bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radio Frequency Induced and Neoclassical Asymmetries and their Effects on Turbulent Impurity Transport in a Tokamak
Authors: Pusztai I. , Landreman M. , Mollén A. , Kazakov Ye. O. , Fülöp T. 
Published: June 2014

AbstractPoloidal asymmetries in the impurity density can be generated by radio frequency heating in the core and by neoclassical effects in the edge of tokamak plasmas. In a pedestal case study, using global neoclassical simulations we find that finite orbit width effects can generate significant poloidal variation in the electrostatic potential, which varies on a small radial scale. Gyrokinetic modeling shows that these poloidal asymmetries can be strong enough to significantly modify turbulent impurity peaking. In the pedestal the E × B drift in the radial electric field can give a larger contribution to the poloidal motion of impurities than that of their parallel streaming. Under such circumstances we find that up‐down asymmetries can also affect impurity peaking. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Integrated Modelling of Nitrogen Seeded JET ILW Discharges for H‐mode and Hybrid Scenarios
Authors: Ivanova‐Stanik I. , Zagórski R. , Telesca G. , Czarnecka A. , Challis C. , Hobirk J. , JET EFDA contributors  
Published: June 2014

AbstractIn this paper numerical simulations with COREDIV code of JET discharges with ITER‐like wall are presented. We concentrate on the JET H‐mode and hybrid scenarios with nitrogen seeding and all simulations have been performed with the same transport model and only the discharge input parameters like auxiliary heating Paux, line average plasma density nline, confinement factor H98, nitrogen input flux ΓpuffN were changed in the calcu lations. The separatrix density nsepe is an input parameter in our model and has been kept equal to 0.4÷0.5nlinein the simulations, with the recycling coefficient adjusted accordingly. It has been shown that COREDIV is able to reproduce basic parameters of nitrogen seeded discharges for both H‐mode and hybrid scenarios. We have achieved reasonable agreement with global plasma parameters like radiations levels, Zeff and tungsten concentrations and the plasma profiles, including density, temperature and radiation are in very good agreement with experimental data. The agreement of the code results with the experimental data might be even better, if the simulations are further tuned taking into account uncertainties to the sputtering model, separatrix density or SOL transport. Simulations show that the observed Zeff level is defined mostly by the low Z impurity content, Be and N2 in the considered shots. It has been found that the tungsten radiation plays always very important role and can not be mitigated even by strong influx of nitrogen. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Modelling the Effect of the Super‐X Divertor in MAST Upgrade on Transition to Detachment and Distribution of Volumetric Power Losses
Authors: Havlíčková E. , Wischmeier M. , Fishpool G. 
Published: June 2014

AbstractA density scan is performed in SOLPS5.0 for two divertor configurations of MAST Upgrade: (i) a short divertor silimiar to configurations in present‐day tokamaks, (ii) the Super‐X divertor. In the simulation, a clear roll‐over of the ion flux and plasma density at the target is observed as the plasma detaches. The separatrix density at which the transition occurs is estimated. In addition, we investigate the ability of the long‐legged divertor to reduce the target power loads and enhance the radiated power at higher collisionalities. We also study how distribution of power losses in the divertor region changes with the modification of geometry and we separately analyze neutral radiation and carbon ion line radiation. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
First EMC3‐EIRENE Simulations with Divertor Legs of LHD in Realistic Device Geometry
Authors: Kawamura G. , Feng Y. , Kobayashi M. , Shoji M. , Morisaki T. , Masuzaki S. , Tomita Y. 
Published: June 2014

AbstractAn extended mesh system for EMC3‐EIRENE has been developed to simulate peripheral plasma including the ergodic and the divertor leg regions of LHD. Both the open and the closed divertor configurations are available. A series of simulations for 8MW input power, five different electron densities at the LCFS (last closed flux surface) and the open/closed configurations were carried out. Approximately 10 times larger neutral pressure was observed under the dome structure compared with the open configuration, which is in good agreement with experimental measurements. In the case of the closed configuration, the leg regions have a large contribution of ionization to hydrogen recycling. In the case of high density discharges, however, electron temperature in the legs becomes low and the major contribution of ionization moves to the ergodic region. Significant influence of configurations is observed in the inboard side of LHD, where closed divertor components are installed but little influence is seen near the LCFS. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Investigation of Oscillations in the Plasma Sheath
Authors: Brida D. , Tskhakaya D. 
Published: June 2014

