Showing papers by "University of California, Santa Cruz published in 2006"

A meta-analytic test of intergroup contact theory.

Abstract: The present article presents a meta-analytic test of intergroup contact theory. With 713 independent samples from 515 studies, the meta-analysis finds that intergroup contact typically reduces intergroup prejudice. Multiple tests indicate that this finding appears not to result from either participant selection or publication biases, and the more rigorous studies yield larger mean effects. These contact effects typically generalize to the entire outgroup, and they emerge across a broad range of outgroup targets and contact settings. Similar patterns also emerge for samples with racial or ethnic targets and samples with other targets. This result suggests that contact theory, devised originally for racial and ethnic encounters, can be extended to other groups. A global indicator of Allport's optimal contact conditions demonstrates that contact under these conditions typically leads to even greater reduction in prejudice. Closer examination demonstrates that these conditions are best conceptualized as an interrelated bundle rather than as independent factors. Further, the meta-analytic findings indicate that these conditions are not essential for prejudice reduction. Hence, future work should focus on negative factors that prevent intergroup contact from diminishing prejudice as well as the development of a more comprehensive theory of intergroup contact.

Geant4 developments and applications

Abstract: Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Its functionality and modeling capabilities continue to be extended, while its performance is enhanced. An overview of recent developments in diverse areas of the toolkit is presented. These include performance optimization for complex setups; improvements for the propagation in fields; new options for event biasing; and additions and improvements in geometry, physics processes and interactive capabilities

The 2.5 m Telescope of the Sloan Digital Sky Survey

Abstract: We describe the design, construction, and performance of the Sloan Digital Sky Survey telescope located at Apache Point Observatory. The telescope is a modified two-corrector Ritchey-Chretien design with a 2.5 m, f/2.25 primary, a 1.08 m secondary, a Gascoigne astigmatism corrector, and one of a pair of interchangeable highly aspheric correctors near the focal plane, one for imaging and the other for spectroscopy. The final focal ratio is f/5. The telescope is instrumented by a wide-area, multiband CCD camera and a pair of fiber-fed double spectrographs. Novel features of the telescope include the following: (1) A 3° diameter (0.65 m) focal plane that has excellent image quality and small geometric distortions over a wide wavelength range (3000-10,600 A) in the imaging mode, and good image quality combined with very small lateral and longitudinal color errors in the spectroscopic mode. The unusual requirement of very low distortion is set by the demands of time-delay-and-integrate (TDI) imaging. (2) Very high precision motion to support open-loop TDI observations. (3) A unique wind baffle/enclosure construction to maximize image quality and minimize construction costs. The telescope had first light in 1998 May and began regular survey operations in 2000.

Ceph: a scalable, high-performance distributed file system

Abstract: We have developed Ceph, a distributed file system that provides excellent performance, reliability, and scalability. Ceph maximizes the separation between data and metadata management by replacing allocation tables with a pseudo-random data distribution function (CRUSH) designed for heterogeneous and dynamic clusters of unreliable object storage devices (OSDs). We leverage device intelligence by distributing data replication, failure detection and recovery to semi-autonomous OSDs running a specialized local object file system. A dynamic distributed metadata cluster provides extremely efficient metadata management and seamlessly adapts to a wide range of general purpose and scientific computing file system workloads. Performance measurements under a variety of workloads show that Ceph has excellent I/O performance and scalable metadata management, supporting more than 250,000 metadata operations per second.

The UCSC Genome Browser Database: update 2006

Abstract: The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

A Tour of Subriemannian Geometries, Their Geodesics and Applications

Abstract: Geodesics in subriemannian manifolds: Dido meets Heisenberg Chow's theorem: Getting from A to B A remarkable horizontal curve Curvature and nilpotentization Singular curves and geodesics A zoo of distributions Cartan's approach The tangent cone and Carnot groups Discrete groups tending to Carnot geometries Open problems Mechanics and geometry of bundles: Metrics on bundles Classical particles in Yang-Mills fields Quantum phases Falling, swimming, and orbiting Appendices: Geometric mechanics Bundles and the Hopf fibration The Sussmann and Ambrose-Singer theorems Calculus of the endpoint map and existence of geodesics Bibliography Index.

