MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters

<p>Abstract</p> <p>Background</p> <p>Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. Data mining is thus essential for deducing significant biological information such as the identification of new biological mechanisms or putative drug targets. While many algorithms and software have been developed for analysing gene expression, the extraction of relevant information from experimental data is still a substantial challenge, requiring significant time and skill.</p> <p>Description</p> <p>MADIBA (MicroArray Data Interface for Biological Annotation) facilitates the assignment of biological meaning to gene expression clusters by automating the post-processing stage. A relational database has been designed to store the data from gene to pathway for <it>Plasmodium</it>, rice and <it>Arabidopsis</it>. Tools within the web interface allow rapid analyses for the identification of the Gene Ontology terms relevant to each cluster; visualising the metabolic pathways where the genes are implicated, their genomic localisations, putative common transcriptional regulatory elements in the upstream sequences, and an analysis specific to the organism being studied.</p> <p>Conclusion</p> <p>MADIBA is an integrated, online tool that will assist researchers in interpreting their results and understand the meaning of the co-expression of a cluster of genes. Functionality of MADIBA was validated by analysing a number of gene clusters from several published experiments – expression profiling of the <it>Plasmodium </it>life cycle, and salt stress treatments of <it>Arabidopsis </it>and rice. In most of the cases, the same conclusions found by the authors were quickly and easily obtained after analysing the gene clusters with MADIBA. </p

Quasilinear hyperbolic Fuchsian systems and AVTD behavior in T2-symmetric vacuum spacetimes

We set up the singular initial value problem for quasilinear hyperbolic Fuchsian systems of first order and establish an existence and uniqueness theory for this problem with smooth data and smooth coefficients (and with even lower regularity). We apply this theory in order to show the existence of smooth (generally not analytic) T2-symmetric solutions to the vacuum Einstein equations, which exhibit AVTD (asymptotically velocity term dominated) behavior in the neighborhood of their singularities and are polarized or half-polarized.Comment: 78 page

Plasma bile acids are not associated with energy metabolism in humans

Bile acids (BA) have recently been shown to increase energy expenditure in mice, but this concept has not been tested in humans. Therefore, we investigated the relationship between plasma BA levels and energy expenditure in humans. Type 2 diabetic (T2DM) patients (n = 12) and gender, age and BMI-matched healthy controls (n = 12) were studied before and after 8 weeks of treatment with a BA sequestrant. In addition, patients with liver cirrhosis (n = 46) were investigated, since these display elevated plasma BA together with increased energy expenditure. This group was compared to gender-, age- and BMI-matched healthy controls (n = 20). Fasting plasma levels of total BA and individual BA species as well as resting energy expenditure were determined. In response to treatment with the BA sequestrant, plasma deoxycholic acid (DCA) levels decreased in controls (-60%, p &lt;0.05) and T2DM (-32%, p &lt;0.05), while chenodeoxycholic acid (CDCA) decreased in controls only (-33%, p &lt;0.05). Energy expenditure did not differ between T2DM and controls at baseline and, in contrast to plasma BA levels, was unaffected by treatment with the BA sequestrant. Total BA as well as individual BA species did not correlate with energy expenditure at any time throughout the study. Patients with cirrhosis displayed on average an increase in energy expenditure of 18% compared to values predicted by the Harris-Benedict equation, and plasma levels of total BA (up to 12-fold) and individual BA (up to 20-fold) were increased over a wide range. However, neither total nor individual plasma BA levels correlated with energy expenditure. In addition, energy expenditure was identical in patients with a cholestatic versus a non-cholestatic origin of liver disease while plasma total BA levels differed four-fold between the groups. In conclusion, in the various (patho) physiological conditions studied, plasma BA levels were not associated with changes in energy expenditure. Therefore, our data do not support an important role of circulating BA in the control of human energy metabolism.</p

Non-Commutative Correction to Thin Shell Collapse in Reissner Nordstro¨\ddot{o}m Geometry

