PATRISTIC: a program for calculating patristic distances and graphically comparing the components of genetic change

BACKGROUND: Phylogenies are commonly used to analyse the differences between genes, genomes and species. Patristic distances calculated from tree branch lengths describe the amount of genetic change represented by a tree and are commonly compared with other measures of mutation to investigate the substitutional processes or the goodness of fit of a tree to the raw data. Up until now no universal tool has been available for calculating patristic distances and correlating them with other genetic distance measures. RESULTS: PATRISTICv1.0 is a java program that calculates patristic distances from large trees in a range of file formats and allows graphical and statistical interpretation of distance matrices calculated by other programs. CONCLUSION: The software overcomes some logistic barriers to analysing signals in sequences. In additional to calculating patristic distances, it provides plots for any combination of matrices, calculates commonly used statistics, allows data such as isolation dates to be entered and reorders matrices with matching species or gene labels. It will be used to analyse rates of mutation and substitutional saturation and the evolution of viruses. It is available at and requires the Java runtime environment

'Tannat' (Vitis vinifera L.) as a model of responses to climate variability

Climate variability influence on the vine is widely studied for its impact on grape final composition and quality. During 1994-2016, thermal and water regimes and their influence on grapevine yield, sanitary status and berry composition were analyzed for 'Tannat' grown in commercial vineyards in the south of Uruguay (Lat 34° 37' S; 56° 17' W). Statistical analysis showed that the principal component analysis (PCA) separated years in three groups: Group 1: rainfall over the growing season higher than the average, limited sanitary status, acidity and yield higher than average, lower sugar content, late harvest. Group 2: greater thermal conditions and water component lower than average, better sanitary status, sugar contents and acidity lower than average, early harvest. Group 3: thermal conditions lower than average, rainfall higher during budbreak-fruitset period and lower than average in the month before harvest, berry size and sugar contents greater than average. Correlations between climate, yield and berry quality variables were established and stages of greater sensitivity to these climate elements were determined. In the studied years, climate variability within the region was high and 'Tannat' showed to be strongly influenced by such variability

Finite element modelling of forging and other metal forming processes

An erratum to this article can be found at : http://dx.doi.org/10.1007/s12289-010-1000-0International audienceThe fundamental mechanical formulation is recalled for simulation of metal forming processes. The basic principles of 3-dimensional finite element discretization and of time integration are summarized. Several important numerical developments for efficient computation of large plastic deformation are briefly described. Various fields of applications to real processes are reviewed. Illustrative examples are mentioned to show the utilization of the commercial computer code Forge3 in industry, as a very flexible tool to design metal forming sequences

Demonstration of the synchrotron-type spectrum of laser-produced Betatron radiation

Betatron X-ray radiation in laser-plasma accelerators is produced when electrons are accelerated and wiggled in the laser-wakefield cavity. This femtosecond source, producing intense X-ray beams in the multi kiloelectronvolt range has been observed at different interaction regime using high power laser from 10 to 100 TW. However, none of the spectral measurement performed were at sufficient resolution, bandwidth and signal to noise ratio to precisely determine the shape of spectra with a single laser shot in order to avoid shot to shot fluctuations. In this letter, the Betatron radiation produced using a 80 TW laser is characterized by using a single photon counting method. We measure in single shot spectra from 8 to 21 keV with a resolution better than 350 eV. The results obtained are in excellent agreement with theoretical predictions and demonstrate the synchrotron type nature of this radiation mechanism. The critical energy is found to be Ec = 5.6 \pm 1 keV for our experimental conditions. In addition, the features of the source at this energy range open novel perspectives for applications in time-resolved X-ray science.Comment: 5 pages, 4 figure

Automatic differentiation is no panacea for phylogenetic gradient computation

Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning. These calculations are readily available for arbitrary models via automatic differentiation implemented in general-purpose machine-learning libraries such as TensorFlow and PyTorch. Although these libraries are highly optimized, it is not clear if their general-purpose nature will limit their algorithmic complexity or implementation speed for the phylogenetic case compared to phylogenetics-specific code. In this paper, we compare six gradient implementations of the phylogenetic likelihood functions, in isolation and also as part of a variational inference procedure. We find that although automatic differentiation can scale approximately linearly in tree size, it is much slower than the carefully-implemented gradient calculation for tree likelihood and ratio transformation operations. We conclude that a mixed approach combining phylogenetic libraries with machine learning libraries will provide the optimal combination of speed and model flexibility moving forward.Comment: 15 pages and 2 figures in main text, plus supplementary material

State selective measurements of HCI produced by strong ultrashort laser clusters interaction

International audienceWe have performed studies of keV x-ray production from (Ar)n , (Kr)n and (Xe)n rare gas clusters (with n between 104 and 106 atoms/cluster) submitted to intense (~10^18 W/cm2) infrared (790 nm) laser pulses. We have determined the photon energies and the absolute photon emission yields as a function of several physical parameters governing the interaction : size and atomic number of the clusters, peak intensity of the laser. Up to 10^6 3 keV photons per pulse at a moderate (10^15/cm3) atomic density have been observed. High resolution spectroscopy studies in the case of (Ar)n clusters have also been performed, giving unambiguous evidence of highly charged (up to heliumlike) ions with K vacancies production. The results obtained indicate that X-rays are emitted before cluster explosion on a subpicosecond time scale, and shed some light on the mechanisms involved in the first stage of the production of the nanoplasma induced from each cluster

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

© Bos et al. The 14th-18th century pandemic of Yersinia pestis caused devastating disease outbreaks in Europe for almost 400 years. The reasons for plague's persistence and abrupt disappearance in Europe are poorly understood, but could have been due to either the presence of now-extinct plague foci in Europe itself, or successive disease introductions from other locations. Here we present five Y. pestis genomes from one of the last European outbreaks of plague, from 1722 in Marseille, France. The lineage identified has not been found in any extant Y. pestis foci sampled to date, and has its ancestry in strains obtained from victims of the 14th century Black Death. These data suggest the existence of a previously uncharacterized historical plague focus that persisted for at least three centuries. We propose that this disease source may have been responsible for the many resurgences of plague in Europe following the Black Death

Molecular epidemiology of clade 1 influenza A viruses (H5N1), southern Indochina Peninsula, 2004-2007

To determine the origin of influenza A virus (H5N1) epizootics in Cambodia, we used maximum-likelihood and Bayesian methods to analyze the genetic sequences of subtype H5N1 strains from Cambodia and neighboring areas. Poultry movements, rather than repeated reintroduction of subtype H5N1 viruses by wild birds, appear to explain virus circulation and perpetuation