bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing the Quiet Sun Scale Magnetic Field
Authors: Title Alan 
Published: August 2011

AbstractObservations with the Solar Optical Telescope on Hinode indicate that the Quiet Sun magnetic field occurs on every scale of convection including granulation. Data reported here show that, regardless of the position on the disk, the polarity in the inner network regions are balanced to 1 part in 72. This is consistent with both local dynamo processes or the creation of surface features by the granulation downflows.
On the formation of ring galaxies
Authors: Wu Yu-Ting , Jiang Ing-Guey 
Published: August 2011

AbstractThe formation scenario of ring galaxies is addressed in this paper. We focus on the P-type ring galaxies presented in Madore, Nelson & Petrillo (2009), particularly on the axis-symmetric ones. Our simulations show that a ring can form through the collision of disc and dwarf galaxies, and the locations, widths, and density contrasts of the ring are well determined. We find that a ring galaxy such as AM 2302-322 can be produced by this collision scenario.
Star formation in galaxy mergers: ISM turbulence, dense gas excess, and scaling relations for disks and starbusts
Authors: Bournaud Frédéric , Powell Leila C. , Chapon Damien , Teyssier Romain 
Published: August 2011

AbstractGalaxy interactions and mergers play a significant, but still debated and poorly understood role in the star formation history of galaxies. Numerical and theoretical models cannot yet explain the main properties of merger-induced starbursts, including their intensity and their spatial extent. Usually, the mechanism invoked in merger-induced starbursts is a global inflow of gas towards the central kpc, resulting in a nuclear starburst. We show here, using high-resolution AMR simulations and comparing to observations of the gas component in mergers, that the triggering of starbursts also results from increased ISM turbulence and velocity dispersions in interacting systems. This forms cold gas that are denser and more massive than in quiescent disk galaxies. The fraction of dense cold gas largely increases, modifying the global density distribution of these systems, and efficient star formation results. Because the starbursting activity is not just from a global compacting of the gas to higher average surface densities, but also from higher turbulence and fragmentation into massive and dense clouds, merging systems can enter a different regime of star formation compared to quiescent disk galaxies. This is in quantitative agreement with recent observations suggesting that disk galaxies and starbursting systems are not the low-activity end and high-activity end of a single regime, but actually follow different scaling relations for their star formation.
The influence of stratification upon small-scale convectively-driven dynamos
Authors: Bushby Paul J. , Proctor Michael R. E. , Weiss Nigel O. 
Published: August 2011

AbstractIn the quiet Sun, convective motions form a characteristic granular pattern, with broad upflows enclosed by a network of narrow downflows. Magnetic fields tend to accumulate in the intergranular lanes, forming localised flux concentrations. One of the most plausible explanations for the appearance of these quiet Sun magnetic features is that they are generated and maintained by dynamo action resulting from the local convective motions at the surface of the Sun. Motivated by this idea, we describe high resolution numerical simulations of nonlinear dynamo action in a (fully) compressible, non-rotating layer of electrically-conducting fluid. The dynamo properties depend crucially upon various aspects of the fluid. For example, the magnetic Reynolds number (Rm) determines the initial growth rate of the magnetic energy, as well as the final saturation level of the dynamo in the nonlinear regime. We focus particularly upon the ways in which the Rm-dependence of the dynamo is influenced by the level of stratification within the domain. Our results can be related, in a qualitative sense, to solar observations.
The Evolution of a Double Diffusive Magnetic Buoyancy Instability
Authors: Silvers Lara J. , Vasil Geoffrey M. , Brummell Nicholas H. , Proctor Michael R. E. 
Published: August 2011

AbstractRecently, Silvers et al. (2009b), using numerical simulations, confirmed the existence of a double diffusive magnetic buoyancy instability of a layer of horizontal magnetic field produced by the interaction of a shear velocity field with a weak vertical field. Here, we demonstrate the longer term nonlinear evolution of such an instability in the simulations. We find that a quasi two-dimensional interchange instability rides (or “surfs”) on the growing shear-induced background downstream field gradients. The region of activity expands since three-dimensional perturbations remain unstable in the wake of this upward-moving activity front, and so the three-dimensional nature becomes more noticeable with time.
Competing kinematic dynamo mechanisms in rotating convection with shear
Authors: Proctor Michael R. E. , Hughes David W. 
Published: August 2011

