Showing papers by "University of California, Santa Cruz published in 2007"

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Abstract: We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

A second generation human haplotype map of over 3.1 million SNPs

Abstract: We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.

Substrate-induced bandgap opening in epitaxial graphene

Abstract: Graphene has shown great application potential as the hostmaterial for next-generation electronic devices. However, despite itsintriguing properties, one of the biggest hurdles for graphene to beuseful as an electronic material is the lack of an energy gap in itselectronic spectra. This, for example, prevents the use of graphene inmaking transistors. Although several proposals have been made to open agap in graphene's electronic spectra, they all require complexengineering of the graphene layer. Here, we show that when graphene isepitaxially grown on SiC substrate, a gap of ~;0.26 eV is produced. Thisgap decreases as the sample thickness increases and eventually approacheszero when the number of layers exceeds four. We propose that the originof this gap is the breaking of sublattice symmetry owing to thegraphene-substrate interaction. We believe that our results highlight apromising direction for band gap engineering of graphene.

Evolution of genes and genomes on the Drosophila phylogeny.

Abstract: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Star Formation in AEGIS Field Galaxies since z = 1.1: The Dominance of Gradually Declining Star Formation, and the Main Sequence of Star-forming Galaxies

Abstract: We analyze star formation (SF) as a function of stellar mass (M☉) and redshift z in the All-Wavelength Extended Groth Strip International Survey. For 2905 field galaxies, complete to 10^10(10^10.8 )M at z < 0.7(1), with Keck spectroscopic redshifts out to z = 1.1, we compile SF rates (SFRs) from emission lines, GALEX, and Spitzer MIPS 24 µm photometry, optical-NIR M* measurements, and HST morphologies. Galaxies with reliable signs of SF form a distinct “main sequence” (MS), with a limited range of SFRs at a given M* and z (1 σ ≾ ±0.3 dex), and log (SFR) approximately proportional to log M*. The range of log (SFR) remains constant to z > 1, while the MS as a whole moves to higher SFR as z increases. The range of the SFR along the MS constrains the amplitude of episodic variations of SF and the effect of mergers on the SFR. Typical galaxies spend ∼67%(95%) of their lifetime since z = 1 within a factor of ≾2(4) of their average SFR at a given M* and z. The dominant mode of the evolution of SF since z ∼ 1 is apparently a gradual decline of the average SFR in most individual galaxies, not a decreasing frequency of starburst episodes, or a decreasing factor by which SFRs are enhanced in starbursts. LIRGs at z ∼ 1 seem to mostly reflect the high SFR typical for massive galaxies at that epoch. The smooth MS may reflect that the same set of few physical processes governs SF prior to additional quenching processes. A gradual process like gas exhaustion may play a dominant role.

Genome-wide detection and characterization of positive selection in human populations

Abstract: With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

Kernel Regression for Image Processing and Reconstruction

Abstract: In this paper, we make contact with the field of nonparametric statistics and present a development and generalization of tools and results for use in image processing and reconstruction. In particular, we adapt and expand kernel regression ideas for use in image denoising, upscaling, interpolation, fusion, and more. Furthermore, we establish key relationships with some popular existing methods and show how several of these algorithms, including the recently popularized bilateral filter, are special cases of the proposed framework. The resulting algorithms and analyses are amply illustrated with practical examples

Evolutionary and biomedical insights from the rhesus macaque genome

Abstract: The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.

Diet and the evolution of human amylase gene copy number variation.

Abstract: Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch. This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis. We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number-variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.

Galaxy luminosity functions to z∼ 1 from DEEP2 and COMBO-17: Implications for red galaxy formation

Abstract: The DEEP2 and COMBO-17 surveys are compared to study luminosity functions of red and blue galaxies to z ~ 1. The two surveys have different methods and sensitivities, but nevertheless results agree. After z ~ 1, M has dimmed by 1.2-1.3 mag for all colors of galaxies, * for blue galaxies has hardly changed, and * for red galaxies has at least doubled (our formal value is ~0.5 dex). Luminosity density jB has fallen by 0.6 dex for blue galaxies but has remained nearly constant for red galaxies. These results imply that the number and total stellar mass of blue galaxies have been substantially constant since z ~ 1, whereas those of red galaxies (near L*) have been significantly rising. To explain the new red galaxies, a ``mixed'' scenario is proposed in which star formation in blue cloud galaxies is quenched, causing them to migrate to the red sequence, where they merge further in a small number of stellar mergers. This mixed scenario matches the local boxy-disky transition for nearby ellipticals, as well as red sequence stellar population scaling laws such as the color-magnitude and Mg-? relations (which are explained as fossil relics from blue progenitors). Blue galaxies enter the red sequence via different quenching modes, each of which peaks at a different characteristic mass and time. The red sequence therefore likely builds up in different ways at different times and masses, and the concept of a single process that is ``downsizing'' (or upsizing) probably does not apply. Our claim in this paper of a rise in the number of red galaxies applies to galaxies near L*. Accurate counts of brighter galaxies on the steep part of the Schechter function require more accurate photometry than is currently available.

