Challenges in clinical genomics

A report on the Genomic Disorders 2012: Genomics of Rare Diseases meeting, Hinxton, UK, 21-23 March 2012

Between Philosophy and Art

Similarity and difference, patterns of variation, consistency and coherence: these are the reference points of the philosopher. Understanding experience, exploring ideas through particular instantiations, novel and innovative thinking: these are the reference points of the artist. However, at certain points in the proceedings of our Symposium titled, Next to Nothing: Art as Performance, this characterisation of philosopher and artist respectively might have been construed the other way around. The commentator/philosophers referenced their philosophical interests through the particular examples/instantiations created by the artist and in virtue of which they were then able to engage with novel and innovative thinking. From the artists’ presentations, on the other hand, emerged a series of contrasts within which philosophical and artistic ideas resonated. This interface of philosopher-artist bore witness to the fact that just as art approaches philosophy in providing its own analysis, philosophy approaches art in being a co-creator of art’s meaning. In what follows, we discuss the conception of philosophy-art that emerged from the Symposium, and the methodological minimalism which we employed in order to achieve it. We conclude by drawing out an implication of the Symposium’s achievement which is that a counterpoint to Institutional theories of art may well be the point from which future directions will take hold, if philosophy-art gains traction

Scaling Relations of Spiral Galaxies

We construct a large data set of global structural parameters for 1300 field and cluster spiral galaxies and explore the joint distribution of luminosity L, optical rotation velocity V, and disk size R at I- and 2MASS K-bands. The I- and K-band velocity-luminosity (VL) relations have log-slopes of 0.29 and 0.27, respectively with sigma_ln(VL)~0.13, and show a small dependence on color and morphological type in the sense that redder, early-type disk galaxies rotate faster than bluer, later-type disk galaxies for most luminosities. The VL relation at I- and K-bands is independent of surface brightness, size and light concentration. The log-slope of the I- and K-band RL relations is a strong function of morphology and varies from 0.25 to 0.5. The average dispersion sigma_ln(RL) decreases from 0.33 at I-band to 0.29 at K, likely due to the 2MASS selection bias against lower surface brightness galaxies. Measurement uncertainties are sigma_ln(V)~0.09, sigma_ln(L)~0.14 and somewhat larger and harder to estimate for ln(R). The color dependence of the VL relation is consistent with expectations from stellar population synthesis models. The VL and RL residuals are largely uncorrelated with each other; the RV-RL residuals show only a weak positive correlation. These correlations suggest that scatter in luminosity is not a significant source of the scatter in the VL and RL relations. The observed scaling relations can be understood in the context of a model of disk galaxies embedded in dark matter halos that invokes low mean spin parameters and dark halo expansion, as we describe in our companion paper (Dutton et al. 2007). We discuss in two appendices various pitfalls of standard analytical derivations of galaxy scaling relations, including the Tully-Fisher relation with different slopes. (Abridged).Comment: Accepted for publication at ApJ. The full document, with high-resolution B&W and colour figures, is available at http://www.astro.queensu.ca/~courteau/papers/VRL2007ApJ.pdf . Our data base for 1303 spiral galaxies is also available at http://www.astro.queensu.ca/~courteau/data/VRL2007.da

Low-Surface-Brightness Galaxies in the Sloan Digital Sky Survey. I. Search Method and Test Sample

In this paper we present results of a pilot study to use imaging data from the Sloan Digital Sky Survey (SDSS) to search for low-surface-brightness (LSB) galaxies. For our pilot study we use a test sample of 92 galaxies from the catalog of Impey et al. (1996) distributed over 93 SDSS fields of the Early Data Release (EDR). Many galaxies from the test sample are either LSB or dwarf galaxies. To deal with the SDSS data most effectively a new photometry software was created, which is described in this paper. We present the results of the selection algorithms applied to these 93 EDR fields. Two galaxies from the Impey et al. test sample are very likely artifacts, as confirmed by follow-up imaging. With our algorithms, we were able to recover 87 of the 90 remaining test sample galaxies, implying a detection rate of $\sim$96.5%. The three missed galaxies fall too close to very bright stars or galaxies. In addition, 42 new galaxies with parameters similar to the test sample objects were found in these EDR fields (i.e., $\sim$47% additional galaxies). We present the main photometric parameters of all identified galaxies and carry out first statistical comparisons. We tested the quality of our photometry by comparing the magnitudes for our test sample galaxies and other bright galaxies with values from the literature. All these tests yielded consistent results. We briefly discuss a few unusual galaxies found in our pilot study, including an LSB galaxy with a two-component disk and ten new giant LSB galaxies.Comment: 36 pages, 16 figures, accepted for publication by AJ, some figures were bitmapped to reduce the siz

Do school crossing guards make crossing roads safer? A quasi-experimental study of pedestrian-motor vehicle collisions in Toronto, Canada