AbstractIn this work different plasma oscillation modes in the plasma sheath (PS) have been identified. For this pur‐pose an electron‐deuterium plasma under different conditions was considered. The plasma was simulated with the fully kinetic massively parallel Particle‐in‐Cell/Monte Carlo code BIT1 [1]. In order to exclude possible artificial boundary effects we simulated a sufficiently large area (10 ‐ 50 cm), so that the PS in the simulation develops fully self‐consistently. Our simulations show that each point in the PS oscillates with a significantly broad frequency spectrum. The largest oscillation amplitudes have the waves which are in resonance with the local plasma frequency for unmagnetized, and with the upper and lower hybrid frequencies for magnetized plasmas. In addition each point exhibits oscillations at resonance frequencies corresponding to other points in the PS. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
On Ion Sound Speed in a High Recycling Plasma Edge
Authors: Eisenstecken T. , Tskhakaya D. 
Published: June 2014

AbstractThe ion sound speed is derived from the propagation speed of small perturbations. For this purpose, we consider particle, momentum and energy conservation equations for the ions and Ohms law for the electrons. We find out that there exist three oscillation modes: two of them correspond to the waves propagating towards the wall and one propagating away from it. One of the modes propagating towards the wall and the mode propagating away from the wall are identified as sound waves. We demonstrate that for the plasma parameters corresponding to the high recycling regime the ion sound speed propagating towards the wall exceeds significantly the commonly given isothermal, or adiabatic sound speeds. Moreover, we show that there exists a layer in front of the wall, where the second mode propagating towards the wall has a positive growth rate. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical Modeling of the Thermal Force for the Kinetic Test‐Ion Transport Simulation Based on the Fokker‐Planck Collision Operator
Authors: Homma Y. , Hatayama A. 
Published: June 2014

AbstractWe present an extended numerical model of the thermal force based on the Fokker‐Planck collision method. Our model is designed for the use of the test particle transport simulation in a fluid‐like magnetized background plasma. By a series of systematic test simulations performed in this study, we have confirmed that our model is able to correctly simulate the thermal force which is caused not only by parallel, but also by perpendicular temperature gradient with respect to the direction of magnetic field. Effective length of collision time step for numerical calculations has also been investigated. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical Scaling with the COREDIV Code of JET Discharges with the ITER‐Like Wall
Authors: Telesca G. , Ivanova‐Stanik I. , Zagörski R. , Brezinsek S. , Giroud C. , Van Ooost G. , JET EFDA contributors  
Published: June 2014

AbstractAfter the code parameters have been fixed by the numerical modeling of a well diagnosed JET pulse, the electron density and the input power have been changed, resulting in 4 density scans (〈ne〉 in the range 3.8 – 8.2 x 1019m‐3) at Pin = 17, 22, 27, 32 MW. At any given power level, W flux decreases with increasing 〈ne〉 as a consequence of the decrease in Te at the target plates. Also the W concentration in the core (cW) decreases, but this not necessarily leads to reduced core radiation. Indeed, while at high Pin the core radiation decreases with density, at low Pin it increases. At high 〈ne〉 the increase in the input power leads to enhanced PradPrad, leaving, however, nearly unchanged the power radiated fraction frad Indeed, the increase in frad withPin is observed only at low 〈ne〉, up to a level of about frad = 0.4. These numerical results, linked to the non‐linear self‐consistent physics of W production and transport, suggest the best conditions are achieved when the level of the electron density is adapted to the level of the available Pin. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Preliminary Comparison of the Conventional and Quasi‐Snowflake Divertor Configurations with the 2D Code EDGE2D/EIRENE in the FAST Tokamak
Authors: Viola B. , Corrigan G. , Harting D. , Maddaluno G. , Mattia M. , Pericoli Ridolfini V. , Zagórski R. 
Published: June 2014

