Showing papers by "University of California, Santa Cruz published in 2013"

The cancer genome atlas pan-cancer analysis project

Abstract: The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.

Integrated genomic characterization of endometrial carcinoma

Abstract: We performed an integrated genomic, transcriptomic and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumours and ∼25% of high-grade endometrioid tumours had extensive copy number alterations, few DNA methylation changes, low oestrogen receptor/progesterone receptor levels, and frequent TP53 mutations. Most endometrioid tumours had few copy number alterations or TP53 mutations, but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A and KRAS and novel mutations in the SWI/SNF chromatin remodelling complex gene ARID5B. A subset of endometrioid tumours that we identified had a markedly increased transversion mutation frequency and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy-number low, and copy-number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may affect post-surgical adjuvant treatment for women with aggressive tumours.

Comprehensivemolecular characterization of clear cell renal cell carcinoma

Abstract: Genetic changes underlying clear cell renal cell carcinoma (ccRCC) include alterations in genes controlling cellular oxygen sensing (for example, VHL) and the maintenance of chromatin states (for example, PBRM1). We surveyed more than 400 tumours using different genomic platforms and identified 19 significantly mutated genes. The PI(3)K/AKT pathway was recurrently mutated, suggesting this pathway as a potential therapeutic target. Widespread DNA hypomethylation was associated with mutation of the H3K36 methyltransferase SETD2, and integrative analysis suggested that mutations involving the SWI/SNF chromatin remodelling complex (PBRM1, ARID1A, SMARCA4) could have far-reaching effects on other pathways. Aggressive cancers demonstrated evidence of a metabolic shift, involving downregulation of genes involved in the TCA cycle, decreased AMPK and PTEN protein levels, upregulation of the pentose phosphate pathway and the glutamine transporter genes, increased acetyl-CoA carboxylase protein, and altered promoter methylation of miR-21 (also known as MIR21) and GRB10. Remodelling cellular metabolism thus constitutes a recurrent pattern in ccRCC that correlates with tumour stage and severity and offers new views on the opportunities for disease treatment.

The Average Star Formation Histories of Galaxies in Dark Matter Halos from z = 0-8

Abstract: We present a robust method to constrain average galaxy star formation rates (SFRs), star formation histories (SFHs), and the intracluster light (ICL) as a function of halo mass. Our results are consistent with observed galaxy stellar mass functions, specific star formation rates (SSFRs), and cosmic star formation rates (CSFRs) from z = 0 to z = 8. We consider the effects of a wide range of uncertainties on our results, including those affecting stellar masses, SFRs, and the halo mass function at the heart of our analysis. As they are relevant to our method, we also present new calibrations of the dark matter halo mass function, halo mass accretion histories, and halo-subhalo merger rates out to z = 8. We also provide new compilations of CSFRs and SSFRs; more recent measurements are now consistent with the buildup of the cosmic stellar mass density at all redshifts. Implications of our work include: halos near 1012 M ☉ are the most efficient at forming stars at all redshifts, the baryon conversion efficiency of massive halos drops markedly after z ~ 2.5 (consistent with theories of cold-mode accretion), the ICL for massive galaxies is expected to be significant out to at least z ~ 1-1.5, and dwarf galaxies at low redshifts have higher stellar mass to halo mass ratios than previous expectations and form later than in most theoretical models. Finally, we provide new fitting formulae for SFHs that are more accurate than the standard declining tau model. Our approach places a wide variety of observations relating to the SFH of galaxies into a self-consistent framework based on the modern understanding of structure formation in ΛCDM. Constraints on the stellar mass-halo mass relationship and SFRs are available for download online.

The baryon oscillation spectroscopic survey of sdss-iii

Abstract: The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large-scale structure. BOSS uses 1.5 million luminous galaxies as faint as i = 19.9 over 10,000 deg2 to measure BAO to redshifts z < 0.7. Observations of neutral hydrogen in the Lyα forest in more than 150,000 quasar spectra (g < 22) will constrain BAO over the redshift range 2.15 < z < 3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyα forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance dA to an accuracy of 1.0% at redshifts z = 0.3 and z = 0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyα forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate DA (z) and H –1(z) parameters to an accuracy of 1.9% at z ~ 2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.

