Digital Beam Trajectory and Orbit System, for the CERN Proton Synchrotron

A new trajectory and orbit measurement system using fast signal sampling and digital signal processing in an FPGA is proposed for the CERN PS. The system uses a constant sampling frequency while the beam revolution frequency changes during acceleration. Synchronization with the beam is accomplished through a numerical PLL algorithm. This algorithm is also capable of treating RF gymnastics like bunch splitting or batch compression with the help of external timing signals. Baseline and position calculation are provided in the FPGA code as well. After having implemented the algorithms in C and MatLab and tested them with data from a test run at the PS, they have now been implemented in the FPGA for online use. Results of measurements on a single beam position monitor in the CERN PS and the SIS-18 at GSI will be presented

Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition interface

Ssd1, a conserved fungal RNA-binding protein, is important in stress responses, cell division and virulence. Ssd1 is closely related to Dis3L2 of the RNase II family of nucleases, but lacks catalytic activity and likely suppresses translation of bound mRNAs. Previous studies identified RNA motifs enriched in Ssd1-associated transcripts, yet the sequence requirements for Ssd1 binding are not defined. Here, we identify precise binding sites of Ssd1 on RNA using in vivo cross-linking and cDNA analysis. These sites are enriched in 5′ untranslated regions of a subset of mRNAs encoding cell wall proteins. We identified a conserved bipartite motif that binds Ssd1 with high affinity in vitro. Active RNase II enzymes have a characteristic, internal RNA binding path; the Ssd1 crystal structure at 1.9 Å resolution shows that remnants of regulatory sequences block this path. Instead, RNA binding activity has relocated to a conserved patch on the surface of the protein. Structure-guided mutations of this surface prevent Ssd1 from binding RNA in vitro and phenocopy Ssd1 deletion in vivo. These studies provide a new framework for understanding the function of a pleiotropic post-transcriptional regulator of gene expression and give insights into the evolution of regulatory and binding elements in the RNase II family

Plasma host protein biomarkers correlating with increasing Mycobacterium tuberculosis infection activity prior to tuberculosis diagnosis in people living with HIV

BACKGROUND: Biomarkers correlating with Mycobacterium tuberculosis infection activity/burden in asymptomatic individuals are urgently needed to identify and treat those at highest risk for developing active tuberculosis (TB). Our main objective was to identify plasma host protein biomarkers that change over time prior to developing TB in people living with HIV (PLHIV). METHODS: Using multiplex MRM-MS, we investigated host protein expressions from 2 years before until time of TB diagnosis in longitudinally collected (every 3-6 months) and stored plasma from PLHIV with incident TB, identified within a South African (SA) and US cohort. We performed temporal trend and discriminant analyses for proteins, and, to assure clinical relevance, we further compared protein levels at TB diagnosis to interferon-gamma release assay (IGRA; SA) or tuberculin-skin test (TST; US) positive and negative cohort subjects without TB. SA and US exploratory data were analyzed separately. FINDINGS: We identified 15 proteins in the SA (n=30) and 10 in the US (n=24) incident TB subjects which both changed from 2 years prior until time of TB diagnosis after controlling for 10% false discovery rate, and were significantly different at time of TB diagnosis compared to non-TB subjects (p<0.01). Five proteins, CD14, A2GL, NID1, SCTM1, and A1AG1, overlapped between both cohorts. Furthermore, after cross-validation, panels of 5 – 12 proteins were able to predict TB up to two years before diagnosis. INTERPRETATION: Host proteins can be biomarkers for increasing Mycobacterium tuberculosis infection activity/burden, incipient TB, and predict TB development in PLHIV. FUNDING: NIH/NIAID AI117927, AI146329, and AI127173 to JMA

Synthetic SXR diagnostic using GEM detectors on WEST: development in the prospect of tungsten monitoring

International audienceWEST (Tungsten Environment in Steady-State Tokamak) will be operating by the end of 2016 as a test bed for the ITER divertor components in long pulse operation. In this context, radiative cooling of highly ionized impurities like tungsten (W) sputtered from Plasma Facing Components (PFC) into the plasma core is a critical issue since even small impurity concentrations below 10-4 degrade significantly plasma performances and can lead to radiative collapse. In the plasma core, tungsten emission is dominant in the Soft X-ray (SXR) range 0.1 keV – 15 keV with complex contributions from line transition, radiative recombination and Bremsstrahlung emission.This paper presents the recent development of a synthetic SXR diagnostic using GEM (Gas Electron Multiplier) detectors. This diagnostic will be used on WEST for W transport studies and will be equipped with two new GEM based poloidal cameras allowing 2D tomographic reconstructions with spectral resolution in energy bands. Thus once GEM response to plasma emissivity is characterized thanks to synthetic diagnostic, it offers new possibilities to disentangle the different SXR contributions in harsh fusion environments like e.g. WEST or ITER with respect to conventional semiconductor diodes working in current mode. Emitted SXR spectrum from the plasma is modelled thanks to ADAS database from given WEST scenario. The synthetic diagnostic includes Lines of Sight (LoS) etendues of the two cameras as well as probability of photoabsorption through filters, photoionization in the detection gas mixture (Ar-CO2), and transport of electron avalanches in the gas through GEM foils as computed with Magboltz. Local SXR emissivity is then retrieved from tomographic inversion using a Minimum Fisher Information (MFI) algorithm