AbstractThe new magnetic configurations for tokamak divertors, snowflake and super‐X, proposed to mitigate the problem of the power exhaust in reactors have clearly evidenced the need for an accurate and reliable modeling of the physics governing the interaction with the plates. The initial effort undertaken jointly by ENEA and IPPLM has been focused to exploit a simple and versatile modeling tool, namely the 2D TECXY code, to obtain preliminary comparison between the conventional and snowflake configurations for the proposed new device FAST that should realize an edge plasma with properties quite close to those of a reactor. The very interesting features found for the snowflake, namely a power load mitigation much larger than expected directly from the change of the magnetic topology, has further pushed us to check these results with the more sophisticated computational tool EDGE2D coupled with the neutral code module EIRENE. After a preparatory work that has been carried out in order to adapt this code combination to deal with non‐conventional, single null equilibria and in particular with second order nulls in the poloidal field generated in the snowflake configuration, in this paper we describe the first activity to compare these codes and discuss the first results obtained for FAST. The outcome of these EDGE2D runs is in qualitative agreement with those of TECXY, confirming the potential benefit obtainable from a snowflake configuration. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Sonographically guided percutaneous treatment of liver abscesses in critically Ill patients
Authors: Zerem Enver , Omerovic Safet , Kunosic Suad 
Published: June 2014

ABSTRACTBackgroundThe management of liver abscess (LA) has shifted toward intravenous broad‐spectrum antibiotics and image‐guided percutaneous needle aspiration (PNA) or percutaneous catheter drainage (PCD).AimTo evaluate the efficacy of percutaneous treatment for patients with LA.MethodsWe performed a retrospective analysis of 264 patients with 354 LA treated by percutaneous management from 1989 to 2012. All patients received appropriate antibiotic therapy. Patients with LA <50 mm in diameter were initially treated by sonographic‐guided PNA and those with LA ≥50 mm were initially treated by ultrasound ultrasound‐guided PCD. Surgery was planned only when there was no clinical improvement after the initial nonsurgical treatment. Primary outcome was the conversion rate to surgery. Secondary outcomes were mortality, length of hospital stay, and the procedure‐related complications.ResultsPNA was performed initially in 116 patients (44%), with 70 of them later requiring PCD due to abscess recurrence. In 148 patients (56%), PCD was performed initially. PCD was performed twice or more in 63 patients. Percutaneous treatment was the definitive and successful treatment in 230 of 264 patients (87.1%). Twenty patients (7.7%) were converted to surgery. Twenty‐one patients (7.9%) died. The median hospital stay was 12 (range, 9–18) days, with complications occurring in 23 patients (8.7%).ConclusionsPercutaneous management with systemic antibiotics is effective and safe and allows resolution of most LA. However, a small proportion of patients with LA still requires surgical drainage. © 2014 Wiley Periodicals, Inc. J Clin Ultrasound 42:527–533, 2014
Purely cystic adrenal lesion in a newborn evolving into a solid neuroblastoma
Authors: Gali Shapira , Anat Ilivitzki 
Published: June 2014

ABSTRACTPurely cystic neuroblatomas are often discovered prenatally. As the main differential diagnosis is adrenal hemorrhage, follow‐up sonography is warranted after birth. Cystic neuroblastomas are expected to evolve into lesions of mixed echogenicity with cystic and solid components. We present a rare case of a purely cystic left‐sided adrenal lesion in a newborn, suggesting an adrenal hemorrhage, which on follow‐up sonography evolved into a purely solid mass with poor vascularization, diagnosed as a cystic neuroblastoma. We suggest that even purely cystic adrenal masses in the newborn should be closely followed up with sonography, as they may represent purely cystic neuroblastomas. © 2014 Wiley Periodicals, Inc. J Clin Ultrasound, 43:126–128, 2015
Finding Minors in Graphs with a Given Path Structure
Authors: Kündgen André , Pelsmajer Michael J. , Ramamurthi Radhika 
Published: June 2014

