Comparative (computational) analysis of the DNA methylation status of trinucleotide repeat expansion diseases

Copyright © 2013 Mohammadmersad Ghorbani et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This article has been made available through the Brunel Open Access Publishing Fund.Previous studies have examined DNA methylation in different trinucleotide repeat diseases. We have combined this data and used a pattern searching algorithm to identify motifs in the DNA surrounding aberrantly methylated CpGs found in the DNA of patients with one of the three trinucleotide repeat (TNR) expansion diseases: fragile X syndrome (FRAXA), myotonic dystrophy type I (DM1), or Friedreich’s ataxia (FRDA). We examined sequences surrounding both the variably methylated (VM) CpGs, which are hypermethylated in patients compared with unaffected controls, and the nonvariably methylated CpGs which remain either always methylated (AM) or never methylated (NM) in both patients and controls. Using the J48 algorithm of WEKA analysis, we identified that two patterns are all that is necessary to classify our three regions CCGG* which is found in VM and not in AM regions and AATT* which distinguished between NM and VM + AM using proportional frequency. Furthermore, comparing our software with MEME software, we have demonstrated that our software identifies more patterns than MEME in these short DNA sequences. Thus, we present evidence that the DNA sequence surrounding CpG can influence its susceptibility to be de novo methylated in a disease state associated with a trinucleotide repeat.European Union Seventh Framework Programme and The Brunel University Graduate Program

1, 2, 3, Stop the Bleed: Analysis of a Bleeding Control Educational Course

Hemorrhaging, or uncontrolled bleeding, accounts for 40% of preventable deaths in the United States that occur after a traumatic injury. The Stop the Bleed campaign was launched in 2015 by the White House National Security Council to educate the public about methods to control and stop bleeding as well as empower individuals to take action if a traumatic accident occurs. The goal of this study was to evaluate the effectiveness of the “Stop the Bleed” bleeding control course to increase knowledge about the topic as well as increase confidence to take action and use the techniques that were taught during the course appropriately. Data was collected via a cross sectional pre-post survey design. At baseline, the participants were asked basic knowledge questions about bleeding control and techniques to use as well as how confident they felt using those skills. After being presented the bleeding control material and practicing the techniques in the hands-on portion of the course, the participants were asked to complete a post-test with similar questions to that of the pre-test. De-identified responses were collected to analyze the changes in the overall knowledge scores and overall confidence scores with the use of the paired-t statistical test on SPSS. The participants (N=32) were employees within the Thomas Jefferson University Campus Security department. The overall score for the knowledge-based questions were analyzed from pre to post and showed that the changes were statistically significant (8.163,

Precise absolute astrometry from the VLBA imaging and polarimetry survey at 5 GHz

We present in this paper accurate positions of 857 sources derived from the astrometric analysis of 16 eleven-hour experiments from the Very Long Baseline Array imaging and polarimetry survey at 5 GHz (VIPS). Among observed sources, positions of 430 objects were not determined before at a milliarcsecond level of accuracy. For 95% of the sources the uncertainty of their positions range from 0.3 to 0.9 mas, with the median value of 0.5 mas. This estimate of accuracy is substantiated by the comparison of positions of 386 sources that were previously observed in astrometric programs simultaneously at 2.3/8.6 GHz. Surprisingly, the ionosphere contribution to group delay was adequately modeled with the use of the total electron contents maps derived from GPS observations and only marginally affected estimates of source coordinates.Comment: Accepted for publication by the Astronomical Journal. 7 pages, 2 tables, 4 figures. Submission contains an ascii file with the catalogue. You can get the catalogue by downloading the source of this paper and extracting file table2.tx

Generalized Bergman kernels on symplectic manifolds

We study the near diagonal asymptotic expansion of the generalized Bergman kernel of the renormalized Bochner-Laplacian on high tensor powers of a positive line bundle over a compact symplectic manifold. We show how to compute the coefficients of the expansion by recurrence and give a closed formula for the first two of them. As consequence, we calculate the density of states function of the Bochner-Laplacian and establish a symplectic version of the convergence of the induced Fubini-Study metric. We also discuss generalizations of the asymptotic expansion for non-compact or singular manifolds as well as their applications. Our approach is inspired by the analytic localization techniques of Bismut-Lebeau.Comment: 48 pages. Add two references on the Hermitian scalar curvatur