fpocket: online tools for protein ensemble pocket detection and tracking

Computational small-molecule binding site detection has several important applications in the biomedical field. Notable interests are the identification of cavities for structure-based drug discovery or functional annotation of structures. fpocket is a small-molecule pocket detection program, relying on the geometric α-sphere theory. The fpocket web server allows: (i) candidate pocket detection—fpocket; (ii) pocket tracking during molecular dynamics, in order to provide insights into pocket dynamics—mdpocket; and (iii) a transposition of mdpocket to the combined analysis of homologous structures—hpocket. These complementary online tools allow to tackle various questions related to the identification and annotation of functional and allosteric sites, transient pockets and pocket preservation within evolution of structural families. The server and documentation are freely available at http://bioserv.rpbs.univ-paris-diderot.fr/fpocket

Deep-water oyster cliffs at La Chapelle Bank (Celtic Margin)

The maiden voyage of Ghent University’s ROV GENESIS on-board R/V Belgica (13-20 June 2006) has succeeded in contributing to several objectives of the EU-projects HERMES and EURODOM, as well as of the ESF Euromargins project MoundForce. After several trials in the Bay of Douarnenez, GENESIS made its first deep-water survey dives off the Banc de la Chapelle, on the Celtic margin, down to 700 m. The French canyon system near the Banc de la Chapelle offered a perfect location for rigorous trials of GENESIS: reported cold-water coral finds, rugged topography and hydrodynamics in a setting linking the shelf seas to the deep marine realm. The area was first surveyed using R/V Belgica’s multibeam echosounder, imaging deep canyons and thalweg channels between prominent spurs where corals had been reported. High resolution seismic sparker lines provided a geological context and linked in to the existing seismostratigraphy.Two successful dives revealed a sandy-muddy seabed with curious bedforms and erosion exposing consolidated sedimentary sequences, often cut by vertical cliffs up to 10m high. At the base of the cliffs, fallen blocks provided settlement sites for sessile organisms whilst the cliffs and protruding banks revealed dense communities of unidentified giant ostreidae (probably Neopycnodonte sp) forming 3D assemblage with occasional cold-water coral colonies (Lophelia pertusa). Though deep-water ‘oyster banks’ of Neopyncodonte cochlear had already been reported in the Bay of Biscay by ..Le Danois (1948) based on dredges, these dramatic seascapes had remained largely hidden to the human eye up to now

A birational mapping with a strange attractor: Post critical set and covariant curves

We consider some two-dimensional birational transformations. One of them is a birational deformation of the H\'enon map. For some of these birational mappings, the post critical set (i.e. the iterates of the critical set) is infinite and we show that this gives straightforwardly the algebraic covariant curves of the transformation when they exist. These covariant curves are used to build the preserved meromorphic two-form. One may have also an infinite post critical set yielding a covariant curve which is not algebraic (transcendent). For two of the birational mappings considered, the post critical set is not infinite and we claim that there is no algebraic covariant curve and no preserved meromorphic two-form. For these two mappings with non infinite post critical sets, attracting sets occur and we show that they pass the usual tests (Lyapunov exponents and the fractal dimension) for being strange attractors. The strange attractor of one of these two mappings is unbounded.Comment: 26 pages, 11 figure

The STAR Silicon Strip Detector (SSD)

The STAR Silicon Strip Detector (SSD) completes the three layers of the Silicon Vertex Tracker (SVT) to make an inner tracking system located inside the Time Projection Chamber (TPC). This additional fourth layer provides two dimensional hit position and energy loss measurements for charged particles, improving the extrapolation of TPC tracks through SVT hits. To match the high multiplicity of central Au+Au collisions at RHIC the double sided silicon strip technology was chosen which makes the SSD a half million channels detector. Dedicated electronics have been designed for both readout and control. Also a novel technique of bonding, the Tape Automated Bonding (TAB), was used to fullfill the large number of bounds to be done. All aspects of the SSD are shortly described here and test performances of produced detection modules as well as simulated results on hit reconstruction are given.Comment: 11 pages, 8 figures, 1 tabl

Les assemblages de coléoptères saproxyliques des vieux chênes verts en région méditerranéenne : rôle d’une structure-clé dans un paysage hétérogène changeant

