The Cross-correlation of MgII Absorption and Galaxies in BOSS

We present a measurement of the cross-correlation of MgII absorption and massive galaxies, using the DR11 main galaxy sample of the Baryon Oscillation Spectroscopic Survey of SDSS-III (CMASS galaxies), and the DR7 quasar spectra of SDSS-II. The cross-correlation is measured by stacking quasar absorption spectra shifted to the redshift of galaxies that are within a certain impact parameter bin of the quasar, after dividing by a quasar continuum model. This results in an average MgII equivalent width as a function of impact parameter from a galaxy, ranging from 50 kpc to more than 10 Mpc in proper units, which includes all MgII absorbers. We show that special care needs to be taken to use an unbiased quasar continuum estimator, to avoid systematic errors in the measurement of the mean stacked MgII equivalent width. The measured cross-correlation follows the expected shape of the galaxy correlation function, although measurement errors are large. We use the cross-correlation amplitude to derive the bias factor of MgII absorbers, finding bMgII = 2.33 \pm? 0.19, where the error accounts only for the statistical uncertainty in measuring the mean equivalent width. This bias factor is larger than that obtained in previous studies and may be affected by modeling uncertainties that we discuss, but if correct it suggests that MgII absorbers at redshift z \simeq 0:5 are spatially distributed on large scales similarly to the CMASS galaxies in BOSS. Keywords: galaxies: haloes, galaxies: formation, quasars: absorption lines, large-scale structure of universeComment: Accepted for publication to MNRAS. Accepted 2014 December 12. Received 2014 November 29; in original form 2014 February

Detection of Ly\beta auto-correlations and Ly\alpha-Ly\beta cross-correlations in BOSS Data Release 9

The Lyman-$\beta$ forest refers to a region in the spectra of distant quasars that lies between the rest-frame Lyman-$\beta$ and Lyman-$\gamma$ emissions. The forest in this region is dominated by a combination of absorption due to resonant Ly$\alpha$ and Ly$\beta$ scattering. When considering the 1D Ly$\beta$ forest in addition to the 1D Ly$\alpha$ forest, the full statistical description of the data requires four 1D power spectra: Ly$\alpha$ and Ly$\beta$ auto-power spectra and the Ly$\alpha$-Ly$\beta$ real and imaginary cross-power spectra. We describe how these can be measured using an optimal quadratic estimator that naturally disentangles Ly$\alpha$ and Ly$\beta$ contributions. Using a sample of approximately 60,000 quasar sight-lines from the BOSS Data Release 9, we make the measurement of the one-dimensional power spectrum of fluctuations due to the Ly$\beta$ resonant scattering. While we have not corrected our measurements for resolution damping of the power and other systematic effects carefully enough to use them for cosmological constraints, we can robustly conclude the following: i) Ly$\beta$ power spectrum and Ly$\alpha$-Ly$\beta$ cross spectra are detected with high statistical significance; ii) the cross-correlation coefficient is $\approx 1$ on large scales; iii) the Ly$\beta$ measurements are contaminated by the associated OVI absorption, which is analogous to the SiIII contamination of the Ly$\alpha$ forest. Measurements of the Ly$\beta$ forest will allow extension of the usable path-length for the Ly$\alpha$ measurements while allowing a better understanding of the physics of intergalactic medium and thus more robust cosmological constraints.Comment: 26 pages, 10 figures; matches version accepted by JCA

The baroclinic secondary instability of the two-dimensional shear layer

The focus of this study is on the numerical investigation of two-dimensional, isovolume, high Reynolds and Froude numbers, variable-density mixing layers. Lagrangian simulations, of both the temporal and the spatial models, are performed. They reveal the breaking-up of the strained vorticity and density-gradient braids, connecting two neighboring primary structures. The secondary instability arises where the vorticity has been intensified by the baroclinic torque. A simplified model of the braid of the variable-density mixing layer, consisting of a strained vorticity and density-gradient filament, is analyzed. It is concluded that the physical mechanism responsible for the secondary instability is the forcing of the vorticity field by the baroclinic torque, itself sensitive to perturbations. This mechanism suggests a rapid route to turbulence for the variable-density mixing layer

Probing the Circumgalactic Medium at High-Redshift Using Composite BOSS Spectra of Strong Lyman-alpha Forest Absorbers

