On the Search for Quasar Light Echoes

The UV radiation from a quasar leaves a characteristic pattern in the distribution of ionized hydrogen throughout the surrounding space. This pattern or light echo propagates through the intergalactic medium at the speed of light, and can be observed by its imprint on the Ly-alpha forest spectra of background sources. As the echo persists after the quasar has switched off, it offers the possibility of searching for dead quasars, and constraining their luminosities and lifetimes. We outline a technique to search for and characterize these light echoes. To test the method, we create artificial Ly-alpha forest spectra from cosmological simulations at z=3, apply light echoes and search for them. We show how the simulations can also be used to quantify the significance level of any detection. We find that light echoes from the brightest quasars could be found in observational data. With absorption line spectra of 100 redshift z~3-3.5 quasars or galaxies in a 1 square degree area, we expect that ~10 echoes from quasars with B band luminosities L_B=3x10^45 ergs/s exist that could be found at 95% confidence, assuming a quasar lifetime of ~10^7 yr. Even a null result from such a search would have interesting implications for our understanding of quasar luminosities and lifetimes.Comment: 9 pages, 7 figures, ApJ in pres

Ionizing radiation fluctuations and large-scale structure in the Lyman-alpha forest

We investigate the large-scale inhomogeneities of the hydrogen ionizing radiation field in the Universe at redshift z=3. Using a raytracing algorithm, we simulate a model in which quasars are the dominant sources of radiation. We make use of large scale N-body simulations of a LambdaCDM universe, and include such effects as finite quasar lifetimes and output on the lightcone, which affects the shape of quasar light echoes. We create Lya forest spectra that would be generated in the presence of such a fluctuating radiation field, finding that the power spectrum of the Lya forest can be suppressed by as much as 15 % for modes with k=0.05-1 Mpc/h. This relatively small effect may have consequences for high precision measurements of the Lya power spectrum on larger scales than have yet been published. We also investigate another radiation field probe, the cross-correlation of quasar positions and the Lya forest. For both quasar lifetimes which we simulate (10^7 yr and 10^8 yr), we expect to see a strong decrease in the Lya absorption close to other quasars (the ``foreground'' proximity effect). We then use data from the Sloan Digital Sky Survey First Data Release to make an observational determination of this statistic. We find no sign of our predicted lack of absorption, but instead increased absorption close to quasars. If the bursts of radiation from quasars last on average < 10^6 yr, then we would not expect to be able to see the foreground effect. However, the strength of the absorption itself seems to be indicative of rare objects, and hence much longer total times of emission per quasar. Variability of quasars in bursts with timescales > 10^4yr and < 10^6 yr could reconcile these two facts.Comment: Submitted to ApJ, 21 pages, 17 postscript figures, emulateapj.st

Cellular mRNAs access second ORFs using a novel amino acid sequence-dependent coupled translation termination-reinitiation mechanism

Polycistronic transcripts are considered rare in the human genome. Initiation of translation of internal ORFs of eukaryotic genes has been shown to use either leaky scanning or highly structured IRES regions to access initiation codons. Studies on mammalian viruses identified a mechanism of coupled translation termination-reinitiation that allows translation of an additional ORF. Here, the ribosome terminating translation of ORF-1 translocates upstream to reinitiate translation of ORF-2. We have devised an algorithm to identify mRNAs in the human transcriptome in which the major ORF-1 overlaps a second ORF capable of encoding a product of at least 50 aa in length. This identified 4368 transcripts representing 2214 genes. We investigated 24 transcripts, 22 of which were shown to express a protein from ORF-2 highlighting that 3' UTRs contain protein-coding potential more frequently than previously suspected. Five transcripts accessed ORF-2 using a process of coupled translation termination-reinitiation. Analysis of one transcript, encoding the CASQ2 protein, showed that the mechanism by which the coupling process of the cellular mRNAs was achieved was novel. This process was not directed by the mRNA sequence but required an aspartate-rich repeat region at the carboxyl terminus of the terminating ORF-1 protein. Introduction of wobble mutations for the aspartate codon had no effect, whereas replacing aspartate for glutamate repeats eliminated translational coupling. This is the first description of a coordinated expression of two proteins from cellular mRNAs using a coupled translation termination-reinitiation process and is the first example of such a process being determined at the amino acid level

Exploring the added value of video-stimulated recall in researching the primary care doctor-patient consultation: a process evaluation