The fourth data release of the Sloan Digital Sky Survey

Abstract: This paper describes the Fourth Data Release of the Sloan Digital Sky Survey (SDSS), including all survey-quality data taken through 2004 June. The data release includes five-band photometric data for 180 million objects selected over 6670 deg2 and 673,280 spectra of galaxies, quasars, and stars selected from 4783 deg2 of those imaging data using the standard SDSS target selection algorithms. These numbers represent a roughly 27% increment over those of the Third Data Release; all the data from previous data releases are included in the present release. The Fourth Data Release also includes an additional 131,840 spectra of objects selected using a variety of alternative algorithms, to address scientific issues ranging from the kinematics of stars in the Milky Way thick disk to populations of faint galaxies and quasars.

Catalog of nearby exoplanets

Abstract: We present a catalog of nearby exoplanets. It contains the 172 known low-mass companions with orbits established through radial velocity and transit measurements around stars within 200 pc. We include five previously unpublished exoplanets orbiting the stars HD 11964, HD 66428, HD 99109, HD 107148, and HD 164922. We update orbits for 83 additional exoplanets, including many whose orbits have not been revised since their announcement, and include radial velocity time series from the Lick, Keck, and Anglo-Australian Observatory planet searches. Both these new and previously published velocities are more precise here due to improvements in our data reduction pipeline, which we applied to archival spectra. We present a brief summary of the global properties of the known exoplanets, including their distributions of orbital semimajor axis, minimum mass, and orbital eccentricity.

The Progenitor stars of gamma-ray bursts

Abstract: Those massive stars that give rise to gamma-ray bursts (GRBs) during their deaths must be endowed with an unusually large amount of angular momentum in their inner regions, 1-2 orders of magnitude greater than the ones that make common pulsars. Yet the inclusion of mass loss and angular momentum transport by magnetic torques during the precollapse evolution is known to sap the core of the necessary rotation. Here we explore the evolution of very rapidly rotating massive stars, including stripped-down helium cores that might result from mergers or mass transfer in a binary, and single stars that rotate unusually rapidly on the main sequence. For the highest possible rotation rates (about 400 km s-1), a novel sort of evolution is encountered in which single stars mix completely on the main sequence, never becoming red giants. Such stars, essentially massive "blue stragglers," produce helium-oxygen cores that rotate unusually rapidly. Such stars might comprise roughly 1% of all stars above 10 M☉ and can, under certain circumstances, retain enough angular momentum to make GRBs. Because this possibility is very sensitive to mass loss, GRBs are much more probable in regions of low metallicity.

An Extension of the Blinder-Oaxaca Decomposition Technique to Logit and Probit Models

Abstract: The Blinder-Oaxaca decomposition technique is widely used to identify and quantify the separate contributions of group differences in measurable characteristics, such as education, experience, marital status, and geographical differences to racial and gender gaps in outcomes. The technique cannot be used directly, however, if the outcome is binary and the coefficients are from a logit or probit model. I describe a relatively simple method of performing a decomposition that uses estimates from a logit or probit model. Expanding on the original application of the technique in Fairlie (1999), I provide a more thorough discussion of how to apply the technique, an analysis of the sensitivity of the decomposition estimates to different parameters, and the calculation of standard errors.

The Field of Streams: Sagittarius and its Siblings

Abstract: We use Sloan Digital Sky Survey (SDSS) Data Release 5 (DR5) u, g, r, i, z photometry to study Milky Way halo substructure in the area around the north Galactic cap. A simple color cut (g - r < 0.4) reveals the tidal stream of the Sagittarius dwarf spheroidal galaxy, as well as a number of other stellar structures in the field. Two branches (A and B) of the Sagittarius stream are clearly visible in an RGB composite image created from three magnitude slices, and there is also evidence for a still more distant wrap behind the A branch. A comparison of these data with numerical models suggests that the shape of the Galactic dark halo is close to spherical.

