Showing papers by "University of California, Santa Cruz published in 2012"
TL;DR: STRUCTURE HARVESTER is presented, a web-based program for collating results generated by the program STRUCTURE, which provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data.
Abstract: We present STRUCTURE HARVESTER (available at http://taylor0.biology.ucla.edu/structureHarvester/
), a web-based program for collating results generated by the program STRUCTURE. The program provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data. In addition, STRUCTURE HARVESTER will reformat data for use in downstream programs, such as CLUMPP.
9,960 citations
Daniel C. Koboldt1, Robert S. Fulton1, Michael D. McLellan1, Heather Schmidt1 +352 more•Institutions (35)
TL;DR: The ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity.
Abstract: We analysed primary breast cancers by genomic DNA copy number arrays, DNA methylation, exome sequencing, messenger RNA arrays, microRNA sequencing and reverse-phase protein arrays. Our ability to integrate information across platforms provided key insights into previously defined gene expression subtypes and demonstrated the existence of four main breast cancer classes when combining data from five platforms, each of which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA and GATA3) occurred at >10% incidence across all breast cancers; however, there were numerous subtype-associated and novel gene mutations including the enrichment of specific mutations in GATA3, PIK3CA and MAP3K1 with the luminal A subtype. We identified two novel protein-expression-defined subgroups, possibly produced by stromal/microenvironmental elements, and integrated analyses identified specific signalling pathways dominant in each molecular subtype including a HER2/phosphorylated HER2/EGFR/phosphorylated EGFR signature within the HER2-enriched expression subtype. Comparison of basal-like breast tumours with high-grade serous ovarian tumours showed many molecular commonalities, indicating a related aetiology and similar therapeutic opportunities. The biological finding of the four main breast cancer subtypes caused by different subsets of genetic and epigenetic abnormalities raises the hypothesis that much of the clinically observable plasticity and heterogeneity occurs within, and not across, these major biological subtypes of breast cancer.
9,355 citations
TL;DR: In this article, a search for the Standard Model Higgs boson in proton-proton collisions with the ATLAS detector at the LHC is presented, which has a significance of 5.9 standard deviations, corresponding to a background fluctuation probability of 1.7×10−9.
9,282 citations
TL;DR: Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression.
Abstract: To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase e (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression.
6,883 citations
Tohoku University1, University of Zurich2, Lawrence Berkeley National Laboratory3, Stanford University4, College of William & Mary5, University of Genoa6, University of Urbino7, CERN8, Budker Institute of Nuclear Physics9, University of California, Irvine10, Cornell University11, Argonne National Laboratory12, ETH Zurich13, Tata Institute of Fundamental Research14, Hillsdale College15, Spanish National Research Council16, Ohio State University17, University of Notre Dame18, Kent State University19, University of California, San Diego20, University of California, Berkeley21, University of Minnesota22, University of Alabama23, University of Helsinki24, Los Alamos National Laboratory25, California Institute of Technology26, George Washington University27, Syracuse University28, Lawrence Livermore National Laboratory29, Oklahoma State University–Stillwater30, University of Washington31, Max Planck Society32, Boston University33, University of California, Los Angeles34, Royal Holloway, University of London35, Université Paris-Saclay36, Fermilab37, University of Pennsylvania38, University of Illinois at Urbana–Champaign39, University of Bristol40, University of Tokyo41, University of Delaware42, Carnegie Mellon University43, University of California, Santa Cruz44, Karlsruhe Institute of Technology45, Heidelberg University46, Florida State University47, Carleton University48, University of Mainz49, University of Edinburgh50, Brookhaven National Laboratory51, Durham University52, University of Lausanne53, Massachusetts Institute of Technology54, University of Southampton55, Nagoya University56, University of Oxford57, Northwestern University58, University of British Columbia59, Columbia University60, Lund University61, University of Sheffield62, University of California, Santa Barbara63, Iowa State University64, University of Alberta65, University of Cambridge66
TL;DR: The Particle Data Group's biennial review as mentioned in this paper summarizes much of particle physics, using data from previous editions, plus 2658 new measurements from 644 papers, and lists, evaluates, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons.
