FLAGCAL:A flagging and calibration package for radio interferometric data

We describe a flagging and calibration pipeline intended for making quick look images from GMRT data. The package identifies and flags corrupted visibilities, computes calibration solutions and interpolates these onto the target source. These flagged calibrated visibilities can be directly imaged using any standard imaging package. The pipeline is written in "C" with the most compute intensive algorithms being parallelized using OpenMP.Comment: 15 Pages, 6 figures, 2 Tables, Accepted for publication in the Experimental Astronomy Journa

Bright Source Subtraction Requirements For Redshifted 21 cm Measurements

The \hi 21 cm transition line is expected to be an important probe into the cosmic dark ages and epoch of reionization. Foreground source removal is one of the principal challenges for the detection of this signal. This paper investigates the extragalactic point source contamination and how accurately bright sources ($\gtrsim 1$ ~Jy) must be removed in order to detect 21 cm emission with upcoming radio telescopes such as the Murchison Widefield Array (MWA). We consider the residual contamination in 21 cm maps and power spectra due to position errors in the sky-model for bright sources, as well as frequency independent calibration errors. We find that a source position accuracy of 0.1 arcsec will suffice for detection of the \hi power spectrum. For calibration errors, 0.05 % accuracy in antenna gain amplitude is required in order to detect the cosmic signal. Both sources of subtraction error produce residuals that are localized to small angular scales, \kperp \gtrsim 0.05 Mpc$^{-1}$, in the two-dimensional power spectrum.Comment: 12 pages, 19 Figures, submitted to Ap

Angular 21 cm Power Spectrum of a Scaling Distribution of Cosmic String Wakes

Cosmic string wakes lead to a large signal in 21 cm redshift maps at redshifts larger than that corresponding to reionization. Here, we compute the angular power spectrum of 21 cm radiation as predicted by a scaling distribution of cosmic strings whose wakes have undergone shock heating.Comment: 13 pages, 6 figures; v2: minor modifications, journal versio

A simulation-calibrated limit on the H i power spectrum from the GMRT Epoch of Reionization experiment

The Giant Metrewave Radio Telescope Epoch of Reionization experiment is an ongoing effort to measure the power spectrum from neutral hydrogen at high redshift. We have previously reported an upper limit of (70 mK)^2 at wavenumbers of k ≈ 0.65 h Mpc^(−1) using a basic piecewise-linear foreground subtraction. In this paper, we explore the use of a singular value decomposition to remove foregrounds with fewer assumptions about the foreground structure. Using this method, we also quantify, for the first time, the signal loss due to the foreground filter and present new power spectra adjusted for this loss, providing a revised measurement of a 2σ upper limit at (248 mK)^2 for k = 0.50 h Mpc^(−1). While this revised limit is larger than previously reported, we believe it to be more robust and still represents the best current constraint on reionization at z ≈ 8.6

The stellar masses and specific star-formation rates of submillimetre galaxies

Establishing the stellar masses (M*), and hence specific star-formation rates (sSFRs) of submillimetre galaxies (SMGs) is crucial for determining their role in the cosmic galaxy/star formation. However, there is as yet no consensus over the typical M* of SMGs. Specifically, even for the same set of SMGs, the reported average M* have ranged over an order of magnitude, from ~5x10^10 Mo to ~5x10^11 Mo. Here we study how different methods of analysis can lead to such widely varying results. We find that, contrary to recent claims in the literature, potential contamination of IRAC 3-8 um photometry from hot dust associated with an active nucleus is not the origin of the published discrepancies in derived M*. Instead, we expose in detail how inferred M* depends on assumptions made in the photometric fitting, and quantify the individual and cumulative effects of different choices of initial mass function, different brands of evolutionary synthesis models, and different forms of assumed star-formation history. We review current observational evidence for and against these alternatives as well as clues from the hydrodynamical simulations, and conclude that, for the most justifiable choices of these model inputs, the average M* of SMGs is ~2x10^11 Mo. We also confirm that this number is perfectly reasonable in the light of the latest measurements of their dynamical masses, and the evolving M* function of the overall galaxy population. M* of this order imply that the average sSFR of SMGs is comparable to that of other star-forming galaxies at z>2, at 2-3 Gyr^-1. This supports the view that, while rare outliers may be found at any M*, most SMGs simply form the top end of the main-sequence of star-forming galaxies at these redshifts. Conversely, this argues strongly against the viewpoint that SMGs are extreme pathological objects, of little relevance in the cosmic history of star-formation.Comment: Accepted to A&A. 13 pages, 5 figures, 3 tables. Main changes: 1) investigation that the main-sequence does not change the location as much as SMGs when changing SFHs; 2) a new table added with all stellar mass estimates for individual SMGs (machine-readable version in the source file). V3: missing references adde

