bluuebunny/crossref_metadata_2025_split huggingface dataset:
GAMER with out-of-core computation
Authors: Schive Hsi-Yu , Tsai Yu-Chih , Chiueh Tzihong 
Published: April 2011

AbstractGAMER is a GPU-accelerated Adaptive-MEsh-Refinement code for astrophysical simulations. In this work, two further extensions of the code are reported. First, we have implemented the MUSCL-Hancock method with the Roe's Riemann solver for the hydrodynamic evolution, by which the accuracy, overall performance and the GPU versus CPU speed-up factor are improved. Second, we have implemented the out-of-core computation, which utilizes the large storage space of multiple hard disks as the additional run-time virtual memory and permits an extremely large problem to be solved in a relatively small-size GPU cluster. The communication overhead associated with the data transfer between the parallel hard disks and the main memory is carefully reduced by overlapping it with the CPU/GPU computations.
A Fast Explicit Scheme for Solving MHD Equations with Ambipolar Diffusion
Authors: Kim Jongsoo 
Published: April 2011

AbstractWe developed a fast numerical scheme for solving ambipolar diffusion MHD equations with the strong coupling approximation, which can be written as the ideal MHD equations with an additional ambipolar diffusion term in the induction equation. The mass, momentum, magnetic fluxes due to the ideal MHD equations can be easily calculated by any Godunov-type schemes. Additional magnetic fluxes due to the ambipolar diffusion term are added in the magnetic fluxes, because of two same spatial gradients operated on the advection fluxes and the ambipolar diffusion term. In this way, we easily kept divergence-free magnetic fields using the constraint transport scheme. In order to overcome a small time step imposed by ambipolar diffusion, we used the super time stepping method. The resultant scheme is fast and robust enough to do the long term evolution of star formation simulations. We also proposed that the decay of alfen by ambipolar diffusion be a good test problem for our codes.
Ambipolar Diffusion Effects on Weakly Ionized Turbulence Molecular Clouds
Authors: Li Pak Shing , McKee Christopher F. , Klein Richard I. 
Published: April 2011

AbstractAmbipolar diffusion (AD) is a key process in molecular clouds (MCs). Non-ideal MHD turbulence simulations are technically very challenging because of the large Alfvén speed of ions in weakly ionized clouds. Using the Heavy-Ion Approximation method (Li, McKee & Klein 2006), we have carried out two-fluid simulations of AD in isothermal, turbulent boxes at a resolution of 5123, to investigate the effect of AD on the weakly ionized turbulence in MCs. Our simulation results show that the neutral gas component of the two-fluid system gradually transforms from an ideal MHD turbulence system to near a pure hydrodynamic turbulence system within the standard AD regime, in which the neutrals and ions are coupled over a flow time. The change of the turbulent state has a profound effect on the weakly ionized MCs.
Radiative Transfer Modeling of Simulation and Observational Data
Authors: Steinacker Jürgen , Henning Thomas , Bacmann Aurore 
Published: April 2011

AbstractRadiative Transfer (RT) is considered to be one of the four Grand Challenges in Computational Astrophysics aside of Astrophysical Fluid Dynamics, N-Body Problems in Astrophysics, and Relativistic Astrophysics. The high dimensionality (7D instead of 4D for MHD) and the underlying integro-differential transport equation have forced coders to implement approximative RT methods in order to fit spectra and images or to treat RT in their HD and MHD codes.The central role of RT in star formation (SF) is based on several facts: a) The dense dusty gas in SF regions alters the radiation substantially making SF one of the most complex applications of RT. b) Radiation transports energy within the object and is therefore an essential part of any dynamical SF model. c) RT calculations tell us which of the processes/structures are visible at what wavelength by which telescope/instrument. Hence, RT is the central tool to analyze simulation results or to explore the scientific capabilities of planned instruments. d) With inverse RT, we can obtain the 1D-3D density and temperature structure from observations, completely decoupled from any (M)HD modeling (and the approximations made within).In this review, we summarize the main difficulties and the currently used computational techniques to calculate the RT in SF regions. Recent applications of 3D continuum RT in molecular clouds and disks around young massive stars are discussed to illustrate the capabilities and limits of current RT modeling.
Galactic star formation in parsec-scale resolution simulations
Authors: Powell Leila C. , Bournaud Frederic , Chapon Damien , Devriendt Julien , Slyz Adrianne , Teyssier Romain 
Published: April 2011