Abstract: This biennial Review summarizes much of particle physics. Using data from previous editions, plus 2658 new measurements from 644 papers, we list, evaluate, and average measured properties of gauge bosons, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as Higgs bosons, heavy neutrinos, and supersymmetric particles. All the particle properties and search limits are listed in Summary Tables. We also give numerous tables, figures, formulae, and reviews of topics such as the Standard Model, particle detectors, probability, and statistics. Among the 112 reviews are many that are new or heavily revised including those on Heavy-Quark and Soft-Collinear Effective Theory, Neutrino Cross Section Measurements, Monte Carlo Event Generators, Lattice QCD, Heavy Quarkonium Spectroscopy, Top Quark, Dark Matter, V-cb & V-ub, Quantum Chromodynamics, High-Energy Collider Parameters, Astrophysical Constants, Cosmological Parameters, and Dark Matter. A booklet is available containing the Summary Tables and abbreviated versions of some of the other sections of this full Review. All tables, listings, and reviews (and errata) are also available on the Particle Data Group website: http://pdg.lbl.gov.
4,465 citations
TL;DR: This work has examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites, and over one-third of GENCODE protein-Coding genes aresupported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas.
Abstract: The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.
4,281 citations
TL;DR: It is shown that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour.
Abstract: Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers.
3,356 citations
University of Western Sydney1, University of Ulm2, University of Tasmania3, Blaise Pascal University4, Institut national de la recherche agronomique5, University of Bordeaux6, Brown University7, National University of Patagonia San Juan Bosco8, James Cook University9, Macquarie University10, University of Alberta11, California State University, Bakersfield12, Leiden University13, University of Guelph14, University of Innsbruck15, University of Edinburgh16, Commonwealth Scientific and Industrial Research Organisation17, University of Trieste18, University of California, Santa Cruz19, University of Utah20, Missouri Botanical Garden21, George Washington University22
TL;DR: In this article, the authors draw together published and unpublished data on the vulnerability of the transport system to drought-induced embolism for a large number of woody species, with a view to examining the likely consequences of climate change for forest biomes.
Abstract: Shifts in rainfall patterns and increasing temperatures associated with climate change are likely to cause widespread forest decline in regions where droughts are predicted to increase in duration and severity(1). One primary cause of productivity loss and plant mortality during drought is hydraulic failure(2-4). Drought stress creates trapped gas emboli in the water transport system, which reduces the ability of plants to supply water to leaves for photosynthetic gas exchange and can ultimately result in desiccation and mortality. At present we lack a clear picture of how thresholds to hydraulic failure vary across a broad range of species and environments, despite many individual experiments. Here we draw together published and unpublished data on the vulnerability of the transport system to drought-induced embolism for a large number of woody species, with a view to examining the likely consequences of climate change for forest biomes. We show that 70% of 226 forest species from 81 sites worldwide operate with narrow (<1 megapascal) hydraulic safety margins against injurious levels of drought stress and therefore potentially face long-term reductions in productivity and survival if temperature and aridity increase as predicted for many regions across the globe(5,6). Safety margins are largely independent of mean annual precipitation, showing that there is global convergence in the vulnerability of forests to drought, with all forest biomes equally vulnerable to hydraulic failure regardless of their current rainfall environment. These findings provide insight into why drought-induced forest decline is occurring not only in arid regions but also in wet forests not normally considered at drought risk(7,8).
1,864 citations
Lawrence Berkeley National Laboratory1, University of California, Berkeley2, Australian Astronomical Observatory3, Pontifical Catholic University of Chile4, Harvard University5, Hamilton College6, University of Utah7, University of Tokyo8, Michigan State University9, Space Telescope Science Institute10, California Institute of Technology11, University of Colorado Boulder12, University of California, Santa Cruz13, University of Waterloo14, University of Chicago15, University of Florida16, Stockholm University17, University of Minnesota18, National Institutes of Natural Sciences, Japan19, Leiden University20, Northwestern University21, University of Bonn22, University of California, Davis23, University of Washington24, Kyoto University25, Pennsylvania State University26, European Southern Observatory27, Lawrence Livermore National Laboratory28, University of Lisbon29, Texas A&M University30, University of Toronto31
TL;DR: In this article, Advanced Camera for Surveys, NICMOS and Keck adaptive-optics-assisted photometry of 20 Type Ia supernovae (SNe Ia) from the Hubble Space Telescope (HST) Cluster Supernova Survey was presented.