AbstractFollowing earlier work by Hughes & Proctor (2009) on the role of velocity shear in convectively driven dynamos, we present preliminary results on the nature of dynamo action due to modified flows derived by filtration from the full convective flow. The results suggest that filtering the flow fields has surprisingly little effect on the dynamo growth rates.
Solar and Stellar Dynamos
Authors: Weiss Nigel O. 
Published: August 2011

AbstractRecords of the solar magnetic field extend back for millennia, and its surface properties have been observed for centuries, while helioseismology has recently revealed the Sun's internal rotation and the presence of a tachocline. Dynamo theory has developed to explain these observations, first with idealized models based on mean-field electrodynamics and, more recently, by direct numerical simulation, notably with the ASH code at Boulder. These results, which suggest that cyclic activity relies on the presence of the tachocline, and that its modulation is chaotic (rather than stochastic), will be critically reviewed. Similar theoretical approaches have been followed in order to explain the magnetic properties of other main-sequence stars, whose fields can be mapped by Zeeman-Doppler imaging. Of particular interest is the behaviour of fully convective, low-mass stars, which lack any tachocline but are nevertheless extremely active.
From convective to stellar dynamos
Authors: Brandenburg Axel , Käpylä Petri J. , Korpi Maarit J. 
Published: August 2011

AbstractConvectively driven dynamos with rotation generating magnetic fields on scales large compared with the scale of the turbulent eddies are being reviewed. It is argued that such fields can be understood as the result of an α effect. Simulations in Cartesian domains show that such large-scale magnetic fields saturate on a time scale compatible with the resistive one, suggesting that the magnitude of the α effect is here still constrained by approximate magnetic helicity conservation. It is argued that, in the absence of shear and/or any other known large-scale dynamo effects, these simulations prove the existence of turbulent α2-type dynamos. Finally, recent results are discussed in the context of solar and stellar dynamos.
Nonlinear Dynamos
Authors: Galloway David 
Published: August 2011

AbstractThis paper discusses nonlinear dynamos where the nonlinearity arises directly via the Lorentz force in the Navier-Stokes equation, and leads to a situation where the Lorentz force and the velocity and the magnetic field are in direct competition over substantial regions of the flow domain. Filamentary and non-filamentary dynamos are contrasted, and the concept of Alfvénic dynamos with almost equal magnetic and kinetic energies is reviewed via examples. So far these remain in the category of toy models; the paper concludes with a discussion of whether similar dynamos are likely to exist in astrophysical objects, and whether they can model the solar cycle.
Juri Toomre and the art of modeling convection zones
Authors: Zahn Jean-Paul 
Published: August 2011

AbstractThermal convection plays a very important role in the structure and evolution of stars, as it is one of the main physical processes that transport heat from their interior where it is released, to the surface where it is radiated into space. Much progress has been achieved in modeling that process during the past 60 years, and I shall recall here how Juri Toomre has greatly contributed to it.
Reduced MHD and Astrophysical Fluid Dynamics
Authors: Arter Wayne 
Published: August 2011

AbstractRecent work has shown a relationship between between the equations of Reduced Magnetohydrodynamics (RMHD), used to model magnetic fusion laboratory experiments, and incompressible magnetoconvection (IMC), employed in the simulation of astrophysical fluid dynamics (AFD), which means that the two systems are mathematically equivalent in certain geometries. Limitations on the modelling of RMHD, which were found over twenty years ago, are reviewed for an AFD audience, together with hitherto unpublished material on the role of finite-time singularities in the discrete equations used to model fluid dynamical systems. Possible implications for turbulence modelling are mentioned.
Influence of Magnetic Helicity in MHD
Authors: Candelaresi Simon , Sordo Fabio Del , Brandenburg Axel 
Published: August 2011

