2DPHOT: A Multi-purpose Environment for the Two-dimensional Analysis of Wide-field Images

We describe 2DPHOT, a general purpose analysis environment for source detection and analysis in deep wide-field images. 2DPHOT is an automated tool to obtain both integrated and surface photometry of galaxies in an image, to perform reliable star-galaxy separation with accurate estimates of contamination at faint flux levels, and to estimate completeness of the image catalog. We describe the analysis strategy on which 2DPHOT is based, and provide a detailed description of the different algorithms implemented in the package. This new environment is intended as a dedicated tool to process the wealth of data from wide-field imaging surveys. To this end, the package is complemented by 2DGUI, an environment that allows multiple processing of data using a range of computing architectures.Comment: Accepted to PAS

Zika virus tropism and interactions in myelinating neural cell cultures: CNS cells and myelin are preferentially affected

The recent global outbreak of Zika virus (ZIKV) infection has been linked to severe neurological disorders affecting the peripheral and central nervous systems (PNS and CNS, respectively). The pathobiology underlying these diverse clinical phenotypes are the subject of intense research; however, even the principal neural cell types vulnerable to productive Zika infection remain poorly characterised. Here we used CNS and PNS myelinating cultures from wild type and Ifnar1 knockout mice to examine neuronal and glial tropism and short-term consequences of direct infection with a Brazilian variant of ZIKV. Cell cultures were infected pre- or post-myelination for various intervals, then stained with cell-type and ZIKV-specific antibodies. In bypassing systemic immunity using ex vivo culture, and the type I interferon response in Ifnar1 deficient cells, we were able to evaluate the intrinsic infectivity of neural cells. Through systematic quantification of ZIKV infected cells in myelinating cultures, we found that ZIKV infection is enhanced in the absence of the type I interferon responses and that CNS cells are considerably more susceptible to infection than PNS cells. In particular, we demonstrate that CNS axons and myelinating oligodendrocytes are especially vulnerable to injury. These results have implications for understanding the pathobiology of neurological symptoms associated with ZIKV infection. Furthermore, we provide a quantifiable ex vivo infection model that can be used for fundamental and therapeutic studies on viral neuroinvasion and its consequences

Search for light massive gauge bosons as an explanation of the (g−2)μ(g-2)_\mu anomaly at MAMI

A massive, but light abelian U(1) gauge boson is a well motivated possible signature of physics beyond the Standard Model of particle physics. In this paper, the search for the signal of such a U(1) gauge boson in electron-positron pair-production at the spectrometer setup of the A1 Collaboration at the Mainz Microtron (MAMI) is described. Exclusion limits in the mass range of 40 MeV up to 300 MeV with a sensitivity in the mixing parameter of down to $\epsilon^2 = 8\times 10^{-7}$ are presented. A large fraction of the parameter space has been excluded where the discrepancy of the measured anomalous magnetic moment of the muon with theory might be explained by an additional U(1) gauge boson.Comment: 4 pages, 3 figure

A Catalog of Distant Compact Groups Using DPOSS

In this paper we present an objectively defined catalog of 459 small, high density groups of galaxies out to z~0.2 in a region of 6260 square degrees in the northern sky derived from the Digitized Second Palomar Observatory Sky Survey. Our catalog extends down to r = 19.0 and has a median redshift of z_med = 0.12, making it complementary to Hickson's catalog for the nearby universe (z_med = 0.03). The depth and angular coverage of this catalog makes it valuable for studies of the general characteristics of small groups of galaxies and how galaxies evolve in and around them. We also examine the relationship between compact groups and large scale structure.Comment: accepted to A