AbstractGiven graphs G and H with , suppose that we have a ‐path in G for each edge in H. There are obvious additional conditions that ensure that G contains H as a rooted subgraph, subdivision, or immersion; we seek conditions that ensure that G contains H as a rooted minor or minor. This naturally leads to studying sets of paths that form an H‐immersion, with the additional property that paths that contain the same vertex must have a common endpoint. We say that H is contractible if, whenever G contains such an H‐immersion, G must also contain a rooted H‐minor. We show, for example, that forests, cycles, K4, and K1, 1, 3 are contractible, but that graphs that are not 6‐colorable and graphs that contain certain subdivisions of K2, 3 are not contractible.
Soybean flour induces a greater increase of the antioxidant defenses in rats fed with a normocaloric diet compared with a hypercaloric diet
Authors: Razzeto Gabriela S , Lucero López Viviana R , Giménez María S , Escudero Nora L 
Published: June 2014

AbstractBACKGROUNDSoybeans, due to their antioxidant properties, present beneficial health effects. The objective was to evaluate if replacing casein with soy flour, modifies antioxidant defenses in rat liver, compared to animals that continued being fed with casein based diets (normocaloric and hypercaloric).RESULTSFour groups of rats were used: CC (control casein), CS (control soy), HC (hypercaloric casein) and HS (hypercaloric soy). Malondialdehyde, in serum and liver, did not present differences. In liver, when comparing CS vs. CC: increased superoxide dismutase 1 (P < 0.001), catalase (P < 0.01) and glutathione reductase (P < 0.05) activities, the total glutathione (P < 0.001) and reduced glutathione (P < 0.05) content and decreased oxidized glutathione content (P < 0.05). In HS vs. HC: increased carbonyl groups (P < 0.01) and superoxide dismutase 1 activity (P < 0.05), and decreased glutathione peroxidase activity (P < 0.01), total glutathione (P < 0.05) and oxidized glutathione content (P < 0.001). In HS vs. CS: decreased glutathione reductase activity (P < 0.01), total glutathione (P < 0.001) and reduced glutathione (P < 0.01) content, and increased oxidized glutathione content (P < 0.05).CONCLUSIONReplacing casein by soybean flour improves antioxidant defenses, mainly in normocaloric diets. © 2014 Society of Chemical Industry
Polymer Thermosets from Multifunctional Polyester Resins Based on Renewable Monomers
Authors: Torron Susana , Semlitsch Stefan , Martinelle Mats , Johansson Mats 
Published: June 2014

The use of monomers based on natural materials as a future supply of raw materials has gained more interest in the last decade. Sources ranging from wood to plant oils and algae are exploited as alternatives to traditional fossil‐based resources for the synthesis of polymeric materials. The use of these raw materials is not only of interest because of its abundance, but also in terms of price, durability, and/or biodegradability. In the present study, a series of resins utilizing a monomer derived from birch bark is prepared. The thermoset resins are formed by reacting an epoxy‐functional ω‐hydroxy fatty acid with methacrylate monomers using enzyme catalysis to form multifunctional resins via a one‐pot synthesis. The derived oligomers are crosslinked through different polymerization routes to produce thermosets with different properties and/or functionalities. This approach allows natural‐based resins with tuned functionalities and mechanical and thermal properties to be obtained.
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Investigating white matter perfusion using optimal sampling strategy arterial spin labeling at 7 Tesla
Authors: Gardener Alexander G. , Jezzard Peter 
Published: June 2014

PurposeCerebral blood flow (CBF) is an informative physiological marker for tissue health. Arterial spin labeling (ASL) is a noninvasive MRI method of measuring this parameter, but it has proven difficult to measure white matter (WM) CBF due to low intrinsic contrast‐to‐noise ratio compared with gray matter (GM). Here we combine ultra‐high field and optimal sampling strategy (OSS) ASL to investigate WM CBF in reasonable scan times.MethodsA FAIR‐based ASL sequence at 7T was combined with a real‐time‐feedback OSS technique, to iteratively improve post‐label image acquisition times (TIs) on a tissue‐ and subject‐specific basis to obtain WM CBF quantification.ResultsIt was found 77% of WM voxels gave a reasonable CBF fit. Averaged WM CBF for these voxels was found to be 16.3 ± 1.5 mL/100 g/min (discarding partial‐volumed voxels). The generated TI schedule was also significantly different when altering the OSS weighted‐tissue‐mask, favoring longer TIs in WM.ConclusionWM CBF could be reasonably quantified in over 75% of identified voxels, from a total preparation and scan time of 15 min. OSS results suggest longer TIs should be used versus general GM ASL settings; this may become more important in WM disease studies. Magn Reson Med 73:2243–2248, 2015. © 2014 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Giant axonal neuropathy: An updated perspective on its pathology and pathogenesis
Authors: Johnson‐Kerner Bethany L. , Roth Lisa , Greene J. Palmer , Wichterle Hynek , Sproule Douglas M. 
Published: June 2014

