Dissecting Galaxy Formation: II. Comparing Substructure in Pure Dark Matter and Baryonic Models

We compare the substructure evolution in pure dark matter (DM) halos with those in the presence of baryons (PDM and BDM). The prime halos have been analyzed by Romano-Diaz et al (2009). Models have been evolved from identical initial conditions using Constrained Realizations, including star formation and feedback. A comprehensive catalog of subhalos has been compiled and properties of subhalos analyzed in the mass range of 10^8 Mo - 10^11 Mo. We find that subhalo mass functions are consistent with a single power law, M_sbh^{alpha}, but detect a nonnegligible shift between these functions, alpha -0.86 for the PDM, and -0.98 for the BDM. Overall, alpha const. in time with variations of +-15%. Second, we find that the radial mass distribution of subhalos can be approximated by a power law, R^{gamma} with a steepening around the radius of a maximal circular velocity, Rvmax, in the prime halos. Gamma ~-1.5 for the PDM and -1 for the BDM, inside Rvmax, and is steeper outside. We detect little spatial bias between the subhalo populations and the DM of the main halos. The subhalo population exhibits much less triaxiality with baryons, in tandem with the prime halo. Finally, we find that, counter-intuitively, the BDM population is depleted at a faster rate than the PDM one within the central 30kpc of the prime. Although the baryons provide a substantial glue to the subhalos, the main halos exhibit the same trend. This assures a more efficient tidal disruption of the BDM subhalos. This effect can be reversed for a more efficient feedback from stellar evolution and supermassive black holes, which will expel baryons from the center and decrease the concentration of the prime halo. We compare our results with via Lactea and Aquarius simulations and other published results.Comment: 12 pages, 9 figures, to be published by the Astrophysical Journa

The value of source data verification in a cancer clinical trial

Background Source data verification (SDV) is a resource intensive method of quality assurance frequently used in clinical trials. There is no empirical evidence to suggest that SDV would impact on comparative treatment effect results from a clinical trial. Methods Data discrepancies and comparative treatment effects obtained following 100% SDV were compared to those based on data without SDV. Overall survival (OS) and Progression-free survival (PFS) were compared using Kaplan-Meier curves, log-rank tests and Cox models. Tumour response classifications and comparative treatment Odds Ratios (ORs) for the outcome objective response rate, and number of Serious Adverse Events (SAEs) were compared. OS estimates based on SDV data were compared against estimates obtained from centrally monitored data. Findings Data discrepancies were identified between different monitoring procedures for the majority of variables examined, with some variation in discrepancy rates. There were no systematic patterns to discrepancies and their impact was negligible on OS, the primary outcome of the trial (HR (95% CI): 1.18(0.99 to 1.41), p = 0.064 with 100% SDV; 1.18(0.99 to 1.42), p = 0.068 without SDV; 1.18(0.99 to 1.40), p = 0.073 with central monitoring). Results were similar for PFS. More extreme discrepancies were found for the subjective outcome overall objective response (OR (95% CI): 1.67(1.04 to 2.68), p = 0.03 with 100% SDV; 2.45(1.49 to 4.04), p = 0.0003 without any SDV) which was mostly due to differing CT scans. Interpretation Quality assurance methods used in clinical trials should be informed by empirical evidence. In this empirical comparison, SDV was expensive and identified random errors that made little impact on results and clinical conclusions of the trial. Central monitoring using an external data source was a more efficient approach for the primary outcome of OS. For the subjective outcome objective response, an independent blinded review committee and tracking system to monitor missing scan data could be more efficient than SDV

Illuminating Choices for Library Prep: A Comparison of Library Preparation Methods for Whole Genome Sequencing of Cryptococcus neoformans Using Illumina HiSeq.

