Relative entropy minimizing noisy non-linear neural network to approximate stochastic processes

A method is provided for designing and training noise-driven recurrent neural networks as models of stochastic processes. The method unifies and generalizes two known separate modeling approaches, Echo State Networks (ESN) and Linear Inverse Modeling (LIM), under the common principle of relative entropy minimization. The power of the new method is demonstrated on a stochastic approximation of the El Nino phenomenon studied in climate research

On the von Karman-Howarth equations for Hall MHD flows

The von Karman-Howarth equations are derived for three-dimensional (3D) Hall magnetohydrodynamics (MHD) in the case of an homogeneous and isotropic turbulence. From these equations, we derive exact scaling laws for the third-order correlation tensors. We show how these relations are compatible with previous heuristic and numerical results. These multi-scale laws provide a relevant tool to investigate the non-linear nature of the high frequency magnetic field fluctuations in the solar wind or, more generally, in any plasma where the Hall effect is important.Comment: 11 page

Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates.

Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins

Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates.

Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins

On spectral scaling laws for incompressible anisotropic MHD turbulence

A heuristic model is given for anisotropic magnetohydrodynamics (MHD) turbulence in the presence of a uniform external magnetic field B_0 {\bf {\hat e}_{\pa}}. The model is valid for both moderate and strong $B_0$ and is able to describe both the strong and weak wave turbulence regimes as well as the transition between them. The main ingredient of the model is the assumption of constant ratio at all scales between \add{the} linear wave period and \add{the} nonlinear turnover timescale. Contrary to the model of critical balance introduced by Goldreich and Sridhar [P. Goldreich and S. Sridhar, ApJ {\bf 438}, 763 (1995)], it is not assumed in addition that this ratio be equal to unity at all scales which allows us to use the Iroshnikov-Kraichnan phenomenology. It is then possible to recover the widely observed anisotropic scaling law \kpa \propto \kpe^{2/3} between parallel and perpendicular wavenumbers (with reference to B_0 {\bf {\hat e}_{\pa}}) and to obtain the universal prediction, $3\alpha + 2\beta = 7$, for the total energy spectrum E(\kpe,\kpa) \sim \kpe^{-\alpha} \kpa^{-\beta}. In particular, with such a prediction the weak Alfv\'en wave turbulence constant-flux solution is recovered and, for the first time, a possible explanation to its precursor found numerically by Galtier et al [S. Galtier et al., J. Plasma Phys. {\bf 63}, 447 (2000)] is given

Oldest Fossil Basidiomycete Clamp Connections

This is the publisher's version, which is being shared with permission. The original version is available from: http://dx.doi.org/10.1007/s10267-010-0065-4A rachis of the fossil filicalean fern Botryopteris antiqua containing abundant septate hyphae with clamp connections is preserved in a late Visean (Mississippian; *330 Ma) chert from Esnost (Autun Basin) in central France. Largely unbranched tubular hyphae pass from cell to cell, but may sometimes produce a branch from a clamp connection. Other clamp-bearing hyphae occur clustered in individual cells or small groups of adjacent host cells. These hyphae may be tubular, catenulate with numerous hyphal swellings, or they may display a combination of both. The Visean hyphae with clamp connections predate Palaeancistrus martinii, the heretofore oldest direct fossil evidence of Basidiomycota, by some 25 Ma