covRNA: discovering covariate associations in large-scale gene expression data

OBJECTIVE: The biological interpretation of gene expression measurements is a challenging task. While ordination methods are routinely used to identify clusters of samples or co-expressed genes, these methods do not take sample or gene annotations into account. We aim to provide a tool that allows users of all backgrounds to assess and visualize the intrinsic correlation structure of complex annotated gene expression data and discover the covariates that jointly affect expression patterns. RESULTS: The Bioconductor package covRNA provides a convenient and fast interface for testing and visualizing complex relationships between sample and gene covariates mediated by gene expression data in an entirely unsupervised setting. The relationships between sample and gene covariates are tested by statistical permutation tests and visualized by ordination. The methods are inspired by the fourthcorner and RLQ analyses used in ecological research for the analysis of species abundance data, that we modified to make them suitable for the distributional characteristics of both, RNA-Seq read counts and microarray intensities, and to provide a high-performance parallelized implementation for the analysis of large-scale gene expression data on multi-core computational systems. CovRNA provides additional modules for unsupervised gene filtering and plotting functions to ensure a smooth and coherent analysis workflow

Conditions for nonexistence of static or stationary, Einstein-Maxwell, non-inheriting black-holes

We consider asymptotically-flat, static and stationary solutions of the Einstein equations representing Einstein-Maxwell space-times in which the Maxwell field is not constant along the Killing vector defining stationarity, so that the symmetry of the space-time is not inherited by the electromagnetic field. We find that static degenerate black hole solutions are not possible and, subject to stronger assumptions, nor are static, non-degenerate or stationary black holes. We describe the possibilities if the stronger assumptions are relaxed.Comment: 19 pages, to appear in GER

Exponential-Potential Scalar Field Universes I: The Bianchi I Models

We obtain a general exact solution of the Einstein field equations for the anisotropic Bianchi type I universes filled with an exponential-potential scalar field and study their dynamics. It is shown, in agreement with previous studies, that for a wide range of initial conditions the late-time behaviour of the models is that of a power-law inflating FRW universe. This property, does not hold, in contrast, when some degree of inhomogeneity is introduced, as discussed in our following paper II.Comment: 16 pages, Plain LaTeX, 1 Figure to be sent on request, to appear in Phys. Rev.

Matrix theory of gravitation

A new classical theory of gravitation within the framework of general relativity is presented. It is based on a matrix formulation of four-dimensional Riemann-spaces and uses no artificial fields or adjustable parameters. The geometrical stress-energy tensor is derived from a matrix-trace Lagrangian, which is not equivalent to the curvature scalar R. To enable a direct comparison with the Einstein-theory a tetrad formalism is utilized, which shows similarities to teleparallel gravitation theories, but uses complex tetrads. Matrix theory might solve a 27-year-old, fundamental problem of those theories (sec. 4.1). For the standard test cases (PPN scheme, Schwarzschild-solution) no differences to the Einstein-theory are found. However, the matrix theory exhibits novel, interesting vacuum solutions.Comment: 24 page

Spinodal Decomposition in a Binary Polymer Mixture: Dynamic Self Consistent Field Theory and Monte Carlo Simulations

We investigate how the dynamics of a single chain influences the kinetics of early stage phase separation in a symmetric binary polymer mixture. We consider quenches from the disordered phase into the region of spinodal instability. On a mean field level we approach this problem with two methods: a dynamical extension of the self consistent field theory for Gaussian chains, with the density variables evolving in time, and the method of the external potential dynamics where the effective external fields are propagated in time. Different wave vector dependencies of the kinetic coefficient are taken into account. These early stages of spinodal decomposition are also studied through Monte Carlo simulations employing the bond fluctuation model that maps the chains -- in our case with 64 effective segments -- on a coarse grained lattice. The results obtained through self consistent field calculations and Monte Carlo simulations can be compared because the time, length, and temperature scales are mapped onto each other through the diffusion constant, the chain extension, and the energy of mixing. The quantitative comparison of the relaxation rate of the global structure factor shows that a kinetic coefficient according to the Rouse model gives a much better agreement than a local, i.e. wave vector independent, kinetic factor. Including fluctuations in the self consistent field calculations leads to a shorter time span of spinodal behaviour and a reduction of the relaxation rate for smaller wave vectors and prevents the relaxation rate from becoming negative for larger values of the wave vector. This is also in agreement with the simulation results.Comment: Phys.Rev.E in prin

