Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.

BACKGROUND: Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial and probabilistic methods that look for coevolving positions in nucleotide or amino acid sequences. RESULTS: We have developed a web-based platform that gives a user-friendly access to two phylogenetic-based methods implementing the Coev model: the evaluation of coevolving scores and the simulation of coevolving positions. We have also extended the capabilities of the Coev model to allow for the generalization of the alphabet used in the Markov model, which can now analyse both nucleotide and amino acid data sets. The simulation of coevolving positions is novel and builds upon the developments of the Coev model. It allows user to simulate pairs of dependent nucleotide or amino acid positions. CONCLUSIONS: The main focus of our paper is the new simulation method we present for coevolving positions. The implementation of this method is embedded within the web platform Coev-web that is freely accessible at http://coev.vital-it.ch/, and was tested in most modern web browsers

Lipome geant parapharynge

L’espace parapharyngé est une région anatomique complexe. Seulement 0,5% des tumeurs de la tête et cou se localisent à ce niveau. elles sont essentiellement représentées par les tumeurs nerveuses, salivaires et vasculaires, les lipomes ont été exceptionnellement décrits. Notre observation a un double intérêt : documenter cette rareté et faire une mise au point sur l’abord chirurgical de cette région.Mots clés :Lipome, espace parapharyngé, chirurgi

A protosolar nebula origin for the ices agglomerated by Comet 67P/Churyumov-Gerasimenko

The nature of the icy material accreted by comets during their formation in the outer regions of the protosolar nebula is a major open question in planetary science. Some scenarios of comet formation predict that these bodies agglomerated from crystalline ices condensed in the protosolar nebula. Concurrently, alternative scenarios suggest that comets accreted amorphous ice originating from the interstellar cloud or from the very distant regions of the protosolar nebula. On the basis of existing laboratory and modeling data, we find that the N$_2$/CO and Ar/CO ratios measured in the coma of the Jupiter family comet 67P/Churyumov-Gerasimenko by the ROSINA instrument aboard the European Space Agency's Rosetta spacecraft match those predicted for gases trapped in clathrates. If these measurements are representative of the bulk N$_2$/CO and Ar/CO ratios in 67P/Churyumov-Gerasimenko, it implies that the ices accreted by the comet formed in the nebula and do not originate from the interstellar medium, supporting the idea that the building blocks of outer solar system bodies have been formed from clathrates and possibly from pure crystalline ices. Moreover, because 67P/Churyumov-Gerasimenko is impoverished in Ar and N$_2$, the volatile enrichments observed in Jupiter's atmosphere cannot be explained solely via the accretion of building blocks with similar compositions and require an additional delivery source. A potential source may be the accretion of gas from the nebula that has been progressively enriched in heavy elements due to photoevaporation.Comment: The Astrophysical Journal Letters, in pres

Reactivity of 3-hydroxy-3-methyl-2-butanone: Photolysis and \OH\ reaction kinetics

International audienceHydroxycarbonyl compounds are important secondary reaction products in the oxidation of Volatile Organic Compounds (VOCs) in the atmosphere. The atmospheric fate of these oxygenated \VOCs\ is however poorly understood, especially the relevance of the photolytic pathway. In this work, a combined investigation of the photolysis and temperature-dependent \OH\ radical reaction of 3-hydroxy-3-methyl-2-butanone (3H3M2B) is presented. A photolysis lifetime of about 4-5 days was estimated with a global quantum yield of 0.10. The \OH\ reaction rate coefficient follows the Arrhenius trend (298-356 K) and could be modelled through the following expression: k3H3M2B(T) = (5.12 ± 0.07) × 10−12 exp(−563 ± 119/T) in cm3 molecule−1 s−1. A 3H3M2B atmospheric lifetime of 15 days towards the \OH\ radical was evaluated. Our results showed that the photolysis pathway is the major degradation channel for 3H3M2B. Photolysis products were identified and quantified in the present work with a carbon balance of around 80% enabling a reaction mechanism to be proposed. The present work underlines the need for further studies on the atmospheric chemistry of oxygenated VOCs

Consistently computing the K -> pi long distance weak transition

First we extract the long-distance (LD) weak matrix element from certain data and give compatible theoretical estimates. We also link this LD scale to the single-quark-line (SQL) transition scale and then test the latter SQL scale against the decuplet weak decay amplitude ratio. Finally, we study LD decay. All of these experimental and theoretical values are in good agreement. We deduce an average value from eleven experimental determinations compared to the theoretical SQL values average.Comment: 19 pages, 9 figures minor change to the Conclusions and abstract sectio

Detection and characterization of Io's atmosphere from high-resolution 4-{\mu}m spectroscopy