TomograPy: A Fast, Instrument-Independent, Solar Tomography Software

Solar tomography has progressed rapidly in recent years thanks to the development of robust algorithms and the availability of more powerful computers. It can today provide crucial insights in solving issues related to the line-of-sight integration present in the data of solar imagers and coronagraphs. However, there remain challenges such as the increase of the available volume of data, the handling of the temporal evolution of the observed structures, and the heterogeneity of the data in multi-spacecraft studies. We present a generic software package that can perform fast tomographic inversions that scales linearly with the number of measurements, linearly with the length of the reconstruction cube (and not the number of voxels) and linearly with the number of cores and can use data from different sources and with a variety of physical models: TomograPy (http://nbarbey.github.com/TomograPy/), an open-source software freely available on the Python Package Index. For performance, TomograPy uses a parallelized-projection algorithm. It relies on the World Coordinate System standard to manage various data sources. A variety of inversion algorithms are provided to perform the tomographic-map estimation. A test suite is provided along with the code to ensure software quality. Since it makes use of the Siddon algorithm it is restricted to rectangular parallelepiped voxels but the spherical geometry of the corona can be handled through proper use of priors. We describe the main features of the code and show three practical examples of multi-spacecraft tomographic inversions using STEREO/EUVI and STEREO/COR1 data. Static and smoothly varying temporal evolution models are presented.Comment: 21 pages, 6 figures, 5 table

Full genome sequence and sfRNA interferon antagonist activity of Zika virus from Recife, Brazil

Background: The outbreak of Zika virus (ZIKV) in the Americas has transformed a previously obscure mosquito-transmitted arbovirus of the Flaviviridae family into a major public health concern. Little is currently known about the evolution and biology of ZIKV and the factors that contribute to the associated pathogenesis. Determining genomic sequences of clinical viral isolates and characterization of elements within these are an important prerequisite to advance our understanding of viral replicative processes and virus-host interactions. Methodology/Principal findings: We obtained a ZIKV isolate from a patient who presented with classical ZIKV-associated symptoms, and used high throughput sequencing and other molecular biology approaches to determine its full genome sequence, including non-coding regions. Genome regions were characterized and compared to the sequences of other isolates where available. Furthermore, we identified a subgenomic flavivirus RNA (sfRNA) in ZIKV-infected cells that has antagonist activity against RIG-I induced type I interferon induction, with a lesser effect on MDA-5 mediated action. Conclusions/Significance: The full-length genome sequence including non-coding regions of a South American ZIKV isolate from a patient with classical symptoms will support efforts to develop genetic tools for this virus. Detection of sfRNA that counteracts interferon responses is likely to be important for further understanding of pathogenesis and virus-host interactions

Modelling diverse root density dynamics and deep nitrogen uptake — a simple approach

We present a 2-D model for simulation of root density and plant nitrogen (N) uptake for crops grown in agricultural systems, based on a modification of the root density equation originally proposed by Gerwitz and Page in J Appl Ecol 11:773–781, (1974). A root system form parameter was introduced to describe the distribution of root length vertically and horizontally in the soil profile. The form parameter can vary from 0 where root density is evenly distributed through the soil profile, to 8 where practically all roots are found near the surface. The root model has other components describing root features, such as specific root length and plant N uptake kinetics. The same approach is used to distribute root length horizontally, allowing simulation of root growth and plant N uptake in row crops. The rooting depth penetration rate and depth distribution of root density were found to be the most important parameters controlling crop N uptake from deeper soil layers. The validity of the root distribution model was tested with field data for white cabbage, red beet, and leek. The model was able to simulate very different root distributions, but it was not able to simulate increasing root density with depth as seen in the experimental results for white cabbage. The model was able to simulate N depletion in different soil layers in two field studies. One included vegetable crops with very different rooting depths and the other compared effects of spring wheat and winter wheat. In both experiments variation in spring soil N availability and depth distribution was varied by the use of cover crops. This shows the model sensitivity to the form parameter value and the ability of the model to reproduce N depletion in soil layers. This work shows that the relatively simple root model developed, driven by degree days and simulated crop growth, can be used to simulate crop soil N uptake and depletion appropriately in low N input crop production systems, with a requirement of few measured parameters

First measurements of the ^16O(e,e'pn)^14N reaction

This paper reports on the first measurement of the ^16O(e,e'pn)^14N reaction. Data were measured in kinematics centred on a super-parallel geometry at energy and momentum transfers of 215 MeV and 316 MeV/c. The experimental resolution was sufficient to distinguish groups of states in the residual nucleus but not good enough to separate individual states. The data show a strong dependence on missing momentum and this dependence appears to be different for two groups of states in the residual nucleus. Theoretical calculations of the reaction using the Pavia code do not reproduce the shape or the magnitude of the data.Comment: 10 pages, 11 figures, 2 tables, Accepted for publication in EPJ