Abstract: We present Advanced Camera for Surveys, NICMOS, and Keck adaptive-optics-assisted photometry of 20 Type Ia supernovae (SNe Ia) from the Hubble Space Telescope (HST) Cluster Supernova Survey. The SNe Ia were discovered over the redshift interval 0.623 1 SNe Ia. We describe how such a sample could be efficiently obtained by targeting cluster fields with WFC3 on board HST. The updated supernova Union2.1 compilation of 580 SNe is available at http://supernova.lbl.gov/Union.
1,784 citations
Max Planck Society1, Massachusetts Institute of Technology2, Harvard University3, University of California, Berkeley4, University of Washington5, Bilkent University6, Chinese Academy of Sciences7, University of California, Santa Cruz8, University of Arizona9, Russian Academy of Sciences10, Howard Hughes Medical Institute11
TL;DR: The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size, and illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.
Abstract: We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
1,690 citations
Duke University1, Fred Hutchinson Cancer Research Center2, New York University3, Harvard University4, Mahidol University5, University of Maryland, Baltimore6, Public Health Research Institute7, Walter Reed Army Institute of Research8, National Institutes of Health9, University of California, Santa Cruz10, Thailand Ministry of Public Health11
TL;DR: V vaccines that are designed to induce higher levels of V1V2 antibodies and lower levels of Env-specific IgA antibodies than are induced by the RV144 vaccine may have improved efficacy against HIV-1 infection.
Abstract: Background In the RV144 trial, the estimated efficacy of a vaccine regimen against human immunodeficiency virus type 1 (HIV-1) was 31.2%. We performed a case–control analysis to identify antibody and cellular immune correlates of infection risk. Methods In pilot studies conducted with RV144 blood samples, 17 antibody or cellular assays met prespecified criteria, of which 6 were chosen for primary analysis to determine the roles of T-cell, IgG antibody, and IgA antibody responses in the modulation of infection risk. Assays were performed on samples from 41 vaccinees who became infected and 205 uninfected vaccinees, obtained 2 weeks after final immunization, to evaluate whether immune-response variables predicted HIV-1 infection through 42 months of follow-up. Results Of six primary variables, two correlated significantly with infection risk: the binding of IgG antibodies to variable regions 1 and 2 (V1V2) of HIV-1 envelope proteins (Env) correlated inversely with the rate of HIV-1 infection (estimated odds...
Christopher P. Ahn1, Rachael Alexandroff2, Carlos Allende Prieto3, Scott F. Anderson4 +256 more•Institutions (65)
TL;DR: In this paper, the authors presented the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS) for the Sloan Digital Sky Survey III (SDSS-III) dataset.
Abstract: The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z ~ 0.52), 102,100 new quasar spectra (median z ~ 2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T eff -0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SEGUE-2. The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the APOGEE along with another year of data from BOSS, followed by the final SDSS-III data release in 2014 December.
TL;DR: A software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms is presented.
Abstract: Motivation: High-throughput sequencing has made the analysis of new model organisms more affordable. Although assembling a new genome can still be costly and difficult, it is possible to use RNA-seq to sequence mRNA. In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values.
Results: We present a software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.
Availability and implementation: Oases is freely available under the GPL license at www.ebi.ac.uk/~zerbino/oases/
Contact: ude.cscu@onibrezd
Supplementary information: Supplementary data are available at Bioinformatics online.
TL;DR: The ability to improve the capacitive properties of TiO(2) electrode materials should open up new opportunities for high-performance supercapacitors.