Long γ-ray bursts and core-collapse supernovae have different environments

Abstract: When massive stars exhaust their fuel, they collapse and often produce the extraordinarily bright explosions known as core-collapse supernovae. On occasion, this stellar collapse also powers an even more brilliant relativistic explosion known as a long-duration γ-ray burst. One would then expect that these long γ-ray bursts and core-collapse supernovae should be found in similar galactic environments. Here we show that this expectation is wrong. We find that the γ-ray bursts are far more concentrated in the very brightest regions of their host galaxies than are the core-collapse supernovae. Furthermore, the host galaxies of the long γ-ray bursts are significantly fainter and more irregular than the hosts of the core-collapse supernovae. Together these results suggest that long-duration γ-ray bursts are associated with the most extremely massive stars and may be restricted to galaxies of limited chemical evolution. Our results directly imply that long γ-ray bursts are relatively rare in galaxies such as our own Milky Way.

An RNA gene expressed during cortical development evolved rapidly in humans

Abstract: The developmental and evolutionary mechanisms behind the emergence of human-specific brain features remain largely unknown. However, the recent ability to compare our genome to that of our closest relative, the chimpanzee, provides new avenues to link genetic and phenotypic changes in the evolution of the human brain. We devised a ranking of regions in the human genome that show significant evolutionary acceleration. Here we report that the most dramatic of these 'human accelerated regions', HAR1, is part of a novel RNA gene (HAR1F) that is expressed specifically in Cajal-Retzius neurons in the developing human neocortex from 7 to 19 gestational weeks, a crucial period for cortical neuron specification and migration. HAR1F is co-expressed with reelin, a product of Cajal-Retzius neurons that is of fundamental importance in specifying the six-layer structure of the human cortex. HAR1 and the other human accelerated regions provide new candidates in the search for uniquely human biology.

Extragalactic Globular Clusters and Galaxy Formation

Abstract: Globular cluster (GC) systems have now been studied in galaxies ranging from dwarfs to giants and spanning the full Hubble sequence of morphological types. Imaging and spectroscopy with the Hubble Space Telescope and large ground-based telescopes have together established that most galaxies have bimodal color distributions that reflect two subpopulations of old GCs: metal-poor and metal-rich. The characteristics of both subpopulations are correlated with those of their parent galaxies. We argue that metal-poor GCs formed in low-mass dark matter halos in the early universe and that their properties reflect biased galaxy assembly. The metal-rich GCs were born in the subsequent dissipational buildup of their parent galaxies and their ages and abundances indicate that most massive early-type galaxies formed the bulk of their stars at early times. Detailed studies of both subpopulations offer some of the strongest constraints on hierarchical galaxy formation that can be obtained in the near-field.

Thermal conductivity reduction and thermoelectric figure of merit increase by embedding nanoparticles in crystalline semiconductors.

Abstract: Atomic substitution in alloys can efficiently scatter phonons, thereby reducing the thermal conductivity in crystalline solids to the "alloy limit." Using In0.53Ga0.47As containing ErAs nanoparticles, we demonstrate thermal conductivity reduction by almost a factor of 2 below the alloy limit and a corresponding increase in the thermoelectric figure of merit by a factor of 2. A theoretical model suggests that while point defects in alloys efficiently scatter short-wavelength phonons, the ErAs nanoparticles provide an additional scattering mechanism for the mid-to-long-wavelength phonons.

