A generalized mechanistic codon model.

Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substitution rate matrix is created using Kronecker product of three 4 × 4 nucleotide substitution matrices, the equilibrium frequency of codons, and the selection rate parameter. The entities of the nucleotide substitution matrices and selection rate are considered as parameters of the model, which are optimized by maximum likelihood. Our fully mechanistic model allows the instantaneous substitution matrix between codons to be fully estimated with only 19 parameters instead of 3,721, by using the biological interdependence existing between positions within codons. We illustrate the properties of our models using computer simulations and assessed its relevance by comparing the AICc measures of our model and other models of codon evolution on simulations and a large range of empirical data sets. We show that our model fits most biological data better compared with the current codon models. Furthermore, the parameters in our model can be interpreted in a similar way as the exchangeability rates found in empirical codon models

Muonium-antimuonium conversion in models with heavy neutrinos

We study muonium-antimuonium conversion and mu+ e- to mu- e+ scattering within two different lepton-flavor-violating models with heavy neutrinos: model I is a typical seesaw that violates lepton number as well as flavor; model II has a neutrino mass texture where lepton number is conserved. We look for the largest possible amplitudes of these processes that are consistent with current bounds. We find that model I has very limited chance of providing an observable signal, except if a finely tuned condition in parameter space occurs. Model II, on the other hand, requires no fine tuning and could cause larger effects. However, the maximum amplitude provided by this model is still two orders of magnitude below the sensitivity of current experiments: one predicts an effective coupling G_MM up to 10^{-4}G_F for heavy neutrino masses near 10 TeV. We have also clarified some discrepancies in previous literature on this subject.Comment: 16 pages, 4 figures, reference adde

On Sterile neutrino explanation of LSND and MiniBooNE anomalies

We examine the compatibility between existing experimental data and a recently proposed explanation of the LSND and MiniBooNE anomalies, given in terms of a sterile neutrino $N$ whose decay is dominated by a radiative mode. We find that current experimental data on $\tau\rightarrow \mu\nu\nu\gamma$ decays are compatible with the sterile neutrino parameters required for the explanation of the anomalies, but $K\rightarrow \mu\nu\gamma$ shows a marginal tension with those parameters. We also propose experimental cuts on radiative $K$ decays that could test the sterile neutrino hypothesis better. Finally, we study the contribution of this sterile neutrino to $K\to\mu\nu e e$, and find that measurements of this process would provide powerful tests for the sterile neutrino explanation of the LSND and MiniBooNE anomalies, if the experimental cut on the invariant mass of the $e^{+}e^{-}$ pair could be reduced from its current value of 145 MeV to a value below 40 MeV.Comment: 6 pages, 2 figures, experimental cut taken into account, some conclusions change

UV-visible Spectra and Gas-Phase Rate Coefficients for the Reaction of 2,3 pentanedione and 2,4-pentanedione with OH Radicals

International audienceThe UV absorption cross-sections of 2,3-pentanedione and 2,4-pentanedione were measured and their reactions with OH were investigated in the gas-phase using a relative rate method. A temperature dependence of the rate coefficients was observed for both reactions over the temperature range 298–338 K. This work provides the first UV cross-section in the gas phase for 2,4-pentanedione and the first kinetic data for the reaction of 2,3-pentanedione with OH radicals as a function of temperature. The tropospheric lifetimes obtained in this work suggest that once emitted into the atmosphere, these species could be quickly degraded close to their emission sources

Improvement of the size estimation of 3D tracked droplets using digital in-line holography with joint estimation reconstruction

International audienceDigital holography is a valuable tool for three-dimensional information extraction. Among existing configurations, the originally proposed setup (i.e. Gabor, or in-line holography), is reasonably immune to variations in the experimental environment making it a method of choice for studies of fluid dynamics. Nevertheless, standard hologram reconstruction techniques, based on numerical light back-propagation are prone to artifacts such as twin images or aliases that limit both the quality and quantity of information extracted from the acquired holograms. To get round this issue, the hologram reconstruction as a parametric inverse problem has been shown to accurately estimate 3D positions and the size of seeding particles directly from the hologram. To push the bounds of accuracy on size estimation still further, we propose to fully exploit the information redundancy of a hologram video sequence using joint estimation reconstruction. Applying this approach in a bench-top experiment, we show that it led to a relative accuracy of 0.13 % (for a 30 µm diameter droplet) for droplet size estimation, and a tracking accuracy of σ x × σ y × σ z = 0.15 × 0.15 × 1 pixels