AbstractThe interstellar medium (ISM) in galaxies is multiphase and cloudy, with stars forming in the very dense, cold gas found in Giant Molecular Clouds (GMCs). Simulating the evolution of an entire galaxy, however, is a computational problem which covers many orders of magnitude, so many simulations cannot reach densities high enough or temperatures low enough to resolve this multiphase nature. Therefore, the formation of GMCs is not captured and the resulting gas distribution is smooth, contrary to observations. We investigate how star formation (SF) proceeds in simulated galaxies when we obtain parsec-scale resolution and more successfully capture the multiphase ISM. Both major mergers and the accretion of cold gas via filaments are dominant contributors to a galaxy's total stellar budget and we examine SF at high resolution in both of these contexts.
Cosmological simulations of low-mass galaxies: some potential issues
Authors: Colín Pedro , Avila-Reese Vladimir , Valenzuela Octavio 
Published: April 2011

AbstractCosmological Adaptive Mesh Refinement simulations are used to study the specific star formation rate (sSFR=SSF/Ms) history and the stellar mass fraction, fs=Ms/MT, of small galaxies, total masses MT between few × 1010 M⊙ to few ×1011 M⊙. Our results are compared with recent observational inferences that show the so-called “downsizing in sSFR” phenomenon: the less massive the galaxy, the higher on average is its sSFR, a trend seen at least since z ~ 1. The simulations are not able to reproduce this phenomenon, in particular the high inferred values of sSFR, as well as the low values of fs constrained from observations. The effects of resolution and sub-grid physics on the SFR and fs of galaxies are discussed.
Comparison between Simulations and Theory: where we stand
Authors: Monaghan Joe J. 
Published: April 2011

AbstractIn this paper I relate progress in the simulation of star formation to a remarkable early (1962) paper by Fowler and Hoyle who analyzed star formation in terms of the relevant energies starting from the formation of a large (100 pc) cloud and ending with the final mass distribution of the stars. The way in which modern simulations have clarified and corrected the Fowler-Hoyle picture, and areas where we could improve our simulations, are discussed.
Concluding Remarks: Playing by the Numbers
Authors: Trimble Virginia 
Published: April 2011

AbstractAdvances in available computing facilities, judiciously employed by our colleagues, have undoubtedly enhanced our understanding of the processes by which stars (and planets) form, from very diffuse gas to something you could almost live around. Nevertheless we remain very far from being able to describe (let alone explain) what is going on in many cases. And this is likely to remain true even as Moore's Law growth begins to hit its head against energy and power considerations. A large fraction of long-standing questions appear to have honest answers of the general form, “yes and no”, “all of the above”, or “some of them are and some of them aren't”. This includes many of my favorites, like triggering, formation of binary populations, and the role of magnetic fields. Rather few questions have actually been retired from the universe of discourse in recent years.
Two faces of patient safety and care quality: a Franco-American comparison
Authors: Degos Laurent , Rodwin Victor G. 
Published: April 2011

AbstractPatient safety, and more broadly the quality of care, is typically discussed with reference to the reduction of preventable adverse events within hospitals and adherence to practice guidelines on care processes. We call it the ‘care-centered approach’ and recognize that the United States is a leader in the field. Another face of patient safety and care quality may be defined as the ‘system-centered approach’. It focuses on access to a timely and effective continuum of health-care services – clinical prevention, primary care and appropriate referral to and receipt of specialty care. Although France's efforts to pursue a care-centered approach to patient safety are limited, its system-centered approach yields some benefits. Based on the evidence we have reviewed for access to primary care (hospital discharges for avoidable hospital conditions), mortality amenable to medical intervention and consumer satisfaction, in the United States and France, there appear to be good grounds for bolstering the system-centered approach in the United States.
Regulating agriculture in the WTO
Authors: Smith Fiona 
Published: April 2011