Background Video-stimulated recall (VSR) is a method whereby researchers show research participants a video of their own behaviour to prompt and enhance their recall and interpretation after the event, e.g. in a post-consultation interview. This paper describes a process evaluation with the aim of understanding what video stimulated recall (VSR) may have added to findings, to describe participants’ responses to, and the acceptability of,VSR and to explore participants’ perceptions of behaviour change in response to being video-recorded. Methods This evaluation took place in the context of a UK study concerning the discussion of osteoarthritis in primary care consultations. Post consultation VSR interviews were conducted with 13 family physicians (general practitioners, GPs) and 17 patients. Thematic analysis of these interviews and the matched 17 consultations was undertaken, and was both inductive and deductive in approach. Results The findings demonstrate VSR appeared to add value by enabling a deeper understanding of participants’ thoughts and reactions to specific parts of consultation dialogue, by facilitating participants to express concerns and possibly speak more candidly and by eliciting a more multi-layered narrative from participants. The method was broadly acceptable to participants; however, levels of mild anxiety and/or distress were reported or observed by both doctor and patient participants and this may explain in part why some participants reported behaviour change as a result of the video. Any reported behaviour change was used to inform analysis. Conclusions This study demonstrates how VSR may enable a more critical, more specific and more in-depth response from participants to events of interest, and in doing so, generates multiple layers of narrative. This results in a method that goes beyond fact finding and description and generates more meaningful explanations of consultation events, getting straight to the core of what is salient to participants

No Evidence for Orbital Loop Currents in Charge Ordered YBa2_2Cu3_3O6+x_{6+x} from Polarized Neutron Diffraction

It has been proposed that the pseudogap state of underdoped cuprate superconductors may be due to a transition to a phase which has circulating currents within each unit cell. Here, we use polarized neutron diffraction to search for the corresponding orbital moments in two samples of underdoped YBa$_2$Cu$_3$O$_{6+x}$ with doping levels $p=0.104$ and 0.123. In contrast to some other reports using polarized neutrons, but in agreement with nuclear magnetic resonance and muon spin rotation measurements, we find no evidence for the appearance of magnetic order below 300 K. Thus, our experiment suggests that such order is not an intrinsic property of high-quality cuprate superconductor single crystals. Our results provide an upper bound for a possible orbital loop moment which depends on the pattern of currents within the unit cell. For example, for the CC-$\theta_{II}$ pattern proposed by Varma, we find that the ordered moment per current loop is less than 0.013 $\mu_B$ for $p=0.104$.Comment: Comments in arXiv:1710.08173v1 fully addresse

Constraining quasar host halo masses with the strength of nearby Lyman-alpha forest absorption

Using cosmological hydrodynamic simulations we measure the mean transmitted flux in the Lyman alpha forest for quasar sightlines that pass near a foreground quasar. We find that the trend of absorption with pixel-quasar separation distance can be fitted using a simple power law form including the usual correlation function parameters r_{0} and \gamma so that ( = \sum exp(-tau_eff*(1+(r/r_{0})^(-\gamma)))). From the simulations we find the relation between r_{0} and quasar mass and formulate this as a way to estimate quasar host dark matter halo masses, quantifying uncertainties due to cosmological and IGM parameters, and redshift errors. With this method, we examine data for ~3000 quasars from the Sloan Digital Sky Survey (SDSS) Data Release 3, assuming that the effect of ionizing radiation from quasars (the so-called transverse proximity effect) is unimportant (no evidence for it is seen in the data.) We find that the best fit host halo mass for SDSS quasars with mean redshift z=3 and absolute G band magnitude -27.5 is log10(M/M_sun) = 12.48^{+0.53}_{-0.89}. We also use the Lyman-Break Galaxy (LBG) and Lyman alpha forest data of Adelberger et al in a similar fashion to constrain the halo mass of LBGs to be log10(M/M_sun) = 11.13^{+0.39}_{-0.55}, a factor of ~20 lower than the bright quasars. In addition, we study the redshift distortions of the Lyman alpha forest around quasars, using the simulations. We use the quadrupole to monopole ratio of the quasar-Lyman alpha forest correlation function as a measure of the squashing effect. We find that this does not have a measurable dependence on halo mass, but may be useful for constraining cosmic geometry.Comment: 10 pages, 11 figures, submitted to MNRA

Weak lensing surveys and the intrinsic correlation of galaxy ellipticities

We explore the possibility that an intrinsic correlation between galaxy ellipticities arising during the galaxy formation process may account for part of the shear signal recently reported by several groups engaged in weak lensing surveys. Using high resolution N-body simulations we measure the projected ellipticities of dark matter halos and their correlations as a function of pair separation. With this simplifying, but not necessarily realistic assumption (halo shapes as a proxy for galaxy shapes), we find a positive detection of correlations up to scales of at least 20 h^-1mpc (limited by the box size). The signal is not strongly affected by variations in the halo finding technique, or by the resolution of the simulations. We translate our 3d results into angular measurements of ellipticity correlation functions and shear variance which can be directly compared to observations. We also measure similar results from simulated angular surveys made by projecting our simulation boxes onto the plane of the sky and applying a radial selection function. Interestingly, the shear variance we measure is a small, but not entirely negligible fraction (from ~10-20 %) of that seen by the observational groups, and the ellipticity correlation functions approximately mimic the functional form expected to be caused by weak lensing. The amplitude depends on the width in redshift of the galaxy distribution. If photometric redshifts are used to pick out a screen of background galaxies with a small width, then the intrinsic correlation may become comparable to the weak lensing signal. Although we are dealing with simulated dark matter halos, whether there is a signal from real galaxies could be checked with a nearby sample with known redshifts.Comment: 12 pages, 11 ps figures, emulateapj.sty, submitted to Ap