Planetary Candidates Observed by Kepler. III. Analysis of the First 16 Months of Data

Abstract: New transiting planet candidates are identified in 16 months (2009 May-2010 September) of data from the Kepler spacecraft. Nearly 5000 periodic transit-like signals are vetted against astrophysical and instrumental false positives yielding 1108 viable new planet candidates, bringing the total count up to over 2300. Improved vetting metrics are employed, contributing to higher catalog reliability. Most notable is the noise-weighted robust averaging of multi-quarter photo-center offsets derived from difference image analysis that identifies likely background eclipsing binaries. Twenty-two months of photometry are used for the purpose of characterizing each of the candidates. Ephemerides (transit epoch, T_0, and orbital period, P) are tabulated as well as the products of light curve modeling: reduced radius (R_P/R_★), reduced semimajor axis (d/R_★), and impact parameter (b). The largest fractional increases are seen for the smallest planet candidates (201% for candidates smaller than 2 R_⊕ compared to 53% for candidates larger than 2 R_⊕) and those at longer orbital periods (124% for candidates outside of 50 day orbits versus 86% for candidates inside of 50 day orbits). The gains are larger than expected from increasing the observing window from 13 months (Quarters 1-5) to 16 months (Quarters 1-6) even in regions of parameter space where one would have expected the previous catalogs to be complete. Analyses of planet frequencies based on previous catalogs will be affected by such incompleteness. The fraction of all planet candidate host stars with multiple candidates has grown from 17% to 20%, and the paucity of short-period giant planets in multiple systems is still evident. The progression toward smaller planets at longer orbital periods with each new catalog release suggests that Earth-size planets in the habitable zone are forthcoming if, indeed, such planets are abundant.

The Multi-object, Fiber-fed Spectrographs for the Sloan Digital Sky Survey and the Baryon Oscillation Spectroscopic Survey

Abstract: We present the design and performance of the multi-object fiber spectrographs for the Sloan Digital Sky Survey (SDSS) and their upgrade for the Baryon Oscillation Spectroscopic Survey (BOSS). Originally commissioned in Fall 1999 on the 2.5 m aperture Sloan Telescope at Apache Point Observatory, the spectrographs produced more than 1.5 million spectra for the SDSS and SDSS-II surveys, enabling a wide variety of Galactic and extra-galactic science including the first observation of baryon acoustic oscillations in 2005. The spectrographs were upgraded in 2009 and are currently in use for BOSS, the flagship survey of the third-generation SDSS-III project. BOSS will measure redshifts of 1.35 million massive galaxies to redshift 0.7 and Lyα absorption of 160,000 high redshift quasars over 10,000 deg2 of sky, making percent level measurements of the absolute cosmic distance scale of the universe and placing tight constraints on the equation of state of dark energy. The twin multi-object fiber spectrographs utilize a simple optical layout with reflective collimators, gratings, all-refractive cameras, and state-of-the-art CCD detectors to produce hundreds of spectra simultaneously in two channels over a bandpass covering the near-ultraviolet to the near-infrared, with a resolving power R = λ/FWHM ~ 2000. Building on proven heritage, the spectrographs were upgraded for BOSS with volume-phase holographic gratings and modern CCD detectors, improving the peak throughput by nearly a factor of two, extending the bandpass to cover 360 nm < λ < 1000 nm, and increasing the number of fibers from 640 to 1000 per exposure. In this paper we describe the original SDSS spectrograph design and the upgrades implemented for BOSS, and document the predicted and measured performances.

Astrocytes mediate synapse elimination through MEGF10 and MERTK pathways

Abstract: To achieve its precise neural connectivity, the developing mammalian nervous system undergoes extensive activity-dependent synapse remodelling. Recently, microglial cells have been shown to be responsible for a portion of synaptic pruning, but the remaining mechanisms remain unknown. Here we report a new role for astrocytes in actively engulfing central nervous system synapses. This process helps to mediate synapse elimination, requires the MEGF10 and MERTK phagocytic pathways, and is strongly dependent on neuronal activity. Developing mice deficient in both astrocyte pathways fail to refine their retinogeniculate connections normally and retain excess functional synapses. Finally, we show that in the adult mouse brain, astrocytes continuously engulf both excitatory and inhibitory synapses. These studies reveal a novel role for astrocytes in mediating synapse elimination in the developing and adult brain, identify MEGF10 and MERTK as critical proteins in the synapse remodelling underlying neural circuit refinement, and have important implications for understanding learning and memory as well as neurological disease processes.

H-TiO(2) @MnO(2) //H-TiO(2) @C core-shell nanowires for high performance and flexible asymmetric supercapacitors.

Abstract: A flexible solid-state asymmetric supercapacitor device with H-TiO(2) @MnO(2) core-shell NWs as the positive electrode and H-TiO(2) @C core-shell NWs as the negative electrode is developed. This device operates in a 1.8 V voltage window and is able to deliver a high specific capacitance of 139.6 F g(-1) and maximum volumetric energy density of 0.30 mWh cm(-3) with excellent cycling performance and good flexibility.

A large-scale evaluation of computational protein function prediction

Abstract: Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.