We report on high-resolution and spatially-resolved spectra of Io in the 4.0 {\mu}m region, recorded with the VLT/CRIRES instrument in 2008 and 2010, which provide the first detection of the {\nu}1 + {\nu}3 band of SO2 in Io's atmosphere. Data are analyzed to constrain the latitudinal, longitudinal, and diurnal distribution of Io's SO2 atmosphere as well as its characteristic temperature. equatorial SO2 column densities clearly show longitudinal asymmetry, but with a maximum of around 1.5e17 cm-2 at central meridian longitude L = 200-220 and a minimum of around 3e16 cm-2 at L = 285-300, the longitudinal pattern somewhat differs from earlier inferences from Ly {\alpha} and thermal IR measurements. Within the accuracy of the measurements, no evolution of the atmospheric density from mid-2008 to mid-2010 can be distinguished. The decrease of the SO2 column density towards high latitude is apparent, and the typical latitudinal extent of the atmosphere found to be (+-) 40{\deg} at half-maximum. The data show moderate diurnal variations of the equatorial atmosphere, which is evidence for a partially sublimation-supported atmospheric component. Compared to local noon, factor of 2 lower densities are observed around 40{\deg} before and 80{\deg} after noon. Best-fit gas temperatures range from 150 to 220 K, with a weighted mean value of 170 (+-) 20 K, which should represent the column-weighted mean kinetic temperature of Io's atmosphere. Finally, although the data include clear thermal emission due to Pillan (in outburst in July 2008) and Loki, no detectable enhancements in the SO2 atmosphere above these volcanic regions are found, with an upper limit of 4e16 cm-2 at Pillan and 1e17 cm-2 at Loki.Comment: Accepted for publication in Icaru

Analytical theory for the initial mass function: CO clumps and prestellar cores

We derive an analytical theory of the prestellar core initial mass function based on an extension of the Press-Schechter statistical formalism. With the same formalism, we also obtain the mass spectrum for the non self-gravitating clumps produced in supersonic flows. The mass spectrum of the self-gravitating cores reproduces very well the observed initial mass function and identifies the different mechanisms responsible for its behaviour. The theory predicts that the shape of the IMF results from two competing contributions, namely a power-law at large scales and an exponential cut-off (lognormal form) centered around the characteristic mass for gravitational collapse. The cut-off exists already in the case of pure thermal collapse, provided that the underlying density field has a lognormal distribution. Whereas pure thermal collapse produces a power-law tail steeper than the Salpeter value, dN/dlog M\propto M^{-x}, with x=1.35, this latter is recovered exactly for the (3D) value of the spectral index of the velocity power spectrum, n\simeq 3.8, found in observations and in numerical simulations of isothermal supersonic turbulence. Indeed, the theory predicts that x=(n+1)/(2n-4) for self-gravitating structures and x=2-n'/3 for non self-gravitating structures, where n' is the power spectrum index of log(rho). We show that, whereas supersonic turbulence promotes the formation of both massive stars and brown dwarfs, it has an overall negative impact on star formation, decreasing the star formation efficiency. This theory provides a novel theoretical foundation to understand the origin of the IMF and to infer its behaviour in different environments. It also provides a complementary approach and useful guidance to numerical simulations exploring star formation, while making testable predictions.Comment: To appear in Ap

Magnetic field structure around cores with very low luminosity objects

Aims. We carried out optical polarimetry of five dense cores, (IRAM 04191, L1521F, L328, L673-7, and L1014) which are found to harbour very low luminosity objects (VeLLOs; Lint ≲ 0.1 L⊙). This study was conducted mainly to understand the role played by the magnetic field in the formation of very low and substellar mass range objects. Methods. Light from the stars, while passing through the dust grains that are aligned with their short axis parallel to an external magnetic field, becomes linearly polarised. The polarisation position angles measured for the stars can provide the plane-of-the sky magnetic field orientation. Because the light in the optical wavelength range is most efficiently polarised by the dust grains typically found at the outer layers of the molecular clouds, optical polarimetry mostly traces the magnetic field orientation of the core envelope. Results. The polarisation observations of stars projected on IRAM 04191, L328, L673-7, and L1014 were obtained in the R-band and those of L1521F were obtained in the V-band. The angular offsets between the envelope magnetic field direction (inferred from optical polarisation measurements) and the outflow position angles from the VeLLOs in IRAM 04191, L1521F, L328, L673-7, and L1014 are found to be 84°, 53°, 24°, 08°, and 15°, respectively. The mean value of the offsets for all the five clouds is ~ 37°. If we exclude IRAM 04191, the mean value reduces to become ~ 25°. In IRAM 04191, the offset between the projected envelope and the inner magnetic field (inferred from the submillimetre data obtained using SCUBA-POL) is found to be ~ 68°. The inner magnetic field, however, is found to be nearly aligned with the projected position angles of the minor axis, the rotation axis of the cloud, and the outflow from the IRAM 04191-IRS. We discuss a possible explanation for the nearly perpendicular orientation between the envelope and core scale magnetic fields in IRAM 04191. The angular offset between the envelope magnetic field direction and the minor axis of IRAM 04191, L1521F, L673-7, and L1014 are 82°, 60°, 47°, and 55°, respectively. The mean value of the offsets between the envelope magnetic field and the minor axis position angles for the four cores is found to be ~ 60°. Conclusions. The results obtained from our study on the limited sample of five cores with VeLLOs show that the outflows in three of them tend to nearly align with the envelope magnetic field

Spin-down of neutron stars by neutrino emission

We study the spin-down of a neutron star during its early stages due to the neutrino emission. The mechanism we consider is the subsequent collisions of the produced neutrinos with the outer shells of the star. We find that this mechanism can indeed slow down the star rotation but only in the first tens of seconds of the core formation, which is when the appropriate conditions of flux and collision rate are met. We find that this mechanism can extract less than 1 % of the star angular momentum, a result which is much less than previously estimated by other authors.Comment: 9 pages, 2 eps figures, RevTeX 4-1. The paper was significantly modified. Now it addresses only the issues of a neutron star spin-down. Version to be published in Phys. Rev.