Abstract: We report a new and general strategy for improving the capacitive properties of TiO2 materials for supercapacitors, involving the synthesis of hydrogenated TiO2 nanotube arrays (NTAs). The hydrogenated TiO2 (denoted as H–TiO2) were obtained by calcination of anodized TiO2 NTAs in hydrogen atmosphere in a range of temperatures between 300 to 600 °C. The H–TiO2 NTAs prepared at 400 °C yields the largest specific capacitance of 3.24 mF cm–2 at a scan rate of 100 mV s–1, which is 40 times higher than the capacitance obtained from air-annealed TiO2 NTAs at the same conditions. Importantly, H–TiO2 NTAs also show remarkable rate capability with 68% areal capacitance retained when the scan rate increase from 10 to 1000 mV s–1, as well as outstanding long-term cycling stability with only 3.1% reduction of initial specific capacitance after 10 000 cycles. The prominent electrochemical capacitive properties of H–TiO2 are attributed to the enhanced carrier density and increased density of hydroxyl group on TiO2 surfa...
University of California, Berkeley1, Ames Research Center2, San Jose State University3, Lowell Observatory4, Jet Propulsion Laboratory5, University of Texas at Austin6, Harvard University7, Las Cumbres Observatory Global Telescope Network8, Space Telescope Science Institute9, Niels Bohr Institute10, National Center for Atmospheric Research11, Aarhus University12, NASA Exoplanet Science Institute13, Massachusetts Institute of Technology14, Fermilab15, University of California, Santa Cruz16, Yale University17, University of Florida18, California Institute of Technology19, University of California, Santa Barbara20, University of Hertfordshire21, San Diego State University22, Carnegie Institution for Science23, Lawrence Hall of Science24, Villanova University25
TL;DR: In this paper, the authors report the distribution of planets as a function of planet radius, orbital period, and stellar effective temperature for orbital periods less than 50 days around solar-type (GK) stars.
Abstract: We report the distribution of planets as a function of planet radius, orbital period, and stellar effective temperature for orbital periods less than 50 days around solar-type (GK) stars. These results are based on the 1235 planets (formally "planet candidates") from the Kepler mission that include a nearly complete set of detected planets as small as 2 R_⊕. For each of the 156,000 target stars, we assess the detectability of planets as a function of planet radius, R_p, and orbital period, P, using a measure of the detection efficiency for each star. We also correct for the geometric probability of transit, R_*/a. We consider first Kepler target stars within the "solar subset" having T_eff = 4100-6100 K, log g = 4.0-4.9, and Kepler magnitude K_p 2 R_⊕ we measure an occurrence of less than 0.001 planets per star. For all planets with orbital periods less than 50 days, we measure occurrence of 0.130 ± 0.008, 0.023 ± 0.003, and 0.013 ± 0.002 planets per star for planets with radii 2-4, 4-8, and 8-32 R_⊕, in agreement with Doppler surveys. We fit occurrence as a function of P to a power-law model with an exponential cutoff below a critical period P_0. For smaller planets, P_0 has larger values, suggesting that the "parking distance" for migrating planets moves outward with decreasing planet size. We also measured planet occurrence over a broader stellar T_eff range of 3600-7100 K, spanning M0 to F2 dwarfs. Over this range, the occurrence of 2-4 R_⊕ planets in the Kepler field increases with decreasing T_eff, with these small planets being seven times more abundant around cool stars (3600-4100 K) than the hottest stars in our sample (6600-7100 K).
TL;DR: A new version of the RegCM regional climate modeling system, RegCM4, has been recently developed and made available for public use as discussed by the authors, which includes new land surface, planetary boundary layer, and air-sea flux schemes, a mixed convection and tropical band configuration, modifications to the pre-existing radiative transfer and boundary layer schemes, and a full upgrade of the model code towards improved flexibility, portability, and user friendliness.
Abstract: A new version of the RegCM regional climate modeling system, RegCM4, has been recently developed and made available for public use. Compared to previous versions, RegCM4 includes new land surface, planetary boundary layer, and air–sea flux schemes, a mixed convection and tropical band configuration, modifications to the pre-existing radiative transfer and boundary layer schemes, and a full upgrade of the model code towards improved flexibility, portability, and user friendliness. The model can be interactively coupled to a 1D lake model, a simplified aerosol scheme (including organic carbon, black carbon, SO4, dust, and sea spray), and a gas phase chemistry module (CBM-Z). After a general description of the model, a series of test experiments are presented over 4 domains prescribed under the CORDEX framework (Africa, South America, East Asia, and Europe) to provide illustrative examples of the model behavior and sensitivities under different climatic regimes. These experiments indicate that, overall, RegCM4 shows an improved performance in several respects compared to previous versions, although further testing by the user community is needed to fully explore its sensitivities and range of applications.
