Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model.

A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. The inference of selection may be confounded by the effects of genetic drift in a system, leading to the development of inference procedures to account for these effects. However, recent work has suggested that deterministic models of evolution may be effective in capturing the effects of selection even under complex models of demography, suggesting the more general application of deterministic approaches to inference. Responding to this literature, we here note a case in which a deterministic model of evolution may give highly misleading inferences, resulting from the nondeterministic properties of mutation in a finite population. We propose an alternative approach that acts to correct for this error, and which we denote the delay-deterministic model. Applying our model to a simple evolutionary system, we demonstrate its performance in quantifying the extent of selection acting within that system. We further consider the application of our model to sequence data from an evolutionary experiment. We outline scenarios in which our model may produce improved results for the inference of selection, noting that such situations can be easily identified via the use of a regular deterministic model

Distant red galaxies in the Hubble Ultra Deep Field

We take advantage of the Hubble Ultra Deep Field (UDF) data to study the restframe optical and ultra violet (UV) morphologies of the novel population of Distant Red Galaxies (DRGs). Six galaxies with J-Ks > 2.3 are found to Ks=21.5, five of which have photometric redshifts z_phot > 2, corresponding to a surface density of 0.9/arcmin^2. The surface brightness distributions of the z_phot > 2 galaxies are better represented by exponential disks than R^{1/4}-laws. Two of the z_phot > 2 galaxies are extended, while three have compact morphologies. The restframe optical morphology of the z_phot > 2 galaxies is quite different from the restframe UV morphology: all the galaxies have red central components which dominate in the NICMOS H_{160}-band images, and distinct off-center blue features which show up in (and often dominate) the ACS images. The mean measured effective radius of the z_phot > 2 galaxies is =1.9+/-1.4 kpc, similar (within the errors) to the mean size of LBGs at similar redshifts. All the DRGs are resolved in the ACS images, while four are resolved in the NICMOS images. Two of the z_phot > 2 galaxies are bright X-ray sources and hence host AGN. The diverse restframe optical and UV morphological properties of DRGs derived here suggest that they have complex stellar populations, consisting of both evolved populations that dominate the mass and the restframe optical light, and younger populations, which show up as patches of star formation in the restframe UV light; in many ways resembling the properties of normal local galaxies. This interpretation is supported by fits to the broadband SEDs, which for all five z_phot > 2 are best represented by models with extended star formation histories and substantial amounts of dust.Comment: Accepted for publication in APJ

Evidence that digital game players neglect age classification systems when deciding which games to play

This article considers players’ experiences seeking out new games to play, and their use of the Australian National Classification Scheme in doing so. The global video game industry is booming, with hundreds of games being released each month across numerous platforms. As a result, players have an unprecedented number of games available when choosing what games to purchase. However, a number of confounding issues around the emergent content of games and the subjective nature of game reviewing makes it difficult to relate what kinds of experiences a given game will facilitate. In this study, we surveyed game players in order to find their game platform and acquisition preferences; strategies and experiences when choosing games; and attitudes towards classification systems. Our findings suggest that players find it difficult to choose what games to purchase, and that existing classification systems are mostly only beneficial when choosing games for minors

The GREATS Hβ\beta+[OIII] Luminosity Function and Galaxy Properties at z∼8\mathbf{z\sim8}: Walking the Way of JWST

The James Webb Space Telescope will allow to spectroscopically study an unprecedented number of galaxies deep into the reionization era, notably by detecting [OIII] and H$\beta$ nebular emission lines. To efficiently prepare such observations, we photometrically select a large sample of galaxies at $z\sim8$ and study their rest-frame optical emission lines. Combining data from the GOODS Re-ionization Era wide-Area Treasury from Spitzer (GREATS) survey and from HST, we perform spectral energy distribution (SED) fitting, using synthetic SEDs from a large grid of photoionization models. The deep Spitzer/IRAC data combined with our models exploring a large parameter space enables to constrain the [OIII]+H$\beta$ fluxes and equivalent widths for our sample, as well as the average physical properties of $z\sim8$ galaxies, such as the ionizing photon production efficiency with $\log(\xi_\mathrm{ion}/\mathrm{erg}^{-1}\hspace{1mm}\mathrm{Hz})\geq25.77$. We find a relatively tight correlation between the [OIII]+H$\beta$ and UV luminosity, which we use to derive for the first time the [OIII]+H$\beta$ luminosity function (LF) at $z\sim8$. The $z\sim8$ [OIII]+H$\beta$ LF is higher at all luminosities compared to lower redshift, as opposed to the UV LF, due to an increase of the [OIII]+H$\beta$ luminosity at a given UV luminosity from $z\sim3$ to $z\sim8$. Finally, using the [OIII]+H$\beta$ LF, we make predictions for JWST/NIRSpec number counts of $z\sim8$ galaxies. We find that the current wide-area extragalactic legacy fields are too shallow to use JWST at maximal efficiency for $z\sim8$ spectroscopy even at 1hr depth and JWST pre-imaging to $\gtrsim30$ mag will be required.Comment: 13 pages, 9 figures, accepted for publication in MNRA

