Comparative analysis of full genomic sequences among different genotypes of dengue virus type 3

<p>Abstract</p> <p>Background</p> <p>Although the previous study demonstrated the envelope protein of dengue viruses is under purifying selection pressure, little is known about the genetic differences of full-length viral genomes of DENV-3. In our study, complete genomic sequencing of DENV-3 strains collected from different geographical locations and isolation years were determined and the sequence diversity as well as selection pressure sites in the DENV genome other than within the E gene were also analyzed.</p> <p>Results</p> <p>Using maximum likelihood and Bayesian approaches, our phylogenetic analysis revealed that the Taiwan's indigenous DENV-3 isolated from 1994 and 1998 dengue/DHF epidemics and one 1999 sporadic case were of the three different genotypes – I, II, and III, each associated with DENV-3 circulating in Indonesia, Thailand and Sri Lanka, respectively. Sequence diversity and selection pressure of different genomic regions among DENV-3 different genotypes was further examined to understand the global DENV-3 evolution. The highest nucleotide sequence diversity among the fully sequenced DENV-3 strains was found in the nonstructural protein 2A (mean ± SD: 5.84 ± 0.54) and envelope protein gene regions (mean ± SD: 5.04 ± 0.32). Further analysis found that positive selection pressure of DENV-3 may occur in the non-structural protein 1 gene region and the positive selection site was detected at position 178 of the NS1 gene.</p> <p>Conclusion</p> <p>Our study confirmed that the envelope protein is under purifying selection pressure although it presented higher sequence diversity. The detection of positive selection pressure in the non-structural protein along genotype II indicated that DENV-3 originated from Southeast Asia needs to monitor the emergence of DENV strains with epidemic potential for better epidemic prevention and vaccine development.</p

Ventricular tachycardia in ischemic cardiomyopathy; a combined endo-epicardial ablation as the first procedure versus a stepwise approach (EPILOGUE) - study protocol for a randomized controlled trial

Background: The role of epicardial substrate ablation of ventricular tachycardia (VT) as a first-line approach in patients with ischemic heart disease is not clearly defined. Epicardial ablation as a first-line option is standard for patients with nonischemic dilated cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy. Several nonrandomized studies, including studies on patients with ischemic heart disease, have shown that epicardial VT ablation improves outcome but this approach was often used after a failed endocardial approach. The aim of this study is to determine whether a combined endo-epicardial scar homogenization as a first-line approach will improve the outcome of VT ablation. Methods/Design: The EPILOGUE study is a multicenter, two-armed, nonblinded, randomized controlled trial. Patients with ischemic heart disease who are referred for VT ablation will be randomly assigned to combined endo-epicardial scar homogenization or endocardial scar homogenization only (control group). The primary outcome is recurrence of sustained VT during a 2-year follow-up. Secondary outcomes include procedural success and safety. Discussion: This study is the first randomized trial that evaluates the role of a combined endo-epicardial scar homogenization versus endocardial scar homogenization for the treatment of ischemic scar-related VT. Trial registration:NL4816807814v0

Quasiclassical description of transport through superconducting contacts

We present a theoretical study of transport properties through superconducting contacts based on a new formulation of boundary conditions that mimics interfaces for the quasiclassical theory of superconductivity. These boundary conditions are based on a description of an interface in terms of a simple Hamiltonian. We show how this Hamiltonian description is incorporated into quasiclassical theory via a T-matrix equation by integrating out irrelevant energy scales right at the onset. The resulting boundary conditions reproduce results obtained by conventional quasiclassical boundary conditions, or by boundary conditions based on the scattering approach. This formalism is well suited for the analysis of magnetically active interfaces as well as for calculating time-dependent properties such as the current-voltage characteristics or as current fluctuations in junctions with arbitrary transmission and bias voltage. This approach is illustrated with the calculation of Josephson currents through a variety of superconducting junctions ranging from conventional to d-wave superconductors, and to the analysis of supercurrent through a ferromagnetic nanoparticle. The calculation of the current-voltage characteristics and of noise is applied to the case of a contact between two d-wave superconductors. In particular, we discuss the use of shot noise for the measurement of charge transferred in a multiple Andreev reflection in d-wave superconductors

