The noise of cluster mass reconstructions from a source redshift distribution

The parameter-free reconstruction of the surface-mass density of clusters of galaxies is one of the principal applications of weak gravitational lensing. From the observable ellipticities of images of background galaxies, the tidal gravitational field (shear) of the mass distribution is estimated, and the corresponding surface mass density is constructed. The noise of the resulting mass map is investigated here, generalizing previous work which included mainly the noise due to the intrinsic galaxy ellipticities. Whereas this dominates the noise budget if the lens is very weak, other sources of noise become important, or even dominant, for the medium-strong lensing regime close to the center of clusters. In particular, shot noise due to a Poisson distribution of galaxy images, and increased shot noise owing to the correlation of galaxies in angular position and redshift, can yield significantly larger levels of noise than that from the intrinsic ellipticities only. We estimate the contributions from these various effects for two widely used smoothing operations, showing that one of them effectively removes the Poisson and the correlation noises related to angular positions of galaxies. Noise sources due to the spread in redshift of galaxies are still present in the optimized estimator and are shown to be relevant in many cases. We show how (even approximate) redshift information can be profitably used to reduce the noise in the mass map. The dependence of the various noise terms on the relevant parameters (lens redshift, strength, smoothing length, redshift distribution of background galaxies) are explicitly calculated and simple estimates are provided.Comment: 18 pages, A&A in pres

NsrR from Streptomyces coelicolor is a nitric oxide-sensing [4Fe-4S] cluster protein with a specialized regulatory function

The Rrf2 family transcription factor NsrR controls expression of genes in a wide range of bacteria in response to nitric oxide (NO). The precise form of the NO-sensing module of NsrR is the subject of controversy because NsrR proteins containing either [2Fe-2S] or [4Fe-4S] clusters have been observed previously. Optical, Mössbauer, resonance Raman spectroscopies and native mass spectrometry demonstrate that Streptomyces coelicolor NsrR (ScNsrR), previously reported to contain a [2Fe-2S] cluster, can be isolated containing a [4Fe-4S] cluster. ChIP-seq experiments indicated that the ScNsrR regulon is small, consisting of only hmpA1, hmpA2, and nsrR itself. The hmpA genes encode NO-detoxifying flavohemoglobins, indicating that ScNsrR has a specialized regulatory function focused on NO detoxification and is not a global regulator like some NsrR orthologues. EMSAs and DNase I footprinting showed that the [4Fe-4S] form of ScNsrR binds specifically and tightly to an 11-bp inverted repeat sequence in the promoter regions of the identified target genes and that DNA binding is abolished following reaction with NO. Resonance Raman data were consistent with cluster coordination by three Cys residues and one oxygen-containing residue, and analysis of ScNsrR variants suggested that highly conserved Glu-85 may be the fourth ligand. Finally, we demonstrate that some low molecular weight thiols, but importantly not physiologically relevant thiols, such as cysteine and an analogue of mycothiol, bind weakly to the [4Fe-4S] cluster, and exposure of this bound form to O2 results in cluster conversion to the [2Fe-2S] form, which does not bind to DNA. These data help to account for the observation of [2Fe-2S] forms of NsrR

Preventable cancer mortality in American Indian and Alaska Native women.

This report describes a series of six studies on cancer in American Indian and Alaska Native (AI/AN) women, with a particular emphasis on cancer of the breast and cervix. Data from the Indian Health Service (IHS) inpatient data system was used to generate estimates of incidence of cancer among AI/AN populations. Additionally, breast cancer rates among Indian women in Arizona and New Mexico were compiled from extensive chart review of the New Mexico Tumor Registry and the IHS Inpatient Data System. Study of the performance of the health care system for cancer screening in women suggest that the major deficiency lies not in a failure to bring women in for screening, but rather to complete the screening after contact has been made and the need for screening recognized. The studies indicate that cancer is generally diagnosed in American Indian women at a more advanced stage and survival experience of Indian cancer patients is worse than non-Indian, even when corrected for later stage at diagnosis. Several of the studies suggest that failure to diagnose cancer in its very early stages appears to be in large part dependent on patient behavior. An alarming number of women do not keep follow-up appointments, even after multiple referrals and rescheduling of appointments. These findings suggest the need for intervention strategies that encourage women to become knowledgeable about cancer and to accept responsibility for their screening. The studies suggest that the relative difficulty in improving screening rates are traced to an inadequate understanding of cancer and its prevention on the part of women in the community