AbstractObservations have shown that the Sun's magnetic field has helical structures. The helicity content in magnetic field configurations is a crucial constraint on the dynamical evolution of the system. Since helicity is connected with the number of links we investigate configurations with interlocked magnetic flux rings and one with unlinked rings. It turns out that it is not the linking of the tubes which affects the magnetic field decay, but the content of magnetic helicity.
The Effect of Scattering on the Temperature Stratification of 3D Model Atmospheres of Metal-Poor Red Giants
Authors: Collet Remo , Hayek Wolfgang , Asplund Martin 
Published: August 2011

AbstractWe study the effects of different approximations of scattering in 3D radiation-hydrodynamics simulations on the photospheric temperature stratification of metal-poor red giant stars. We find that assuming a Planckian source function and neglecting the contribution of scattering to extinction in optically thin layers provides a good approximation of the effects of coherent scattering on the photospheric temperature balance.
Multi-season photometry of the newly-discovered roAp star HD75445
Authors: Engelbrecht C. A. , Frescura F. A. M. , Frank B. S. , Nicol P. R. 
Published: August 2011

AbstractHD75445 was recently announced by Kochukhov et al. (2009) to be a low-amplitude roAp star, based on spectroscopic measurements. We present putative pulsation frequencies of HD75445 determined from 22 hours of Johnson B photometry obtained in 2008, 2009 and 2010. We present the first photometric periodicities detected in this star. We make a marginal detection of one of Kochukhov et al. (2009)'s spectroscopic periods, along with a range of confidently detected periodicities covering the low-frequency end of the roAp instability spectrum and the high-frequency end of the Delta Scuti instability spectrum.
Solar wind, mass and momentum losses during the solar cycle
Authors: Pinto R. , Brun S. , Jouve L. , Grappin R. 
Published: August 2011

AbstractWe study the connections between the sun's convection zone evolution and the dynamics of the solar wind and corona. We input the magnetic fields generated by a 2.5D axisymmetric kinematic dynamo code (STELEM) into a 2.5D axisymmetric coronal MHD code (DIP). The computations were carried out for an 11 year cycle. We show that the solar wind's velocity and mass flux vary in latitude and in time in good agreement with the well known time-latitude assymptotic wind speed diagram. Overall sun's mass loss rate, momentum flux and magnetic breaking torque are maximal near the solar minimum.
Magnetic confinement of the solar tachocline: influence of turbulent convective motions
Authors: Strugarek Antoine , Brun Allan Sacha , Zahn Jean-Paul 
Published: August 2011

AbstractWe present the results of 3D simulations, performed with the ASH code, of the nonlinear, magnetic coupling between the convective and radiative zones in the Sun, through the tachocline. Contrary to the predictions of Gough & McIntyre (1998), a fossil magnetic field, deeply buried initially in the solar interior, will penetrate into the convection zone. According to Ferraro's law of iso-rotation, the differential rotation of the convective zone will thus expand into the radiation zone, along the field lines of the poloidal field.
ChimeraScan: a tool for identifying chimeric transcription in sequencing data
Authors: Iyer Matthew K. , Chinnaiyan Arul M. , Maher Christopher A. 
Published: August 2011

Abstract
Summary: Next generation sequencing (NGS) technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts in high-throughput transcriptome sequencing data.
Availability: http://chimerascan.googlecode.com
Contact: cmaher@dom.wustl.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
A phylogenetic mixture model for the identification of functionally divergent protein residues
Authors: Gaston Daniel , Susko Edward , Roger Andrew J. 
Published: August 2011

