Resonant Kelvin-Helmholtz modes in sheared relativistic flows
Qualitatively new aspects of the (linear and non-linear) stability of sheared relativistic (slab) jets are analyzed. The linear problem has been solved for a wide range of jet models well inside the ultrarelativistic domain (flow Lorentz factors up to 20; specific internal energies $\approx 60c^2$). As a distinct feature of our work, we have combined the analytical linear approach with high-resolution relativistic hydrodynamical simulations, which has allowed us i) to identify, in the linear regime, resonant modes specific to the relativistic shear layer ii) to confirm the result of the linear analysis with numerical simulations and, iii) more interestingly, to follow the instability develo…
Health and disease imprinted in the time variability of the human microbiome
Human microbiota plays an important role in determining changes from health to disease. Increasing research activity is dedicated to understand its diversity and variability. We analyse 16S rRNA and whole genome sequencing (WGS) data from the gut microbiota of 97 individuals monitored in time. Temporal fluctuations in the microbiome reveal significant differences due to factors that affect the microbiota such as dietary changes, antibiotic intake, early gut development or disease. Here we show that a fluctuation scaling law describes the temporal variability of the system and that a noise-induced phase transition is central in the route to disease. The universal law distinguishes healthy fr…
Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles
Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp. and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation.
Metagenomic dynamics in Olea europaea after root damage and Verticillium dahliae infection
AbstractThe olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt of olive, which causes significant economic damage in numerous areas of this crop. We have analyzed the temporal metagenomic samples of a transcriptomic study in Olea europaea roots and leaves after root-damage and after a root Verticillium dahliae infection (Jimenez-Ruiz et al. 2017). Our results indicate that this infection, although led by Verticillium, is driven not by a single species but by a polymicrobial community, including their natural endophytes, which acts as a consort…
Relativistic Magnetohydrodynamics: Renormalized eigenvectors and full wave decomposition Riemann solver
We obtain renormalized sets of right and left eigenvectors of the flux vector Jacobians of the relativistic MHD equations, which are regular and span a complete basis in any physical state including degenerate ones. The renormalization procedure relies on the characterization of the degeneracy types in terms of the normal and tangential components of the magnetic field to the wavefront in the fluid rest frame. Proper expressions of the renormalized eigenvectors in conserved variables are obtained through the corresponding matrix transformations. Our work completes previous analysis that present different sets of right eigenvectors for non-degenerate and degenerate states, and can be seen as…
Oxidative stress in the oral cavity is driven by individualspecific bacterial communities
The term “bacterial dysbiosis” is being used quite extensively in metagenomic studies, however, the identification of harmful bacteria often fails due to large overlap between the bacterial species found in healthy volunteers and patients. We hypothesized that the pathogenic oral bacteria are individual-specific and they correlate with oxidative stress markers in saliva which reflect the inflammatory processes in the oral cavity. Temporally direct and lagged correlations between the markers and bacterial taxa were computed individually for 26 volunteers who provided saliva samples during one month (21.2 ± 2.7 samples/volunteer, 551 samples in total). The volunteers’ microbiomes differed sig…
Robust Analysis of Time Series in Virome Metagenomics
Metagenomics is a powerful tool for assessing the functional and taxonomic contents in biological samples as it makes feasible to study, simultaneously, the whole living community related to a host organism or medium: all the microbes, including virus, bacteria, archaea, fungi, and protists. New DNA and RNA sequencing technologies are dramatically decreasing the cost per sequenced base, so metagenomic sequencing is becoming more and more widespread in biomedical and environmental research. This is opening the possibility of complete longitudinal metagenomic studies, which could unravel the dynamics of microbial communities including intra-microbiome and host-microbiome interactions through …
Not just BLAST nt: WGS database joins the party
AbstractSince its introduction in 1990 and with over 50k citations, the NCBI BLAST family has been an essential tool of in silico molecular biology. The BLAST nt database, based on the traditional divisions of GenBank, has been the default and most comprehensive database for nucleotide BLAST searches and for taxonomic classification software in metagenomics. Here we argue that this is no longer the case. Currently, the NCBI WGS database contains one billion reads (almost five times more than GenBank), and with 4.4 trillion nucleotides, WGS has about 14 times more nucleotides than GenBank. This ratio is growing with time. We advocate a change in the database paradigm in taxonomic classificat…
Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling
AbstractWe propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia.
Stability of three-dimensional relativistic jets: implications for jet collimation
The stable propagation of jets in FRII sources is remarkable if one takes into account that large-scale jets are subjected to potentially highly disruptive three-dimensional (3D) Kelvin-Helmholtz instabilities. Numerical simulations can address this problem and help clarify the causes of this remarkable stability. Following previous studies of the stability of relativistic flows in two dimensions (2D), it is our aim to test and extend the conclusions of such works to three dimensions. We present numerical simulations for the study of the stability properties of 3D, sheared, relativistic flows. This work uses a fully parallelized code Ratpenat that solves equations of relativistic hydrodynam…
Spectral evolution of superluminal components in parsec-scale jets
27 pages, 18 figures, 1 table, 1 appendix.-- Pre-print archive.
