Stability of a frictional, cohesive layer on a viscous substratum: validity of asymptotic solution and influence of material properties

This study deals with the stability of a stratified structure composed of a cohesive and frictional overburden, a viscous substratum, and a rigid basement. That structure should be seen as a prototype for various salt tectonics and lithospheric plates stability analyses. The destabilizing factors are the density contrast, the tectonic compressive stress, and the possible erosion and deposition at the top surface. The overburden stiffness, a nonlinear function of in situ stress, has a stabilizing role. Two solutions are extracted from the variational formulation of the stability problem previously proposed [Leroy and Triantafyllidis, 1996]: the first is analytical and is obtained by disregarding gravity, and the second is numerical and is based on the finite element method. The latter is used to assess the validity of the previously presented asymptotic solution. It is shown that the asymptotic solution is accurate even for values of the small parameter, defined as the perturbation wavenumber times the overburden thickness, as large as 0.4. Furthermore, the possibility for the cohesive material in the overburden to accommodate part of the deformation by slip along a population of small pervasive faults is accounted for by the introduction of a deformation theory of plasticity. Stability predictions based on this theory indicate that structural modes, such as folding, and localized faulting modes are triggered for similar stress magnitudes. The parametric study presented includes the previously undetected influences of the stress gradient with depth and of the work hardening properties of the competent overburden. The role of erosion and deposition in destabilizing shallow overburdens, regardless of the magnitude of the tectonic stress, is also established. The stability predictions are then applied to a folded section through the Campos basin, offshore Brazil, revealing that the deformation theory of plasticity is necessary to explain the buckling that occurred during the Albian

Fracture of disordered solids in compression as a critical phenomenon: I. Statistical mechanics formalism

This is the first of a series of three articles that treats fracture localization as a critical phenomenon. This first article establishes a statistical mechanics based on ensemble averages when fluctuations through time play no role in defining the ensemble. Ensembles are obtained by dividing a huge rock sample into many mesoscopic volumes. Because rocks are a disordered collection of grains in cohesive contact, we expect that once shear strain is applied and cracks begin to arrive in the system, the mesoscopic volumes will have a wide distribution of different crack states. These mesoscopic volumes are the members of our ensembles. We determine the probability of observing a mesoscopic volume to be in a given crack state by maximizing Shannon's measure of the emergent crack disorder subject to constraints coming from the energy-balance of brittle fracture. The laws of thermodynamics, the partition function, and the quantification of temperature are obtained for such cracking systems.Comment: 11 pages, 2 figure

SMYD1, the myogenic activator, is a direct target of serum response factor and myogenin

SMYD1 is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. We demonstrated that the expression of SMYD1 is restricted in the heart and skeletal muscle tissues in human. To reveal the regulatory mechanisms of SMYD1 expression during myogenesis and cardiogenesis, we cloned and characterized the human SMYD1 promoter, which contains highly conserved serum response factor (SRF) and myogenin binding sites. Overexpression of SRF and myogenin significantly increased the endogenous expression level of Smyd1 in C2C12 cells, respectively. Deletion of Srf in the heart of mouse embryos dramatically decreased the expression level of Smyd1 mRNA and the expression of Smyd1 can be rescued by exogenous SRF introduction in SRF null ES cells during differentiation. Furthermore, we demonstrated that SRF binds to the CArG site and myogenin binds to the E-box element on Smyd1 promoter region using EMSA and ChIP assays. Moreover, forced expression of SMYD1 accelerates myoblast differentiation and myotube formation in C2C12 cells. Taken together, these studies demonstrated that SMYD1 is a key regulator of myogenic differentiation and acts as a downstream target of muscle regulatory factors, SRF and myogenin

Switched-current filter structure for synthesizing arbitrary characteristics based on follow-the-leader feedback configuration

This document is the Accepted Manuscript version of the following article: Wenshan Zhao, Yigang He, and Yichuang Sun, ‘Switched-current filter structure for synthesizing arbitrary characteristics based on follow-the-leader feedback configuration’, Analog Integrated Circuits and Signal Processing, (2015), Vol. 82 (2): 479-486. The version of record is available online at doi: 10.1007/s10470-014-0477-8 © Springer Science+Business Media New York 2015Peer reviewedFinal Accepted Versio