Abstract
Motivation: To understand the evolution of molecular function within protein families, it is important to identify those amino acid residues responsible for functional divergence; i.e. those sites in a protein family that affect cofactor, protein or substrate binding preferences; affinity; catalysis; flexibility; or folding. Type I functional divergence (FD) results from changes in conservation (evolutionary rate) at a site between protein subfamilies, whereas type II FD occurs when there has been a shift in preferences for different amino acid chemical properties. A variety of methods have been developed for identifying both site types in protein subfamilies, both from phylogenetic and information-theoretic angles. However, evaluation of the performance of these methods has typically relied upon a handful of reasonably well-characterized biological datasets or analyses of a single biological example. While experimental validation of many truly functionally divergent sites (true positives) can be relatively straightforward, determining that particular sites do not contribute to functional divergence (i.e. false positives and true negatives) is much more difficult, resulting in noisy ‘gold standard’ examples.
Results:We describe a novel, phylogeny-based functional divergence classifier, FunDi. Unlike previous approaches, FunDi uses a unified mixture model-based approach to detect type I and type II FD. To assess FunDi's overall classification performance relative to other methods, we introduce two methods for simulating functionally divergent datasets. We find that the FunDi method performs better than several other predictors over a wide variety of simulation conditions.
Availability:http://rogerlab.biochem.dal.ca/Software
Contact: andrew.roger@dal.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Conserved and differential gene interactions in dynamical biological systems
Authors: Ouyang Zhengyu , Song Mingzhou , Güth Robert , Ha Thomas J. , Larouche Matt , Goldowitz Dan 
Published: August 2011

Abstract
Motivation: While biological systems operated from a common genome can be conserved in various ways, they can also manifest highly diverse dynamics and functions. This is because the same set of genes can interact differentially across specific molecular contexts. For example, differential gene interactions give rise to various stages of morphogenesis during cerebellar development. However, after over a decade of efforts toward reverse engineering biological networks from high-throughput omic data, gene networks of most organisms remain sketchy. This hindrance has motivated us to develop comparative modeling to highlight conserved and differential gene interactions across experimental conditions, without reconstructing complete gene networks first.
Results: We established a comparative dynamical system modeling (CDSM) approach to identify conserved and differential interactions across molecular contexts. In CDSM, interactions are represented by ordinary differential equations and compared across conditions through statistical heterogeneity and homogeneity tests. CDSM demonstrated a consistent superiority over differential correlation and reconstruct-then-compare in simulation studies. We exploited CDSM to elucidate gene interactions important for cellular processes poorly understood during mouse cerebellar development. We generated hypotheses on 66 differential genetic interactions involved in expansion of the external granule layer. These interactions are implicated in cell cycle, differentiation, apoptosis and morphogenesis. Additional 1639 differential interactions among gene clusters were also identified when we compared gene interactions during the presence of Rhombic lip versus the presence of distinct internal granule layer. Moreover, compared with differential correlation and reconstruct-then-compare, CDSM makes fewer assumptions on data and thus is applicable to a wider range of biological assays.
Availability: Source code in C++ and R is available for non-commercial organizations upon request from the corresponding author. The cerebellum gene expression dataset used in this article is available upon request from the Goldowitz lab (dang@cmmt.ubc.ca, http://grits.dglab.org/).
Contact: joemsong@cs.nmsu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters
Authors: Despalins Arnaud , Marsit Souhir , Oberto Jacques 
Published: August 2011

Abstract
Summary: Absynte (Archaeal and Bacterial Synteny Explorer) is a web-based service designed to display local syntenies in completely sequenced prokaryotic chromosomes. The genomic contexts are determined with a multiple center star clustering topology on the basis of a user-provided protein sequence and all (or a set of) chromosomes from the publicly available archaeal and bacterial genomes. The results consist in a dynamic web page where a consistent color-coding permits a rapid visual evaluation of the relative positioning of genes with similar sequences within the synteny. Each gene composing the synteny can be further queried interactively using either local or remote databases. Absynte results can be exported in .CSV or high-resolution, .PDF formats for printing, archival, further editing or publication purposes. Performance, real-time computation, user-friendliness and daily database updates constitute the principal advantages of Absynte over similar web services.
Availability: http://archaea.u-psud.fr/absynte
Contact: jacques.oberto@igmors.u-psud.fr
Protein Quality and Physical Characteristics of Kisra (Fermented Sorghum Pancake‐like Flatbread) Made from Tannin and Non‐Tannin Sorghum Cultivars
Authors: AwadElkareem Amir Mahgoub , Taylor John R. N. 
Published: August 2011