Evaluating Appearance Models for Recognition, Reacquisition, and Tracking

Abstract: Traditionally, appearance models for recognition, reacquisition and tracking problems have been evaluated independently using metrics applied to a complete system. It is shown that appearance models for these three problems can be evaluated using a cumulative matching curve on a standardized dataset, and that this one curve can be converted to a synthetic reacquisition or disambiguation rate for tracking. A challenging new dataset for viewpoint invariant pedestrian recognition (VIPeR) is provided as an example. This dataset contains 632 pedestrian image pairs from arbitrary viewpoints. Several baseline methods are tested on this dataset and the results are presented as a benchmark for future appearance models and matchin methods.

The UCSC genome browser database: update 2007

Abstract: The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

Regional Climate Modeling for the Developing World: The ICTP RegCM3 and RegCNET

Abstract: Regional climate models are important research tools available to scientists around the world, including in economically developing nations (EDNs). The Earth Systems Physics (ESP) group of the Abdus Salam International Centre for Theoretical Physics (ICTP) maintains and distributes a state-of-the-science regional climate model called the ICTP Regional Climate Model version 3 (RegCM3), which is currently being used by a large research community for a diverse range of climate-related studies. The RegCM3 is the central, but not only, tool of the ICTP-maintained Regional Climate Research Network (RegCNET) aimed at creating south–south and north–south scientific interactions on the topic of climate and associated impacts research and modeling. In this paper, RegCNET, RegCM3, and illustrative results from RegCM3 benchmark simulations applied over south Asia, Africa, and South America are presented. It is shown that RegCM3 performs reasonably well over these regions and is therefore useful for climate studies in...

Cats and dogs, hair and a hero: A quintet of new milky way companions

Abstract: We present five new satellites of the Milky Way discovered in Sloan Digital Sky Survey (SDSS) imaging data, four of which were followed-up with either the Subaru or the Isaac Newton Telescopes. They include four probable new dwarf galaxies--one each in the constellations of Coma Berenices, Canes Venatici, Leo and Hercules--together with one unusually extended globular cluster, Segue 1. We provide distances, absolute magnitudes, half-light radii and color-magnitude diagrams for all five satellites. The morphological features of the color-magnitude diagrams are generally well described by the ridge line of the old, metal-poor globular cluster M92. In the last two years, a total of ten new Milky Way satellites with effective surface brightness {mu}{sub v} {approx}> 28 mag arcsec{sup -2} have been discovered in SDSS data. They are less luminous, more irregular and appear to be more metal-poor than the previously-known nine Milky Way dwarf spheroidals. The relationship between these objects and other populations is discussed. We note that there is a paucity of objects with half-light radii between {approx} 40 pc and {approx} 100 pc. We conjecture that this may represent the division between star clusters and dwarf galaxies.

Spatial-Depth Super Resolution for Range Images

Abstract: We present a new post-processing step to enhance the resolution of range images. Using one or two registered and potentially high-resolution color images as reference, we iteratively refine the input low-resolution range image, in terms of both its spatial resolution and depth precision. Evaluation using the Middlebury benchmark shows across-the-board improvement for sub-pixel accuracy. We also demonstrated its effectiveness for spatial resolution enhancement up to 100 times with a single reference image.

The Fifth Data Release of the Sloan Digital Sky Survey

Abstract: This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS). DR5 includes all survey quality data taken through 2005 June and represents the completion of the SDSS-I project (whose successor, SDSS-II, will continue through mid-2008). It includes five-band photometric data for 217 million objects selected over 8000 deg^2 and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 deg^2 of that imaging data. These numbers represent a roughly 20% increment over those of the Fourth Data Release; all the data from previous data releases are included in the present release. In addition to "standard" SDSS observations, DR5 includes repeat scans of the southern equatorial stripe, imaging scans across M31 and the core of the Perseus Cluster of galaxies, and the first spectroscopic data from SEGUE, a survey to explore the kinematics and chemical evolution of the Galaxy. The catalog database incorporates several new features, including photometric redshifts of galaxies, tables of matched objects in overlap regions of the imaging survey, and tools that allow precise computations of survey geometry for statistical investigations.