A study of spring-summer saproxylic fauna was conducted in a Mediterranean landscape under land use change in order to estimate the relative infl uence of landscape composition vs tree characteristics on beetles’ biodiversity. The composition of the species assemblages and the number of taxa sampled appeared more infl uenced by the characteristics of the sampled Holm oak trees than by the surrounding landscape matrix. The number and the diameter of trunks, the number of cavities and the quantity of visible dead wood were positively correlated either with the total number of taxa or with the observation of specifi c taxa. Mediterranean species did not show an overall preference for open surroundings, and mycetophagous beetles were not particularly selecting woody mesophilous conditions. Our results confi rm the determinant role of old trees as keystone structures for the saproxylic fauna, but, up to now, this role does not seem to be affected by the changes in the landscape that resulted from land abandonment. However, specifi c forest management practices need to be implemented to maintain a population of old Holm oak trees in the absence of the traditional land use practices that favoured themUne étude de la faune saproxylique a été conduite au printemps et en été dans un paysage méditerranéen soumis à des changements d'occupation des terres afin d'estimer l'influence relative de la composition paysagère vs les caractéristiques des arbres sur la biodiversité des coléoptères. La composition des assemblages d'espèces et le nombre de taxons échantillonnés sont apparus plus influencés par les caractéristiques des chênes verts que par la matrice paysagère environnante. Le nombre et le diamètre des troncs, le nombre de cavités et la quantité de bois mort visible étaient positivement corrélés soit avec le nombre total de taxons soit avec l'observation de taxons spécifiques. Les espèces méditerranéennes n'ont pas montré de préférence pour des environnements ouverts et les coléoptères mycétophages ne sélectionnaient pas particulièrement les conditions de boisements mésophiles. Nos résultats confirment le rôle déterminant des vieux arbres en tant que structures-clés pour la faune saproxylique mais jusqu'à présent ce rôle n'apparaît pas affecté par les changements paysagers résultant de l'abandon des terres. Cependant des pratiques spécifiques de gestion forestière demandent à être mises en oeuvre afin de maintenir une population de vieux chênes verts en l'absence des pratiques traditionnelles d'occupation des terres qui les ont favorisés

SoLid : Search for Oscillations with Lithium-6 Detector at the SCK-CEN BR2 reactor

Sterile neutrinos have been considered as a possible explanation for the recent reactor and Gallium anomalies arising from reanalysis of reactor flux and calibration data of previous neutrino experiments. A way to test this hypothesis is to look for distortions of the anti-neutrino energy caused by oscillation from active to sterile neutrino at close stand-off (similar to 6-8m) of a compact reactor core. Due to the low rate of anti-neutrino interactions the main challenge in such measurement is to control the high level of gamma rays and neutron background. The SoLid experiment is a proposal to search for active-to-sterile anti-neutrino oscillation at very short baseline of the SCK center dot CEN BR2 research reactor. This experiment uses a novel approach to detect anti-neutrino with a highly segmented detector based on Lithium-6. With the combination of high granularity, high neutron-gamma discrimination using 6LiF:ZnS(Ag) and precise localization of the Inverse Beta Decay products, a better experimental sensitivity can be achieved compared to other state-of-the-art technology. This compact system requires minimum passive shielding allowing for very close stand off to the reactor. The experimental set up of the SoLid experiment and the BR2 reactor will be presented. The new principle of neutrino detection and the detector design with expected performance will be described. The expected sensitivity to new oscillations of the SoLid detector as well as the first measurements made with the 8 kg prototype detector deployed at the BR2 reactor in 2013-2014 will be reported

Multi-time-over-threshold technique for photomultiplier signal processing: Description and characterization of the SCOTT ASIC

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Zinc-gallium oxynitride powders: effect of the oxide precursor synthesis route

International audienceZinc-gallium oxynitride powders (ZnGaON) were synthesized by nitridation of ZnGa2O4 oxide precursor obtained by polymeric precursors (PP) and solid state reaction (SSR) methods and the influence of the synthesis route of ZnGa2O4 on the final compound ZnGaON was investigated. Crystalline single phase ZnGa2O4 was obtained at 1100 oC / 12 h by SSR and at 600 oC / 2 h by PP with different grain sizes and specific surface areas according to the synthesis route. After nitridation, ZnGaON oxynitrides with a GaN würtzite-type structure were obtained in both cases, however at lower temperatures for PP samples. The microstructure and the specific surface area were strongly dependent on the oxide synthesis method and on the nitridation temperature (42 m2g-1 and 5 m2g-1 for PP and SSR oxides treated at 700 °C, respectively). The composition analyses showed a strong loss of Zn for the PP samples, favored by the increase of ammonolysis temperature and by the higher specific surface area