ABSTRACTGiant axonal neuropathy (GAN) is a rare pediatric neurodegenerative disease. It is best known for the “giant” axons caused by accumulations of intermediate filaments. The disease is progressive, with onset around age 3 years and death by the third decade of life. GAN results from recessive mutations in the GAN gene encoding gigaxonin, and our analysis of all reported mutations shows that they are distributed throughout the protein structure. Precisely how these mutations cause the disease remains to be determined. In addition to changes in peripheral nerves that are similar to those seen in neuropathies such as Charcot–Marie–Tooth type 2, GAN patients exhibit a wide range of central nervous system signs. These features, corroborated by degeneration of central tracts apparent from postmortem pathology, indicate that GAN is also a progressive neurodegenerative disease. To reflect this phenotype more precisely, we therefore propose that the disease should be more appropriately referred to as “giant axonal neurodegeneration.” Muscle Nerve 50: 467–476, 2014
Structural and thermodynamic characterization of the recognition of the S100‐binding peptides TRTK12 and p53 by calmodulin
Authors: Wafer Lucas N. , Tzul Franco O. , Pandharipande Pranav P. , McCallum Scott A. , Makhatadze George I. 
Published: June 2014

AbstractCalmodulin (CaM) is a multifunctional messenger protein that activates a wide variety of signaling pathways in eukaryotic cells in a calcium‐dependent manner. CaM has been proposed to be functionally distinct from the S100 proteins, a related family of eukaryotic calcium‐binding proteins. Previously, it was demonstrated that peptides derived from the actin‐capping protein, TRTK12, and the tumor‐suppressor protein, p53, interact with multiple members of the S100 proteins. To test the specificity of these peptides, they were screened using isothermal titration calorimetry against 16 members of the human S100 protein family, as well as CaM, which served as a negative control. Interestingly, both the TRTK12 and p53 peptides were found to interact with CaM. These interactions were further confirmed by both fluorescence and nuclear magnetic resonance spectroscopies. These peptides have distinct sequences from the known CaM target sequences. The TRTK12 peptide was found to independently interact with both CaM domains and bind with a stoichiometry of 2:1 and dissociations constants Kd,C‐term = 2 ± 1 µM and Kd,N‐term = 14 ± 1 µM. In contrast, the p53 peptide was found to interact only with the C‐terminal domain of CaM, Kd,C‐term =2 ± 1 µM, 25°C. Using NMR spectroscopy, the locations of the peptide binding sites were mapped onto the structure of CaM. The binding sites for both peptides were found to overlap with the binding interface for previously identified targets on both domains of CaM. This study demonstrates the plasticity of CaM in target binding and may suggest a possible overlap in target specificity between CaM and the S100 proteins.
Method to increase the yield of eukaryotic membrane protein expression in Saccharomyces cerevisiae for structural and functional studies
Authors: Parker Joanne L. , Newstead Simon 
Published: June 2014

AbstractDespite recent successes in the structure determination of eukaryotic membrane proteins, the total number of structures of these important proteins is severely underrepresented in the Protein Data Bank. Although prokaryotic homologues provide valuable mechanistic insight, they often lack crucial details, such as post‐translational modification and additional intra or extracellular domains that are important for understanding the function and regulation of these proteins in eukaryotic cells. The production of milligram quantities of recombinant protein is still a serious obstacle to the structural and functional characterization of these proteins. Here, we report a modification to a previously described over expression system using the simple eukaryote Saccharomyces cerevisiae that can increase overall protein yield and improve downstream purification procedures. Using a metabolic marker under the control of a truncated promoter, we show that expression levels for several membrane transporters are increased fourfold. We further demonstrate that the increase in expression for our test proteins resulted in a concomitant increase in functional protein. Using this system, we were able to increase the expression level of a plant transporter, NRT1.1, which was a key factor in its structural and functional characterization.