Analysis versus synthesis in signal priors

Abstract: The concept of prior probability for signals plays a key role in the successful solution of many inverse problems. Much of the literature on this topic can be divided between analysis-based and synthesis-based priors. Analysis-based priors assign probability to a signal through various forward measurements of it, while synthesis-based priors seek a reconstruction of the signal as a combination of atom signals. The algebraic similarity between the two suggests that they could be strongly related; however, in the absence of a detailed study, contradicting approaches have emerged. While the computationally intensive synthesis approach is receiving ever-increasing attention and is notably preferred, other works hypothesize that the two might actually be much closer, going as far as to suggest that one can approximate the other. In this paper we describe the two prior classes in detail, focusing on the distinction between them. We show that although in the simpler complete and undercomplete formulations the two approaches are equivalent, in their overcomplete formulation they depart. Focusing on the l1 case, we present a novel approach for comparing the two types of priors based on high-dimensional polytopal geometry. We arrive at a series of theoretical and numerical results establishing the existence of an unbridgeable gap between the two.

UV Luminosity Functions at z~4, 5, and 6 from the Hubble Ultra Deep Field and Other Deep Hubble Space Telescope ACS Fields: Evolution and Star Formation History*

Abstract: We use the ACS BViz data from the HUDF and all other deep HST ACS fields (including the GOODS fields) to find large samples of star-forming galaxies at z ~ 4 and ~5 and to extend our previous z ~ 6 sample. These samples contain 4671, 1416, and 627 B-, V-, and i-dropouts, respectively, and reach to extremely low luminosities [(0.01-0.04)L or MUV ~ -16 to -17], allowing us to determine the rest-frame UV LF and faint-end slope ? at z ~ 4-6 to high accuracy. We find faint-end slopes ? = -1.73 ? 0.05, -1.66 ? 0.09, and -1.74 ? 0.16 at z ~ 4, ~5, and ~6, respectively, suggesting that the faint-end slope is very steep and shows little evolution with cosmic time. We find that M brightens considerably in the 0.7 Gyr from z ~ 6 to ~4 (by ~0.7 mag from M = -20.24 ? 0.19 to -20.98 ? 0.10). The observed increase in the characteristic luminosity over this range is almost identical to that expected for the halo mass function, suggesting that the observed evolution is likely due to the hierarchical coalescence and merging of galaxies. The evolution in * is not significant. The UV luminosity density at z ~ 6 is modestly lower than (0.45 ? 0.09 times) that at z ~ 4 (integrated to -17.5 mag) although a larger change is seen in the dust-corrected SFR density. We thoroughly examine published LF results and assess the reasons for their wide dispersion. We argue that the results reported here are the most robust available. The extremely steep faint-end slopes ? found here suggest that lower luminosity galaxies play a significant role in reionizing the universe. Finally, recent search results for galaxies at z ~ 7-8 are used to extend our estimates of the evolution of M* from z ~ 7-8 to z ~ 4.

A checklist for ecological management of landscapes for conservation

Abstract: The management of landscapes for biological conservation and ecologically sustainable natural resource use are crucial global issues. Research for over two decades has resulted in a large literature, yet there is little consensus on the applicability or even the existence of general principles or broad considerations that could guide landscape conservation. We assess six major themes in the ecology and conservation of landscapes. We identify 13 important issues that need to be considered in developing approaches to landscape conservation. They include recognizing the importance of landscape mosaics (including the integration of terrestrial and aquatic areas), recognizing interactions between vegetation cover and vegetation configuration, using an appropriate landscape conceptual model, maintaining the capacity to recover from disturbance and managing landscapes in an adaptive framework. These considerations are influenced by landscape context, species assemblages and management goals and do not translate directly into on-the-ground management guidelines but they should be recognized by researchers and resource managers when developing guidelines for specific cases. Two crucial overarching issues are: (i) a clearly articulated vision for landscape conservation and (ii) quantifiable objectives that offer unambiguous signposts for measuring progress.