This paper investigates the polytropic matter shell collapse in the non-commutative Reissner-Nordstr$\ddot{o}$m geometry. Using the Israel criteria, equation of motion for the polytropic matter shell is derived. In order to explore the physical aspects of this equation, the most general equation of state, $p=k{\rho}^{({1+\frac{1}{n}})}$, has been used for finite and infinite values of $n$. The effective potentials corresponding to the equation of motion have been used to explain different states of the matter shell collapse. The numerical solution of the equation of motion predicts collapse as well as expansion depending on the choice of initial data. Further, in order to include the non-commutative correction, we modify the matter components and re-formulate the equation of motion as well as the corresponding effective potentials by including non-commutative factor and charge parameter. It is concluded that charge reduces the velocity of the expanding or collapsing matter shell but does not bring the shell to static position. While the non-commutative factor with generic matter favors the formation of black hole.Comment: 18 pages,17 figure

On the exact gravitational lens equation in spherically symmetric and static spacetimes

Lensing in a spherically symmetric and static spacetime is considered, based on the lightlike geodesic equation without approximations. After fixing two radius values r_O and r_S, lensing for an observation event somewhere at r_O and static light sources distributed at r_S is coded in a lens equation that is explicitly given in terms of integrals over the metric coefficients. The lens equation relates two angle variables and can be easily plotted if the metric coefficients have been specified; this allows to visualize in a convenient way all relevant lensing properties, giving image positions, apparent brightnesses, image distortions, etc. Two examples are treated: Lensing by a Barriola-Vilenkin monopole and lensing by an Ellis wormhole.Comment: REVTEX, 11 pages, 12 eps-figures, figures partly improved, minor revision

Schwarzschild black hole surrounded by quintessence: Null geodesics

We have studied the null geodesics of the Schwarzschild black hole surrounded by quintessence matter. Quintessence matter is a candidate for dark energy. Here, we have done a detailed analysis of the geodesics and exact solutions are presented in terms of Jacobi-elliptic integrals for all possible energy and angular momentum of the photons. The circular orbits of the photons are studied in detail. As an application of the null geodesics, the angle of deflection of the photons are computed.Comment: 25 pages, 20 figures. typos corrected and some of the notation change

Absence of Adiponutrin (PNPLA3) and Monoacylglycerol Lipase Synergistically Increases Weight Gain and Aggravates Steatohepatitis in Mice

Altered lipid metabolic pathways including hydrolysis of triglycerides are key players in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Whether adiponutrin (patatin-like phospholipase domain containing protein-3-PNPLA3) and monoacylglycerol lipase (MGL) synergistically contribute to disease progression remains unclear. We generated double knockout (DKO) mice lacking both Mgl and Pnpla3; DKO mice were compared to Mgl-/- after a challenge by high-fat diet (HFD) for 12 weeks to induce steatosis. Serum biochemistry, liver transaminases as well as histology were analyzed. Fatty acid (FA) profiling was assessed in liver and adipose tissue by gas chromatography. Markers of inflammation and lipid metabolism were analyzed. Bone marrow derived macrophages (BMDMs) were isolated and treated with oleic acid. Combined deficiency of Mgl and Pnpla3 resulted in weight gain on a chow diet; when challenged by HFD, DKO mice showed increased hepatic FA synthesis and diminished beta-oxidation compared to Mgl-/-.DKO mice exhibited more pronounced hepatic steatosis with inflammation and recruitment of immune cells to the liver associated with accumulation of saturated FAs. Primary BMDMs isolated from the DKO mice showed increased inflammatory activities, which could be reversed by oleic acid supplementation. Pnpla3 deficiency aggravates the effects of Mgl deletion on steatosis and inflammation in the liver under HFD challenge

Dynamics of Charged Plane Symmetric Gravitational Collapse

In this paper, we study dynamics of the charged plane symmetric gravitational collapse. For this purpose, we discuss non-adiabatic flow of a viscous fluid and deduce the results for adiabatic case. The Einstein and Maxwell field equations are formulated for general plane symmetric spacetime in the interior. Junction conditions between the interior and exterior regions are derived. For the non-adiabatic case, the exterior is taken as plane symmetric charged Vaidya spacetime while for the adiabatic case, it is described by plane Reissner-Nordstr$\ddot{o}$m spacetime. Using Misner and Sharp formalism, we obtain dynamical equations to investigate the effects of different forces over the rate of collapse. In non-adiabatic case, a dynamical equation is joined with transport equation of heat flux. Finally, a relation between the Weyl tensor and energy density is found.Comment: 21 pages, accepted for publication Gen. Relativ. Gra