Dipolar Interactions in Superconductor-Ferromagnet Heterostructures

We consider a simple model for a superlattice composed of a thin magnetic film placed between two bulk superconductors. The magnetic film is modelled by a planar but otherwise arbitrary distribution of magnetic dipoles and the superconductors are treated in the London approximation. Due to the linearity of the problem, we are able to compute the magnetic energy of the film in the presence of the superconductors. We show that in the case of small wavenumbers compared to the inverse London penetration depth, the magnetic energy resembles the energy of a distribution of magnetisation in a two dimensional space. Possible experimental applications of these results are discussed.Comment: RevTeX, 29 pages, 3 figures. To be published in Phys. Rev. B. Changes were made (including adding fig. 3), to conform with the referee's report. Reference 54 was also adde

BoscoR: Extending R from the desktop to the Grid

In this paper, we describe a framework to execute R functions on remote resources from the desktop using Bosco. The R language is attractive to researchers because of its high level programming constructs which lower the barrier of entry for use. As the use of the R programming language in HPC and High Throughput Computing (HTC) has grown, so too has the need for parallel libraries in order to utilize computing resources. Bosco is middleware that uses common protocols to manage job submissions to a variety of remote computational platforms and resources. The researcher is able to control and monitor remote submission from their interactive R IDE, such as RStudio. Bosco is capable of managing many concurrent tasks submitted to remote resources while providing feedback to the interactive R environment. We will also show how this framework can be used to access national infrastructure such as the Open Science Grid. Through interviews with R users, and their feedback after using BoscoR, we learned how R users work and designed BoscoR to fit their needs. We incorporated their feedback to improve BoscoR by adding much needed features, such as remote package management. A key design goal was to have a flat learning curve in using BoscoR for any R user

Genetic diversity and origins of the homoploid type hybrid Phytophthora×alni

Assessing the process that gives rise to hybrid pathogens is central to understanding the evolution of emerging plant diseases. Phytophthora xalni, a pathogen of alder, results from the homoploid hybridization of two related species, Phytophthora uniformis and Phytophthora xmultiformis. Describing the genetic characteristics of P. xalni should help us understand how reproductive mechanisms and historical processes shaped the population structure of this emerging hybrid pathogen. The population genetic structure of P. xalni and the relationship with its parental species were investigated using 12 microsatellites and one mitochondrial DNA (mtDNA) marker on a European collection of 379 isolates. Populations of P. xalni were dominated by one multilocus genotype (MLG). The frequency of this dominant MLG increased after the disease emergence together with a decline in diversity, suggesting that it was favored by a genetic mechanism such as drift or selection. Combined microsatellite and mtDNA results confirmed that P. xalni originated from multiple hybridization events that involved different genotypes of the progenitors. Our detailed analyses point to a geographic structure that mirrors that observed for P. uniformis in Europe. The study provides more insights on the contribution of P. uniformis, an invasive species in Europe, to the emergence of Phytophthora-induced alder decline. IMPORTANCE Our study describes an original approach to assess the population genetics of polyploid organisms using microsatellite markers. By studying the parental subgenomes present in the interspecific hybrid P. xalni, we were able to assess the geographical and temporal structure of European populations of the hybrid, shedding new light on the evolution of an emerging plant pathogen. In turn, the study of the parental subgenomes permitted us to assess some genetic characteristics of the parental species of P. xalni, P. uniformis, and P. xmultiformis, which are seldom sampled in nature. The subgenomes found in P. xalni represent a picture of the "fossilized" diversity of the parental species

OH and RO 2 radicals at Dome C (East Antarctica): first observations and assessment of photochemical budget

International audienceMeasurements of OH and total peroxy RO 2 (HO 2 + organic peroxy) radicals were performed in December 2011/January 2012 at the Dome C Concordia station (East Antarctica, 75.1˚S / 123.3˚E) in the frame of the Oxi-dant Production over Antarctic Land and its Export (OPALE) project. The goal of these first on the East Antarctica plateau radical measurements was to estimate the oxidative capacity and assess the role of snow emissions on the radical budget in this part of Antarctica. The OH concentration levels were found to be in general similar to those observed at South Pole. However, based on the analysis of the OH sources and sinks derived from the available measurements of NO x , HONO, HCHO, H 2 O 2 and others, it has been concluded that, in contrast to South Pole, the photolysis of HONO is the major OH source at Dome C site. The role of HONO as the major source of OH is also supported by an excellent correlation of OH with the production rate of OH from the HONO photolysis. The observed diurnal profiles of OH and RO 2 are discussed in relation with boundary dynamics and the variability of photolysis and snow emissions rates