The Sunyaev-Zel'dovich effect in WMAP data

Using WMAP 5 year data, we look for the average Sunyaev-Zel'dovich effect (SZE) signal from clusters of galaxies by stacking the regions around hundreds of known X-ray clusters. We detect the average SZE at a very high significance level. The average cluster signal is spatially resolved in the W band. This mean signal is compared with the expected signal from the same clusters calculated on the basis of archival ROSAT data. From the comparison we conclude that the observed SZE seems to be less than the expected signal derived from X-ray measurements when a standard beta-model is assumed for the gas distribution. This conclusion is model dependent. Our predictions depend mostly on the assumptions made about the core radius of clusters and the slope of the gas density profile. Models with steeper profiles are able to simultaneously fit both X-ray and WMAP data better than a beta-model. However, the agreement is not perfect and we find that it is still difficult to make the X-ray and SZE results agree. A model assuming point source contamination in SZE clusters renders a better fit to the one-dimensional SZE profiles thus suggesting that contamination from point sources could be contributing to a diminution of the SZE signal. Selecting a model that better fits both X-ray and WMAP data away from the very central region, we estimate the level of contamination and find that on average, the point source contamination is on the level of 16 mJy (at 41 GHz), 26 mJy (at 61 GHz) and 18 mJy (at 94 GHz). These estimated fluxes are marginally consistent with the estimated contamination derived from radio and infrared surveys thus suggesting that the combination of a steeper gas profile and the contribution from point sources allows us to consistently explain the X-ray emission and SZE in galaxy clusters as measured by ROSAT and WMAP.Comment: 17 pages and 17 figures. Submited to MNRA

The source counts of submillimetre galaxies detected at 1.1 mm

The source counts of galaxies discovered at sub-millimetre and millimetre wavelengths provide important information on the evolution of infrared-bright galaxies. We combine the data from six blank-field surveys carried out at 1.1 mm with AzTEC, totalling 1.6 square degrees in area with root-mean-square depths ranging from 0.4 to 1.7 mJy, and derive the strongest constraints to date on the 1.1 mm source counts at flux densities S(1100) = 1-12 mJy. Using additional data from the AzTEC Cluster Environment Survey to extend the counts to S(1100) ~ 20 mJy, we see tentative evidence for an enhancement relative to the exponential drop in the counts at S(1100) ~ 13 mJy and a smooth connection to the bright source counts at >20 mJy measured by the South Pole Telescope; this excess may be due to strong lensing effects. We compare these counts to predictions from several semi-analytical and phenomenological models and find that for most the agreement is quite good at flux densities > 4 mJy; however, we find significant discrepancies (>3sigma) between the models and the observed 1.1 mm counts at lower flux densities, and none of them are consistent with the observed turnover in the Euclidean-normalised counts at S(1100) < 2 mJy. Our new results therefore may require modifications to existing evolutionary models for low luminosity galaxies. Alternatively, the discrepancy between the measured counts at the faint end and predictions from phenomenological models could arise from limited knowledge of the spectral energy distributions of faint galaxies in the local Universe.Comment: 16 pages, 3 figures, 4 tables; accepted for publication in MNRA