We present composite spectra constructed from a sample of 242,150 Lyman-alpha (Lya) forest absorbers at redshifts 2.4<z<3.1 identified in quasar spectra from the Baryon Oscillation Spectroscopic Survey (BOSS) as part of Data Release 9 of the Sloan Digital Sky Survey III. We select forest absorbers by their flux in bins 138 km/s wide (approximately the size of the BOSS resolution element). We split these absorbers into five samples spanning the range of flux -0.05 < F<0.45. Tests on a smaller sample of high-resolution spectra show that our three strongest absorption bins would probe circumgalactic regions (projected separation < 300 proper kpc and |Delta v| < 300km/s) in about 60% of cases for very high signal-to-noise ratio. Within this subset, weakening Lya absorption is associated with decreasing purity of circumgalactic selection once BOSS noise is included. Our weaker two Lya absorption samples are dominated by the intergalactic medium. We present composite spectra of these samples and a catalogue of measured absorption features from HI and 13 metal ionization species, all of which we make available to the community. We compare measurements of seven Lyman series transitions in our composite spectra to single line models and obtain further constraints from their associated excess Lyman limit opacity. This analysis provides results consistent with column densities over the range 14.4 <~ Log (N_HI) <~ 16.45. We compare our measurements of metal absorption to a variety of simple single-line, single-phase models for a preliminary interpretation. Our results imply clumping on scales down to ~30 pc and near-solar metallicities in the circumgalactic samples, while high-ionization metal absorption consistent with typical IGM densities and metallicities is visible in all samples.Comment: 23 pages, 15 figures, 5 tables, link to downloadable data included. Accepted by MNRAS 2014 March 20. New sections 3.4 and 6.1 limiting the occurrence and impact of Lyman limit system

Implications for Chk1 Regulation: The 1.7 Å Crystal Structure of Human Cell Cycle Checkpoint Kinase Chk1

AbstractThe checkpoint kinase Chk1 is an important mediator of cell cycle arrest following DNA damage. The 1.7 Å resolution crystal structures of the human Chk1 kinase domain and its binary complex with an ATP analog has revealed an identical open kinase conformation. The secondary structure and side chain interactions stabilize the activation loop of Chk1 and enable kinase activity without phosphorylation of the catalytic domain. Molecular modeling of the interaction of a Cdc25C peptide with Chk1 has uncovered several conserved residues that are important for substrate selectivity. In addition, we found that the less conserved C-terminal region negatively impacts Chk1 kinase activity

Seeds of Change: Corn Seed Mixtures for Resistance Management and Integrated Pest Management

The use of mixtures of transgenic insecticidal seed and nontransgenic seed to provide an in-field refuge for susceptible insects in insect-resistance-management (IRM) plans has been considered for at least two decades. However, the U.S. Environmental Protection Agency has only recently authorized the practice. This commentary explores issues that regulators, industry, and other stakeholders should consider as the use of biotechnology increases and seed mixtures are implemented as a major tactic for IRM. We discuss how block refuges and seed mixtures in transgenic insecticidal corn, Zea mays L., production will influence integrated pest management (IPM) and the evolution of pest resistance. We conclude that seed mixtures will make pest monitoring more difficult and that seed mixtures may make IRM riskier because of larval behavior and greater adoption of insecticidal corn. Conversely, block refuges present a different suite of risks because of adult pest behavior and the lower compliance with IRM rules expected from farmers. It is likely that secondary pests not targeted by the insecticidal corn as well as natural enemies will respond differently to block refuges and seed mixtures

3D-HST: A wide-field grism spectroscopic survey with the Hubble Space Telescope

We present 3D-HST, a near-infrared spectroscopic Treasury program with the Hubble Space Telescope for studying the processes that shape galaxies in the distant Universe. 3D-HST provides rest-frame optical spectra for a sample of ~7000 galaxies at 1<z<3.5, the epoch when 60% of all star formation took place, the number density of quasars peaked, the first galaxies stopped forming stars, and the structural regularity that we see in galaxies today must have emerged. 3D-HST will cover 3/4 (625 sq.arcmin) of the CANDELS survey area with two orbits of primary WFC3/G141 grism coverage and two to four parallel orbits with the ACS/G800L grism. In the IR these exposure times yield a continuum signal-to-noise of ~5 per resolution element at H~23.1 and a 5sigma emission line sensitivity of 5x10-17 erg/s/cm2 for typical objects, improving by a factor of ~2 for compact sources in images with low sky background levels. The WFC3/G141 spectra provide continuous wavelength coverage from 1.1-1.6 um at a spatial resolution of ~0."13, which, combined with their depth, makes them a unique resource for studying galaxy evolution. We present the preliminary reduction and analysis of the grism observations, including emission line and redshift measurements from combined fits to the extracted grism spectra and photometry from ancillary multi-wavelength catalogs. The present analysis yields redshift estimates with a precision of sigma(z)=0.0034(1+z), or sigma(v)~1000 km/s. We illustrate how the generalized nature of the survey yields near-infrared spectra of remarkable quality for many different types of objects, including a quasar at z=4.7, quiescent galaxies at z~2, and the most distant T-type brown dwarf star known. The CANDELS and 3D-HST surveys combined will provide the definitive imaging and spectroscopic dataset for studies of the 1<z<3.5 Universe until the launch of the James Webb Space Telescope.Comment: Replacement reflects version now accepted by ApJS. A preliminary data release intended to provide a general illustration of the WFC3 grism data is available at http://3dhst.research.yale.edu

