DEFORMATION TRANSVERSE SHEAR BENDING STATE OF A THIN PLATE LAYER OF AN ANISOTROPIC GEOLOGICAL MEDIUM FROM THE ACTION OF CONCENTRATED ENERGY IMPULSES

A method is proposed for study the structural stability of the deformation state of structural blocks of the earth's crust, approximated in the form of plate layers of the geological medium when transverse shear bending from the action of concentrated energy impulses. Advances here are carried out in the two directions. First, in contrast to the previous article, the physical and mechanical model of the geological medium is endowed with anisotropic properties, which makes it possible to increase the adequacy of the obtained numerical results to the specifics of the real problem. Secondly, instead of the simplest bilinear 4-node finite elements, the special spectral non-algebraic 8-node finite iso-parametric finite elements are used, the use of which significantly increases both the accuracy of calculations and their reliability in the sense of ensuring the robustness of calculations for relatively small values of the plate thickness. It should be noted that the Finite Element Method uses exclusively only algebraic finite elements (power polynomials in the h-version and orthogonal polynomials in the p-version). It is known from approximation theory that the use of spectral non-algebraic approximations improves the quality of approximations. Therefore, their introduction into the structure of finite element calculations can improve the quality of modeling in the study of the strain-stress-state (SSS) of the geological medium. A structural block (SB) is understood as a plate layer with plan dimensions exceeding the thickness by more than 10 times. The identification of hazardous zones in the rock massive due to stress concentration is complemented by the development of mechanical, mathematical and computational tools for modeling the curvature of the earth's crust during bending based on the classical theory of Kirchhoff and refined Reissner-Mindlin theory. Test calculations have shown that the accuracy of the calculation and the quality of geometric modeling of fragments of an anisotropic geological environment based on the refined 8-node spectral finite element is significantly better than for the 8-node algebraic finit

Differential Evolution Approach to Detect Recent Admixture

The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools that can infer multiple origins. Misclassification of such individuals can lead to incorrect and costly misinterpretations of genomic data, primarily in disease studies and drug trials. We present an advanced tool to infer ancestry that can identify the biogeographic origins of highly mixed individuals. reAdmix is an online tool available at http://chcb.saban-chla.usc.edu/reAdmix/.Comment: presented at ISMB 2014, VariSI

The mysterious orphans of Mycoplasmataceae

Background: The length of a protein sequence is largely determined by its function, i.e. each functional group is associated with an optimal size. However, comparative genomics revealed that proteins length may be affected by additional factors. In 2002 it was shown that in bacterium Escherichia coli and the archaeon Archaeoglobus fulgidus, protein sequences with no homologs are, on average, shorter than those with homologs. Most experts now agree that the length distributions are distinctly different between protein sequences with and without homologs in bacterial and archaeal genomes. In this study, we examine this postulate by a comprehensive analysis of all annotated prokaryotic genomes and focusing on certain exceptions. Results: We compared lengths distributions of having homologs proteins (HHPs) and non-having homologs proteins (orphans or ORFans) in all currently annotated completely sequenced prokaryotic genomes. As expected, the HHPs and ORFans have strikingly different length distributions in almost all genomes. As previously established, the HHPs, indeed, are, on average, longer than the ORFans, and the length distributions for the ORFans have a relatively narrow peak, in contrast to the HHPs, whose lengths spread over a wider range of values. However, about thirty genomes do not obey these rules. Practically all genomes of Mycoplasma and Ureaplasma have atypical ORFans distributions, with the mean lengths of ORFan larger than the mean lengths of HHPs. These genera constitute over 80% of atypical genomes. Conclusions: We confirmed on a ubiquitous set of genomes the previous observation that HHPs and ORFans have different gene length distributions. We also showed that Mycoplasmataceae genomes have distinctive distributions of ORFans lengths. We offer several possible biological explanations of this phenomenon

Tectonic Processes Modeling For High-Level Radioactive Waste Disposal

The possibility of using deep geological formations to dispose of high-level radioactive waste (HLW) is a subject raising heated debate among scientists. In Russia, the idea of constructing HLW repository in the Niznekansky granitoid massif (NKM) in Krasnoyarsk area is widely discussed. To solve this problem we are elaborating a technology associated with time – space stability prediction of the geological environment, which is subject to geodynamic processes evolutionary effects. It is based on the prediction of isolation properties stability in a structural tectonic block of the Earth’s crust for a given time. The danger is in the possibility that the selected structural block may be broken by new tectonic faults or movements on a passive fault may be activated and thus underground water may penetrate to HLW containers

GC3 biology in corn, rice, sorghum and other grasses

<p>Abstract</p> <p>Background</p> <p>The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates.</p> <p>Results</p> <p>Here we demonstrate that in certain organisms the amount of GC at the wobble position (GC₃) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC₃content: they (1) provide more targets for methylation, (2) exhibit more variable expression, (3) more frequently possess upstream TATA boxes, (4) are predominant in certain classes of genes (e.g., stress responsive genes) and (5) have a GC₃content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC₃bimodality in grasses.</p> <p>Conclusions</p> <p>Our findings suggest that high levels of GC₃typify a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC₃bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation.</p

Local ancestry prediction with PyLAE

We developed PyLAE, a new tool for determining local ancestry along a genome using whole-genome sequencing data or high-density genotyping experiments. PyLAE can process an arbitrarily large number of ancestral populations (with or without an informative prior). Since PyLAE does not involve estimating many parameters, it can process thousands of genomes within a day. PyLAE can run on phased or unphased genomic data. We have shown how PyLAE can be applied to the identification of differentially enriched pathways between populations. The local ancestry approach results in higher enrichment scores compared to whole-genome approaches. We benchmarked PyLAE using the 1000 Genomes dataset, comparing the aggregated predictions with the global admixture results and the current gold standard program RFMix. Computational efficiency, minimal requirements for data pre-processing, straightforward presentation of results, and ease of installation make PyLAE a valuable tool to study admixed populations

benchNGS : An approach to benchmark short reads alignment tools

In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when the NGS reads are quite different from the available reference genome. We propose a benchmark to assess accuracy of short reads mapping based on the pre-computed global alignment of related genome sequences. In this paper we propose a benchmark to assess accuracy of the short reads mapping based on the pre-computed global alignment of closely related genome sequences. We outline the method and also present a short report of an experiment performed on five popular alignment tools based on the pairwise alignments of Escherichia coli O6 CFT073 genome with genomes of seven other bacteria.Comment: 1 figur