MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

High-throughput metabolomic experiments aim at identifying and ultimately quantifying all metabolites present in biological systems. The metabolites are interconnected through metabolic reactions, generally grouped into metabolic pathways. Classical metabolic maps provide a relational context to help interpret metabolomics experiments and a wide range of tools have been developed to help place metabolites within metabolic pathways. However, the representation of metabolites within separate disconnected pathways overlooks most of the connectivity of the metabolome. By definition, reference pathways cannot integrate novel pathways nor show relationships between metabolites that may be linked by common neighbours without being considered as joint members of a classical biochemical pathway. MetExplore is a web server that offers the possibility to link metabolites identified in untargeted metabolomics experiments within the context of genome-scale reconstructed metabolic networks. The analysis pipeline comprises mapping metabolomics data onto the specific metabolic network of an organism, then applying graph-based methods and advanced visualization tools to enhance data analysis. The MetExplore web server is freely accessible at http://metexplore.toulouse.inra.fr

Synaptic targets of photoreceptors specialized to detect color and skylight polarization in Drosophila

Color and polarization provide complementary information about the world and are detected by specialized photoreceptors. However, the downstream neural circuits that process these distinct modalities are incompletely understood in any animal. Using electron microscopy, we have systematically reconstructed the synaptic targets of the photoreceptors specialized to detect color and skylight polarization in Drosophila, and we have used light microscopy to confirm many of our findings. We identified known and novel downstream targets that are selective for different wavelengths or polarized light, and followed their projections to other areas in the optic lobes and the central brain. Our results revealed many synapses along the photoreceptor axons between brain regions, new pathways in the optic lobes, and spatially segregated projections to central brain regions. Strikingly, photoreceptors in the polarization-sensitive dorsal rim area target fewer cell types, and lack strong connections to the lobula, a neuropil involved in color processing. Our reconstruction identifies shared wiring and modality-specific specializations for color and polarization vision, and provides a comprehensive view of the first steps of the pathways processing color and polarized light inputs

Photometric redshifts and clustering of emission line galaxies selected jointly by DES and eBOSS

We present the results of the first test plates of the extended Baryon Oscillation Spectroscopic Survey. This paper focuses on the emission line galaxies (ELG) population targetted from the Dark Energy Survey (DES) photometry. We analyse the success rate, efficiency, redshift distribution, and clustering properties of the targets. From the 9000 spectroscopic redshifts targetted, 4600 have been selected from the DES photometry. The total success rate for redshifts between 0.6 and 1.2 is 71\% and 68\% respectively for a bright and faint, on average more distant, samples including redshifts measured from a single strong emission line. We find a mean redshift of 0.8 and 0.87, with 15 and 13\% of unknown redshifts respectively for the bright and faint samples. In the redshift range 0.6<z<1.2, for the most secure spectroscopic redshifts, the mean redshift for the bright and faint sample is 0.85 and 0.9 respectively. Star contamination is lower than 2\%. We measure a galaxy bias averaged on scales of 1 and 10~Mpc/h of 1.72 \pm 0.1 for the bright sample and of 1.78 \pm 0.12 for the faint sample. The error on the galaxy bias have been obtained propagating the errors in the correlation function to the fitted parameters. This redshift evolution for the galaxy bias is in agreement with theoretical expectations for a galaxy population with MB-5\log h < -21.0. We note that biasing is derived from the galaxy clustering relative to a model for the mass fluctuations. We investigate the quality of the DES photometric redshifts and find that the outlier fraction can be reduced using a comparison between template fitting and neural network, or using a random forest algorithm

Astrometric calibration and performance of the Dark Energy Camera

We characterize the ability of the Dark Energy Camera (DECam) to perform relative astrometry across its 500~Mpix, 3 deg^2 science field of view, and across 4 years of operation. This is done using internal comparisons of ~4x10^7 measurements of high-S/N stellar images obtained in repeat visits to fields of moderate stellar density, with the telescope dithered to move the sources around the array. An empirical astrometric model includes terms for: optical distortions; stray electric fields in the CCD detectors; chromatic terms in the instrumental and atmospheric optics; shifts in CCD relative positions of up to ~10 um when the DECam temperature cycles; and low-order distortions to each exposure from changes in atmospheric refraction and telescope alignment. Errors in this astrometric model are dominated by stochastic variations with typical amplitudes of 10-30 mas (in a 30 s exposure) and 5-10 arcmin coherence length, plausibly attributed to Kolmogorov-spectrum atmospheric turbulence. The size of these atmospheric distortions is not closely related to the seeing. Given an astrometric reference catalog at density ~0.7 arcmin^{-2}, e.g. from Gaia, the typical atmospheric distortions can be interpolated to 7 mas RMS accuracy (for 30 s exposures) with 1 arcmin coherence length for residual errors. Remaining detectable error contributors are 2-4 mas RMS from unmodelled stray electric fields in the devices, and another 2-4 mas RMS from focal plane shifts between camera thermal cycles. Thus the astrometric solution for a single DECam exposure is accurate to 3-6 mas (0.02 pixels, or 300 nm) on the focal plane, plus the stochastic atmospheric distortion.Comment: Submitted to PAS

COSMOGRAIL XVI: Time delays for the quadruply imaged quasar DES J0408-5354 with high-cadence photometric monitoring