Grid Interoperation with ARC Middleware for the CMS Experiment

The Compact Muon Solenoid (CMS) is one of the general purpose experiments at the CERN Large Hadron Collider (LHC). CMS computing relies on different grid infrastructures to provide computational and storage resources. The major grid middleware stacks used for CMS computing are gLite, Open Science Grid (OSG) and ARC (Advanced Resource Connector). Helsinki Institute of Physics (HIP) hosts one of the Tier-2 centers for CMS computing. CMS Tier-2 centers operate software systems for data transfers (PhEDEx), Monte Carlo production (ProdAgent) and data analysis (CRAB). In order to provide the Tier-2 services for CMS, HIP uses tools and components from both ARC and gLite grid middleware stacks. Interoperation between grid systems is a challenging problem and HIP uses two different solutions to provide the needed services. The first solution is based on gLite-ARC grid level interoperability. This allows to use ARC resources in CMS without modifying the CMS application software. The second solution is based on developing specific ARC plugins in CMS software

Renewal processes and fluctuation analysis of molecular motor stepping

We model the dynamics of a processive or rotary molecular motor using a renewal processes, in line with the work initiated by Svoboda, Mitra and Block. We apply a functional technique to compute different types of multiple-time correlation functions of the renewal process, which have applications to bead-assay experiments performed both with processive molecular motors, such as myosin V and kinesin, and rotary motors, such as F1-ATPase

Domain wall roughening in dipolar films in the presence of disorder

We derive a low-energy Hamiltonian for the elastic energy of a N\'eel domain wall in a thin film with in-plane magnetization, where we consider the contribution of the long-range dipolar interaction beyond the quadratic approximation. We show that such a Hamiltonian is analogous to the Hamiltonian of a one-dimensional polaron in an external random potential. We use a replica variational method to compute the roughening exponent of the domain wall for the case of two-dimensional dipolar interactions.Comment: REVTEX, 35 pages, 2 figures. The text suffered minor changes and references 1,2 and 12 were added to conform with the referee's repor

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Mice deficient in CD38 develop an attenuated form of collagen type II-induced arthritis

CD38, a type II transmembrane glycoprotein expressed in many cells of the immune system, is involved in cell signaling, migration and differentiation. Studies in CD38 deficient mice (CD38 KO mice) indicate that this molecule controls inflammatory immune responses, although its involvement in these responses depends on the disease model analyzed. Here, we explored the role of CD38 in the control of autoimmune responses using chicken collagen type II (col II) immunized C57BL/6-CD38 KO mice as a model of collagen-induced arthritis (CIA). We demonstrate that CD38 KO mice develop an attenuated CIA that is accompanied by a limited joint induction of IL-1β and IL-6 expression, by the lack of induction of IFNγ expression in the joints and by a reduction in the percentages of invariant NKT (iNKT) cells in the spleen. Immunized CD38 KO mice produce high levels of circulating IgG1 and low of IgG2a anti-col II antibodies in association with reduced percentages of Th1 cells in the draining lymph nodes. Altogether, our results show that CD38 participates in the pathogenesis of CIA controlling the number of iNKT cells and promoting Th1 inflammatory responses

Epistatic Roles for Pseudomonas aeruginosa MutS and DinB (DNA Pol IV) in Coping with Reactive Oxygen Species-Induced DNA Damage

Pseudomonas aeruginosa is especially adept at colonizing the airways of individuals afflicted with the autosomal recessive disease cystic fibrosis (CF). CF patients suffer from chronic airway inflammation, which contributes to lung deterioration. Once established in the airways, P. aeruginosa continuously adapts to the changing environment, in part through acquisition of beneficial mutations via a process termed pathoadaptation. MutS and DinB are proposed to play opposing roles in P. aeruginosa pathoadaptation: MutS acts in replication-coupled mismatch repair, which acts to limit spontaneous mutations; in contrast, DinB (DNA polymerase IV) catalyzes error-prone bypass of DNA lesions, contributing to mutations. As part of an ongoing effort to understand mechanisms underlying P. aeruginosa pathoadaptation, we characterized hydrogen peroxide (H2O2)-induced phenotypes of isogenic P. aeruginosa strains bearing different combinations of mutS and dinB alleles. Our results demonstrate an unexpected epistatic relationship between mutS and dinB with respect to H2O2-induced cell killing involving error-prone repair and/or tolerance of oxidized DNA lesions. In striking contrast to these error-prone roles, both MutS and DinB played largely accurate roles in coping with DNA lesions induced by ultraviolet light, mitomycin C, or 4-nitroquinilone 1-oxide. Models discussing roles for MutS and DinB functionality in DNA damage-induced mutagenesis, particularly during CF airway colonization and subsequent P. aeruginosa pathoadaptation are discussed