Global turbulence simulations of the tokamak edge region with GRILLIX

Turbulent dynamics in the scrape-off layer (SOL) of magnetic fusion devices is intermittent with large fluctuations in density and pressure. Therefore, a model is required that allows perturbations of similar or even larger magnitude to the time-averaged background value. The fluid-turbulence code GRILLIX is extended to such a global model, which consistently accounts for large variation in plasma parameters. Derived from the drift reduced Braginskii equations, the new GRILLIX model includes electromagnetic and electron-thermal dynamics, retains global parametric dependencies and the Boussinesq approximation is not applied. The penalisation technique is combined with the flux-coordinate independent (FCI) approach [F. Hariri and M. Ottaviani, Comput.Phys.Commun. 184:2419, (2013); A. Stegmeir et al., Comput.Phys.Commun. 198:139, (2016)], which allows to study realistic diverted geometries with X-point(s) and general boundary contours. We characterise results from turbulence simulations and investigate the effect of geometry by comparing simulations in circular geometry with toroidal limiter against realistic diverted geometry at otherwise comparable parameters. Turbulence is found to be intermittent with relative fluctuation levels of up to 40% showing that a global description is indeed important. At the same time via direct comparison, we find that the Boussinesq approximation has only a small quantitative impact in a turbulent environment. In comparison to circular geometry the fluctuations are reduced in diverted geometry, which is related to a different zonal flow structure. Moreover, the fluctuation level has a more complex spatial distribution in diverted geometry. Due to local magnetic shear, which differs fundamentally in circular and diverted geometry, turbulent structures become strongly distorted in the perpendicular direction and are eventually damped away towards the X-point

Increasing the Fine Structure Visibility of the Hinode SOT Ca II H Filtergrams

We present the improved so-called Madmax (OMC) operator selecting maxima of convexities computed in multiple directions around each pixel rewritten in MatLab and shown to be very efficient for pattern recognition. The aim of the algorithm is to trace the bright hair-like features (for ex. chromospheric thin jets or spicules) of solar ultimate observations polluted by a noise of different origins. This popular spatial operator uses the second derivative in the optimally selected direction for which its absolute value has a maximum value. Accordingly, it uses the positivity of the resulting intensity signal affected by a superposed noise. The results are illustrated using a test artificially generated image and real SOT (Hinode) images are also used, to make your own choice of the sensitive parameters to use in improving the visibility of images.Comment: 12 pages, 3 figurs, submitted in Solar Physic

Mitochondrial encephalocardio-myopathy with early neonatal onset due to TMEM70 mutation

Objective Mitochondrial disturbances of energy-generating systems in childhood are a heterogeneous group of disorders. The aim of this multi-site survey was to characterise the natural course of a novel mitochondrial disease with ATP synthase deficiency and mutation in the TMEM70 gene. Methods Retrospective clinical data and metabolic profiles were collected and evaluated in 25 patients (14 boys, 11 girls) from seven European countries with a c. 317-2A -> G mutation in the TMEM70 gene. Results Severe muscular hypotonia (in 92% of newborns), apnoic spells (92%), hypertrophic cardiomyopathy (HCMP; 76%) and profound lactic acidosis (lactate 5-36 mmol/l; 92%) with hyperammonaemia (100-520 mu mol/l; 86%) were present from birth. Ten patients died within the first 6 weeks of life. Most patients surviving the neonatal period had persisting muscular hypotonia and developed psychomotor delay. HCMP was non-progressive and even disappeared in some children. Hypospadia was present in 54% of the boys and cryptorchidism in 67%. Increased excretion of lactate and 3-methylglutaconic acid (3-MGC) was observed in all patients. In four surviving patients, life-threatening hyperammonaemia occurred during childhood, triggered by acute gastroenteritis and prolonged fasting. Conclusions ATP synthase deficiency with mutation in TMEM70 should be considered in the diagnosis and management of critically ill neonates with early neonatal onset of muscular hypotonia, HCMP and hypospadias in boys accompanied by lactic acidosis, hyperammonaemia and 3-MGC-uria. However, phenotype severity may vary significantly. The disease occurs frequently in the Roma population and molecular-genetic analysis of the TMEM70 gene is sufficient for diagnosis without need of muscle biopsy in affected children

Solving Medium-Density Subset Sum Problems in Expected Polynomial Time: An Enumeration Approach

The subset sum problem (SSP) can be briefly stated as: given a target integer $E$ and a set $A$ containing $n$ positive integer $a_j$, find a subset of $A$ summing to $E$. The \textit{density} $d$ of an SSP instance is defined by the ratio of $n$ to $m$, where $m$ is the logarithm of the largest integer within $A$. Based on the structural and statistical properties of subset sums, we present an improved enumeration scheme for SSP, and implement it as a complete and exact algorithm (EnumPlus). The algorithm always equivalently reduces an instance to be low-density, and then solve it by enumeration. Through this approach, we show the possibility to design a sole algorithm that can efficiently solve arbitrary density instance in a uniform way. Furthermore, our algorithm has considerable performance advantage over previous algorithms. Firstly, it extends the density scope, in which SSP can be solved in expected polynomial time. Specifically, It solves SSP in expected $O(n\log{n})$ time when density $d \geq c\cdot \sqrt{n}/\log{n}$, while the previously best density scope is $d \geq c\cdot n/(\log{n})^{2}$. In addition, the overall expected time and space requirement in the average case are proven to be $O(n^5\log n)$ and $O(n^5)$ respectively. Secondly, in the worst case, it slightly improves the previously best time complexity of exact algorithms for SSP. Specifically, the worst-case time complexity of our algorithm is proved to be $O((n-6)2^{n/2}+n)$, while the previously best result is $O(n2^{n/2})$.Comment: 11 pages, 1 figur

