A Factor Graph Approach to Automated GO Annotation

As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum.Fil: Spetale, Flavio Ezequiel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Krsticevic, Flavia Jorgelina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Roda, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; ArgentinaFil: Bulacio, Pilar Estela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas. Universidad Nacional de Rosario. Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas; Argentin

Catastrophic ice lake collapse in Aram Chaos, Mars

Hesperian chaotic terrains have been recognized as the source of outflow channels formed by catastrophic outflows. Four main scenarios have been proposed for the formation of chaotic terrains that involve different amounts of water and single or multiple outflow events. Here, we test these scenarios with morphological and structural analyses of imagery and elevation data for Aram Chaos in conjunction with numerical modeling of the morphological evolution of the catastrophic carving of the outflow valley. The morphological and geological analyses of Aram Chaos suggest large-scale collapse and subsidence (1500 m) of the entire area, which is consistent with a massive expulsion of liquid water from the subsurface in one single event. The combined observations suggest a complex process starting with the outflow of water from two small channels, followed by continuous groundwater sapping and headward erosion and ending with a catastrophic lake rim collapse and carving of the Aram Valley, which is synchronous with the 2.5 Ga stage of the Ares Vallis formation. The water volume and formative time scale required to carve the Aram channels indicate that a single, rapid (maximum tens of days) and catastrophic (flood volume of 9.3?104 km3) event carved the outflow channel. We conclude that a sub-ice lake collapse model can best explain the features of the Aram Chaos Valley system as well as the time scale required for its formation.Comment: 20 pages, 17 figures. Icarus, 201

Relativistic simulations of rotational core collapse : II. Collapse dynamics and gravitational radiation

We have performed hydrodynamic simulations of relativistic rotational supernova core collapse in axisymmetry and have computed the gravitational radiation emitted by such an event. The Einstein equations are formulated using the conformally flat metric approximation, and the corresponding hydrodynamic equations are written as a first-order flux-conservative hyperbolic system. Details of the methodology and of the numerical code have been given in an accompanying paper. We have simulated the evolution of 26 models in both Newtonian and relativistic gravity. The initial configurations are di erentially rotating relativistic 4=3-polytropes in equilibrium which have a central density of 10^10 g cm^−3. Collapse is initiated by decreasing the adiabatic index to some prescribed fixed value. The equation of state consists of a polytropic and a thermal part for a more realistic treatment of shock waves. Any microphysics like electron capture and neutrino transport is neglected. Our simulations show that the three di erent types of rotational supernova core collapse and gravitational waveforms identified in previous Newtonian simulations (regular collapse, multiple bounce collapse, and rapid collapse) are also present in relativistic gravity. However, rotational core collapse with multiple bounces is only possible in a much narrower parameter range in relativistic gravity. The relativistic models cover almost the same range of gravitational wave amplitudes (4x10^−21 <= h^TT 3x10^−20 for a source at a distance of 10 kpc) and frequencies (60 Hz <= ν <= 1000 Hz) as the corresponding Newtonian ones. Averaged over all models, the total energy radiated in the form of gravitational waves is 8.2 10^−8 Moc^2 in the relativistic case, and 3.6 10^−8 Moc^2 in the Newtonian case. For all collapse models that are of the same type in both Newtonian and relativistic gravity, the gravitational wave signal is of lower amplitude. If the collapse type changes, either weaker or stronger signals are found in the relativistic case. For a given model, relativistic gravity can cause a large increase of the characteristic signal frequency of up to a factor of five, which may have important consequences for the signal detection. Our study implies that the prospects for detection of gravitational wave signals from axisymmetric supernova rotational core collapse do not improve when taking into account relativistic gravity. The gravitational wave signals obtained in our study are within the sensitivity range of the first generation laser interferometer detectors if the source is located within the Local Group. An online catalogue containing the gravitational wave signal amplitudes and spectra of all our models is available at the URL http://www.mpa-garching.mpg.de/Hydro/hydro.html.Font Roda, Jose Antonio, [email protected]

A new general relativistic magnetohydrodynamics code for dynamical spacetimes

We present a new numerical code that solves the general relativistic magneto-hydrodynamical (GRMHD) equations coupled to the Einstein equations for the evolution of a dynamical spacetime within a conformally-flat approximation. This code has been developed with the main objective of studying astrophysical scenarios in which both, high magnetic fields and strong gravitational fields appear, such as the magneto-rotational collapse of stellar cores, the collapsar model of GRBs, and the evolution of neutron stars. The code is based on an existing and thoroughly tested purely hydrodynamical code and on its extension to accommodate weakly magnetized fluids (passive magnetic-field approximation). These codes have been applied in the past to simulate the aforementioned scenarios with increasing levels of sophistication in the input physics. The numerical code we present here is based on high-resolution shock- capturing schemes to solve the GRMHD equations, which are cast in first-order, flux-conservative hyperbolic form, together with the flux constraint transport method to ensure the solenoidal condition of the magnetic field. Since the astrophysical applications envisaged do not deviate significantly from spherical symmetry, the conformal flatness condition approximation is used for the formulation of the Einstein equations; this has repeatedly shown to yield very good agreement with full general relativistic simulations of core- collapse supernovae and the evolution of isolated neutron stars. In addition, the code can handle several equations of state, from simple analytical expressions to microphysical tabulated ones. In this paper we present stringent tests of our new GRMHD numerical code, which show its ability to handle all aspects appearing in the astrophysical scenarios for which the code is intended, namely relativistic shocks, highly magnetized fluids, and equilibrium configurations of magnetized neutron stars. As an application, magneto- rotational core-collapse simulations of a realistic progenitor are presented and the results compared with our previous findings in the passive magnetic-field [email protected]; [email protected]