Study design for development of novel safety biomarkers of drug-induced liver injury by the translational safety biomarker pipeline (TransBioLine) consortium: a study protocol for a nested case–control study

A lack of biomarkers that detect drug-induced liver injury (DILI) accurately continues to hinder early- and late-stage drug development and remains a challenge in clinical practice. The Innovative Medicines Initiative’s TransBioLine consortium comprising academic and industry partners is developing a prospective repository of deeply phenotyped cases and controls with biological samples during liver injury progression to facilitate biomarker discovery, evaluation, validation and qualification.In a nested case–control design, patients who meet one of these criteria, alanine transaminase (ALT) ≥ 5 × the upper limit of normal (ULN), alkaline phosphatase ≥ 2 × ULN or ALT ≥ 3 ULN with total bilirubin > 2 × ULN, are enrolled. After completed clinical investigations, Roussel Uclaf Causality Assessment and expert panel review are used to adjudicate episodes as DILI or alternative liver diseases (acute non-DILI controls). Two blood samples are taken: at recruitment and follow-up. Sample size is as follows: 300 cases of DILI and 130 acute non-DILI controls. Additional cross-sectional cohorts (1 visit) are as follows: Healthy volunteers (n = 120), controls with chronic alcohol-related or non-alcoholic fatty liver disease (n = 100 each) and patients with psoriasis or rheumatoid arthritis (n = 100, 50 treated with methotrexate) are enrolled. Candidate biomarkers prioritised for evaluation include osteopontin, glutamate dehydrogenase, cytokeratin-18 (full length and caspase cleaved), macrophage-colony-stimulating factor 1 receptor and high mobility group protein B1 as well as bile acids, sphingolipids and microRNAs. The TransBioLine project is enabling biomarker discovery and validation that could improve detection, diagnostic accuracy and prognostication of DILI in premarketing clinical trials and for clinical healthcare application

Herschel-ATLAS/GAMA: SDSS cross-correlation induced by weak lensing

We report a highly significant (>10σ) spatial correlation between galaxies with S350 μm ≥ 30 mJy detected in the equatorial fields of the Herschel Astrophysical Terahertz Large Area Survey (H-ATLAS) with estimated redshifts ≳ 1.5, and Sloan Digital Sky Survey (SDSS) or Galaxy And Mass Assembly (GAMA) galaxies at 0.2 ≤ z ≤ 0.6. The significance of the cross-correlation is much higher than those reported so far for samples with non-overlapping redshift distributions selected in other wavebands. Extensive, realistic simulations of clustered sub-mm galaxies amplified by foreground structures confirm that the cross-correlation can be explained by weak gravitational lensing (μ < 2). The simulations also show that the measured amplitude and range of angular scales of the signal are larger than can be accounted for by galaxy–galaxy weak lensing. However, for scales ≲ 2 arcmin, the signal can be reproduced if SDSS/GAMA galaxies act as signposts of galaxy groups/clusters with halo masses in the range 1013.2–1014.5 M⊙. The signal detected on larger scales appears to reflect the clustering of such haloes

Applying polygenic risk scoring for psychiatric disorders to a large family with bipolar disorder and major depressive disorder

Psychiatric disorders are thought to have a complex genetic pathology consisting of interplay of common and rare variation. Traditionally, pedigrees are used to shed light on the latter only, while here we discuss the application of polygenic risk scores to also highlight patterns of common genetic risk. We analyze polygenic risk scores for psychiatric disorders in a large pedigree (n similar to 260) in which 30% of family members suffer from major depressive disorder or bipolar disorder. Studying patterns of assortative mating and anticipation, it appears increased polygenic risk is contributed by affected individuals who married into the family, resulting in an increasing genetic risk over generations. This may explain the observation of anticipation in mood disorders, whereby onset is earlier and the severity increases over the generations of a family. Joint analyses of rare and common variation may be a powerful way to understand the familial genetics of psychiatric disorders