MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. Through this work, which consists of a protocol, a toolbox, and tutorials of two use cases, we make our methods available to the broader scientific community. The protocol describes, in a step-wise manner, the workflow of data integration and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, this protocol constitutes a comprehensive guide to the intra-model analysis of extracellular metabolomic data and a resource offering a broad set of computational analysis tools for a wide biomedical and non-biomedical research community

Cosmic microwave anisotropies in an inhomogeneous compact flat universe

The anisotropies of the cosmic microwave background (CMB) are computed for the half-turn space E_2 which represents a compact flat model of the Universe, i.e. one with finite volume. This model is inhomogeneous in the sense that the statistical properties of the CMB depend on the position of the observer within the fundamental cell. It is shown that the half-turn space describes the observed CMB anisotropies on large scales better than the concordance model with infinite volume. For most observer positions it matches the temperature correlation function even slightly better than the well studied 3-torus topology

Hot pixel contamination in the CMB correlation function?

Recently, it was suggested that the map-making procedure, which is applied to the time-ordered CMB data by the WMAP team, might be flawed by hot pixels. This could lead to a bias in the pixels having an angular distance of about 141 degrees from hot pixels due to the differential measuring process of the satellite WMAP. Here, the bias is confirmed, and the temperature two-point correlation function C(theta) is reevaluated by excluding the affected pixels. It is shown that the most significant effect occurs in C(theta) at the largest angles near theta = 180 degrees. Furthermore, the corrected correlation function C(theta) is applied to the cubic topology of the Universe, and it is found that such a multi-connected universe matches the temperature correlation better than the LCDM concordance model, provided the cubic length scale is close to L=4 measured in units of the Hubble length

CMB Anisotropy of Spherical Spaces

The first-year WMAP data taken at their face value hint that the Universe might be slightly positively curved and therefore necessarily finite, since all spherical (Clifford-Klein) space forms M^3 = S^3/Gamma, given by the quotient of S^3 by a group Gamma of covering transformations, possess this property. We examine the anisotropy of the cosmic microwave background (CMB) for all typical groups Gamma corresponding to homogeneous universes. The CMB angular power spectrum and the temperature correlation function are computed for the homogeneous spaces as a function of the total energy density parameter Omega_tot in the large range [1.01, 1.20] and are compared with the WMAP data. We find that out of the infinitely many homogeneous spaces only the three corresponding to the binary dihedral group T*, the binary octahedral group O*, and the binary icosahedral group I* are in agreement with the WMAP observations. Furthermore, if Omega_tot is restricted to the interval [1.00, 1.04], the space described by T* is excluded since it requires a value of Omega_tot which is probably too large being in the range [1.06, 1.07]. We thus conclude that there remain only the two homogeneous spherical spaces S^3/O* and S^3/I* with Omega_tot of about 1.038 and 1.018, respectively, as possible topologies for our Universe.Comment: A version with high resolution sky maps can be obtained at http://www.physik.uni-ulm.de/theo/qc

The Topology and Size of the Universe from the Cosmic Microwave Background

We study the possibility that the universe has compact topologies T^3, T^2 x R^1, or S^1 x R^2 using the seven-year WMAP data. The maximum likelihood 95% confidence intervals for the size L of the compact direction are 1.7 < L/L_0 < 2.1, 1.8 < L/L_0 < 2.0, 1.2 < L/L_0 < 2.1 for the three cases, respectively, where L_0=14.4 Gpc is the distance to the last scattering surface. An infinite universe is compatible with the data at 4.3 sigma. We find using a Bayesian analysis that the most probable universe has topology T^2 x R^1, with L/L_0=1.9.Comment: Additional checks, Monte-Carlo skies, and study of dipole contamination added. References added. 13 pages, 11 figure

Segmentierung des Gehirns auf der Basis von MR-Daten

Es wird ein Segmentierungsverfahren vorgestellt, das bei T1-gewichteten MR Aufnahmen Liquor, Cortex und weisse Materie trennt. Das Verfahren korrigiert in mehreren Schritten aufnahmetechnisch bedingte Artefakte und bestimmt die Substanzen durch 2 globale Schwellen. Das Verfahren erfordert an mehreren Stellen eine interaktive Justierung von Parametern und ist entsprechend flexibel