TL;DR: In this article, the authors presented improved synthesis models of the evolving spectrum of the UV/X-ray diffuse background, updating and extending their previous results, and provided tables of predicted H I and He II photoionization and photoheating rates for use, e.g., in cosmological hydrodynamics simulations of the Lyα forest and a new metallicity-dependent calibration to the UV luminosity density-star formation rate density relation.
Abstract: We present improved synthesis models of the evolving spectrum of the UV/X-ray diffuse background, updating and extending our previous results. Five new main components are added to our radiative transfer code CUBA: (1) the sawtooth modulation of the background intensity from resonant line absorption in the Lyman series of cosmic hydrogen and helium; (2) the X-ray emission from the obscured and unobscured quasars that gives origin to the X-ray background; (3) a piecewise parameterization of the distribution in redshift and column density of intergalactic absorbers that fits recent measurements of the mean free path of 1 ryd photons; (4) an accurate treatment of the photoionization structure of absorbers, which enters in the calculation of the helium continuum opacity and recombination emissivity; and (5) the UV emission from star-forming galaxies at all redshifts. We provide tables of the predicted H I and He II photoionization and photoheating rates for use, e.g., in cosmological hydrodynamics simulations of the Lyα forest and a new metallicity-dependent calibration to the UV luminosity density-star formation rate density relation. A "minimal cosmic reionization model" is also presented in which the galaxy UV emissivity traces recent determinations of the cosmic history of star formation, the luminosity-weighted escape fraction of hydrogen-ionizing radiation increases rapidly with look-back time, the clumping factor of the high-redshift intergalactic medium evolves following the results of hydrodynamic simulations, and Population III stars and miniquasars make a negligible contribution to the metagalactic flux. The model provides a good fit to the hydrogen-ionization rates inferred from flux decrement and proximity effect measurements, predicts that cosmological H II (He III) regions overlap at redshift 6.7 (2.8), and yields an optical depth to Thomson scattering, τes = 0.084 that is in agreement with Wilkinson Microwave Anisotropy Probe results. Our new background intensities and spectra are sensitive to a number of poorly determined input parameters and suffer from various degeneracies. Their predictive power should be constantly tested against new observations. We are therefore making our redshift-dependent UV/X emissivities and CUBA outputs freely available for public use at http://www.ucolick.org/~pmadau/CUBA.
Washington University in St. Louis1, Mayo Clinic2, University of California, Santa Cruz3, University of Texas MD Anderson Cancer Center4, University of California, San Francisco5, Duke University6, Good Samaritan Hospital7, University of Texas Southwestern Medical Center8, Howard Hughes Medical Institute9
TL;DR: To correlate the variable clinical features of oestrogen-receptor-positive breast cancer with somatic alterations, pretreatment tumour biopsies accrued from patients in two studies of neoadjuvant aromatase inhibitor therapy are studied by massively parallel sequencing and analysis.
Abstract: Whole-genome analysis of oestrogen-receptor-positive tumours in patients treated with aromatase inhibitors show that distinct phenotypes are associated with specific patterns of somatic mutations; however, most recurrent mutations are relatively infrequent so prospective clinical trials will require comprehensive sequencing and large study populations.
TL;DR: The UCSC Genome Browser database is provided, which has been previously featured in the Database issue of this journal, and several features to improve usability are introduced, including new navigation menus.
Abstract: The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.
Lamont–Doherty Earth Observatory1, University of Bristol2, Wesleyan University3, Yale University4, National Oceanography Centre, Southampton5, Utrecht University6, University of Hawaii at Manoa7, Pennsylvania State University8, University of Southern California9, Museum für Naturkunde10, University of North Carolina at Chapel Hill11, University of California, Santa Cruz12, Cardiff University13, Institute of Arctic and Alpine Research14, University of South Florida St. Petersburg15, Autonomous University of Barcelona16, VU University Amsterdam17, Claremont McKenna College18
TL;DR: This paper reviewed events exhibiting evidence for elevated atmospheric CO2, global warming, and ocean acidification over the past ~300 million years of Earth's history, some with contemporaneous extinction or evolutionary turnover among marine calcifiers.