Au Nanostructure-Decorated TiO2 Nanowires Exhibiting Photoactivity Across Entire UV-visible Region for Photoelectrochemical Water Splitting

Abstract: Here we demonstrate that the photoactivity of Au-decorated TiO2 electrodes for photoelectrochemical water oxidation can be effectively enhanced in the entire UV–visible region from 300 to 800 nm by manipulating the shape of the decorated Au nanostructures. The samples were prepared by carefully depositing Au nanoparticles (NPs), Au nanorods (NRs), and a mixture of Au NPs and NRs on the surface of TiO2 nanowire arrays. As compared with bare TiO2, Au NP-decorated TiO2 nanowire electrodes exhibited significantly enhanced photoactivity in both the UV and visible regions. For Au NR-decorated TiO2 electrodes, the photoactivity enhancement was, however, observed in the visible region only, with the largest photocurrent generation achieved at 710 nm. Significantly, TiO2 nanowires deposited with a mixture of Au NPs and NRs showed enhanced photoactivity in the entire UV–visible region. Monochromatic incident photon-to-electron conversion efficiency measurements indicated that excitation of surface plasmon resonance...

The DEEP2 Galaxy Redshift Survey: Design, Observations, Data Reduction, and Redshifts

Abstract: We describe the design and data analysis of the DEEP2 Galaxy Redshift Survey, the densest and largest high-precision redshift survey of galaxies at z ~ 1 completed to date. The survey was designed to conduct a comprehensive census of massive galaxies, their properties, environments, and large-scale structure down to absolute magnitude M_B = −20 at z ~ 1 via ~90 nights of observation on the Keck telescope. The survey covers an area of 2.8 deg^2 divided into four separate fields observed to a limiting apparent magnitude of R_(AB) = 24.1. Objects with z ≾0.7 are readily identifiable using BRI photometry and rejected in three of the four DEEP2 fields, allowing galaxies with z > 0.7 to be targeted ~2.5 times more efficiently than in a purely magnitude-limited sample. Approximately 60% of eligible targets are chosen for spectroscopy, yielding nearly 53,000 spectra and more than 38,000 reliable redshift measurements. Most of the targets that fail to yield secure redshifts are blue objects that lie beyond z ~ 1.45, where the [O ii] 3727 A doublet lies in the infrared. The DEIMOS 1200 line mm^(−1) grating used for the survey delivers high spectral resolution (R ~ 6000), accurate and secure redshifts, and unique internal kinematic information. Extensive ancillary data are available in the DEEP2 fields, particularly in the Extended Groth Strip, which has evolved into one of the richest multiwavelength regions on the sky. This paper is intended as a handbook for users of the DEEP2 Data Release 4, which includes all DEEP2 spectra and redshifts, as well as for the DEEP2 DEIMOS data reduction pipelines. Extensive details are provided on object selection, mask design, biases in target selection and redshift measurements, the spec2d two-dimensional data-reduction pipeline, the spec1d automated redshift pipeline, and the zspec visual redshift verification process, along with examples of instrumental signatures or other artifacts that in some cases remain after data reduction. Redshift errors and catastrophic failure rates are assessed through more than 2000 objects with duplicate observations. Sky subtraction is essentially photon-limited even under bright OH sky lines; we describe the strategies that permitted this, based on high image stability, accurate wavelength solutions, and powerful B-spline modeling methods. We also investigate the impact of targets that appear to be single objects in ground-based targeting imaging but prove to be composite in Hubble Space Telescope data; they constitute several percent of targets at z ~ 1, approaching ~5%–10% at z > 1.5. Summary data are given that demonstrate the superiority of DEEP2 over other deep high-precision redshift surveys at z ~ 1 in terms of redshift accuracy, sample number density, and amount of spectral information. We also provide an overview of the scientific highlights of the DEEP2 survey thus far.

The Universal Stellar Mass-Stellar Metallicity Relation for Dwarf Galaxies

Abstract: We present spectroscopic metallicities of individual stars in seven gas-rich dwarf irregular galaxies (dIrrs), and we show that dIrrs obey the same mass-metallicity relation as the dwarf spheroidal (dSph) satellites of both the Milky Way and M31: Z_* ∝ M_*^(0.30±0.02). The uniformity of the relation is in contradiction to previous estimates of metallicity based on photometry. This relationship is roughly continuous with the stellar mass-stellar metallicity relation for galaxies as massive as M_* = 10^(12) M_☉. Although the average metallicities of dwarf galaxies depend only on stellar mass, the shapes of their metallicity distributions depend on galaxy type. The metallicity distributions of dIrrs resemble simple, leaky box chemical evolution models, whereas dSphs require an additional parameter, such as gas accretion, to explain the shapes of their metallicity distributions. Furthermore, the metallicity distributions of the more luminous dSphs have sharp, metal-rich cut-offs that are consistent with the sudden truncation of star formation due to ram pressure stripping.

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.