New search strategy for high z intervening absorbers: GRB021004, a pilot study

We present near-infrared narrow- and broad-band imaging of the field of GRB021004, performed with ISAAC on the UT1 of the ESO Very Large Telescope. The narrow-band filters were chosen to match prominent emission lines at the redshift of the absorption-line systems found against the early-time afterglow of GRB021004: [OIII] at z=1.38 and Halpha at z=1.60, respectively. For the z=1.38 system we find an emission-line source at an impact parameter of 16", which is somewhat larger than the typical impact parameters of a sample of MgII absorbers at redshifts around unity. Assuming that this tentative redshift-identification is correct, the star formation rate of the galaxy is 13 +- 2 Msun/year. Our study reaches star-formation rate limits (5 sigma) of 5.7 Msun/year at z=1.38, and 7.7 Msun/year at z=1.60. These limits correspond to a depth of roughly 0.13 L*. Any galaxy counterpart of the absorbers nearer to the line of sight either has to be fainter than this limit or not be an emission-line source.Comment: 4 pages, 3 figures, accepted for publication in A&A letter

Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica

Surveillance of antimicrobial resistance (AMR) in non-typhoidal Salmonella enterica (NTS), is essential for monitoring transmission of resistance from the food chain to humans, and for establishing effective treatment protocols. We evaluated the prediction of phenotypic resistance in NTS from genotypic profiles derived from whole genome sequencing (WGS). Genes and chromosomal mutations responsible for phenotypic resistance were sought in WGS data from 3,491 NTS isolates received by Public Health England’s Gastrointestinal Bacteria Reference Unit between April 2014 and March 2015. Inferred genotypic AMR profiles were compared with phenotypic susceptibilities determined for fifteen antimicrobials using EUCAST guidelines. Discrepancies between phenotypic and genotypic profiles for one or more antimicrobials were detected for 76 isolates (2.18%) although only 88/52,365 (0.17%) isolate/antimicrobial combinations were discordant. Of the discrepant results, the largest number were associated with streptomycin (67.05%, n = 59). Pan-susceptibility was observed in 2,190 isolates (62.73%). Overall, resistance to tetracyclines was most common (26.27% of isolates, n = 917) followed by sulphonamides (23.72%, n = 828) and ampicillin (21.43%, n = 748). Multidrug resistance (MDR), i.e., resistance to three or more antimicrobial classes, was detected in 848 isolates (24.29%) with resistance to ampicillin, streptomycin, sulphonamides and tetracyclines being the most common MDR profile (n = 231; 27.24%). For isolates with this profile, all but one were S. Typhimurium and 94.81% (n = 219) had the resistance determinants blaTEM-1, strA-strB, sul2 and tet(A). Extended-spectrum β-lactamase genes were identified in 41 isolates (1.17%) and multiple mutations in chromosomal genes associated with ciprofloxacin resistance in 82 isolates (2.35%). This study showed that WGS is suitable as a rapid means of determining AMR patterns of NTS for public health surveillance

A wide-field spectroscopic survey of the cluster of galaxies Cl0024+1654: I. The catalogue

We present the catalogue of a wide-field CFHT/WHT spectroscopic survey of the lensing cluster Cl0024+1654 at z=0.395. This catalogue contains 618 new spectra, of which 581 have identified redshifts. Adding redshifts available from the literature, the final catalogue contains data for 687 objects with redshifts identified for 650 of them. 295 galaxies have redshifts in the range 0.37<z<0.41, i. e. are cluster members or lie in the immediate neighbourhood of the cluster. The area covered by the survey is 21x25 arcmin2 in size, corresponding to 4x4.8 h^-2 Mpc2 at the cluster redshift. The survey is 45% complete down to V=22 over the whole field covered; within 3 arcmin of the cluster centre the completeness exceeds 80% at the same magnitude. A detailed completeness analysis is presented. The catalogue gives astrometric position, redshift, V magnitude and V-I colour, as well as the equivalent widths for a number of lines. Apart from the cluster Cl0024+1654 itself, three other structures are identified in redshift space: a group of galaxies at z=0.38, just in front of Cl0024+1654 and probably interacting with it, a close pair of groups of galaxies at z~0.495 and an overdensity of galaxies at z~0.18 with no obvious centre. The spectroscopic catalogue will be used to trace the three-dimensional structure of the cluster Cl0024+1654 as well as study the physical properties of the galaxies in the cluster and in its environment.Comment: 14 pages - figures included - A&A (re)submitted versio

