Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/[email protected]

Couplings of the Rho Meson in a Holographic dual of QCD with Regge Trajectories

The couplings $g_{\rho HH}$ of the $\rho$ meson with any hadron H are calculated in a holographic dual of QCD where the Regge trajectories for mesons are manifest. The resulting couplings grow linearly with the exciting number of H, thus are far from universal. A simple argument has been given for this behavior based on quasi-classical picture of excited hadrons. It seems that in holographic duals with exact Regge trajectories the $g_{\rho HH}$ universality should be violated. The $\rho$-dominance for the electromagnetic form factors of H are also strongly violated, except for the lowest state, the pion. Quite unexpected, the form factor of the pion is completely saturated by the contribution of the $\rho$. The asymptotic behavior of the form factors are also calculated, and are found to be perfectly accordant with the prediction of conformal symmetry and pertubative QCD.Comment: 9 page

XMMU J100750.5+125818: A strong lensing cluster at z=1.082

We report on the discovery of the X-ray luminous cluster XMMU J100750.5+125818 at redshift 1.082 based on 19 spectroscopic members, which displays several strong lensing features. SED modeling of the lensed arc features from multicolor imaging with the VLT and the LBT reveals likely redshifts ~2.7 for the most prominent of the lensed background galaxies. Mass estimates are derived for different radii from the velocity dispersion of the cluster members, M_200 ~ 1.8 10^{14} Msun, from the X-ray spectral parameters, M_500 ~ 1.0 10^{14} Msun, and the largest lensing arc, M_SL ~ 2.3 10^{13} Msun. The projected spatial distribution of cluster galaxies appears to be elongated, and the brightest galaxy lies off center with respect to the X-ray emission indicating a not yet relaxed structure. XMMU J100750.5+125818 offers excellent diagnostics of the inner mass distribution of a distant cluster with a combination of strong and weak lensing, optical and X-ray spectroscopy.Comment: A&A, accepted for publicatio

SO/Sp Monopoles and Branes with Orientifold 3 Plane

We study BPS monopoles in 4 dimensional N=4 SO(N) and $Sp(N)$ super Yang-Mills theories realized as the low energy effective theory of $N$ (physical and its mirror) parallel D3 branes and an {\it Orientifold 3 plane} with D1 branes stretched between them in type IIB string theory. Monopoles on D3 branes give the natural understanding by embedding in SU(N) through the constraints on both the asymptotic Higgs field (corresponding to the horizontal positions of D3 branes) and the magnetic charges (corresponding to the number of D1 branes) imposed by the O3 plane. The compatibility conditions of Nahm data for monopoles for these groups can be interpreted very naturally through the D1 branes in the presence of O3 plane.Comment: 18 pages, Latex with RevTex, 1 table, 4 figures, v2: Clarified the introduction and improved on the supersymmetric theory on D1 branes in page 7 and 8 and this final version to appear in Phys.Rev.

The probability to initiate X chromosome inactivation is determined by the X to autosomal ratio and x chromosome specific allelic properties.

Background: In female mammalian cells, random X chromosome inactivation (XCI) equalizes the dosage of X-encoded gene products to that in male cells. XCI is a stochastic process, in which each X chromosome has a probability to be inactivated. To obtain more insight in the factors setting up this probability, we studied the role of the X to autosome (X:A) ratio in initiation of XCI, and have used the experimental data in a computer simulation model to study the cellular population dynamics of XCI. Methodology/Principal Findings: To obtain more insight in the role of the X:A ratio in initiation of XCI, we generated triploid mouse ES cells by fusion of haploid round spermatids with diploid female and male ES cells. These fusion experiments resulted in only XXY triploid ES cells. XYY and XXX ES lines were absent, suggesting cell death related either to insufficient X-chromosomal gene dosage (XYY) or to inheritance of an epigenetically modified X chromosome (XXX). Analysis of active (Xa) and inactive (Xi) X chromosomes in the obtained triploid XXY lines indicated that the initiation frequency of XCI is low, resulting in a mixed population of XaXiY and XaXaY cells, in which the XaXiY cells have a small proliferative advantage. This result, and findings on XCI in diploid and tetraploid ES cell lines with different X:A ratios, provides evidence that the X:A ratio determines the probability for a given X chromosome to be inactivated. Furthermore, we found that the kinetics of the XCI process can be simulated using a probability for an X chromosome to be inactivated that is proportional to the X:A ratio. These simulation studies re-emphasize our hypothesis that the probability is a function of the concentration of an X-encoded activator of XCI, and of X chromosome specific allelic properties determining the threshold for this activator. Conclusions: The present findings reveal that the probability for an X chromosome to be inactivated is proportional to the X:A ratio. This finding supports the presence of an X-encoded activator of the XCI process. © 2009 Monkhorst et al

One-way multigrid method in electronic structure calculations

We propose a simple and efficient one-way multigrid method for self-consistent electronic structure calculations based on iterative diagonalization. Total energy calculations are performed on several different levels of grids starting from the coarsest grid, with wave functions transferred to each finer level. The only changes compared to a single grid calculation are interpolation and orthonormalization steps outside the original total energy calculation and required only for transferring between grids. This feature results in a minimal amount of code change, and enables us to employ a sophisticated interpolation method and noninteger ratio of grid spacings. Calculations employing a preconditioned conjugate gradient method are presented for two examples, a quantum dot and a charged molecular system. Use of three grid levels with grid spacings 2h, 1.5h, and h decreases the computer time by about a factor of 5 compared to single level calculations.Comment: 10 pages, 2 figures, to appear in Phys. Rev. B, Rapid Communication

Simcluster: clustering enumeration gene expression data on the simplex space

Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST "digital northern", are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space.

Here we present a software tool, Simcluster, designed to perform clustering analysis for data on the simplex space. We present Simcluster as a stand-alone command-line C package and as a user-friendly on-line tool. Both versions are available at: http://xerad.systemsbiology.net/simcluster.

Simcluster is designed in accordance with a well-established mathematical framework for compositional data analysis, which provides principled procedures for dealing with the simplex space, and is thus applicable in a number of contexts, including enumeration-based gene expression data