Biotic interactions and plant invasions

Abstract: Introduced plant populations lose interactions with enemies, mutualists and competitors from their native ranges, and gain interactions with new species, under new abiotic conditions. From a biogeographical perspective, differences in the assemblage of interacting species, as well as in abiotic conditions, may explain the demographic success of the introduced plant populations relative to conspecifics in their native range. Within invaded communities, the new interactions and conditions experienced by the invader may influence both its demographic success and its effects on native biodiversity. Here, we examine indirect effects involving enemies, mutualists and competitors of introduced plants, and effects of abiotic conditions on biotic interactions. We then synthesize ideas building on Darwin’s idea that the kinds of new interactions gained by an introduced population will depend on its relatedness to native populations. This yields a heuristic framework to explain how biotic interactions and abiotic conditions influence invader success. We conclude that species introductions generally alter plants interactions with enemies, mutualists and competitors, and that there is increasing evidence that these altered interactions jointly influence the success of introduced populations. Ecology Letters (2006) 9: 726‐740

Robust rendezvous for mobile autonomous agents via proximity graphs in arbitrary dimensions

Abstract: This paper presents coordination algorithms for networks of mobile autonomous agents. The objective of the proposed algorithms is to achieve rendezvous, that is, agreement over the location of the agents in the network. We provide analysis and design results for multiagent networks in arbitrary dimensions under weak requirements on the switching and failing communication topology. The novel correctness proof relies on proximity graphs and their properties and on a general LaSalle invariance principle for nondeterministic discrete-time dynamical systems

The mass assembly history of field galaxies: detection of an evolving mass limit for star forming galaxies

Abstract: We characterize the mass-dependent evolution of more than 8000 galaxies using spectroscopic redshifts from the DEEP2 Galaxy Redshift Survey in the range 0.4 < z < 1.4 and stellar masses calculated from K-band photometry obtained at Palomar Observatory. This sample spans more than 1.5 deg^2 in four independent fields. Using rest-frame U - B color and [O II] equivalent widths, we distinguish star-forming from passive populations in order to explore the nature of "downsizing"—a pattern in which the sites of active star formation shift from high-mass galaxies at early times to lower mass systems at later epochs. We identify a mass limit, M_Q, above which star formation appears to be quenched and show that the physical mechanisms responsible for downsizing can thus be empirically quantified by charting the evolution in this threshold mass. We find that M_Q decreases with time by a factor of ~3 across our redshift range according to M_Q α (1 + z)^(3.5). To further constrain possible quenching mechanisms, we investigate how downsizing depends on local galaxy environment using the projected third-nearest-neighbor statistic D_(p,3). For the majority of galaxies near the median density, there is no significant correlation between downsizing and environment. However, a trend is observed in the comparison between environments that are more than 3 times overdense or underdense relative to the median. Here, downsizing appears accelerated in overdense regions that host higher numbers of massive, early-type galaxies as compared to the underdense regions. Our results significantly constrain recent suggestions for the origin of downsizing and indicate that the process for quenching star formation must, primarily, be internally driven

Late Quaternary Extinctions: State of the Debate

Abstract: Between fifty and ten thousand years ago, most large mammals became extinct everywhere except Africa. Slow-breeding animals also were hard hit, regardless of size. This unusual extinction of large and slow-breeding animals provides some of the strongest support for a human contribution to their extinction and is consistent with various human hunting models, but it is difficult to explain by models relying solely on environmental change. It is an oversimplification, however, to say that a wave of hunting-induced extinctions swept continents immediately after first human contact. Results from recent studies suggest that humans precipitated extinction in many parts of the globe through combined direct (hunting) and perhaps indirect (competition, habitat alteration) impacts, but that the timing and geography of extinction might have been different and the worldwide magnitude less, had not climatic change coincided with human impacts in many places.