Abstract: Ocean acidification may have severe consequences for marine ecosystems; however, assessing its future impact is difficult because laboratory experiments and field observations are limited by their reduced ecologic complexity and sample period, respectively. In contrast, the geological record contains long-term evidence for a variety of global environmental perturbations, including ocean acidification plus their associated biotic responses. We review events exhibiting evidence for elevated atmospheric CO2, global warming, and ocean acidification over the past ~300 million years of Earth’s history, some with contemporaneous extinction or evolutionary turnover among marine calcifiers. Although similarities exist, no past event perfectly parallels future projections in terms of disrupting the balance of ocean carbonate chemistry—a consequence of the unprecedented rapidity of CO2 release currently taking place.
TL;DR: The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome and its third year of investigations in the mouse genome.
Abstract: The Encyclopedia of DNA Elements (ENCODE), http://encodeproject.org, has completed its fifth year of scientific collaboration to create a comprehensive catalog of functional elements in the human genome, and its third year of investigations in the mouse genome. Since the last report in this journal, the ENCODE human data repertoire has grown by 898 new experiments (totaling 2886), accompanied by a major integrative analysis. In the mouse genome, results from 404 new experiments became available this year, increasing the total to 583, collected during the course of the project. The University of California, Santa Cruz, makes this data available on the public Genome Browser http://genome.ucsc.edu for visual browsing and data mining. Download of raw and processed data files are all supported. The ENCODE portal provides specialized tools and information about the ENCODE data sets.
University of Bologna1, University of Barcelona2, INAF3, University of Edinburgh4, Centre national de la recherche scientifique5, University of Toulouse6, European Southern Observatory7, California Institute of Technology8, ETH Zurich9, Max Planck Society10, Paris Diderot University11, University of Vienna12, Spanish National Research Council13, University of Insubria14, Institute for the Physics and Mathematics of the Universe15, University of Nottingham16, National Taiwan Normal University17, Johns Hopkins University18, Space Telescope Science Institute19, Institut d'Astrophysique de Paris20, University of California, Santa Cruz21, Lawrence Livermore National Laboratory22, University of California, Davis23
TL;DR: In this paper, the authors presented new improved constraints on the Hubble parameter H(z) in the redshift range 0.15 -1.1, obtained from the differential spectroscopic evolution of early-type galaxies as a function of redshift.
Abstract: We present new improved constraints on the Hubble parameter H(z) in the redshift range 0.15 \textless z \textless 1.1, obtained from the differential spectroscopic evolution of early-type galaxies as a function of redshift. We extract a large sample of early-type galaxies ( 11000) from several spectroscopic surveys, spanning almost 8 billion years of cosmic lookback time (0.15 \textless z \textless 1.42). We select the most massive, red elliptical galaxies, passively evolving and without signature of ongoing star formation. Those galaxies can be used as standard cosmic chronometers, as firstly proposed by Jimenez & Loeb (2002), whose (life! Nit age evolution as a function of cosmic time directly probes H (z). We analyze the 4000 angstrom break (D4000) as a function of redshift, use stellar population synthesis models to theoretically calibrate the dependence of the differential age evolution on the differential D4000, and estimate the Hubble parameter taking into account both statistical and systematical errors. We provide 8 new measurements of H(z) (see table 4), and determine its change in H(z) to a precision of 5-12% mapping homogeneously the redshift range up to z 1.1; for the first time, we place a constraint on 11(z) at z not equal 0 with a precision comparable with the one achieved for the Hubble constant (about 5-6% at z similar to 0.2), and covered a redshift range (0.5 \textless z \textless 0.8) which is crucial to distinguish many different quintessence cosmologies. These measurements have been tested to best match a ACDM model, clearly providing a statistically robust indication that the Universe is undergoing an accelerated expansion. This method shows the potentiality to open a new avenue in constrain a variety of alternative cosmologies, especially when future surveys (e.g. Euclid) will open the possibility to extend it up to z similar to 2.