Josephson currents through spin-active interfaces

The Josephson coupling of two isotropic s-wave superconductors through a small, magnetically active junction is studied. This is done as a function of junction transparency and of the degree of spin-mixing occurring in the barrier. In the tunneling limit, the critical current shows an anomalous 1/T temperature dependence at low temperatures and for certain magnetic realizations of the junction. The behavior of the Josephson current is governed by Andreev bound states appearing within the superconducting gap and the position of these states in energy is tunable with the magnetic properties of the barrier. This study is done using the equilibrium part of the quasiclassical Zaitsev-Millis-Rainer-Sauls boundary condition for spin-active interfaces and a general solution of the boundary condition is found. This solution is a generalization of the one recently presented by Eschrig [M. Eschrig, Phys. Rev B 61, 9061 (2000)] for spin-conserving interfaces and allows an effective treatment of the problem of a superconductor in proximity to a magnetically active material.Comment: 8 pages + 3 eps figure

Galaxy Clusters Associated with Short GRBs. II. Predictions for the Rate of Short GRBs in Field and Cluster Early-Type Galaxies

We determine the relative rates of short GRBs in cluster and field early-type galaxies as a function of the age probability distribution of their progenitors, P(\tau) \propto \tau^n. This analysis takes advantage of the difference in the growth of stellar mass in clusters and in the field, which arises from the combined effects of the galaxy stellar mass function, the early-type fraction, and the dependence of star formation history on mass and environment. This approach complements the use of the early- to late-type host galaxy ratio, with the added benefit that the star formation histories of early-type galaxies are simpler than those of late-type galaxies, and any systematic differences between progenitors in early- and late-type galaxies are removed. We find that the ratio varies from R(cluster)/R(field) ~ 0.5 for n = -2 to ~ 3 for n = 2. Current observations indicate a ratio of about 2, corresponding to n ~ 0 - 1. This is similar to the value inferred from the ratio of short GRBs in early- and late-type hosts, but it differs from the value of n ~ -1 for NS binaries in the Milky Way. We stress that this general approach can be easily modified with improved knowledge of the effects of environment and mass on the build-up of stellar mass, as well as the effect of globular clusters on the short GRB rate. It can also be used to assess the age distribution of Type Ia supernova progenitors.Comment: ApJ accepted versio

Cohort profile: a collaborative multicentre study of retinal optical coherence tomography in 539 patients with neuromyelitis optica spectrum disorders (CROCTINO)

PURPOSE: Optical coherence tomography (OCT) captures retinal damage in neuromyelitis optica spectrum disorders (NMOSD). Previous studies investigating OCT in NMOSD have been limited by the rareness and heterogeneity of the disease. The goal of this study was to establish an image repository platform, which will facilitate neuroimaging studies in NMOSD. Here we summarise the profile of the Collaborative OCT in NMOSD repository as the initial effort in establishing this platform. This repository should prove invaluable for studies using OCT to investigate NMOSD. PARTICIPANTS: The current cohort includes data from 539 patients with NMOSD and 114 healthy controls. These were collected at 22 participating centres from North and South America, Asia and Europe. The dataset consists of demographic details, diagnosis, antibody status, clinical disability, visual function, history of optic neuritis and other NMOSD defining attacks, and OCT source data from three different OCT devices. FINDINGS TO DATE: The cohort informs similar demographic and clinical characteristics as those of previously published NMOSD cohorts. The image repository platform and centre network continue to be available for future prospective neuroimaging studies in NMOSD. For the conduct of the study, we have refined OCT image quality criteria and developed a cross-device intraretinal segmentation pipeline. FUTURE PLANS: We are pursuing several scientific projects based on the repository, such as analysing retinal layer thickness measurements, in this cohort in an attempt to identify differences between distinct disease phenotypes, demographics and ethnicities. The dataset will be available for further projects to interested, qualified parties, such as those using specialised image analysis or artificial intelligence applications