The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use

The effects of baryon physics, black holes and AGN feedback on the mass distribution in clusters of galaxies

The spatial distribution of matter in clusters of galaxies is mainly determined by the dominant dark matter component, however, physical processes involving baryonic matter are able to modify it significantly. We analyse a set of 500 pc resolution cosmological simulations of a cluster of galaxies with mass comparable to Virgo, performed with the AMR code RAMSES. We compare the mass density profiles of the dark, stellar and gaseous matter components of the cluster that result from different assumptions for the subgrid baryonic physics and galaxy formation processes. First, the prediction of a gravity only N-body simulation is compared to that of a hydrodynamical simulation with standard galaxy formation recipes, then all results are compared to a hydrodynamical simulation which includes thermal AGN feedback from Super Massive Black Holes (SMBH). We find the usual effects of overcooling and adiabatic contraction in the run with standard galaxy formation physics, but very different results are found when implementing SMBHs and AGN feedback. Star formation is strongly quenched, producing lower stellar densities throughout the cluster, and much less cold gas is available for star formation at low redshifts. At redshift z = 0 we find a flat density core of radius 10 kpc in both of the dark and stellar matter density profiles. We specu- late on the possible formation mechanisms able to produce such cores and we conclude that they can be produced through the coupling of different processes: (I) dynamical friction from the decay of black hole orbits during galaxy mergers; (II) AGN driven gas outflows producing fluctuations of the gravitational potential causing the removal of collisionless matter from the central region of the cluster; (III) adiabatic expansion in response to the slow expulsion of gas from the central region of the cluster during the quiescent mode of AGN activity.Comment: Published on MNRAS - 13 pages, 4 tables, 9 figure

The impact of a wireless audio system on communication in robotic-assisted laparoscopic surgery: A prospective controlled trial.

BACKGROUND: Robotic surgery presents a challenge to effective teamwork and communication in the operating theatre (OR). Our objective was to evaluate the effect of using a wireless audio headset device on communication, efficiency and patient outcome in robotic surgery. METHODS AND FINDINGS: A prospective controlled trial of team members participating in gynecologic and urologic robotic procedures between January and March 2015. In the first phase, all surgeries were performed without headsets (control), followed by the intervention phase where all team members used the wireless headsets. Noise levels were measured during both phases. After each case, all team members evaluated the quality of communication, performance, teamwork and mental load using a validated 14-point questionnaire graded on a 1-10 scale. Higher overall scores indicated better communication and efficiency. Clinical and surgical data of all patients in the study were retrieved, analyzed and correlated with the survey results. The study included 137 procedures, yielding 843 questionnaires with an overall response rate of 89% (843/943). Self-reported communication quality was better in cases where headsets were used (113.0 ± 1.6 vs. 101.4 ± 1.6; p \u3c .001). Use of headsets reduced the percentage of time with a noise level above 70 dB at the console (8.2% ± 0.6 vs. 5.3% ± 0.6, p \u3c .001), but had no significant effect on length of surgery nor postoperative complications. CONCLUSIONS: The use of wireless headset devices improved quality of communication between team members and reduced the peak noise level in the robotic OR

A Relationship between Supermassive Black Hole Mass and the Total Gravitational Mass of the Host Galaxy

We investigate the correlation between the mass of a central supermassive black hole and the total gravitational mass of the host galaxy (M_tot). The results are based on 43 galaxy-scale strong gravitational lenses from the Sloan Lens ACS (SLACS) Survey whose black hole masses were estimated through two scaling relations: the relation between black hole mass and Sersic index (M_bh - n) and the relation between black hole mass and stellar velocity dispersion (M_bh - sigma). We use the enclosed mass within R_200, the radius within which the density profile of the early type galaxy exceeds the critical density of the Universe by a factor of 200, determined by gravitational lens models fitted to HST imaging data, as a tracer of the total gravitational mass. The best fit correlation, where M_bh is determined from M_bh - sigma relation, is log(M_bh) = (8.18 +/- 0.11) + (1.55 +/- 0.31) (log(M_tot) - 13.0) over 2 orders of magnitude in M_bh. From a variety of tests, we find that we cannot reliably infer a connection between M_bh and M_tot from the M_bh - n relation. The M_bh - M_tot relation provides some of the first, direct observational evidence to test the prediction that supermassive black hole properties are determined by the halo properties of the host galaxy.Comment: 29 pages, 10 figures, Accepted for publication in Ap

Testing Models of Intrinsic Brightness Variations in Type Ia Supernovae, and their Impact on Measuring Cosmological Parameters