European Southern Observatory1, Yale University2, Leiden University3, Max Planck Society4, Harvard University5, University of Wisconsin–Milwaukee6, University of Arizona7, University of California, Santa Cruz8, Tufts University9, Carnegie Learning10, California Institute of Technology11, University of Wisconsin-Madison12
TL;DR: 3D-HST as discussed by the authors is a near-infrared spectroscopic Treasury program with the Hubble Space Telescope for studying the physical processes that shape galaxies in the distant universe.
Abstract: We present 3D-HST, a near-infrared spectroscopic Treasury program with the Hubble Space Telescope for studying
the physical processes that shape galaxies in the distant universe. 3D-HST provides rest-frame optical spectra for
a sample of ∼7000 galaxies at 1 < z < 3.5, the epoch when ∼60% of all star formation took place, the number
density of quasars peaked, the first galaxies stopped forming stars, and the structural regularity that we see in
galaxies today must have emerged. 3D-HST will cover three quarters (625 arcmin^2) of the CANDELS Treasury
survey area with two orbits of primary WFC3/G141 grism coverage and two to four orbits with the ACS/G800L
grism in parallel. In the IR, these exposure times yield a continuum signal-to-noise ratio of ∼5 per resolution element
at H_140 ∼ 23.1 and a 5σ emission-line sensitivity of ∼5 × 10^(−17) erg s^−1 cm^(−2) for typical objects, improving by
a factor of ∼2 for compact sources in images with low sky background levels. The WFC3/G141 spectra provide
continuous wavelength coverage from 1.1 to 1.6μm at a spatial resolution of ∼0."13, which, combined with their
depth, makes them a unique resource for studying galaxy evolution. We present an overview of the preliminary
reduction and analysis of the grism observations, including emission-line and redshift measurements from combined
fits to the extracted grism spectra and photometry from ancillary multi-wavelength catalogs. The present analysis
yields redshift estimates with a precision of σ(z) = 0.0034(1 + z), or σ(v) ≈ 1000 km s^(−1). We illustrate how
the generalized nature of the survey yields near-infrared spectra of remarkable quality for many different types
of objects, including a quasar at z = 4.7, quiescent galaxies at z ∼ 2, and the most distant T-type brown dwarf
star known. The combination of the CANDELS and 3D-HST surveys will provide the definitive imaging and
spectroscopic data set for studies of the 1 < z < 3.5 universe until the launch of the James Webb Space Telescope.
TL;DR: This year the Genome Browser has introduced ‘track data hubs’, which allow theGenome Browser to provide access to remotely located sets of annotations, and several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image.
Abstract: The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011. Further, a large number of annotation tracks have been either added, updated by contributors, or remapped to the latest human reference genome. Among these are new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods. Growing beyond the local database, this year we have introduced ‘track data hubs’, which allow the Genome Browser to provide access to remotely located sets of annotations. This feature is designed to significantly extend the number and variety of annotation tracks that are publicly available for visualization and analysis from within our site. We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image.
Space Telescope Science Institute1, Max Planck Society2, California Institute of Technology3, Massachusetts Institute of Technology4, Harvard University5, University of Provence6, University of Arizona7, National Autonomous University of Mexico8, University of California, San Diego9, University of Hawaii10, University of California, Santa Cruz11, INAF12
TL;DR: In this paper, the authors used the large samples of luminous active galactic nuclei and high-redshift star-forming galaxies in COSMOS to redefine the AGN selection criteria for use in deep IRAC surveys.
Abstract: Spitzer/IRAC selection is a powerful tool for identifying luminous active galactic nuclei (AGNs). For deep IRAC data, however, the AGN selection wedges currently in use are heavily contaminated by star-forming galaxies, especially at high redshift. Using the large samples of luminous AGNs and high-redshift star-forming galaxies in COSMOS, we redefine the AGN selection criteria for use in deep IRAC surveys. The new IRAC criteria are designed to be both highly complete and reliable, and incorporate the best aspects of the current AGN selection wedges and of infrared power-law selection while excluding high-redshift star-forming galaxies selected via the BzK, distant red galaxy, Lyman-break galaxy, and submillimeter galaxy criteria. At QSO luminosities of log L_(2-10keV)(erg s^(–1)) ≥44, the new IRAC criteria recover 75% of the hard X-ray and IRAC-detected XMM-COSMOS sample, yet only 38% of the IRAC AGN candidates have X-ray counterparts, a fraction that rises to 52% in regions with Chandra exposures of 50-160 ks. X-ray stacking of the individually X-ray non-detected AGN candidates leads to a hard X-ray signal indicative of heavily obscured to mildly Compton-thick obscuration (log N H (cm^(–2)) = 23.5 ± 0.4). While IRAC selection recovers a substantial fraction of luminous unobscured and obscured AGNs, it is incomplete to low-luminosity and host-dominated AGNs.