Spectral Statistics of the Two-Body Random Ensemble Revisited

Using longer spectra we re-analyze spectral properties of the two-body random ensemble studied thirty years ago. At the center of the spectra the old results are largely confirmed, and we show that the non-ergodicity is essentially due to the variance of the lowest moments of the spectra. The longer spectra allow to test and reach the limits of validity of French's correction for the number variance. At the edge of the spectra we discuss the problems of unfolding in more detail. With a Gaussian unfolding of each spectrum the nearest neighbour spacing distribution between ground state and first exited state is shown to be stable. Using such an unfolding the distribution tends toward a semi-Poisson distribution for longer spectra. For comparison with the nuclear table ensemble we could use such unfolding obtaining similar results as in the early papers, but an ensemble with realistic splitting gives reasonable results if we just normalize the spacings in accordance with the procedure used for the data.Comment: 11 pages, 7 figure

Dynamics of Viscous Dissipative Plane Symmetric Gravitational Collapse

We present dynamical description of gravitational collapse in view of Misner and Sharp's formalism. Matter under consideration is a complicated fluid consistent with plane symmetry which we assume to undergo dissipation in the form of heat flow, radiation, shear and bulk viscosity. Junction conditions are studied for a general spacetime in the interior and Vaidya spacetime in the exterior regions. Dynamical equations are obtained and coupled with causal transport equations derived in context of M$\ddot{u}$ller Israel Stewart theory. The role of dissipative quantities over collapse is investigated.Comment: 17 pages, accepted for publication in Gen. Relativ. Gra

Diffusive spin transport

Information to be stored and transported requires physical carriers. The quantum bit of information (qubit) can for instance be realised as the spin 1/2 degree of freedom of a massive particle like an electron or as the spin 1 polarisation of a massless photon. In this lecture, I first use irreducible representations of the rotation group to characterise the spin dynamics in a least redundant manner. Specifically, I describe the decoherence dynamics of an arbitrary spin S coupled to a randomly fluctuating magnetic field in the Liouville space formalism. Secondly, I discuss the diffusive dynamics of the particle's position in space due to the presence of randomly placed impurities. Combining these two dynamics yields a coherent, unified picture of diffusive spin transport, as applicable to mesoscopic electronic devices or photons propagating in cold atomic clouds.Comment: Lecture notes, published in A. Buchleitner, C. Viviescas, and M. Tiersch (Eds.), "Entanglement and Decoherence. Foundations and Modern Trends", Lecture Notes in Physics 768, Springer, Berlin (2009

Pervasive protein thermal stability variation during the cell cycle

Quantitative mass spectrometry has established proteome-wide regulation of protein abundance and post-translational modifications in various biological processes. Here, we used quantitative mass spectrometry to systematically analyze the thermal stability and solubility of proteins on a proteome-wide scale during the eukaryotic cell cycle. We demonstrate pervasive variation of these biophysical parameters with most changes occurring in mitosis and G1. Various cellular pathways and components vary in thermal stability, such as cell-cycle factors, polymerases, and chromatin remodelers. We demonstrate that protein thermal stability serves as a proxy for enzyme activity, DNA binding, and complex formation in situ. Strikingly, a large cohort of intrinsically disordered and mitotically phosphorylated proteins is stabilized and solubilized in mitosis, suggesting a fundamental remodeling of the biophysical environment of the mitotic cell. Our data represent a rich resource for cell, structural, and systems biologists interested in proteome regulation during biological transitions

How does the electromagnetic field couple to gravity, in particular to metric, nonmetricity, torsion, and curvature?

The coupling of the electromagnetic field to gravity is an age-old problem. Presently, there is a resurgence of interest in it, mainly for two reasons: (i) Experimental investigations are under way with ever increasing precision, be it in the laboratory or by observing outer space. (ii) One desires to test out alternatives to Einstein's gravitational theory, in particular those of a gauge-theoretical nature, like Einstein-Cartan theory or metric-affine gravity. A clean discussion requires a reflection on the foundations of electrodynamics. If one bases electrodynamics on the conservation laws of electric charge and magnetic flux, one finds Maxwell's equations expressed in terms of the excitation H=(D,H) and the field strength F=(E,B) without any intervention of the metric or the linear connection of spacetime. In other words, there is still no coupling to gravity. Only the constitutive law H= functional(F) mediates such a coupling. We discuss the different ways of how metric, nonmetricity, torsion, and curvature can come into play here. Along the way, we touch on non-local laws (Mashhoon), non-linear ones (Born-Infeld, Heisenberg-Euler, Plebanski), linear ones, including the Abelian axion (Ni), and find a method for deriving the metric from linear electrodynamics (Toupin, Schoenberg). Finally, we discuss possible non-minimal coupling schemes.Comment: Latex2e, 26 pages. Contribution to "Testing Relativistic Gravity in Space: Gyroscopes, Clocks, Interferometers ...", Proceedings of the 220th Heraeus-Seminar, 22 - 27 August 1999 in Bad Honnef, C. Laemmerzahl et al. (eds.). Springer, Berlin (2000) to be published (Revised version uses Springer Latex macros; Sec. 6 substantially rewritten; appendices removed; the list of references updated