Determination of propofol by GC/MS and fast GC/MS-TOF in two cases of poisoning

Two cases of suspected acute and lethal intoxication caused by propofol were delivered by the judicial authority to the Department of Sciences for Health Promotion and Mother-Child Care in Palermo, Sicily. In the first case a female nurse was found in a hotel room, where she lived with her mother; four 10 mg/mL vials and two 20 mg/mL vials of propofol were found near the decedent along with syringes and needles. In the second case a male nurse was found in the operating room of a hospital, along with a used syringe. In both cases a preliminary systematic and toxicological analysis indicated the presence of propofol in the blood and urine. As a result, a method for the quantitative determination of propofol in biological fluids was optimized and validated using a liquid-liquid extraction protocol followed by GC/MS and fast GC/MS-TOF. In the first case, the concentration of propofol in blood was determined to be 8.1 \u3bcg/mL while the concentration of propofol in the second case was calculated at 1.2 \u3bcg/mL. Additionally, the tissue distribution of propofol was determined for both cases. Brain and liver concentrations of propofol were, respectively, 31.1 and 52.2 \u3bcg/g in Case 1 and 4.7 and 49.1 \u3bcg/g in Case 2. Data emerging from the autopsy findings, histopathological exams as well as the toxicological results aided in establishing that the deaths were due to poisoning, however, the manner of death in each were different: homicide in Case 1 and suicide in Case 2

Audit économique et financier du secteur forestier au Cameroun : rapport final, septembre 2006

1. Le secteur forestier camerounais a connu une profonde évolution en une décennie. La réforme la plus spectaculaire a été le passage d'un système d'attribution discrétionnaires des permis forestiers à un mécanisme d'adjudication, comprenant une présélection, une offre technique et une offre financière - cette dernière étant pondérée à 70%. Depuis 1997, les ventes de coupe (2.500 ha, d'une durée de 1 à 2 ans) et les concessions (jusqu'à 200.000 ha, 15 ans renouvelables) ont été attribuées sur cette base. Outre cette mise en concurrence des investisseurs, le mécanisme comporte une dimension de gouvernance, à travers l'instauration d'un double niveau d'Observateurs Indépendants (OI). Un OI assiste à toutes adjudications, rapporte sur les éventuelles irrégularités ou dysfonctionnement, et propose des améliorations. Un second niveau d'observation indépendante, pour l'amélioration des procédures de détection des infractions de terrain, a associé l'ONG Global Witness et les services de contrôle du Ministère en charge des forêts. Depuis 2004, c'est une autre ONG internationale (Resource Extraction Monitoring) qui a pris le relais. 2. En matière de gestion forestière, le pays dispose depuis 2001 de normes nationales d'aménagement, et ce processus progresse maintenant rapidement dans les concessions. C'est le seul pays de la sous-région qui se soit doté d'un plan de zonage (du sud forestier) identifiant les objectifs d'affectation des espaces boisés. Depuis 2000, l'administration a entrepris de classer les forêts à vocation de production ou de conservation, afin de constituer légalement un domaine forestier permanent. Les concertations locales avec les villageois et les communes ont amené à modifier les limites prévisionnelles du plan de zonage, généralement en faveur d'une utilisation par les populations locales. Des communes commencent à disposer de leurs propres forêts. En outre, 67 forêts communautaires ont été constituées depuis 1997 (sur 180 demandes reçues), sur environ 240.000 et ce nombre serait de plus de 80 fin 2005. Depuis 2002, les villageois bénéficient d'un droit de préemption sur les futures "ventes de coupe" prévues dans le domaine national, afin d'y constituer des forêts communautaires. Enfin, le gouvernement a décidé de ne pas allouer, au moins provisoirement, 9 UFA (unité forestière d'aménagement) correspondant à 867.000 ha de forêt dense pour en faire des réserves de diversité biologique. (Résumé d'auteur

A device to characterize optical fibres

ATLAS is a general purpose experiment approved for the LHC collider at CERN. An important component of the detector is the central hadronic calorimeter; for its construction more than 600,000 Wave Length Shifting (WLS) fibres (corresponding to a total length of 1,120 Km) have been used. We have built and put into operation a dedicated instrument for the measurement of light yield and attenuation length over groups of 20 fibres at a time. The overall accuracy achieved in the measurement of light yield (attenuation length) is 1.5% (3%). We also report the results obtained using this method in the quality control of a large sample of fibres.Comment: 17 pages 20 figeres submitted to NIM journa

Effects of vessel traffic on relative abundance and behaviour of cetaceans : the case of the bottlenose dolphins in the Archipelago de La Maddalena, north-western Mediterranean sea

Acknowledgements This study was part of the Tursiops Project of the Dolphin Research Centre of Caprera, La Maddalena. Financial and logistical support was provided by the Centro Turistico Studentesco (CTS) and by the National Park of the Archipelago de La Maddalena. We thank the Natural Reserve of Bocche di Bonifacio for the support provided during data collection. The authors thank the numerous volunteers of the Caprera Dolphin Research Centre and especially Marco Ferraro, Mirko Ugo, Angela Pira and Maurizio Piras whose assistance during field observation and skills as a boat driver were invaluable.Peer reviewedPostprin