Tomographic capabilities of the new GEM based SXR diagnostic of WEST

International audienceThe tokamak WEST (Tungsten Environment in Steady-State Tokamak) will start operating by the end of 2016 as a test bed for the ITER divertor components in long pulse operation. In this context, radiative cooling of heavy impurities like tungsten (W) in the Soft X-ray (SXR) range [0.1 keV; 20 keV] is a critical issue for the plasma core performances. Thus reliable tools are required to monitor the local impurity density and avoid W accumulation. The WEST SXR diagnostic will be equipped with two new GEM (Gas Electron Multiplier) based poloidal cameras allowing to perform 2D tomographic reconstructions in tunable energy bands. In this paper tomographic capabilities of the Minimum Fisher Information (MFI) algorithm developed for Tore Supra and upgraded for WEST are investigated, in particular through a set of emissivity phantoms and the standard WEST scenario including reconstruction errors, influence of noise as well as computational time

Studies of viomycin, an anti-tuberculosis antibiotic: Copper(II) coordination, DNA degradation and the impact on delta ribozyme cleavage activity

Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidrug-resistant tuberculosis. In this paper we provide the characteristics of its acid base properties, coordination preferences towards the Cu(II) ions, as well as the reactivity of the resulting complexes against plasmid DNA and HDV ribozyme. Careful coordination studies throughout the wide pH range allow for the characterisation of all the Cu(II)-viomycin complex species. The assignment of proton chemical shifts was achieved by NMR experiments, while the DTF level of theory was applied to support molecular structures of the studied complexes. The experiments with the plasmid DNA reveal that at the physiological levels of hydrogen peroxide the Cu(II)-viomycin complex is more aggressive against DNA than uncomplexed metal ions. Moreover, the degradation of DNA by viomycin can be carried out without the presence of transition metal ions. In the studies of antigenomic delta ribozyme catalytic activity, viomycin and its complex are shown to modulate the ribozyme functioning. The molecular modelling approach allows the indication of two different locations of viomycin binding sites to the ribozyme

Classification of Light-Induced Desorption of Alkali Atoms in Glass Cells Used in Atomic Physics Experiments

We attempt to provide physical interpretations of light-induced desorption phenomena that have recently been observed for alkali atoms on glass surfaces of alkali vapor cells used in atomic physics experiments. We find that the observed desorption phenomena are closely related to recent studies in surface science, and can probably be understood in the context of these results. If classified in terms of the photon-energy dependence, the coverage and the bonding state of the alkali adsorbates, the phenomena fall into two categories: It appears very likely that the neutralization of isolated ionic adsorbates by photo-excited electron transfer from the substrate is the origin of the desorption induced by ultraviolet light in ultrahigh vacuum cells. The desorption observed in low temperature cells, on the other hand, which is resonantly dependent on photon energy in the visible light range, is quite similar to light-induced desorption stimulated by localized electronic excitation on metallic aggregates. More detailed studies of light-induced desorption events from surfaces well characterized with respect to alkali coverage-dependent ionicity and aggregate morphology appear highly desirable for the development of more efficient alkali atom sources suitable to improve a variety of atomic physics experiments.Comment: 6 pages, 1 figure; minor corrections made, published in e-Journal of Surface Science and Nanotechnology at http://www.jstage.jst.go.jp/article/ejssnt/4/0/4_63/_articl

GRB 080319B: A Naked-Eye Stellar Blast from the Distant Universe

Long duration gamma-ray bursts (GRBs) release copious amounts of energy across the entire electromagnetic spectrum, and so provide a window into the process of black hole formation from the collapse of a massive star. Over the last forty years, our understanding of the GRB phenomenon has progressed dramatically; nevertheless, fortuitous circumstances occasionally arise that provide access to a regime not yet probed. GRB 080319B presented such an opportunity, with extraordinarily bright prompt optical emission that peaked at a visual magnitude of 5.3, making it briefly visible with the naked eye. It was captured in exquisite detail by wide-field telescopes, imaging the burst location from before the time of the explosion. The combination of these unique optical data with simultaneous gamma-ray observations provides powerful diagnostics of the detailed physics of this explosion within seconds of its formation. Here we show that the prompt optical and gamma-ray emissions from this event likely arise from different spectral components within the same physical region located at a large distance from the source, implying an extremely relativistic outflow. The chromatic behaviour of the broadband afterglow is consistent with viewing the GRB down the very narrow inner core of a two-component jet that is expanding into a wind-like environment consistent with the massive star origin of long GRBs. These circumstances can explain the extreme properties of this GRB.Comment: 43 pages, 18 figures, 3 tables, submitted to Nature May 11, 200