UV Luminosity Functions at z~4, 5, and 6 from the HUDF and other Deep HST ACS Fields: Evolution and Star Formation History

Abstract: We use the ACS BViz data from the HUDF and all other deep HST ACS fields (including the GOODS fields) to find large samples of star-forming galaxies at z~4 and z~5 and to extend our previous z~6 sample. These samples contain 4671, 1416, and 627 B, V, and i dropouts, respectively, and reach to extremely low luminosities (0.01-0.04 L* or M(UV)~-16 to -17), allowing us to determine the rest-frame UV luminosity function (LF) and faint-end slope alpha at z~4-6 to high accuracy. We find faint-end slopes alpha of -1.73+/-0.05 at z~4, -1.66+/-0.09 at z~5, and -1.74+/-0.16 at z~6 -- suggesting that the faint-end slope is very steep and shows little evolution with cosmic time. We find that M*(UV) brightens considerably in the 0.7 Gyr from z~6 to z~4 (by ~0.7 mag from M*=-20.24+/-0.19 to M*=-20.98+/-0.10). The observed increase in the characteristic luminosity over this range is almost identical to that expected for the halo mass function -- suggesting that the observed evolution is likely due to the hierarchical coalescence and merging of galaxies. The evolution in phi* is not significant. The UV luminosity density at z~6 is modestly lower (0.45+/-0.09 times) than that at z~4 (integrated to -17.5 AB mag) though a larger change is seen in the dust-corrected star-formation rate density. We thoroughly examine published LF results and assess the reasons for their wide dispersion. We argue that the results reported here are the most robust available. The extremely steep faint-end slopes alpha found here suggest that lower luminosity galaxies play a significant role in reionizing the universe. Finally, we consider recent search results for galaxies at z~7-8 and use them to extend our estimates of the evolution in M* from z~7-8 to z~4.

Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

Abstract: The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species. Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely related species, D. melanogaster and D. yakuba. We discovered previously unknown, large-scale fluctuations of polymorphism and divergence along chromosome arms, and significantly less polymorphism and faster divergence on the X chromosome. We generated a comprehensive list of functional elements in the D. simulans genome influenced by adaptive evolution. Finally, we characterized genomic patterns of base composition for coding and noncoding sequence. These results suggest several new hypotheses regarding the genetic and biological mechanisms controlling polymorphism and divergence across the Drosophila genome, and provide a rich resource for the investigation of adaptive evolution and functional variation in D. simulans.

Formation and Evolution of Galaxy Dark Matter Halos and Their Substructure

Abstract: We use the "Via Lactea" simulation to study the co-evolution of a Milky Way-sized ΛCDM halo and its subhalo population. While most of the host halo mass is accreted over the first 6 Gyr in a series of major mergers, the physical mass distribution [not Mvir(z)] remains practically constant since z = 1. The same is true in a large sample of ΛCDM galaxy halos. Subhalo mass loss peaks between the turnaround and virialization epochs of a given mass shell, and the abundance of substructure within the shell freezes afterward. Of the z = 1 subhalos, 97% have a surviving bound remnant at the present epoch. The retained mass fraction is larger for initially lighter subhalos: today satellites with maximum circular velocities Vmax = 10 km s-1 at z = 1 have about 40% of the mass they had back then. At the first pericenter passage a larger average mass fraction is lost than during each following orbit. Tides remove mass in the substructure from the outside in, leading to higher concentrations compared to field halos of the same mass. This effect, combined with the earlier formation epoch of the inner satellites, results in strongly increasing subhalo concentrations toward the Galactic center. We present individual evolutionary tracks and present-day properties of the likely hosts of the dwarf satellites around the Milky Way. The formation histories of "field halos" that lie beyond the Via Lactea host today are found to strongly depend on the density of their environment. This is caused by tidal mass loss that affects many field halos on eccentric orbits.

Phylogenetic signal in plant pathogen–host range

Abstract: What determines which plant species are susceptible to a given plant pathogen is poorly understood. Experimental inoculations with fungal pathogens of plant leaves in a tropical rain forest show that most fungal pathogens are polyphagous but that most plant species in a local community are resistant to any given pathogen. The likelihood that a pathogen can infect two plant species decreases continuously with phylogenetic distance between the plants, even to ancient evolutionary distances. This phylogenetic signal in host range allows us to predict the likely host range of plant pathogens in a local community, providing an important tool for plant ecology, design of agronomic systems, quarantine regulations in international trade, and risk analysis of biological control agents. In particular, the results suggest that the rate of spread and ecological impacts of a disease through a natural plant community will depend strongly on the phylogenetic structure of the community itself and that current regulatory approaches strongly underestimate the local risks of global movement of plant pathogens or their hosts.

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Abstract: Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.