The Impact of Strong Gravitational Lensing on Observed Lyman-Break Galaxy Numbers at 4<z<8 in the GOODS and the XDF Blank Fields

Detection of Lyman-Break Galaxies (LBGs) at high-redshift can be affected by gravitational lensing induced by foreground deflectors not only in galaxy clusters, but also in blank fields. We quantify the impact of strong magnification in the samples of $B$, $V$, $i$, $z$ $\&$ $Y$ LBGs ($4\lesssim z \lesssim8$) observed in the XDF and GOODS/CANDELS fields, by investigating the proximity of dropouts to foreground objects. We find that $\sim6\%$ of bright LBGs ($m_{H_{160}}2$) by foreground objects. This fraction decreases from $\sim 3.5\%$ at $z\sim6$ to $\sim1.5\%$ at $z\sim4$. Since the observed fraction of strongly lensed galaxies is a function of the shape of the luminosity function (LF), it can be used to derive Schechter parameters, $\alpha$ and $M_{\star}$, independently from galaxy number counts. Our magnification bias analysis yields Schechter-function parameters in close agreement with those determined from galaxy counts albeit with larger uncertainties. Extrapolation of our analysis to $z\gtrsim 8$ suggests that future surveys with JSWT, WFIRST and EUCLID should find excess LBGs at the bright-end, even if there is an intrinsic exponential cutoff of number counts. Finally, we highlight how the magnification bias measurement near the detection limit can be used as probe of the population of galaxies too faint to be detected. Preliminary results using this novel idea suggest that the magnification bias at $M_{UV}\sim -18$ is not as strong as expected if $\alpha\lesssim -1.7$ extends well below the current detection limits in the XDF. At face value this implies a flattening of the LF at $M_{UV}\gtrsim-16.5$. However, selection effects and completeness estimates are difficult to quantify precisely. Thus, we do not rule out a steep LF extending to $M_{UV}\gtrsim -15$.Comment: Submitted to ApJ on 18/12/201

Imprints of Environment on Cluster and Field Late-type Galaxies at z~1

We present a comparison of late-type galaxies (Sa and later) in intermediate redshift clusters and the field using ACS imaging of four cluster fields: CL0152-1357, CL1056-0337 (MS1054), CL1604+4304, and CL1604+4321. Concentration, asymmetry, and clumpiness parameters are calculated for each galaxy in blue (F606W or F625W) and red (F775W or F814W) filters. Galaxy half-light radii, disk scale lengths, color gradients, and overall color are compared. We find marginally significant differences in the asymmetry distributions of spiral and irregular galaxies in the X-ray luminous and X-ray faint clusters. The massive clusters contain fewer galaxies with large asymmetries. The physical sizes of the cluster and field populations are similar; no significant differences are found in half-light radii or disk scale lengths. The most significant difference is in rest-frame $U-B$ color. Late-type cluster galaxies are significantly redder, $\sim 0.3$ magnitudes at rest-frame $U-B$, than their field counterparts. Moreover, the intermediate-redshift cluster galaxies tend to have blue inward color gradients, in contrast to the field galaxies, but similar to late-type galaxies in low redshift clusters. These blue inward color gradients are likely to be the result of enhanced nuclear star formation rates relative to the outer disk. Based on the significant rest-frame color difference, we conclude that late-type cluster members at $z\sim0.9$ are not a pristine infalling field population; some difference in past and/or current star formation history is already present. This points to high redshift ``groups'', or filaments with densities similar to present-day groups, as the sites where the first major effects of environment are imprinted.Comment: updated titl

First Frontier Field Constraints on the Cosmic Star-Formation Rate Density at z~10 - The Impact of Lensing Shear on Completeness of High-Redshift Galaxy Samples