Galaxy Cluster Correlation Function to z ~ 1.5 in the IRAC Shallow Cluster Survey

We present the galaxy cluster autocorrelation function of 277 galaxy cluster candidates with 0.25 \le z \le 1.5 in a 7 deg^2 area of the IRAC Shallow Cluster Survey. We find strong clustering throughout our galaxy cluster sample, as expected for these massive structures. Specifically, at = 0.5 we find a correlation length of r_0 = 17.40^{+3.98}_{-3.10} h^-1 Mpc, in excellent agreement with the Las Campanas Distant Cluster Survey, the only other non-local measurement. At higher redshift, = 1, we find that strong clustering persists, with a correlation length of r_0=19.14^{+5.65}_{-4.56} h^-1 Mpc. A comparison with high resolution cosmological simulations indicates these are clusters with halo masses of \sim 10^{14} Msun, a result supported by estimates of dynamical mass for a subset of the sample. In a stable clustering picture, these clusters will evolve into massive (10^{15} Msun) clusters by the present day.Comment: 4 pages, 4 figures, 1 table. ApJ Letters, in pres

Evolution of the Cluster Mass and Correlation Functions in LCDM Cosmology

The evolution of the cluster mass function and the cluster correlation function from z = 0 to z = 3 are determined using 10^6 clusters obtained from high-resolution simulations of the current best-fit LCDM cosmology (\Omega_m = 0.27, \sigma_8 = 0.84, h = 0.7). The results provide predictions for comparisons with future observations of high redshift clusters. A comparison of the predicted mass function of low redshift clusters with observations from early Sloan Digital Sky Survey data, and the predicted abundance of massive distant clusters with observational results, favor a slightly larger amplitude of mass fluctuations (\sigma_8 = 0.9) and lower density parameter (\Omega_m = 0.2); these values are consistent within 1-\sigma with the current observational and model uncertainties. The cluster correlation function strength increases with redshift for a given mass limit; the clusters were more strongly correlated in the past, due to their increasing bias with redshift - the bias reaches b = 100 at z = 2 for M > 5 x 10^13 h^-1 M_sun. The richness-dependent cluster correlation function, represented by the correlation scale versus cluster mean separation relation, R0-d, is generally consistent with observations. This relation can be approximated as R_0 = 1.7 d^0.6 h^-1 Mpc for d = 20 - 60 h^-1 Mpc. The R0-d relation exhibits surprisingly little evolution with redshift for z < 2; this can provide a new test of the current LCDM model when compared with future observations of high redshift clusters.Comment: 20 pages, 9 figures, accepted for publication in Ap

Bias, redshift space distortions and primordial nongaussianity of nonlinear transformations: application to Lyman alpha forest

On large scales a nonlinear transformation of matter density field can be viewed as a biased tracer of the density field itself. A nonlinear transformation also modifies the redshift space distortions in the same limit, giving rise to a velocity bias. In models with primordial nongaussianity a nonlinear transformation generates a scale dependent bias on large scales. We derive analytic expressions for these for a general nonlinear transformation. These biases can be expressed entirely in terms of the one point distribution function (PDF) of the final field and the parameters of the transformation. Our analysis allows one to devise nonlinear transformations with nearly arbitrary bias properties, which can be used to increase the signal in the large scale clustering limit. We apply the results to the ionizing equilibrium model of Lyman-alpha forest, in which Lyman-alpha flux F is related to the density perturbation delta via a nonlinear transformation. Velocity bias can be expressed as an average over the Lyman-alpha flux PDF. At z=2.4 we predict the velocity bias of -0.1, compared to the observed value of -0.13 +/- 0.03. Bias and primordial nongaussianity bias depend on the parameters of the transformation. Measurements of bias can thus be used to constrain these parameters, and for reasonable values of the ionizing background intensity we can match the predictions to observations. Matching to the observed values we predict the ratio of primordial nongaussianity bias to bias to have the opposite sign and lower magnitude than the corresponding values for the highly biased galaxies, but this depends on the model parameters and can also vanish or change the sign.Comment: 18 pages, 1 figur