Time Series Analysis of the Microbiota of Children Suffering From Acute Infectious Diarrhea and Their Recovery After Treatment
WOS: 000434952800001
Recentrifuge: Robust comparative analysis and contamination removal for metagenomics
Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Contamination is particularly critical in low microbial biomass body sites and environments, where it can comprise most of a sample if not all. Recentrifuge implements a robust method for the removal of negative-control and crossover taxa from the rest of samples. With Recentrifuge, researchers can analyze results f…
The role of Kelvin-Helmholtz instability in the internal structure of relativistic outflows. The case of the jet in 3C 273
Relativistic outflows represent one of the best-suited tools to probe the physics of AGN. Numerical modelling of internal structure of the relativistic outflows on parsec scales provides important clues about the conditions and dynamics of the material in the immediate vicinity of the central black holes in AGN. We investigate possible causes of the structural patterns and regularities observed in the parsec-scale jet of the well-known quasar 3C 273. We present here the results from a 3D relativistic hydrodynamics numerical simulation based on the parameters given for the jet by Lobanov & Zensus (2001), and one in which the effects of jet precession and the injection of discrete compone…
Health and Disease Imprinted in the Time Variability of the Human Microbiome
The human microbiota correlates closely with the health status of its host. This article analyzes the microbial composition of several subjects under different conditions over time spans that ranged from days to months. Using the Langevin equation as the basis of our mathematical framework to evaluate microbial temporal stability, we proved that stable microbiotas can be distinguished from unstable microbiotas. This initial step will help us to determine how temporal microbiota stability is related to a subject’s health status and to develop a more comprehensive framework that will provide greater insight into this complex system.
3D Relativistic Hydrodynamics
We review the evolution of the numerical techniques applied in relativistic hydrodynamics since the sixties until today. We focus our attention on the state-of- the-art high-resolution shock-capturing methods and the astrophysical applications involving three-dimensional simulations.
Numerical 3+1 general relativistic magnetohydrodynamics: a local characteristic approach
We present a general procedure to solve numerically the general relativistic magnetohydrodynamics (GRMHD) equations within the framework of the 3+1 formalism. The work reported here extends our previous investigation in general relativistic hydrodynamics (Banyuls et al. 1997) where magnetic fields were not considered. The GRMHD equations are written in conservative form to exploit their hyperbolic character in the solution procedure. All theoretical ingredients necessary to build up high-resolution shock-capturing schemes based on the solution of local Riemann problems (i.e. Godunov-type schemes) are described. In particular, we use a renormalized set of regular eigenvectors of the flux Jac…
Stellar hydrodynamics with glaister's riemann solver: An approach to the stellar collapse
La resolution de Remann approximee de la solution des equations d'Euler de la dynamique des gaz 1 D, developpee par Glaister P. (1988, J. Comput. Phys., 74) est introduite dans un code hydrodynamique lagrangien et appliquee a l'effondrement stellaire a symetrie spherique
Jet stability and the generation of superluminal and stationary components
We present a numerical simulation of the response of an expanding relativistic jet to the ejection of a superluminal component. The simulation has been performed with a relativistic time-dependent hydrodynamical code from which simulated radio maps are computed by integrating the transfer equations for synchrotron radiation. The interaction of the superluminal component with the underlying jet results in the formation of multiple conical shocks behind the main perturbation. These trailing components can be easily distinguished because they appear to be released from the primary superluminal component, instead of being ejected from the core. Their oblique nature should also result in distinc…
The internal structure of overpressured, magnetized, relativistic jets
This work presents the first characterization of the internal structure of overpressured steady superfast magnetosonic relativistic jets in connection with their dominant type of energy. To this aim, relativistic magnetohydrodynamic simulations of different jet models threaded by a helical magnetic field have been analyzed covering a wide region in the magnetosonic Mach number - specific internal energy plane. The merit of this plane is that models dominated by different types of energy (internal energy: hot jets; rest-mass energy: kinetically dominated jets; magnetic energy: Poynting-flux dominated jets) occupy well separated regions. The analyzed models also cover a wide range of magnetiz…
Recollimation shocks in relativistic jets
Recollimation shocks (RS) appear associated with relativistic flows propagating through pressure mismatched atmospheres. Astrophysical scenarios invoking the presence of such shocks include jets from AGNs and X-ray binaries and GRBs. We shall start reviewing the theoretical background behind the structure of RS in overpressured jets. Next, basing on numerical simulations, we will focus on the properties of RS in relativistic steady jets threaded by helical magnetic fields depending on the dominant type of energy. Synthetic radio maps from the simulation of the synchrotron emission for a selection of models in the context of parsec-scale extragalactic jets will also be discussed.© 2018 World…
Assessment of a high-resolution central scheme for the solution of the relativistic hydrodynamics equations
We assess the suitability of a recent high-resolution central scheme developed by Kurganov & Tadmor (2000) for the solution of the relativistic hydrodynamics equations. The novelty of this approach relies on the absence of Riemann solvers in the solution procedure. The computations we present are performed in one and two spatial dimensions in Minkowski spacetime. Standard numerical experiments such as shock tubes and the relativistic flat-faced step test are performed. As an astrophysical application the article includes two-dimensional simulations of the propagation of relativistic jets using both Cartesian and cylindrical coordinates. The simulations reported clearly show the capabili…