ABSTRACTKisra is a naturally lactic acid bacteria‐ and yeast‐fermented sorghum thin pancake‐like flatbread produced in Sudan. Kisra has considerable potential as the basis for development of a gluten‐free sandwich wrap. To help direct cultivar selection for commercial production of these products, two white, tan plant non‐tannin Type I, one white Type II tannin, and one red Type III tannin sorghum cultivars were evaluated with respect to kisra protein quality and physical characteristics. Kisra from the non‐tannin sorghums were flexible and had an open‐textured structure with many regular gas cells, whereas those from the tannin sorghums were more brittle, denser in structure, and contained far fewer and smaller gas cells. Kisra from the tannin sorghums had the lowest reactive lysine content, in vitro protein digestibility, and Protein Digestibility Corrected Amino Score (PDCAAS), with values being lowest for the Type III sorghum. PDCAAS of kisra from the Type III sorghum was only 0.12, less than half of that from the Type I sorghums. As the tannins in tannin sorghums adversely affect kisra protein quality and physical characteristics, white tan plant, non‐tannin sorghum cultivars are most suitable for kisra production and for development of wrap‐type sorghum‐based baked goods.
Enzymatic Process for Corn Dry‐Grind High‐Solids Fermentation
Authors: Kaur Prabhjot , Rausch Kent D. , Tumbleson M. E. , Singh Vijay 
Published: August 2011

ABSTRACTA modified dry‐grind process that combined the use of conventional amylases (glucoamylase [GA]), phytase, and granular starch hydrolyzing enzymes (GSHE) to achieve low liquefaction viscosities and low glucose concentrations during simultaneous saccharification and fermentation (SSF) with a high slurry solids content (>33% w/w) was developed. Doses of GSHE and GA were optimized for the modified process. At 35% solids content, the modified process had 80% lower slurry viscosity, 24% lower peak glucose concentration, 7.5% higher final ethanol concentration, and 51% higher fermentation rate compared with the conventional dry‐grind process. At 40% solids content, the modified process had lower viscosities, lower peak and residual glucose concentrations, and higher ethanol concentrations than the conventional process; however, the results were in contrast to those for 35% solids content. At 40% solids content, SSF did not run to completion for conventional or modified processes, and more than 2.5% w/v of residual glucose was left in the fermentation broth. Final ethanol concentration achieved with the modified process at 40% solids content was 19.5% v/v, similar to the ethanol concentration achieved with the modified process at 35% solids content. At 35% slurry solids content, a GSHE level of 1.25 μL/g db of corn and a GA level of 0.25 μL/g db of corn were selected as optimum enzyme doses for the modified process.
The value of work‐based projects in management education
Authors: Rogers Beth 
Published: August 2011

PurposeNational policy appears to be supportive of part‐time management education, but many researchers have observed difficult challenges in this type of skills development. This paper seeks to discuss how academic assessments that are also work‐based projects could benefit all stakeholders in management education.Design/methodology/approachThis premise is based on prior literature sources together with an example from the author's own teaching practice – a part‐time Master's programme focused on sales managers.FindingsIt is possible for company sponsors and their employees to achieve considerable benefits from management education when assignments are used to address their change projects.Originality/valueThis paper demonstrates how, even in the most outcome‐oriented of management functions, part‐time education can provide mutual value for all stakeholders.
A missing link: national economic aspirations and training and learning in firms
Authors: Sloman Martyn 
Published: August 2011

PurposeThe purpose of this paper is to consider critically Government policy options in achieving growth through skills acquisition and deployment.Design/methodology/approachThe approach takes the form of a review of policies drawing on literature from a number of countries.FindingsGovernment has a tendency to offer macro‐solutions to a micro problem and is impotent as a result. The main hope lies in long‐term development through the education system.Practical implicationsThe paper argues for a change in perspective from Government and a shift away from unhelpful initiatives. It calls for a long‐term investment in education.Originality/valueThe paper links the Government's macro‐economic policies with the micro‐ implications at the level of the firm.