We present time-delay measurements for the new quadruply imaged quasar DES J0408-5354, the first quadruply imaged quasar found in the Dark Energy Survey (DES). Our result is made possible by implementing a new observational strategy using almost daily observations with the MPIA 2.2m telescope at La Silla observatory and deep exposures reaching a signal-to-noise ratio of about 1000 per quasar image. This data quality allows us to catch small photometric variations (a few mmag rms) of the quasar, acting on temporal scales much shorter than microlensing, hence making the time delay measurement very robust against microlensing. In only 7 months we measure very accurately one of the time delays in DES J0408-5354: Dt(AB) = -112.1 +- 2.1 days (1.8%) using only the MPIA 2.2m data. In combination with data taken with the 1.2m Euler Swiss telescope, we also measure two delays involving the D component of the system Dt(AD) = -155.5 +- 12.8 days (8.2%) and Dt(BD) = -42.4 +- 17.6 days (41%), where all the error bars include systematics. Turning these time delays into cosmological constraints will require deep HST imaging or ground-based Adaptive Optics (AO), and information on the velocity field of the lensing galaxy.Comment: 9 pages, 5 figures, accepted for publication in Astronomy & Astrophysic

Causal propagation of geometrical fields in relativistic cosmology

We employ the extended 1+3 orthonormal frame formalism for fluid spacetime geometries $({\cal M}, {\bf g}, {\bf u})$, which contains the Bianchi field equations for the Weyl curvature, to derive a 44-D evolution system of first-order symmetric hyperbolic form for a set of geometrically defined dynamical field variables. Describing the matter source fields phenomenologically in terms of a barotropic perfect fluid, the propagation velocities $v$ (with respect to matter-comoving observers that Fermi-propagate their spatial reference frames) of disturbances in the matter and the gravitational field, represented as wavefronts by the characteristic 3-surfaces of the system, are obtained. In particular, the Weyl curvature is found to account for two (non-Lorentz-invariant) Coulomb-like characteristic eigenfields propagating with $v = 0$ and four transverse characteristic eigenfields propagating with $|v| = 1$, which are well known, and four (non-Lorentz-invariant) longitudinal characteristic eigenfields propagating with |v| = \sfrac{1}{2}. The implications of this result are discussed in some detail and a parallel is drawn to the propagation of irregularities in the matter distribution. In a worked example, we specialise the equations to cosmological models in locally rotationally symmetric class II and include the constraints into the set of causally propagating dynamical variables.Comment: 25 pages, RevTeX (10pt), accepted for publication by Physical Review

H0LiCOW X: Spectroscopic/imaging survey and galaxy-group identification around the strong gravitational lens system WFI2033-4723

Galaxies and galaxy groups located along the line of sight towards gravitationally lensed quasars produce high-order perturbations of the gravitational potential at the lens position. When these perturbation are too large, they can induce a systematic error on $H_0$ of a few-percent if the lens system is used for cosmological inference and the perturbers are not explicitly accounted for in the lens model. In this work, we present a detailed characterization of the environment of the lens system WFI2033-4723 ($z_{\rm src} = 1.662$, $z_{\rm lens}$ = 0.6575), one of the core targets of the H0LICOW project for which we present cosmological inferences in a companion paper (Rusu et al. 2019). We use the Gemini and ESO-Very Large telescopes to measure the spectroscopic redshifts of the brightest galaxies towards the lens, and use the ESO-MUSE integral field spectrograph to measure the velocity-dispersion of the lens ($\sigma_{\rm {los}}= 250^{+15}_{-21}$ km/s) and of several nearby galaxies. In addition, we measure photometric redshifts and stellar masses of all galaxies down to $i < 23$ mag, mainly based on Dark Energy Survey imaging (DR1). Our new catalog, complemented with literature data, more than doubles the number of known galaxy spectroscopic redshifts in the direct vicinity of the lens, expanding to 116 (64) the number of spectroscopic redshifts for galaxies separated by less than 3 arcmin (2 arcmin) from the lens. Using the flexion-shift as a measure of the amplitude of the gravitational perturbation, we identify 2 galaxy groups and 3 galaxies that require specific attention in the lens models. The ESO MUSE data enable us to measure the velocity-dispersions of three of these galaxies. These results are essential for the cosmological inference analysis presented in Rusu et al. (2019).Comment: Matches the version accepted for publication by MNRAS. Note that this paper previously appeared as H0LICOW X

Forward Global Photometric Calibration of the Dark Energy Survey

Many scientific goals for the Dark Energy Survey (DES) require calibration of optical/NIR broadband $b = grizY$ photometry that is stable in time and uniform over the celestial sky to one percent or better. It is also necessary to limit to similar accuracy systematic uncertainty in the calibrated broadband magnitudes due to uncertainty in the spectrum of the source. Here we present a "Forward Global Calibration Method (FGCM)" for photometric calibration of the DES, and we present results of its application to the first three years of the survey (Y3A1). The FGCM combines data taken with auxiliary instrumentation at the observatory with data from the broad-band survey imaging itself and models of the instrument and atmosphere to estimate the spatial- and time-dependence of the passbands of individual DES survey exposures. "Standard" passbands are chosen that are typical of the passbands encountered during the survey. The passband of any individual observation is combined with an estimate of the source spectral shape to yield a magnitude $m_b^{\mathrm{std}}$ in the standard system. This "chromatic correction" to the standard system is necessary to achieve sub-percent calibrations. The FGCM achieves reproducible and stable photometric calibration of standard magnitudes $m_b^{\mathrm{std}}$ of stellar sources over the multi-year Y3A1 data sample with residual random calibration errors of $\sigma=5-6\,\mathrm{mmag}$ per exposure. The accuracy of the calibration is uniform across the $5000\,\mathrm{deg}^2$ DES footprint to within $\sigma=7\,\mathrm{mmag}$. The systematic uncertainties of magnitudes in the standard system due to the spectra of sources are less than $5\,\mathrm{mmag}$ for main sequence stars with $0.5<g-i<3.0$.Comment: 25 pages, submitted to A