TL;DR: The authors draw on a theoretical and meta-analytic review to present a model that integrates group and individual RD, and suggest that RD measures that include justice-related affect, match the outcome level of analysis, and use higher quality measures yield significantly stronger relationships.
Abstract: Relative deprivation (RD) is the judgment that one is worse off compared to some standard accompanied by feelings of anger and resentment. Social scientists use RD to predict a wide range of significant outcome variables: collective action, individual achievement and deviance, intergroup attitudes, and physical and mental health. But the results are often weak and inconsistent. The authors draw on a theoretical and meta-analytic review (210 studies composing 293 independent samples, 421 tests, and 186,073 respondents) to present a model that integrates group and individual RD. RD measures that (a) include justice-related affect, (b) match the outcome level of analysis, and (c) use higher quality measures yield significantly stronger relationships. Future research should focus on appropriate RD measurement, angry resentment, and the inclusion of theoretically relevant situational appraisals. Such methodological improvements would revitalize RD as a useful social psychological predictor of a wide range of i...
TL;DR: Recent advances in the young and evolving field of biodiversity and ecosystem functioning are reviewed, the extent to which the field is becoming a predictive science is explored, and how the field needs to develop in order to aid worldwide efforts to achieve environmental sustainability in the face of rising rates of extinction is explored.
Abstract: Ecosystems worldwide are rapidly losing taxonomic, phylogenetic, genetic, and functional diversity as a result of human appropriation of natural resources, modification of habitats and climate, and the spread of pathogenic, exotic, and domestic plants and animals. Twenty years of intense theoretical and empirical research have shown that such biotic impoverishment can markedly alter the biogeochemical and dynamic properties of ecosystems, but frontiers remain in linking this research to the complexity of wild nature, and in applying it to pressing environmental issues such as food, water, energy, and biosecurity. The question before us is whether these advances can take us beyond merely invoking the precautionary principle of conserving biodiversity to a predictive science that informs practical and specific solutions to mitigate and adapt to its loss.
TL;DR: In this article, the BaBar data sample was used to investigate the sensitivity of BaBar ratios to new physics contributions in the form of a charged Higgs boson in the type II two-Higgs doublet model.
Abstract: Based on the full BaBar data sample, we report improved measurements of the ratios R(D(*)) = B(B -> D(*) Tau Nu)/B(B -> D(*) l Nu), where l is either e or mu. These ratios are sensitive to new physics contributions in the form of a charged Higgs boson. We measure R(D) = 0.440 +- 0.058 +- 0.042 and R(D*) = 0.332 +- 0.024 +- 0.018, which exceed the Standard Model expectations by 2.0 sigma and 2.7 sigma, respectively. Taken together, our results disagree with these expectations at the 3.4 sigma level. This excess cannot be explained by a charged Higgs boson in the type II two-Higgs-doublet model. We also report the observation of the decay B -> D Tau Nu, with a significance of 6.8 sigma.
TL;DR: The Fermi Large Area Telescope measured separate cosmic-ray electron and positron spectra to distinguish the two species by exploiting Earth's shadow, and it is confirmed that the fraction rises with energy in the 20-100 GeV range.
Abstract: We measured separate cosmic-ray electron and positron spectra with the Fermi Large Area Telescope. Because the instrument does not have an onboard magnet, we distinguish the two species by exploiting the Earth's shadow, which is offset in opposite directions for opposite charges due to the Earth's magnetic field. We estimate and subtract the cosmic-ray proton background using two different methods that produce consistent results. We report the electron-only spectrum, the positron-only spectrum, and the positron fraction between 20 GeV and 200 GeV. We confirm that the fraction rises with energy in the 20--100 GeV range and determine for the first time that it continues to rise between 100 and 200 GeV.