For spectroscopically confirmed Type Ia supernovae we evaluate models of intrinsic brightness variations with detailed data/Monte Carlo comparisons of the dispersion in the following quantities: Hubble-diagram scatter, color difference (B-V-c) between the true B-V color and the fitted color (c) from the SALT-II light curve model, and photometric redshift residual. The data sample includes 251 ugriz light curves from the 3-season Sloan Digital Sky Survey-II, and 191 griz light curves from the Supernova Legacy Survey 3-year data release. We find that the simplest model of a wavelength-independent (coherent) scatter is not adequate, and that to describe the data the intrinsic scatter model must have wavelength-dependent variations. We use Monte Carlo simulations to examine the standard approach of adding a coherent scatter term in quadrature to the distance-modulus uncertainty in order to bring the reduced chi2 to unity when fitting a Hubble diagram. If the light curve fits include model uncertainties with the correct wavelength dependence of the scatter, we find that the bias on the dark energy equation of state parameter $w$ is negligible. However, incorrect model uncertainties can lead to a significant bias on the distance moduli, with up to ~0.05 mag redshift-dependent variation. For the recent SNLS3 cosmology results we estimate that this effect introduces an additional systematic uncertainty on $w$ of ~0.02, well below the total uncertainty. However, this uncertainty depends on the samples used, and thus this small $w$-uncertainty is not guaranteed in future cosmology results.Comment: accepted by Ap

A hierarchy of voids: Much ado about nothing

We present a model for the distribution of void sizes and its evolution in the context of hierarchical scenarios of gravitational structure formation. We find that at any cosmic epoch the voids have a size distribution which is well-peaked about a characteristic void size which evolves self-similarly in time. This is in distinct contrast to the distribution of virialized halo masses which does not have a small-scale cut-off. In our model, the fate of voids is ruled by two processes. The first process affects those voids which are embedded in larger underdense regions: the evolution is effectively one in which a larger void is made up by the mergers of smaller voids, and is analogous to how massive clusters form from the mergers of less massive progenitors. The second process is unique to voids, and occurs to voids which happen to be embedded within a larger scale overdensity: these voids get squeezed out of existence as the overdensity collapses around them. It is this second process which produces the cut-off at small scales. In the excursion set formulation of cluster abundance and evolution, solution of the cloud-in-cloud problem, i.e., counting as clusters only those objects which are not embedded in larger clusters, requires study of random walks crossing one barrier. We show that a similar formulation of void evolution requires study of a two-barrier problem: one barrier is required to account for voids-in-voids, and the other for voids-in-clouds. Thus, in our model, the void size distribution is a function of two parameters, one of which reflects the dynamics of void formation, and the other the formation of collapsed objects.Comment: 23 pages, 9 figures, submitted to MNRA

Photometric Properties of Void Galaxies in the Sloan Digital Sky Survey DR7 Data Release

Using the sample presented in Pan:2011, we analyse the photometric properties of 88,794 void galaxies and compare them to galaxies in higher density environments with the same absolute magnitude distribution. In Pan et al. (2011), we found a total of 1054 dynamically distinct voids in the SDSS with radius larger than 10h^-1 Mpc. The voids are underdense, with delta rho/rho < -0.9 in their centers. Here we study the photometric properties of these void galaxies. We look at the u - r colours as an indication of star formation activity and the inverse concentration index as an indication of galaxy type. We find that void galaxies are statistically bluer than galaxies found in higher density environments with the same magnitude distribution. We examine the colours of the galaxies as a function of magnitude, and we fit each colour distribution with a double-Gaussian model for the red and blue subpopulations. As we move from bright to dwarf galaxies, the population of red galaxies steadily decreases and the fraction of blue galaxies increases in both voids and walls, however the fraction of blue galaxies in the voids is always higher and bluer than in the walls. We also split the void and wall galaxies into samples depending on galaxy type. We find that late type void galaxies are bluer than late type wall galaxies and the same holds for early galaxies. We also find that early type, dwarf void galaxies are blue in colour. We also study the properties of void galaxies as a function of their distance from the center of the void. We find very little variation in the properties, such as magnitude, colour and type, of void galaxies as a function of their location in the void. The only exception is that the dwarf void galaxies may live closer to the center. The centers of voids have very similar density contrast and hence all void galaxies live in very similar density environments (ABRIDGED)Comment: 10 pages, 25 figure