Empirical Models for Dark Matter Halos. I. Nonparametric Construction of Density Profiles and Comparison with Parametric Models

Abstract: We use techniques from nonparametric function estimation theory to extract the density profiles, and their derivatives, from a set of N-body dark matter halos. We consider halos generated from ΛCDM simulations of gravitational clustering, as well as isolated spherical collapses. The logarithmic density slopes γ ≡ d log ρ/d log r of the ΛCDM halos are found to vary as power laws in radius, reaching values of γ ≈ -1 at the innermost resolved radii, ~10-2rvir. This behavior is significantly different from that of broken-power-law models like the Navarro-Frenk-White (NFW) profile but similar to that of models like de Vaucouleurs's. Accordingly, we compare the N-body density profiles with various parametric models to find which provide the best fit. We consider an NFW-like model with arbitrary inner slope; Dehnen & McLaughlin's anisotropic model; Einasto's model (identical in functional form to Sersic's model but fitted to the space density); and the density model of Prugniel & Simien that was designed to match the deprojected form of Sersic's R1/n law. Overall, the best-fitting model to the ΛCDM halos is Einasto's, although the Prugniel-Simien and Dehnen-McLaughlin models also perform well. With regard to the spherical-collapse halos, both the Prugniel-Simien and Einasto models describe the density profiles well, with an rms scatter some 4 times smaller than that obtained with either the NFW-like model or the three-parameter Dehnen-McLaughlin model. Finally, we confirm recent claims of a systematic variation in profile shape with halo mass.

The shape of dark matter haloes : dependence on mass, redshift, radius and formation

Abstract: Using six high-resolution dissipationless simulations with a varying box size in a flat Lambda cold dark matter (ACDM) universe, we study the mass and redshift dependence of dark matter halo shapes for M vir = 9.0 x 10" - 2.0 x 10 14 h -1 M ⊙ , over the redshift range z = 0-3, and for two values of σ 8 = 0.75 and 0.9. Remarkably, we find that the redshift, mass and σ 8 dependence of the mean smallest-to-largest axis ratio of haloes is well described by the simple power-law relation (s) = (0.54 ± 0.02)(M vir /M * ) -0.050±0.003 , where s is measured at 0.3R vir , and the z and σ 8 dependences are governed by the characteristic non-linear mass, M * = M * (z, σ 8 ). We find that the scatter about the mean s is well described by a Gaussian with a ∼ 0.1, for all masses and redshifts. We compare our results to a variety of previous works on halo shapes and find that reported differences between studies are primarily explained by differences in their methodologies. We address the evolutionary aspects of individual halo shapes by following the shapes of the haloes through ∼100 snapshots in time. We determine the formation scalefactor a c as defined by Wechsler et al. and find that it can be related to the halo shape at z = 0 and its evolution over time.

An optical supernova associated with the X-ray flash XRF 060218.

Abstract: Long-duration gamma-ray bursts (GRBs) are associated with type Ic supernovae(1) that are more luminous than average(2-5) and that eject material at very high velocities. Less-luminous supernovae were not hitherto known to be associated with GRBs, and therefore GRB - supernovae were thought to be rare events(6). Whether X-ray flashes - analogues of GRBs, but with lower luminosities and fewer gamma-rays - can also be associated with supernovae, and whether they are intrinsically 'weak' events or typical GRBs viewed off the axis of the burst(7), is unclear. Here we report the optical discovery and follow-up observations of the type Ic supernova SN 2006aj associated with X-ray flash XRF 060218. Supernova 2006aj is intrinsically less luminous than the GRB - supernovae, but more luminous than many supernovae not accompanied by a GRB. The ejecta velocities derived from our spectra are intermediate between these two groups, which is consistent with the weakness of both the GRB output(8) and the supernova radio flux(9). Our data, combined with radio and X-ray observations(8-10), suggest that XRF 060218 is an intrinsically weak and soft event, rather than a classical GRB observed off-axis. This extends the GRB - supernova connection to X-ray flashes and fainter supernovae, implying a common origin. Events such as XRF 060218 are probably more numerous than GRB - supernovae.