We search the complete Hubble Frontier Field dataset of Abell 2744 and its parallel field for z~10 sources to further refine the evolution of the cosmic star-formation rate density (SFRD) at z>8. We independently confirm two images of the recently discovered triply-imaged z~9.8 source by Zitrin et al. (2014) and set an upper limit for similar z~10 galaxies with red colors of J_125-H_160>1.2 in the parallel field of Abell 2744. We utilize extensive simulations to derive the effective selection volume of Lyman-break galaxies at z~10, both in the lensed cluster field and in the adjacent parallel field. Particular care is taken to include position-dependent lensing shear to accurately account for the expected sizes and morphologies of highly-magnified sources. We show that both source blending and shear reduce the completeness at a given observed magnitude in the cluster, particularly near the critical curves. These effects have a significant, but largely overlooked, impact on the detectability of high-redshift sources behind clusters, and substantially reduce the expected number of highly-magnified sources. The detections and limits from both pointings result in a SFRD which is higher by 0.4+-0.4 dex than previous estimates at z~10 from blank fields. Nevertheless, the combination of these new results with all other estimates remain consistent with a rapidly declining SFRD in the 170 Myr from z~8 to z~10 as predicted by cosmological simulations and dark-matter halo evolution in LambdaCDM. Once biases introduced by magnification-dependent completeness are accounted for, the full six cluster and parallel Frontier Field program will be an extremely powerful new dataset to probe the evolution of the galaxy population at z>8 before the advent of the JWST.Comment: 10 pages, 7 figures, changed to match accepted version to appear in Ap

z~2-9 Galaxies Magnified by the Hubble Frontier Field Clusters II: Luminosity Functions and Constraints on a Faint-End Turnover

We present new determinations of the rest-UV luminosity functions (LFs) at z=2-9 to extremely low luminosities (>-14 mag) from a sample of >2500 lensed galaxies found behind the HFF clusters. For the first time, we present faint-end slope results from lensed samples that are fully consistent with blank-field results over the redshift range z=2-9, while reaching to much lower luminosities than possible from the blank-field studies. Combining the deep lensed sample with the large blank-field samples allows us to set the tight constraints on the faint-end slope alpha of the z=2-9 UV LFs and its evolution. We find a smooth flattening in alpha from -2.28+/-0.10 (z=9) to -1.53+/-0.03 (z=2) with cosmic time (d(alpha)/dz=-0.11+/-0.01), fully consistent with dark matter halo buildup. We utilize these new results to present new measurements of the evolution in the UV luminosity density rho(UV) brightward of -13 mag from z~9 to z~2. Accounting for the SFR densities to faint luminosities implied by our LF results, we find that unobscured star formation dominates the SFR density at z>~4, with obscured star formation dominant thereafter. Having shown we can quantify the faint-end slope alpha of the LF accurately with our lensed HFF samples, we also quantify the apparent curvature in the shape of the UV LF through a curvature parameter delta. The constraints on the curvature delta strongly rule out the presence of a turn-over brightward of -13.1 mag at z~3, -14.3 mag at z~6, and -15.5 mag at all other redshifts between z~9 to z~2.Comment: 31 pages, 16 figures, 7 tables, in submission to AAS Journals, including some minor updates based on feedback we have received from the communit

Assessing the effect of dynamics on the closed-loop protein-folding hypothesis

The closed-loop (loop-n-lock) hypothesis of protein folding suggests that loops of about 25 residues, closed through interactions between the loop ends (locks), play an important role in protein structure. Coarse-grain elastic network simulations, and examination of loop lengths in a diverse set of proteins, each supports a bias towards loops of close to 25 residues in length between residues of high stability. Previous studies have established a correlation between total contact distance (TCD), a metric of sequence distances between contacting residues (cf. contact order), and the log-folding rate of a protein. In a set of 43 proteins, we identify an improved correlation ( r 2 = 0.76), when the metric is restricted to residues contacting the locks, compared to the equivalent result when all residues are considered ( r 2 = 0.65). This provides qualified support for the hypothesis, albeit with an increased emphasis upon the importance of a much larger set of residues surrounding the locks. Evidence of a similar-sized protein core/extended nucleus (with significant overlap) was obtained from TCD calculations in which residues were successively eliminated according to their hydrophobicity and connectivity, and from molecular dynamics simulations. Our results suggest that while folding is determined by a subset of residues that can be predicted by application of the closed-loop hypothesis, the original hypothesis is too simplistic; efficient protein folding is dependent on a considerably larger subset of residues than those involved in lock formation. </jats:p