentary OVX group had a significantly worse modified Mankin score (7.7 ± 1.4) than the OVX-RUN group (4.8 ± 1.0), whose scores did not differ significantly from the other 2 non-operated groups. The articular cartilage in the sedentary OVX rats was relatively thinner, hypocellular, and had more clefts than in the other 3 groups.</p> <p>Conclusion</p> <p>This study suggests that long-term exercise protects articular cartilage in OVX rats but does not retard the loss of bone mass seen in after menopause.</p