Sharp interface limits of phase-field models

The use of continuum phase-field models to describe the motion of well-defined interfaces is discussed for a class of phenomena, that includes order/disorder transitions, spinodal decomposition and Ostwald ripening, dendritic growth, and the solidification of eutectic alloys. The projection operator method is used to extract the ``sharp interface limit'' from phase field models which have interfaces that are diffuse on a length scale $\xi$. In particular,phase-field equations are mapped onto sharp interface equations in the limits $\xi \kappa \ll 1$ and $\xi v/D \ll 1$, where $\kappa$ and $v$ are respectively the interface curvature and velocity and $D$ is the diffusion constant in the bulk. The calculations provide one general set of sharp interface equations that incorporate the Gibbs-Thomson condition, the Allen-Cahn equation and the Kardar-Parisi-Zhang equation.Comment: 17 pages, 9 figure

The VIRMOS deep imaging survey II: CFH12K BVRI optical data for the 0226-04 deep field

(abridged) In this paper we describe in detail the reduction, preparation and reliability of the photometric catalogues which comprise the 1.2 deg^2 CFH12K-VIRMOS deep field. The survey reaches a limiting magnitude of BAB~26.5, VAB~26.2, RAB~25.9 IAB~25.0 and contains 90,729 extended sources in the magnitude range 18.0<IAB<24.0. We demonstrate our catalogues are free from systematic biases and are complete and reliable down these limits. We estimate that the upper limit on bin-to-bin systematic photometric errors for the I- limited sample is ~10% in this magnitude range. We estimate that 68% of the catalogues sources have absolute per co-ordinate astrometric uncertainties less than ~0.38" and ~0.32" (alpha,delta). Our internal (filter-to-filter) per co-ordinate astrometric uncertainties are 0.08" and 0.08" (alpha,delta). We quantify the completeness of our survey in the joint space defined by object total magnitude and peak surface brightness. Finally, we present numerous comparisons between our catalogues and published literature data: galaxy and star counts, galaxy and stellar colours, and the clustering of both point-like and extended populations. In all cases our measurements are in excellent agreement with literature data to IAB<24.0. This combination of depth and areal coverage makes this multi-colour catalogue a solid foundation to select galaxies for follow-up spectroscopy with VIMOS on the ESO-VLT and a unique database to study the formation and evolution of the faint galaxy population to z~1 and beyond.Comment: 18 pages, 23 figures, accepted for publication in A&

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

© 2016 Rinke et al. High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100-1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics

Substructure in lensing clusters and simulations

We present high-resolution mass reconstructions for five massive cluster-lenses spanning a redshift range from $z = 0.18$--0.57 utilising archival {\it Hubble Space Telescope} ({\it HST}) data and applying galaxy-galaxy lensing techniques. These detailed mass models were obtained from the observations by combining constraints from the strong and weak lensing regimes. We ascribe local weak distortions in the shear maps to perturbations induced by the presence of galaxy haloes around individual bright early-type cluster member galaxies. This technique constrains the mass enclosed within an aperture for these subhaloes. We are sensitive to a specific mass range for these subhaloes, $10^{11}$ -- 10^{12.5} \msun, which we associate with galaxy-scale subhaloes. Adopting a parametric model for the subhaloes, we also derive their velocity dispersion function and the aperture radius function. The mass spectrum of substructure in the inner regions of the observed clusters is directly compared with that in simulated clusters extracted from the {\it Millennium Simulation}. The massfunction, aperture radii and velocity dispersion function are compared in detail. Overall, we find good agreement between the distribution of substructure properties retrieved using the lensing analysis and those obtained from the simulation (truncated abstract).Comment: 15 pages, 5 figures, 2 tables, in press MNRA