Genetic analyses reveal cryptic introgression in secretive marsh bird populations

Hybridization is common in bird populations but can be challenging for management, especially if one of the two parent species is of greater conservation concern than the other. King rails (Rallus elegans) and clapper rails (R. crepitans) are two marsh bird species with similar morphologies, behaviors, and overlapping distributions. The two species are found along a salinity gradient with the king rail in freshwater marshes and the clapper in estuarine marshes. However, this separation is not absolute; they are occasionally sympatric, and there are reports of interbreeding. In Virginia, USA, both king and clapper rails are identified by the state as Species of Greater Conservation Need, although clappers are thought to be more abundant and king rails have a higher priority ranking. We used a mitochondrial DNA marker and 13 diagnostic nuclear single nucleotide polymorphisms (SNPs) to identify species, classify the degree of introgression, and explore the evolutionary history of introgression in two putative clapper rail focal populations along a salinity gradient in coastal Virginia. Genetic analyses revealed cryptic introgression with site‐specific rates of admixture. We identified a pattern of introgression where clapper rail alleles predominate in brackish marshes. These results suggest clapper rails may be displacing king rails in Virginia coastal waterways, most likely as a result of ecological selection. As introgression can result in various outcomes from outbreeding depression to local adaptation, continued monitoring of these populations would allow further exploration of hybrid fitness and inform conservation management

Dysregulated autophagy in restrictive cardiomyopathy due to Pro209Leu mutation in BAG3

Myofibrillary myopathies (MFM) are hereditary myopathies histologically characterized by degeneration of myofibrils and aggregation of proteins in striated muscle. Cardiomyopathy is common in MFM but the pathophysiological mechanisms are not well understood. The BAG3-Pro209Leu mutation is associated with early onset MFM and severe restrictive cardiomyopathy (RCM), often necessitating heart transplantation during childhood. We report on a young male patient with a BAG3-Pro209Leu mutation who underwent heart transplantation at eight years of age. Detailed morphological analyses of the explanted heart tissue showed intracytoplasmic inclusions, aggregation of BAG3 and desmin, disintegration of myofibers and Z-disk alterations. The presence of undegraded autophagosomes, seen by electron microscopy, as well as increased levels of p62, LC3-I and WIPI1, detected by immunohistochemistry and western blot analyses, indicated a dysregulation of autophagy. Parkin and PINK1, proteins involved in mitophagy, were slightly increased whereas mitochondrial OXPHOS activities were not altered. These findings indicate that altered autophagy plays a role in the pathogenesis and rapid progression of RCM in MFM caused by the BAG3-Pro209Leu mutation, which could have implications for future therapeutic strategies

Universality of Symmetry and Mixed-symmetry Collective Nuclear States

The global correlation in the observed variation with mass number of the $E2$ and summed $M1$ transition strengths is examined for rare earth nuclei. It is shown that a theory of correlated $S$ and $D$ fermion pairs with a simple pairing plus quadrupole interaction leads naturally to this universality. Thus a unified and quantitative description emerges for low-lying quadrupole and dipole strengths.Comment: In press, Phys. Rev. Lett. 199

GPS phase scintillation and proxy index at high latitudes during a moderate geomagnetic storm

The amplitude and phase scintillation indices are customarily obtained by specialised GPS Ionospheric Scintillation and TEC Monitors (GISTMs) from L1 signal recorded at the rate of 50 Hz. The scintillation indices S[subscript 4] and σ[subscript Φ] are stored in real time from an array of high-rate scintillation receivers of the Canadian High Arctic Ionospheric Network (CHAIN). Ionospheric phase scintillation was observed at high latitudes during a moderate geomagnetic storm (Dst = −61 nT) that was caused by a moderate solar wind plasma stream compounded with the impact of two coronal mass ejections. The most intense phase scintillation (σ[subscript Φ] ~ 1 rad) occurred in the cusp and the polar cap where it was co-located with a strong ionospheric convection, an extended tongue of ionisation and dense polar cap patches that were observed with ionosondes and HF radars. At sub-auroral latitudes, a sub-auroral polarisation stream that was observed by mid-latitude radars was associated with weak scintillation (defined arbitrarily as σ[subscript Φ] 0.1 rad and DPR > 2 mm s[superscript −1], both mapped as a function of magnetic latitude and magnetic local time, are very similar.National Science Foundation (U.S.) (Grant ATM-0856093