Pulsational pair instability as an explanation for the most luminous supernovae

Abstract: The extremely luminous supernova SN 2006gy (ref. 1) challenges the traditional view that the collapse of a stellar core is the only mechanism by which a massive star makes a supernova, because it seems too luminous by more than a factor of ten. Here we report that the brightest supernovae in the modern Universe arise from collisions between shells of matter ejected by massive stars that undergo an interior instability arising from the production of electron-positron pairs. This 'pair instability' leads to explosive burning that is insufficient to unbind the star, but ejects many solar masses of the envelope. After the first explosion, the remaining core contracts and searches for a stable burning state. When the next explosion occurs, several solar masses of material are again ejected, which collide with the earlier ejecta. This collision can radiate 10(50) erg of light, about a factor of ten more than an ordinary supernova. Our model is in good agreement with the observed light curve for SN 2006gy and also shows that some massive stars can produce more than one supernova-like outburst.

The All-Wavelength Extended Groth Strip International Survey(AEGIS) Data Sets

Abstract: In this the first of a series of Letters, we present a panchromatic data set in the Extended Groth Strip region of the sky. Our survey, the All-Wavelength Extended Groth Strip International Survey (AEGIS), aims to study the physical properties and evolutionary processes of galaxies at z ~ 1. It includes the following deep, wide-field imaging data sets: Chandra/ACIS X-ray, GALEX ultraviolet, CFHT/MegaCam Legacy Survey optical, CFHT/CFH12K optical, Hubble Space Telescope/ACS optical and NICMOS near-infrared, Palomar/WIRC near-infrared, Spitzer/IRAC mid-infrared, Spitzer/MIPS far-infrared, and VLA radio continuum. In addition, this region of the sky has been targeted for extensive spectroscopy using the Deep Imaging Multi-Object Spectrograph (DEIMOS) on the Keck II 10 m telescope. Our survey is compared to other large multiwavelength surveys in terms of depth and sky coverage.

Slow slip events and seismic tremor at circum-Pacific subduction zones

Abstract: [1] It has been known for a long time that slip accompanying earthquakes accounts for only a fraction of plate tectonic displacements. However, only recently has a fuller spectrum of strain release processes, including normal, slow, and silent earthquakes (or slow slip events) and continuous and episodic slip, been observed and generated by numerical simulations of the earthquake cycle. Despite a profusion of observations and modeling studies the physical mechanism of slow slip events remains elusive. The concurrence of seismic tremor with slow slip episodes in Cascadia and southwestern Japan provides insight into the process of slow slip. A perceived similarity between subduction zone and volcanic tremor has led to suggestions that slow slip involves fluid migration on or near the plate interface. Alternatively, evidence is accumulating to support the notion that tremor results from shear failure during slow slip. Global observations of the location, spatial extent, magnitude, duration, slip rate, and periodicity of these aseismic slip transients indicate significant variation that may be exploited to better understand their generation. Most slow slip events occur just downdip of the seismogenic zone, consistent with rate- and state-dependent frictional modeling that requires unstable to stable transitional properties for slow slip generation. At a few convergent margins the occurrence of slow slip events within the seismogenic zone makes it highly likely that transitions in frictional properties exist there and are the loci of slow slip nucleation. Slow slip events perturb the surrounding stress field and may either increase or relieve stress on a fault, bringing it closer to or farther from earthquake failure, respectively. This paper presents a review of slow slip events and related seismic tremor observed at plate boundaries worldwide, with a focus on circum-Pacific subduction zones. Trends in global observations of slow slip events suggest that (1) slow slip is a common phenomena observed at almost all subduction zones with instrumentation capable of recording it, (2) different frictional properties likely control fast versus slow slip, (3) the depth range of slow slip may be related to the thermal properties of the plate interface, and (4) the equivalent seismic moment of slow slip events is proportional to their duration (Moατ), different from the Moατ3 scaling observed for earthquakes.

The UCSC Genome Browser Database: 2008 update.

Abstract: The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

Revisiting Carbon Flux Through the Ocean's Twilight Zone

Abstract: The oceanic biological pump drives sequestration of carbon dioxide in the deep sea via sinking particles. Rapid biological consumption and remineralization of carbon in the "twilight zone" (depths between the euphotic zone and 1000 meters) reduce the efficiency of sequestration. By using neutrally buoyant sediment traps to sample this chronically understudied realm, we measured a transfer efficiency of sinking particulate organic carbon between 150 and 500 meters of 20 and 50% at two contrasting sites. This large variability in transfer efficiency is poorly represented in biogeochemical models. If applied globally, this is equivalent to a difference in carbon sequestration of more than 3 petagrams of carbon per year.