The determinants of the global digital divide: a cross-country analysis of computer and internet penetration

Abstract: To identify the determinants of cross-country disparities in personal computer and Internet penetration, we examine a panel of 161 countries over the 1999-2001 period. Our candidate variables include economic variables (income per capita, years of schooling, illiteracy, trade openness), demographic variables (youth and aged dependency ratios, urbanization rate), infrastructure indicators (telephone density, electricity consumption), telecommunications pricing measures, and regulatory quality. With the exception of trade openness and the telecom pricing measures, these variables enter in as statistically significant in most specifications for computer use. A similar pattern holds true for Internet use, except that telephone density and aged dependency matter less. The global digital divide is mainly – but by no means entirely – accounted for by income differentials. For computers, telephone density and regulatory quality are of second and third importance, while for the Internet, this ordering is reversed. The region specific explanations for large disparities in computer and Internet penetration are generally very similar. Our results suggest that public investment in human capital, telecommunications infrastructure, and the regulatory infrastructure can mitigate the gap in PC and Internet use.

The Dependence of Halo Clustering on Halo Formation History, Concentration, and Occupation

Abstract: We investigate the dependence of dark matter halo clustering on halo formation time, density profile concentration, and subhalo occupation number, using high-resolution numerical simulations of a ?CDM cosmology. We confirm results that halo clustering is a function of halo formation time at fixed mass and that this trend depends on halo mass. For the first time, we show unequivocally that halo clustering is a function of halo concentration and show that the dependence of halo bias on concentration, mass, and redshift can be accurately parameterized in a simple way: b(M,c|z) = b(M|z)b(c|M/M). Interestingly, the scaling between bias and concentration changes sign with the value of M/M: high-concentration (early forming) objects cluster more strongly for M M, while low-concentration (late forming) objects cluster more strongly for rare high-mass halos, M M. We show the first explicit demonstration that host dark halo clustering depends on the halo occupation number (of dark matter subhalos) at fixed mass and discuss implications for halo model calculations of dark matter power spectra and galaxy clustering statistics. The effect of these halo properties on clustering is strongest for early-forming dwarf-mass halos, which are significantly more clustered than typical halos of their mass. Our results suggest that isolated low-mass galaxies (e.g., low surface brightness dwarfs) should have more slowly rising rotation curves than their more clustered counterparts and may have consequences for the dearth of dwarf galaxies in voids. They also imply that self-calibrating richness-selected cluster samples with their clustering properties might overestimate cluster masses and bias cosmological parameter estimation.

Galaxies in the Hubble Ultra Deep Field. I. Detection, Multiband Photometry, Photometric Redshifts, and Morphology

Abstract: We present aperture-matched point-spread function (PSF)-corrected BVi'z'JH photometry and Bayesian photometric redshifts (BPZ) for objects detected in the Hubble Ultra Deep Field (UDF), 8042 of which are detected at the 10 σ level (e.g., i' < 29.01 or z' < 28.43). Most of our objects are defined identically to those in the public STScI catalogs, enabling a straightforward object-by-object comparison. We have combined detections from i', z', J + H, and B + V + i' + z' images into a single comprehensive segmentation map. Using a new program called SExSeg, we are able to force this segmentation map into SExtractor for photometric analysis. The resulting photometry is corrected for the wider NIC3 PSFs using our ColorPro software. We also correct for the ACS z'-band PSF halo. Offsets are applied to our NIC3 magnitudes, which are found to be too faint relative to the ACS fluxes. Based on BPZ spectral energy distribution (SED) fits to objects of known spectroscopic redshift, we derived corrections of -0.30 ± 0.03 mag in J and -0.18 ± 0.04 mag in H. Our offsets appear to be supported by a recent recalibration of the UDF NIC3 images combined with nonlinearity measured in NICMOS itself. The UDF reveals a large population of faint blue galaxies (presumably young starbursts), bluer than those observed in the original Hubble Deep Fields. To accommodate these galaxies, we have added two new starburst templates to the SED library used in previous BPZ papers. The resulting photometric redshifts are accurate to within 0.04(1 + zspec) out to z < 6. Our BPZ results include a full redshift probability distribution for each galaxy. By adding these distributions, we obtain the redshift probability histogram for galaxies in the UDF. Median redshifts are also provided for different magnitude-limited samples. Finally, we measure galaxy morphology, including Sersic index and asymmetry. Simulations allow us to quantify the reliability of our morphological results. Our full catalog, along with our software packages SExSeg and ColorPro, is available from our ACS Web site.