BACKGROUND: The presence of school crossing guards has been associated with more walking and more pedestrian-motor vehicle collisions (PMVCs) in area-level cross-sectional analyses. The objectives of the study were to (1) Determine the effect on PMVC rates of newly implemented crossing guards in Toronto, Canada (2) Determine where collisions were located in relation to crossing guards throughout the city, and whether they occurred during school travel times. METHODS: School crossing guards with 50 m buffers were mapped along with police-reported child PMVCs from 2000–2011. (1) A quasi-experimental study identified all age collision counts near newly implemented guards before and after implementation, modeled using repeated measures Poisson regression adjusted for season and built environment variables. (2) A retrospective cohort study of all child PMVCS throughout the city to determine the proportions of child PMVCs which occurred during school travel times and at guard locations. RESULTS: There were 27,827 PMVCs, with 260 PMVCs at the locations of 58 newly implemented guards. Repeated measures adjusted Poisson regression found PMVCs rates remained unchanged at guard locations after implementation (IRR 1.02, 95 % CI 0.74, 1.39). There were 568 guards citywide with 1850 child PMVCs that occurred at guard locations. The majority of child PMVCs occurred outside school travel times (n = 1155, 62 %) and of those that occurred during school travel times, only 95 (13.7 %) were at a guard location. CONCLUSIONS: School crossing guards are a simple roadway modification to increase walking to school without apparent detrimental safety effects. Other more permanent interventions are necessary to address the frequency of child PMVCs occurring away from the location of crossing guards, and outside of school travel times

Biology of Genomes: making sense of sequence

A report on the Biology of Genomes meeting held at Cold Spring Harbor Laboratory, NY, USA, 5-9 May 2009

The species-area relationship and evolution

Models relating to the Species-Area curve are usually defined at the species level, and concerned only with ecological timescales. We examine an individual-based model of co-evolution on a spatial lattice based on the Tangled Nature model, and show that reproduction, mutation and dispersion by diffusion in an interacting system produces power-law Species-Area Relations as observed in ecological measurements at medium scales. We find that co-evolutionary habitats form, allowing high diversity levels in a spatially homogenous system, and these are maintained for exponentially increasing time when increasing system size.Comment: 21 pages, 5 figures. This is the final, accepted draf

The ACS Nearby Galaxy Survey Treasury VI. The Ancient Star Forming disk of NGC 404

We present HST/WFPC2 observations across the disk of the nearby isolated dwarf S0 galaxy NGC 404, which hosts an extended gas disk. Our deepest field reaches the red clump and main-sequence stars with ages <500 Myr. Although we detect trace amounts of star formation at times more recent than 10 Gyr for all fields, the proportion of red giant stars to asymptotic giants and main sequence stars suggests that the disk is dominated by an ancient (>10 Gyr) population. Detailed modeling of the color-magnitude diagram suggests that ~70% of the stellar mass in the NGC 404 disk formed by z~2 (10 Gyr ago) and at least ~90% formed prior to z~1 (8 Gyr ago). These results indicate that the stellar populations of the NGC 404 disk are on average significantly older than those of other nearby disk galaxies, suggesting that early and late type disks may have different long-term evolutionary histories, not simply differences in their recent star formation rates. Comparisons of the spatial distribution of the young stellar mass and FUV emission in GALEX images show that the brightest FUV regions contain the youngest stars, but that some young stars (<160 Myr) lie outside of these regions. FUV luminosity appears to be strongly affected by both age and stellar mass within individual regions. Finally, we use our measurements to infer the relationship between the star formation rate and the gas density of the disk at previous epochs. We find that most of the history of the NGC 404 disk is consistent with star formation that has decreased with the gas density according to the Schmidt law. However, 0.5-1 Gyr ago, the star formation rate was unusually low for the inferred gas density, consistent with the possibility that there was a gas accretion event that reignited star formation ~0.5 Gyr ago. Such an event could explain why this S0 galaxy hosts an extended gas disk.Comment: 28 pages, 20 figures, 1 table, accepted for publication in Ap

Quantifying unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects

As new proposals aim to sequence ever larger collection of humans, it is critical to have a quantitative framework to evaluate the statistical power of these projects. We developed a new algorithm, UnseenEst, and applied it to the exomes of 60,706 individuals to estimate the frequency distribution of all protein-coding variants, including rare variants that have not been observed yet in the current cohorts. Our results quantified the number of new variants that we expect to identify as sequencing cohorts reach hundreds of thousands of individuals. With 500K individuals, we find that we expect to capture 7.5% of all possible loss-of-function variants and 12% of all possible missense variants. We also estimate that 2,900 genes have loss-of-function frequency of <0.00001 in healthy humans, consistent with very strong intolerance to gene inactivation.United States. National Institutes of Health (U54DK105566)United States. National Institutes of Health (R01GM104371