Broad Absorption Line Variability in Repeat Quasar Observations from the Sloan Digital Sky Survey

We present a time-variability analysis of 29 broad absorption line quasars (BALQSOs) observed in two epochs by the Sloan Digital Sky Survey (SDSS). These spectra are selected from a larger sample of BALQSOs with multiple observations by virtue of exhibiting a broad CIV $\lambda$1549 absorption trough separated from the rest frame of the associated emission peak by more than 3600 km s$^{-1}$. Detached troughs facilitate higher precision variability measurements, since the measurement of the absorption in these objects is not complicated by variation in the emission line flux. We have undertaken a statistical analysis of these detached-trough BALQSO spectra to explore the relationships between BAL features that are seen to vary and the dynamics of emission from the quasar central engine. We have measured variability within our sample, which includes three strongly variable BALs. We have also verified that the statistical behavior of the overall sample agrees with current model predictions and previous studies of BAL variability. Specifically, we observe that the strongest BAL variability occurs among the smallest equivalent width features and at velocities exceeding 12,000 km s$^{-1}$, as predicted by recent disk-wind modeling.Comment: 11 pages, 7 figures. Accepted for publication in Ap

The glitch-induced identity changes of PSR J1119-6127

We demonstrate that the high-magnetic field pulsar J1119-6127 exhibits three different types of behaviour in the radio band. Trailing the "normal" profile peak there is an "intermittent" peak and these components are flanked by two additional components showing very erratic "RRAT-like" emission. Both the intermittent and RRAT-like events are extremely rare and are preceded by a large amplitude glitch in the spin-down parameters. The post-glitch spin-down rate is smaller than the pre-glitch rate. This type of relaxation is very unusual for the pulsar population as a whole, but is observed in the glitch recovery of a RRAT. The abnormal emission behaviour in PSR J1119-6127 was observed up to three months after the epoch of the large glitch, suggestive of changes in the magnetospheric conditions during the fast part of the recovery process. We argue that both the anomalous recoveries and the emission changes could be related to reconfigurations of the magnetic field. Apart from the glitches, the spin-down of PSR J1119-6127 is relatively stable, allowing us to refine the measurement of the braking index (n=2.684\pm0.002) using more than 12 years of timing data. The properties of this pulsar are discussed in light of the growing evidence that RRATs do not form a distinct class of pulsar, but rather are a combination of different extreme emission types seen in other neutron stars. Different sub-classes of the RRATs can potentially be separated by calculating the lower limit on the modulation index of their emission. We speculate that if the abnormal behaviour in PSR J1119-6127 is indeed glitch induced then there might exist a population of neutron stars which only become visible in the radio band for a short duration in the immediate aftermath of glitch activity. These neutron stars will be visible in the radio band as sources that only emit some clustered pulses every so many years.Comment: 20 pages, 10 figures, Accepted for publication in MNRA

The SDSS-III Baryon Oscillation Spectroscopic Survey: Quasar Target Selection for Data Release Nine

The SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS), a five-year spectroscopic survey of 10,000 deg^2, achieved first light in late 2009. One of the key goals of BOSS is to measure the signature of baryon acoustic oscillations in the distribution of Ly-alpha absorption from the spectra of a sample of ~150,000 z>2.2 quasars. Along with measuring the angular diameter distance at z\approx2.5, BOSS will provide the first direct measurement of the expansion rate of the Universe at z > 2. One of the biggest challenges in achieving this goal is an efficient target selection algorithm for quasars over 2.2 < z < 3.5, where their colors overlap those of stars. During the first year of the BOSS survey, quasar target selection methods were developed and tested to meet the requirement of delivering at least 15 quasars deg^-2 in this redshift range, out of 40 targets deg^-2. To achieve these surface densities, the magnitude limit of the quasar targets was set at g <= 22.0 or r<=21.85. While detection of the BAO signature in the Ly-alpha absorption in quasar spectra does not require a uniform target selection, many other astrophysical studies do. We therefore defined a uniformly-selected subsample of 20 targets deg^-2, for which the selection efficiency is just over 50%. This "CORE" subsample will be fixed for Years Two through Five of the survey. In this paper we describe the evolution and implementation of the BOSS quasar target selection algorithms during the first two years of BOSS operations. We analyze the spectra obtained during the first year. 11,263 new z>2.2 quasars were spectroscopically confirmed by BOSS. Our current algorithms select an average of 15 z > 2.2 quasars deg^-2 from 40 targets deg^-2 using single-epoch SDSS imaging. Multi-epoch optical data and data at other wavelengths can further improve the efficiency and completeness of BOSS quasar target selection. [Abridged]Comment: 33 pages, 26 figures, 12 tables and a whole bunch of quasars. Submitted to Ap