AbstractThis article argues there is value in exploring the resonance between the regulation of international agricultural trade as a specific topic and the general notion of international trade regulation in the World Trade Organisation (WTO). It explores particular problems to illuminate more general concerns. In this ascendant way of looking at things, certain aspects of agricultural trade regulation have direct resonance for other areas covered by the WTO agreements. We might see these additional dimensions as addressing a different series of questions: the nature of agreement and the different ways in which agreement can manifest itself. The two dimensions are the nature of international agricultural trade as a polycentric problem and the way accepted concepts and categories influence how we see problems in international agricultural trade. Polycentrism goes to the nature of the stability of the Agreement on Agriculture, whereas the question of concepts and categories concerns the way in which we represent the problem as coherent to ourselves.
Law is not (best considered) an essentially contested concept
Authors: Ehrenberg Kenneth M. 
Published: April 2011

AbsrtactI argue that law is not best considered an essentially contested concept. After first explaining the notion of essential contestability and disaggregating law into several related concepts, I show that the most basic and general concept of law does not fit within the criteria offered for essential contestation. I buttress this claim with the explanation that essential contestation is itself a framework for understanding complex concepts and therefore should only be applied when it would yield a greater understanding of uses of the concept to which it is applied. I then show that, even if law meets some basic criteria of essential contestation, applying the appellation does not helpfully illuminate the most general concept of law and therefore it should not be used, while allowing that it might be more useful for the related concept of the rule of law.
Optical two-tone generation and SSB modulation using electro-optic modulator with suppressing redundant spectrum components
Authors: Enokihara Akira , Kawai Tadashi , Kawanishi Tetsuya 
Published: April 2011

Doubled frequency optical two-tone generation and optical single sideband (SSB) modulation by the dual-electrode-type electro-optic (EO) modulator with a single Mach–Zehnder (MZ) interferometer were considered. We theoretically showed that redundant spectrum components in the modulated optical signals, which are caused by the imbalance of light splitting ratio between the two arms of the interferometer, are significantly suppressed by controlling the input power ratio of RF modulation signals applied to each electrode. This effect was confirmed by the experiment, where an optical two-tone with the redundant components 49.8 dB lower than the primary two-tone components in intensity level was obtained. This method is also valid for suppression of undesired frequency components of RF signals that are generated at a photo detector from the optical two-tone waves propagated through a dispersive optical fiber.
Extended X-ray absorption fine structure studies of magnetic nanoparticles
Authors: Agarwal A. , Singh M. K. , Kaneko T. , Nagamatsu S.-I. , Konishi T. , Fujikawa T. 
Published: April 2011

We have synthesized nickel by means of pulsed laser ablation. A nickel disc was used for ablation with the focused output of fundamental harmonic from Nd:YAG laser. X-ray diffraction result shows that the synthesized nanoparticles are of pure metallic nickel with a face-centred cubic structure and the average particle size is 35 nm. The extended X-ray absorption fine structure (EXAFS) studies of pure nickel foil and the synthesized nanoparticles show similar structures. The position of the main peak is same in these nanoparticles with reference to the nickel foil. The only difference was observed in the reduction of the amplitude. The nearest-neighbour distance is similar as for pure nickel foil. The Debye–Waller factor is also similar. There is no trace of oxide and hydroxide in the EXAFS data, suggesting that the synthesized nanoparticles contain only nickel metal.
TNO1 Is Involved in Salt Tolerance and Vacuolar Trafficking in Arabidopsis
Authors: Kim Sang-Jin , Bassham Diane C. 
Published: April 2011

