Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors

This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Beam heat load analysis with COLDDIAG: a cold vacuum chamber for diagnostics

The knowledge of the heat intake from the electron beam is essential to design the cryogenic layout of superconducting insertion devices. With the aim of measuring the beam heat load to a cold bore and understanding the responsible mechanisms, a cold vacuum chamber for diagnostics (COLDDIAG) has been built. The instrumentation comprises temperature sensors, pressure gauges, mass spectrometers and retarding field analyzers, which allow to study the beam heat load and the influence of the cryosorbed gas layer. COLDDIAG was installed in the storage ring of the Diamond Light Source from September 2012 to August 2013. During this time measurements were performed for a wide range of machine conditions, employing the various measuring capabilities of the device. Here we report on the analysis of the measured beam heat load, pressure and gas content, as well as the low energy charged particle flux and spectrum as a function of the electron beam parameters

GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information

GeneCodis is a web server application for functional analysis of gene lists that integrates different sources of information and finds modular patterns of interrelated annotations. This integrative approach has proved to be useful for the interpretation of high-throughput experiments and therefore a new version of the system has been developed to expand its functionality and scope. GeneCodis now expands the functional information with regulatory patterns and user-defined annotations, offering the possibility of integrating all sources of information in the same analysis. Traditional singular enrichment is now permitted and more organisms and gene identifiers have been added to the database. The application has been re-engineered to improve performance, accessibility and scalability. In addition, GeneCodis can now be accessed through a public SOAP web services interface, enabling users to perform analysis from their own scripts and workflows. The application is freely available at http://genecodis.dacya.ucm.e

Confirmation of and Variable Energy Injection by a Near-Relativistic Outflow in APM 08279+5255

We present results from multi-epoch spectral analysis of XMM-Newton and Chandra observations of the broad absorption line (BAL) quasar APM 08279+5255. Our analysis shows significant X-ray BALs in all epochs with rest-frame energies lying in the range of ~ 6.7-18 keV. The X-ray BALs and 0.2-10 keV continuum show significant variability on timescales as short as 3.3 days (proper time) implying a source size-scale of ~ 10 r_g, where r_g is the gravitational radius. We find a large gradient in the outflow velocity of the X-ray absorbers with projected outflow velocities of up to 0.76 c. The maximum outflow velocity constrains the angle between the wind velocity and our line of sight to be less than ~ 22 degrees. We identify the following components of the outflow: (a) Highly ionized X-ray absorbing material (2.9 < logxi < 3.9) and a column density of log N_H ~ 23 outflowing at velocities of up to 0.76 c. (b) Low-ionization X-ray absorbing gas with log N_H ~ 22.8. We find that flatter spectra appear to result in lower outflow velocities. Based on our spectral analysis of observations of APM 08279+5255 over a period of 1.2 years (proper time) we estimate the mass-outflow rate and efficiency of the outflow to have varied between 16(-8,+12) M_solar yr^-1 and 64(-40,+66) M_solar yr^-1 and 0.18(-0.11,+0.15) to 1.7(-1.2+1.9), respectively. Assuming that the outflow properties of APM 08279+5255 are a common property of most quasars at similar redshifts, our results then imply that quasar winds are massive and energetic enough to influence significantly the formation of the host galaxy, provide significant metal enrichment to the interstellar medium and intergalactic medium, and are a viable mechanism for feedback at redshifts near the peak in the number density of galaxy mergers.Comment: 27 pages, includes 12 figures, accepted for publication in Ap

Cosmological entropy and generalized second law of thermodynamics in F(R,G)F(R,G) theory of gravity

We consider a spatially flat Friedmann-Lemaitre-Robertson-Walker space time and investigate the second law and the generalized second law of thermodynamics for apparent horizon in generalized modified Gauss Bonnet theory of gravity (whose action contains a general function of Gauss Bonnet invariant and the Ricci scalar: $F(R,G)$). By assuming that the apparent horizon is in thermal equilibrium with the matter inside it, conditions which must be satisfied by $F(R,G)$ are derived and elucidated through two examples: a quasi-de Sitter space-time and a universe with power law expansion.Comment: 10 pages, minor changes, typos corrected, accepted for publication in Europhysics Letter

The 2-79 keV X-ray Spectrum of the Circinus Galaxy with NuSTAR, XMM-Newton and Chandra: a Fully Compton-Thick AGN

The Circinus galaxy is one of the nearest obscured AGN, making it an ideal target for detailed study. Combining archival Chandra and XMM-Newton data with new NuSTAR observations, we model the 2-79 keV spectrum to constrain the primary AGN continuum and to derive physical parameters for the obscuring material. Chandra's high angular resolution allows a separation of nuclear and off-nuclear galactic emission. In the off-nuclear diffuse emission we find signatures of strong cold reflection, including high equivalent-width neutral Fe lines. This Compton-scattered off-nuclear emission amounts to 18% of the nuclear flux in the Fe line region, but becomes comparable to the nuclear emission above 30 keV. The new analysis no longer supports a prominent transmitted AGN component in the observed band. We find that the nuclear spectrum is consistent with Compton-scattering by an optically-thick torus, where the intrinsic spectrum is a powerlaw of photon index $\Gamma = 2.2-2.4$, the torus has an equatorial column density of $N_{\rm H} = (6-10)\times10^{24}$cm$^{-2}$ and the intrinsic AGN $2-10$ keV luminosity is $(2.3-5.1)\times 10^{42}$ erg/s. These values place Circinus along the same relations as unobscured AGN in accretion rate-vs-$\Gamma$ and $L_X$-vs-$L_{IR}$ phase space. NuSTAR's high sensitivity and low background allow us to study the short time-scale variability of Circinus at X-ray energies above 10 keV for the first time. The lack of detected variability favors a Compton-thick absorber, in line with the the spectral fitting results.Comment: Accepted for publication in Ap

Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit.

Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in Bacillus subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment

P16-37. HIV controllers with weak CD8+ T cell responses maintain a tight control of infection despite carrying infectious viruses

International audienc