Matrix Element Distribution as a Signature of Entanglement Generation

We explore connections between an operator's matrix element distribution and its entanglement generation. Operators with matrix element distributions similar to those of random matrices generate states of high multi-partite entanglement. This occurs even when other statistical properties of the operators do not conincide with random matrices. Similarly, operators with some statistical properties of random matrices may not exhibit random matrix element distributions and will not produce states with high levels of multi-partite entanglement. Finally, we show that operators with similar matrix element distributions generate similar amounts of entanglement.Comment: 7 pages, 6 figures, to be published PRA, partially supersedes quant-ph/0405053, expands quant-ph/050211

Mapeamento de Competências Necessárias aos Chefes de Parques Nacionais: Uma Proposta a Partir do Modelo de Cheetham e Chivers

Essa pesquisa teve como objetivo geral mapear as competências necessárias para o cargo de chefe de parque nacional, uma das doze categorias de Unidades de Conservação existentes no Brasil, geridas pelo Instituto Chico Mendes de Conservação da Biodiversidade ICMBio. Os parques nacionais são unidades de conservação que tem como objetivo básico a preservação de ecossistemas naturais de grande relevância ecológica e beleza cênica, realização de pesquisas científicas e o desenvolvimento de atividades de educação e interpretação ambiental, recreação em contato com a natureza e turismo ecológico. Por meio de uma metodologia qualitativa com aplicação de entrevistas semiestruturadas e utilizando-se a análise interpretativa a partir da codificação (Gibbs, 2009) foi gerado o produto final, um mapa de competências para a função de chefe de parque nacional que poderá ser aplicado na seleção de servidores para o cargo e ainda para orientar o desenvolvimento de competências, cujo conteúdo o insere na linha de pesquisa Gestão de Operações no Setor Público

Noise Reduction in Images: Some Recent Edge-Preserving Methods

We introduce some recent and very recent smoothing methods which focus on the preservation of boundaries, spikes and canyons in presence of noise. We try to point out basic principles they have in common; the most important one is the robustness aspect. It is reflected by the use of `cup functions' in the statistical loss functions instead of squares; such cup functions were introduced early in robust statistics to down weight outliers. Basically, they are variants of truncated squares. We discuss all the methods in the common framework of `energy functions', i.e we associate to (most of) the algorithms a `loss function' in such a fashion that the output of the algorithm or the `estimate' is a global or local minimum of this loss function. The third aspect we pursue is the correspondence between loss functions and their local minima and nonlinear filters. We shall argue that the nonlinear filters can be interpreted as variants of gradient descent on the loss functions. This way we can show that some (robust) M-estimators and some nonlinear filters produce almost the same result

Topology of the universe from COBE-DMR; a wavelet approach

In this paper we pursue a new technique to search for evidence of a finite Universe, making use of a spherical mexican-hat wavelet decomposition of the microwave background fluctuations. Using the information provided by the wavelet coefficients at several scales we test whether compact orientable flat topologies are consistent with the COBE-DMR data. We consider topological sizes ranging from half to twice the horizon size. A scale-scale correlation test indicates that non-trivial topologies with appropriate topological sizes are as consistent with the COBE-DMR data as an infinite universe. Among the finite models the data seems to prefer a Universe which is about the size of the horizon for all but the hypertorus and the triple-twist torus. For the latter the wavelet technique does not seem a good discriminator of scales for the range of topological sizes considered here, while a hypertorus has a preferred size which is 80% of the horizon. This analysis allows us to find a best fit topological size for each model, although cosmic variance might limit our ability to distinguish some of the topologies.Comment: 10 pages, 13 figures (12 coloured), submitted to MNRAS. Figures 1,2 and 3 are not included but a complete version of the paper with high resolution figures can be downloaded from (http://www.mrao.cam.ac.uk/~graca/topol/