TurbuStat: Turbulence Statistics in Python

We present TurbuStat (v1.0): a Python package for computing turbulence statistics in spectral-line data cubes. TurbuStat includes implementations of fourteen methods for recovering turbulent properties from observational data. Additional features of the software include: distance metrics for comparing two data sets; a segmented linear model for fitting lines with a break-point; a two-dimensional elliptical power-law model; multi-core fast-fourier-transform support; a suite for producing simulated observations of fractional Brownian Motion fields, including two-dimensional images and optically-thin HI data cubes; and functions for creating realistic world coordinate system information for synthetic observations. This paper summarizes the TurbuStat package and provides representative examples using several different methods. TurbuStat is an open-source package and we welcome community feedback and contributions.Comment: Accepted in AJ. 21 pages, 8 figure

Low-Mach-number turbulence in interstellar gas revealed by radio polarization gradients

The interstellar medium of the Milky Way is multi-phase, magnetized and turbulent. Turbulence in the interstellar medium produces a global cascade of random gas motions, spanning scales ranging from 100 parsecs to 1000 kilometres. Fundamental parameters of interstellar turbulence such as the sonic Mach number (the speed of sound) have been difficult to determine because observations have lacked the sensitivity and resolution to directly image the small-scale structure associated with turbulent motion. Observations of linear polarization and Faraday rotation in radio emission from the Milky Way have identified unusual polarized structures that often have no counterparts in the total radiation intensity or at other wavelengths, and whose physical significance has been unclear. Here we report that the gradient of the Stokes vector (Q,U), where Q and U are parameters describing the polarization state of radiation, provides an image of magnetized turbulence in diffuse ionized gas, manifested as a complex filamentary web of discontinuities in gas density and magnetic field. Through comparison with simulations, we demonstrate that turbulence in the warm ionized medium has a relatively low sonic Mach number, M_s <~ 2. The development of statistical tools for the analysis of polarization gradients will allow accurate determinations of the Mach number, Reynolds number and magnetic field strength in interstellar turbulence over a wide range of conditions.Comment: 5 pages, 3 figures, published in Nature on 13 Oct 201

Density Studies of MHD Interstellar Turbulence: Statistical Moments, Correlations and Bispectrum

We present a number of statistical tools for obtaining studying turbulence in molecular clouds and diffuse interstellar medium. For our tests we used of three-dimensional 512 cube compressible MHD isothermal simulations performed for different sonic and Alfvenic Mach numbers. We introduce the bispectrum, a new tool for statistical studies of the interstellar medium which, unlike an ordinary power spectrum of turbulence, preserves the phase information of the stochastic field. We show that the bispectra of the 3D stochastic density field and of column densities, available from observations, are similar. We use the bispectrum technique to define the role of non-linear wave-wave interactions in the turbulent energy cascade. We also obtained the bispectrum function for density and column densities with varying magnetic field strength. Larger values of sonic Mach number result in increased correlations for modes with different wavenumbers. This effect becomes more evident with increasing magnetic field intensity. In addition to the bispectrum, we calculated the 3rd and 4th statistical moments of density and column density, namely, skewness and kurtosis, respectively. We found a strong dependence of skewness and kurtosis with the sonic Mach number. In particular, as this number increases, so does the asymmetry of the density distribution. We also studied the correlations of 2D column density with dispersion of velocities and magnetic field, as well as the correlations of 3D density with magentic and kinetic energy and Alfven Mach number for comparison. Our results show that column density is linearly correlated with magnetic field for high sonic Mach number. This trend is independent of the turbulent kinetic energy and can be used to characterize inhomogeneities of physical properties in low density clumps in the ISM.Comment: apj emulated, 18 pages, 11 figures. Accepted to Astrophysical Journa

Observational Diagnostics for Two-Fluid Turbulence in Molecular Clouds As Suggested by Simulations

We present high resolution simulations of two-fluid (ion-neutral) MHD turbulence with resolutions as large as 512^3. The simulations are supersonic and mildly sub-Alfvenic, in keeping with the conditions present in molecular clouds. Such turbulence is thought to influence star formation processes in molecular clouds because typical cores form on length scales that are comparable to the dissipation scales of this turbulence in the ions. The simulations are motivated by the fact that recent studies of isophotologue lines in molecular clouds have found significant differences in the linewidth-size relationship for neutral and ion species. The goals of this paper are to explain those observations using simulations and analytic theory, present a new set of density-based diagnostics by drawing on similar diagnostics that have been obtained by studying single-fluid turbulence, and show that our two-fluid simulations play a vital role in reconciling alternative models of star formation. The velocity-dependent diagnostics display a complementarity with the density-dependent diagnostics. We find that the linewidth-size relationships show a prominent difference between ions and neutrals when the line of sight is orthogonal to the mean field. This is because the MHD waves in the ions differ from hydrodynamic waves in the neutrals. We also find that the density probability distribution functions (PDFs) show prominent differences between the ions and neutrals when the line of sight is parallel to the mean field. This is because the velocity fluctuations in the ions tend to produce column density fluctuations along field lines. When the magnetic field makes an angle to the line of sight, both observable differences should be visible. These diagnostics should be easy for observers to test. This analysis assumes optically thin lines and a mean magnetic field that is uniform in direction within a cloud.Comment: 23 pages, 10 figures. Corrected typos (including an author name

The completion of the Mammalian Gene Collection (MGC)

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide

Living on the edge: utilising lidar data to assess the importance of vegetation structure for avian diversity in fragmented woodlands and their edges

Context: In agricultural landscapes, small woodland patches can be important wildlife refuges. Their value in maintaining biodiversity may, however, be compromised by isolation, and so knowledge about the role of habitat structure is vital to understand the drivers of diversity. This study examined how avian diversity and abundance were related to habitat structure in four small woods in an agricultural landscape in eastern England. Objectives: The aims were to examine the edge effect on bird diversity and abundance, and the contributory role of vegetation structure. Specifically: what is the role of vegetation structure on edge effects, and which edge structures support the greatest bird diversity? Methods: Annual breeding bird census data for 28 species were combined with airborne lidar data in linear mixed models fitted separately at (i) the whole wood level, and (ii) for the woodland edges only. Results: Despite relatively small woodland areas (4.9–9.4 ha), bird diversity increased significantly towards the edges, being driven in part by vegetation structure. At the whole woods level, diversity was positively associated with increased vegetation above 0.5 m and especially with increasing vegetation density in the understorey layer, which was more abundant at the woodland edges. Diversity along the edges was largely driven by the density of vegetation below 4 m. Conclusions: The results demonstrate that bird diversity was maximised by a diverse vegetation structure across the wood and especially a dense understorey along the edge. These findings can assist bird conservation by guiding habitat management of remaining woodland patches

In vivo and in vitro synthesis of CM-proteins (A-hordeins) from barley (Hordeum vulgare L.)

CM-proteins from barley endosperm (CMa, CMb, CMc, CMd), which are the main components of the A-hordein fraction, are synthesized most actively 10 to 30 d after anthesis (maximum at 15–20 d). They are synthesized by membranebound polysomes as precursors of higher apparent molecular weight (13,000–21,000) than the mature proteins (12,000–16,000). The largest in vitro product (21,000) is the putative precursor of protein CMd (16,000), as it is selected with anti-CMd monospecific IgG's, and is coded by an mRNA of greater sedimentation coefficient (9 S) than those encoding the other three proteins (7.5 S). CM-proteins always appear in the soluble fraction, following different homogenization and subcellular fractionation procedures, indicating that these proteins are transferred to the soluble fraction after processing