The UCSC Known Genes

Abstract: The University of California Santa Cruz (UCSC) Known Genes dataset is constructed by a fully automated process, based on protein data from Swiss-Prot/TrEMBL (UniProt) and the associated mRNA data from Genbank. The detailed steps of this process are described. Extensive cross-references from this dataset to other genomic and proteomic data were constructed. For each known gene, a details page is provided containing rich information about the gene, together with extensive links to other relevant genomic, proteomic and pathway data. As of July 2005, the UCSC Known Genes are available for human, mouse and rat genomes. The Known Genes serves as a foundation to support several key programs: the Genome Browser, Proteome Browser, Gene Sorter and Table Browser offered at the UCSC website. All the associated data files and program source code are also available. They can be accessed at http://genome.ucsc.edu. The genomic coverage of UCSC Known Genes, RefSeq, Ensembl Genes, H-Invitational and CCDS is analyzed. Although UCSC Known Genes offers the highest genomic and CDS coverage among major human and mouse gene sets, more detailed analysis suggests all of them could be further improved. Contact: fanhsu@soe.ucsc.edu

A distal enhancer and an ultraconserved exon are derived from a novel retroposon

Abstract: Hundreds of highly conserved distal cis-regulatory elements have been characterized so far in vertebrate genomes. Many thousands more are predicted on the basis of comparative genomics. However, in stark contrast to the genes that they regulate, in invertebrates virtually none of these regions can be traced by using sequence similarity, leaving their evolutionary origins obscure. Here we show that a class of conserved, primarily non-coding regions in tetrapods originated from a previously unknown short interspersed repetitive element (SINE) retroposon family that was active in the Sarcopterygii (lobe-finned fishes and terrestrial vertebrates) in the Silurian period at least 410 million years ago (ref. 4), and seems to be recently active in the 'living fossil' Indonesian coelacanth, Latimeria menadoensis. Using a mouse enhancer assay we show that one copy, 0.5 million bases from the neuro-developmental gene ISL1, is an enhancer that recapitulates multiple aspects of Isl1 expression patterns. Several other copies represent new, possibly regulatory, alternatively spliced exons in the middle of pre-existing Sarcopterygian genes. One of these, a more than 200-base-pair ultraconserved region, 100% identical in mammals, and 80% identical to the coelacanth SINE, contains a 31-amino-acid-residue alternatively spliced exon of the messenger RNA processing gene PCBP2 (ref. 6). These add to a growing list of examples in which relics of transposable elements have acquired a function that serves their host, a process termed 'exaptation', and provide an origin for at least some of the many highly conserved vertebrate-specific genomic sequences.

A new γ-ray burst classification scheme from GRB 060614

Abstract: Gamma-ray bursts (GRBs) are known to come in two duration classes, separated at ~2 s. Long-duration bursts originate from star-forming regions in galaxies, have accompanying supernovae when these are near enough to observe and are probably caused by massive-star collapsars. Recent observations show that short-duration bursts originate in regions within their host galaxies that have lower star-formation rates, consistent with binary neutron star or neutron star–black hole mergers. Moreover, although their hosts are predominantly nearby galaxies, no supernovae have been so far associated with short-duration GRBs. Here we report that the bright, nearby GRB 060614 does not fit into either class. Its ~102-s duration groups it with long-duration GRBs, while its temporal lag and peak luminosity fall entirely within the short-duration GRB subclass. Moreover, very deep optical observations exclude an accompanying supernova, similar to short-duration GRBs. This combination of a long-duration event without an accompanying supernova poses a challenge to both the collapsar and the merging-neutron-star interpretations and opens the door to a new GRB classification scheme that straddles both long- and short-duration bursts.