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

<p>Abstract</p> <p>Background</p> <p>The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation.</p> <p>Results</p> <p>A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from <url>http://dna.uio.no/swipe/</url> under the GNU Affero General Public License.</p> <p>Conclusions</p> <p>Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.</p

Measuring our universe from galaxy redshift surveys

Galaxy redshift surveys have achieved significant progress over the last couple of decades. Those surveys tell us in the most straightforward way what our local universe looks like. While the galaxy distribution traces the bright side of the universe, detailed quantitative analyses of the data have even revealed the dark side of the universe dominated by non-baryonic dark matter as well as more mysterious dark energy (or Einstein's cosmological constant). We describe several methodologies of using galaxy redshift surveys as cosmological probes, and then summarize the recent results from the existing surveys. Finally we present our views on the future of redshift surveys in the era of Precision Cosmology.Comment: 82 pages, 31 figures, invited review article published in Living Reviews in Relativity, http://www.livingreviews.org/lrr-2004-

FRA2A is a CGG repeat expansion associated with silencing of AFF3

Folate-sensitive fragile sites (FSFS) are a rare cytogenetically visible subset of dynamic mutations. Of the eight molecularly characterized FSFS, four are associated with intellectual disability (ID). Cytogenetic expression results from CGG tri-nucleotide-repeat expansion mutation associated with local CpG hypermethylation and transcriptional silencing. The best studied is the FRAXA site in the FMR1 gene, where large expansions cause fragile X syndrome, the most common inherited ID syndrome. Here we studied three families with FRA2A expression at 2q11 associated with a wide spectrum of neurodevelopmental phenotypes. We identified a polymorphic CGG repeat in a conserved, brain-active alternative promoter of the AFF3 gene, an autosomal homolog of the X-linked AFF2/FMR2 gene: Expansion of the AFF2 CGG repeat causes FRAXE ID. We found that FRA2A-expressing individuals have mosaic expansions of the AFF3 CGG repeat in the range of several hundred repeat units. Moreover, bisulfite sequencing and pyrosequencing both suggest AFF3 promoter hypermethylation. cSNP-analysis demonstrates monoallelic expression of the AFF3 gene in FRA2A carriers thus predicting that FRA2A expression results in functional haploinsufficiency for AFF3 at least in a subset of tissues. By whole-mount in situ hybridization the mouse AFF3 ortholog shows strong regional expression in the developing brain, somites and limb buds in 9.5-12.5dpc mouse embryos. Our data suggest that there may be an association between FRA2A and a delay in the acquisition of motor and language skills in the families studied here. However, additional cases are required to firmly establish a causal relationship

Point-Free, Set-Free Concrete Linear Algebra

International audienceWe show how a simple variant of Gaussian elimination can be used to model abstract linear algebra directly, using matrices only to represent all categories of objects, with operations such as subspace intersection and sum. We can even provide effective support for direct sums and subalgebras. We have formalized this work in Coq, and used it to develop all of the group representation theory required for the proof of the Odd Order Theorem, including results such as the Jacobson Density Theorem, Clifford's Theorem, the Jordan-Holder Theorem for modules, the Wedderburn Structure Theorem for semisimple rings (the basis for character theory).On présente une formalisation en Coq de l'algèbre linéaire où tous les objets sont représentés par des matrices, y compris les sous-espaces. Ce développement a été utilisé pour élaborer la formalisation des éléments de théorie de la représentation nécessaires à la prévue du théorème de Feit-Thompson

Down-Regulation of Myogenin Can Reverse Terminal Muscle Cell Differentiation

Certain higher vertebrates developed the ability to reverse muscle cell differentiation (dedifferentiation) as an additional mechanism to regenerate muscle. Mammals, on the other hand, show limited ability to reverse muscle cell differentiation. Myogenic Regulatory Factors (MRFs), MyoD, myogenin, Myf5 and Myf6 are basic-helix-loop-helix (bHLH) transcription factors essential towards the regulation of myogenesis