Phospho.ELM:a database of experimentally verified phosphorylation sites in eukaryotic proteins

BACKGROUND: Post-translational phosphorylation is one of the most common protein modifications. Phosphoserine, threonine and tyrosine residues play critical roles in the regulation of many cellular processes. The fast growing number of research reports on protein phosphorylation points to a general need for an accurate database dedicated to phosphorylation to provide easily retrievable information on phosphoproteins.DESCRIPTION: Phospho.ELM http://phospho.elm.eu.org is a new resource containing experimentally verified phosphorylation sites manually curated from the literature and is developed as part of the ELM (Eukaryotic Linear Motif) resource. Phospho.ELM constitutes the largest searchable collection of phosphorylation sites available to the research community. The Phospho.ELM entries store information about substrate proteins with the exact positions of residues known to be phosphorylated by cellular kinases. Additional annotation includes literature references, subcellular compartment, tissue distribution, and information about the signaling pathways involved as well as links to the molecular interaction database MINT. Phospho.ELM version 2.0 contains 1703 phosphorylation site instances for 556 phosphorylated proteins.CONCLUSION: Phospho.ELM will be a valuable tool both for molecular biologists working on protein phosphorylation sites and for bioinformaticians developing computational predictions on the specificity of phosphorylation reactions.</p

Multiphase reactions using solid foams

The present invention relates to a gas-liquid-solid (GLS) process comprising contacting reactants on a solid foam material, wherein the solid foam material has a surface to volume ratio of at least 250 m2/m3. This foam material may include a catalyst composition or a catalyst material may be supported on the foam material. The foam material proyides improved mass transfer and favourable hydrodynamic parameters when compared to conventional packings so that an enhanced contact between reactants and an improved reactor performance is achieved

Multiphase reactions using solid foams

The present invention relates to a gas-liquid-solid (GLS) process comprising contacting reactants on a solid foam material, wherein the solid foam material has a surface to volume ratio of at least 250 m2/m3. This foam material may include a catalyst composition or a catalyst material may be supported on the foam material. The foam material proyides improved mass transfer and favourable hydrodynamic parameters when compared to conventional packings so that an enhanced contact between reactants and an improved reactor performance is achieved

Where to place which sensor to measure sedentary behaviour? A method development and comparison among various sensor placements and signal types

Background: Sedentary Behaviour (SB) is associated with several chronic diseases and especially office workers are at increased risk. SB is defined by a sitting or reclined body posture with an energy expenditure ≤1.5 METs. However, current objective methods to measure SB are not consistent with its definition. There is no consensus on which sensor placement and type to be used. Aim: To compare the accuracy of newly developed artificial intelligence models for 15 sensor placements in combination with four signal types (accelerometer only/plus gyroscope and/or magnetometer) to detect posture and physical in-/activity while desk-based activities. Method: Signal features for the model development were extracted from sensor raw data of 30 office workers performing 10 desk-based tasks, each lasting 5 minutes. Direct observation (posture) and indirect calorimetry (in-/activity) served as reference criteria. The best classification model for each sensor was identified and compared among the sensor placements, both using Friedman and post-hoc Wilcoxon tests (p≤0.05). Results: Posture was most accurately measured with a lower body sensor, while in-/activity was most accurately measured with an upper body or waist sensor. The inclusion of additional signal types improved the posture classification for some placements, while the acceleration signal already contained the relevant signal information for the in-/activity classification. Overall, the thigh accelerometer most accurately classified desk-based SB. Conclusion: This study favours, in line with previous work, the measurement of SB with a thigh worn accelerometer, and adds the information that this sensor is also accurate in measuring physical in-/activity while sitting and standing.Swiss National Science FoundationAccepte

Background studies and shielding effects for the TPC detector of the CAST experiment

Sunset solar axions traversing the intense magnetic field of the CERN Axion Solar Telescope (CAST) experiment may be detected in a Time Projection Chamber (TPC) detector, as X-rays signals. These signals could be masked, however, by the inhomogeneous background of materials in the experimental site. A detailed analysis, based on the detector characteristics, the background radiation at the CAST site, simulations and experimental results, has allowed us to design a shielding which reduces the background level by a factor of ~4 compared to the detector without shielding, depending on its position, in the energy range between 1 and 10 keV. Moreover, this shielding has improved the homogeneity of background measured by the TPC.Comment: 14 pages, 5 figures, accepted in New Journal of Physic