Maladie de kimura: À propos d’un cas

Introduction :  Mots-clés : Maladie de Kimura, parotide, chirurgie.La maladie de Kimura ou lymphogranulome éosinophile est une pathologie inflammatoire chronique très rare, d’étiologie inconnue. Nous rapportons un cas de maladie de Kimura à localisation parotidienne et à travers une revue de la littérature, rappelons les principales caractéristiques cliniques, paracliniques, thérapeutiques et évolutives de cette pathologie. Matériel et méthodes : Patient de 17 ans qui a consulté devant l’apparition d’une tuméfaction de la région parotidienne gauche évoluant depuis un an et sans paralysie faciale. Résultats : L’échographie cervico-parotidienne a révélé une parotide gauche hypertrophiée siège de multiples nodules hypoéchogènes. La tomodensitométrie cervico-faciale a mis en évidence une glande parotide gauche augmentée de taille et de structure hétérogène nodulaire sans adénopathies cervicales. La cytopontion était non concluante. Le patient a bénéficié d’une parotidectomie exofaciale gauche et l’étude anatomopathologique de la pièce opératoire revenue en faveur de la maladie de Kimura. Les suites opératoires étaient simples. Le recul est d’un an sans récidive. Discussion : La Maladie de Kimura se caractérise cliniquement par des nodules sous cutanés de localisation cervicofaciale, une augmentation du volume des glandes salivaires et des adénopathies satellites. Son diagnostic est histologique reposant sur l’identification d’une hyperplasie follicullaire avec des abcès à polynucléaires éosinophiles. Le traitement est chirurgical le plus souvent mais dans certains cas la corticothérapie est proposée. Ce diagnostic doit cependant rester à l’esprit devant toute masse cervico-faciale

NGC 7538 : Multiwavelength Study of Stellar Cluster Regions associated with IRS 1-3 and IRS 9 sources

We present deep and high-resolution (FWHM ~ 0.4 arcsec) near-infrared (NIR) imaging observations of the NGC 7538 IRS 1-3 region (in JHK bands), and IRS 9 region (in HK bands) using the 8.2m Subaru telescope. The NIR analysis is complemented with GMRT low-frequency observations at 325, 610, and 1280 MHz, molecular line observations of H13CO+ (J=1-0), and archival Chandra X-ray observations. Using the 'J-H/H-K' diagram, 144 Class II and 24 Class I young stellar object (YSO) candidates are identified in the IRS 1-3 region. Further analysis using 'K/H-K' diagram yields 145 and 96 red sources in the IRS 1-3 and IRS 9 regions, respectively. A total of 27 sources are found to have X-ray counterparts. The YSO mass function (MF), constructed using a theoretical mass-luminosity relation, shows peaks at substellar (~0.08-0.18 Msolar) and intermediate (~1-1.78 Msolar) mass ranges for the IRS 1-3 region. The MF can be fitted by a power law in the low mass regime with a slope of Gamma ~ 0.54-0.75, which is much shallower than the Salpeter value of 1.35. An upper limit of 10.2 is obtained for the star to brown dwarf ratio in the IRS 1-3 region. GMRT maps show a compact HII region associated with the IRS 1-3 sources, whose spectral index of 0.87+-0.11 suggests optical thickness. This compact region is resolved into three separate peaks in higher resolution 1280 MHz map, and the 'East' sub-peak coincides with the IRS 2 source. H13CO+ (J=1-0) emission reveals peaks in both IRS 1-3 and IRS 9 regions, none of which are coincident with visible nebular emission, suggesting the presence of dense cloud nearby. The virial masses are approximately of the order of 1000 Msolar and 500 Msolar for the clumps in IRS 1-3 and IRS 9 regions, respectively.Comment: 27 pages, 18 figures, 5 tables. Accepted for publication in MNRA

Years of RXTE Monitoring of Anomalous X-ray Pulsar 4U 0142+61: Long-Term Variability

We report on 10 years of monitoring of the 8.7-s Anomalous X-ray Pulsar 4U 0142+61 using the Rossi X-Ray Timing Explorer (RXTE). This pulsar exhibited stable rotation from 2000 March until 2006 February: the RMS phase residual for a spin-down model which includes nu, nudot, and nuddot is 2.3%. We report a possible phase-coherent timing solution valid over a 10-yr span extending back to March 1996. A glitch may have occured between 1998 and 2000, but is not required by the existing timing data. The pulse profile has been evolving since 2000. In particular, the dip of emission between its two peaks got shallower between 2002 and 2006, as if the profile were evolving back to its pre-2000 morphology, following an earlier event, which possibly also included the glitch suggested by the timing data. These profile variations are seen in the 2-4 keV band but not in 6-8 keV. We also detect a slow increase in the pulsed flux between 2002 May and 2004 December, such that it has risen by 36+/-3% over 2.6 years in the 2-10 keV band. The pulsed flux variability and the narrow-band pulse profile changes present interesting challenges to aspects of the magnetar model.Comment: 28 pages, 8 figures, accepted by Ap

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