Abstract
The Arabidopsis (Arabidopsis thaliana) soluble N-ethylmaleimide-sensitive factor attachment protein receptor SYP41 is involved in vesicle fusion at the trans-Golgi network (TGN) and interacts with AtVPS45, SYP61, and VTI12. These proteins are involved in diverse cellular processes, including vacuole biogenesis and stress tolerance. A previously uncharacterized protein, named TNO1 (for TGN-localized SYP41-interacting protein), was identified by coimmunoprecipitation as a SYP41-interacting protein. TNO1 was found to localize to the TGN by immunofluorescence microscopy. A tno1 mutant showed increased sensitivity to high concentrations of NaCl, KCl, and LiCl and also to mannitol-induced osmotic stress. Localization of SYP61, which is involved in the salt stress response, was disrupted in the tno1 mutant. Vacuolar proteins were partially secreted to the apoplast in the tno1 mutant, suggesting that TNO1 is required for efficient protein trafficking to the vacuole. The tno1 mutant had delayed formation of the brefeldin A (BFA) compartment in cotyledons upon application of BFA, suggesting less efficient membrane fusion processes in the mutant. Unlike most TGN proteins, TNO1 does not relocate to the BFA compartment upon BFA treatment. These data demonstrate that TNO1 is involved in vacuolar trafficking and salt tolerance, potentially via roles in vesicle fusion and in maintaining TGN structure or identity.
Arabidopsis thaliana High-Affinity Phosphate Transporters Exhibit Multiple Levels of Posttranslational Regulation
Authors: Bayle Vincent , Arrighi Jean-François , Creff Audrey , Nespoulous Claude , Vialaret Jérôme , Rossignol Michel , Gonzalez Esperanza , Paz-Ares Javier , Nussaume Laurent 
Published: April 2011

Abstract
In Arabidopsis thaliana, the PHOSPHATE TRANSPORTER1 (PHT1) family encodes the high-affinity phosphate transporters. They are transcriptionally induced by phosphate starvation and require PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR (PHF1) to exit the endoplasmic reticulum (ER), indicating intracellular traffic as an additional level of regulation of PHT1 activity. Our study revealed that PHF1 acts on PHT1, upstream of vesicle coat protein COPII formation, and that additional regulatory events occur during PHT1 trafficking and determine its ER exit and plasma membrane stability. Phosphoproteomic and mutagenesis analyses revealed modulation of PHT1;1 ER export by Ser-514 phosphorylation status. Confocal microscopy analysis of root tip cells showed that PHT1;1 is localized to the plasma membrane and is present in intracellular endocytic compartments. More precisely, PHT1;1 was localized to sorting endosomes associated with prevacuolar compartments. Kinetic analysis of PHT1;1 stability and targeting suggested a modulation of PHT1 internalization from the plasma membrane to the endosomes, followed by either subsequent recycling (in low Pi) or vacuolar degradation (in high Pi). For the latter condition, we identified a rapid mechanism that reduces the pool of PHT1 proteins present at the plasma membrane. This mechanism is regulated by the Pi concentration in the medium and appears to be independent of degradation mechanisms potentially regulated by the PHO2 ubiquitin conjugase. We propose a model for differential trafficking of PHT1 to the plasma membrane or vacuole as a function of phosphate concentration.
p2 of Rice stripe virus (RSV) interacts with OsSGS3 and is a silencing suppressor
Authors: DU ZHENGUO , XIAO DONGLAI , WU JIANGUO , JIA DONGSHENG , YUAN ZHENGJIE , LIU YING , HU LIUYANG , HAN ZHAO , WEI TAIYUN , LIN QIYING , WU ZUJIAN , XIE LIANHUI 
Published: April 2011

SUMMARYA rice cDNA library was screened by a galactosidase 4 (Gal4)‐based yeast two‐hybrid system with Rice stripe virus (RSV) p2 as bait. The results revealed that RSV p2 interacted with a rice protein exhibiting a high degree of identity with Arabidopsis thaliana suppressor of gene silencing 3 (AtSGS3). The interaction was confirmed by bimolecular fluorescence complementation assay. SGS3 has been shown to be involved in sense transgene‐induced RNA silencing and in the biogenesis of trans‐acting small interfering RNAs (ta‐siRNAs), possibly functioning as a cofactor of RNA‐dependent RNA polymerase 6 (RDR6). Given the intimate relationships between virus and RNA silencing, further experiments were conducted to show that p2 was a silencing suppressor. In addition, p2 enhanced the accumulation and pathogenicity of Potato virus X in Nicotiana benthamiana. Five genes that have been demonstrated to be targets of TAS3‐derived ta‐siRNAs were up‐regulated in RSV‐infected rice. The implications of these findings are discussed.
The determination of water‐soluble vitamins and in vitro digestibility of selected Czech cheeses
Authors: Altangerel Bayanmunkh , Sengee Zultsetseg , Kramarova Daniela , Rop Otakar , Hoza Ignac 
Published: April 2011