XMM-Newton and INTEGRAL observations of the black hole candidate XTE J1817-330

The galactic black hole candidate XTE J1817-330 was discovered in outburst by RXTE in January 2006. We present here the results of an XMM-Newton Target of opportunity observation (TOO), performed on 13 March 2006 (44 days after the maximum), and an INTEGRAL observation performed on 15-18 February 2006 (18 days after the maximum). The EPIC-pn camera on-board XMM-Newton was used in the fast read-out Burst mode to avoid photon pile-up, while the RGSs were used in Spectroscopy high count-rate mode. We fit both the XMM-Newton and the INTEGRAL spectra with a two-component model consisting of a thermal accretion disk and a comptonizing hot corona. The soft X-ray spectrum is dominated by an accretion disk component, with a maximum temperature decreasing from 0.96+/-0.04 keV at the time of the INTEGRAL observation to 0.70+/-m0.01 keV on 13 March. The Optical Monitors on board INTEGRAL and XMM-Newton showed the source with magnitudes V: 11.3-11.4, U:15.0-15.1 and UVW1:14.7-14.8. The soft X-ray spectrum, together with the optical and UV data, show a low hydrogen column density towards the source, and several absorption lines, most likely of interstellar origin, are detected in the RGS spectrum: OI K-alpha, OI K-beta, OII, OIII and OVII, which trace both cold and hot components of the ISM. The soft X-ray spectrum indicates the presence of a black hole, with an estimate for the upper limit of the mass of 6.0(+4.0/-2.5) Msun.Comment: Accepted for publication in A&

Origins and composition of fine atmospheric carbonaceous aerosol in the Sierra Nevada Mountains, California

In this paper we report chemically resolved measurements of organic aerosol (OA) and related tracers during the Biosphere Effects on Aerosols and Photochemistry Experiment (BEARPEX) at the Blodgett Forest Research Station, California from 15 August–10 October 2007. OA contributed the majority of the mass to the fine atmospheric particles and was predominately oxygenated (OOA). The highest concentrations of OA were during sporadic wildfire influence when aged plumes were impacting the site. In situ measurements of particle phase molecular markers were dominated by secondary compounds and along with gas phase compounds could be categorized into six factors or sources: (1) aged biomass burning emissions and oxidized urban emissions, (2) oxidized urban emissions (3) oxidation products of monoterpene emissions, (4) monoterpene emissions, (5) anthropogenic emissions and (6) local methyl chavicol emissions and oxidation products. There were multiple biogenic components that contributed to OA at this site whose contributions varied diurnally, seasonally and in response to changing meteorological conditions, e.g. temperature and precipitation events. Concentrations of isoprene oxidation products were larger when temperatures were higher during the first half of the campaign (15 August–12 September) due to more substantial emissions of isoprene and enhanced photochemistry. The oxidation of methyl chavicol, an oxygenated terpene emitted by ponderosa pine trees, contributed similarly to OA throughout the campaign. In contrast, the abundances of monoterpene oxidation products in the particle phase were greater during the cooler conditions in the latter half of the campaign (13 September–10 October), even though emissions of the precursors were lower, although the mechanism is not known. OA was correlated with the anthropogenic tracers 2-propyl nitrate and carbon monoxide (CO), consistent with previous observations, while being comprised of mostly non-fossil carbon (>75%). The correlation between OA and an anthropogenic tracer does not necessarily identify the source of the carbon as being anthropogenic but instead suggests a coupling between the anthropogenic and biogenic components in the air mass that might be related to the source of the oxidant and/or the aerosol sulfate. Observations of organosulfates of isoprene and α-pinene provided evidence for the likely importance of aerosol sulfate in spite of neutralized aerosol although acidic plumes might have played a role upwind of the site. This is in contrast to laboratory studies where strongly acidic seed aerosols were needed in order to form these compounds. These compounds together represented only a minor fraction (<1%) of the total OA mass, which may be the result of the neutralized aerosol at the site or because only a small number of organosulfates were quantified. The low contribution of organosulfates to total OA suggests that other mechanisms, e.g. NO_x enhancement of oxidant levels, are likely responsible for the majority of the anthropogenic enhancement of biogenic secondary organic aerosol observed at this site

Probing the outer edge of an accretion disk : a Her X-1 turn-on observed with RXTE

We present the analysis of Rossi X-ray Timing Explorer (RXTE) observations of the turn-on phase of a 35 day cycle of the X-ray binary Her X-1. During the early phases of the turn-on, the energy spectrum is composed of X-rays scattered into the line of sight plus heavily absorbed X-rays. The energy spectra in the 3–17 keV range can be described by a partial covering model, where one of the components is influenced by photoelectric absorption and Thomson scattering in cold material plus an iron emission line at 6.5 keV. In this paper we show the evolution of spectral parameters as well as the evolution of the pulse profile during the turn-on. We describe this evolution using Monte Carlo simulations which self-consistently describe the evolution of the X-ray pulse profile and of the energy spectrum