SummaryWater‐soluble vitamins, in vitro organic matter digestibility (OMD) and dry matter digestibility (DMD) values were determined in various different Czech cheeses. An HPLC method for the simultaneous determination of niacin, pantothenic acid and pyridoxine in cheese was established. Different hydrolysis conditions and enzymes were used to release these vitamins from their complex form. The cheeses contained on average 2.04 mg of niacin, 3.24 mg of pantothenic acid and 2.16 mg of pyridoxine per 100 g of fresh mass. An enzymatic method was applied for the evaluation of OMD and DMD in cheeses. In vitro digestibility values ranged from 83.29% to 99.99% for organic matter (OMD) and 83.33% to 99.87% for dry matter (DMD) after two different enzymatic digestions (pepsin, pancreatin). In addition, cheeses incubated with pepsin plus pancreatin, OMD and DMD were strongly digested (99.04–99.83%, 97.73–99.74%).
Fluidized bed and tray drying of thinly sliced mango (Mangifera indica) pretreated with ascorbic and citric acid
Authors: Villegas‐Santiago Juliana , Calderon‐Santoyo Monserrat , Ragazzo‐Sánchez Arturo , Salgado‐Cervantes Marco Antonio , Luna‐Solano Guadalupe 
Published: April 2011

SummaryThe purpose of this work was to determine the influence of air temperature, sample diameter and antioxidants on water activity, moisture content and colour difference of thinly sliced mango in a fluidized bed and tray dryer. Mango samples were treated with antioxidants solutions (ascorbic and citric acid) before the drying process. Fluidized bed and tray drying of control and treated samples were carried out at two temperatures: 50 and 60 °C. A fractional factorial design 24−1 was used in both drying methods. The Newton semi‐theoretical model was found to represent thin‐layer drying kinetics of mango. For both drying types, moisture content of thinly sliced mango was well characterised (R2 ≥ 0.975) by the model. The temperature increment increases the drying constant and decreases the equilibrium moisture content and water activity of the dehydrated samples. Colour closest to the original colour of fresh mango was obtained when 2 cm diameter mango pretreated with citric acid (1%) was dehydrated by fluidized bed at 60 °C. In addition, it was observed that the drying time at equilibrium by using fluidized bed was lower (60 min) than the tray dryer (120 min).
Essential oil composition and antibacterial activity of the grapefruit (Citrus Paradisi. L) peel essential oils obtained by solvent‐free microwave extraction: comparison with hydrodistillation
Authors: Uysal Burcu , Sozmen Fazli , Aktas Ozgur , Oksal Birsen S. , Kose Elif Odabas 
Published: April 2011

SummaryThe chemical composition of the essential oil (EO) obtained by solvent‐free microwave extraction (SFME) and hydrodistillation (HD) from the peel of grapefruit (Citrus Paradisi. L) was analysed by gas chromatography/mass spectrometry (GC/MS). Totally, twenty‐five components were identified in the EO. Limonene was observed as dominant (91.5–88.6%) for two extraction methods, SFME and HD, respectively. β‐Pinene (0.8–1.2%), linalool (1.1–0.7%), α‐terpinene (0.7–1.0%) and the other minor components were also detected. Disc diffusion method was applied to determine the antibacterial properties of the EO. The results showed that the EO of grapefruit peel had a wide spectrum of antimicrobial activities against Staphylococcus aureus, Enterococcus faecalis, Staphylococcus epidermidis, Escherichia coli, Salmonella typhimurium, Serratia marcescens and Proteus vulgaris, with their inhibition zones ranging from 11 to 53 mm.