Abstract: The rich fossil record of equids has made them a model for evolutionary processes. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560-780 thousand years before present (kyr BP). Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43 kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski's horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0-4.5 million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus. We also find that horse population size fluctuated multiple times over the past 2 Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski's and domestic horse populations diverged 38-72 kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski's horse investigated. This supports the contention that Przewalski's horses represent the last surviving wild horse population. We find similar levels of genetic variation among Przewalski's and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski's horse. Such regions could correspond to loci selected early during domestication.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Abstract: Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

Modeling the Panchromatic Spectral Energy Distributions of Galaxies

Abstract: The spectral energy distributions (SEDs) of galaxies are shaped by nearly every physical property of the system, including the star-formation history, metal content, abundance pattern, dust mass, grain size distribution, star-dust geometry, and interstellar radiation field. The principal goal of stellar population synthesis (SPS) is to extract these variables from observed SEDs. In this review I provide an overview of the SPS technique and discuss what can be reliably measured from galaxy SEDs. Topics include stellar masses, star-formation rates and histories, metallicities and abundance patterns, dust properties, and the stellar initial mass function.

The Crust of the Moon as Seen by GRAIL

Abstract: High-resolution gravity data obtained from the dual Gravity Recovery and Interior Laboratory (GRAIL) spacecraft show that the bulk density of the Moon's highlands crust is 2550 kilograms per cubic meter, substantially lower than generally assumed. When combined with remote sensing and sample data, this density implies an average crustal porosity of 12% to depths of at least a few kilometers. Lateral variations in crustal porosity correlate with the largest impact basins, whereas lateral variations in crustal density correlate with crustal composition. The low-bulk crustal density allows construction of a global crustal thickness model that satisfies the Apollo seismic constraints, and with an average crustal thickness between 34 and 43 kilometers, the bulk refractory element composition of the Moon is not required to be enriched with respect to that of Earth.

The UCSC genome browser and associated tools

Abstract: The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting.

High energy density asymmetric quasi-solid-state supercapacitor based on porous vanadium nitride nanowire anode.

Abstract: To push the energy density limit of asymmetric supercapacitors (ASCs), a new class of anode materials is needed. Vanadium nitride (VN) holds great promise as anode material for ASCs due to its large specific capacitance, high electrical conductivity, and wide operation windows in negative potential. However, its poor electrochemical stability severely limits its application in SCs. In this work, we demonstrated high energy density, stable, quasi-solid-state ASC device based on porous VN nanowire anode and VOx nanowire cathode for the first time. The VOx//VN-ASC device exhibited a stable electrochemical window of 1.8 V and excellent cycling stability with only 12.5% decrease of capacitance after 10 000 cycles. More importantly, the VOx//VN-ASC device achieved a high energy density of 0.61 mWh cm–3 at current density of 0.5 mA cm–2 and a high power density of 0.85 W cm–3 at current density of 5 mA cm–2. These values are substantially enhanced compared to most of the reported quasi/all-solid-state SC devices...

Measurement of an excess of B̄→D(*) τ-ν̄τ decays and implications for charged Higgs bosons

Abstract: The concept for this analysis is to a large degree based on earlier BABAR work and we acknowledge the guidance provided by M. Mazur. The authors consulted with theorists A. Datta, S. Westhoff, S. Fajfer, J. Kamenik, and I. Nisandzic on the calculations of the charged Higgs contributions to the decay rates. We are grateful for the extraordinary contributions of our PEP-II colleagues in achieving the excellent luminosity and machine conditions that have made this work possible. The success of this project also relied critically on the expertise and dedication of the computing organizations that support BABAR. The collaborating institutions wish to thank SLAC for its support and the kind hospitality extended to them. This work is supported by the U.S. Department of Energy and National Science Foundation, the Natural Sciences and Engineering Research Council (Canada), the Commissariat a l'Energie Atomique and Institut National de Physique Nucleaire et de Physique des Particules (France), the Bundesministerium fur Bildung und Forschung and Deutsche Forschungsgemeinschaft (Germany), the Istituto Nazionale di Fisica Nucleare (Italy), the Foundation for Fundamental Research on Matter (Netherlands), the Research Council of Norway, the Ministry of Education and Science of the Russian Federation, Ministerio de Economia y Competitividad (Spain), and the Science and Technology Facilities Council (United Kingdom). Individuals have received support from the Marie-Curie IEF program (European Union) and the A. P. Sloan Foundation (USA).

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Abstract: Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. (Continued on next page)

A Tour of Modern Image Filtering: New Insights and Methods, Both Practical and Theoretical

Abstract: In this article, the author presents a practical and accessible framework to understand some of the basic underpinnings of these methods, with the intention of leading the reader to a broad understanding of how they interrelate. The author also illustrates connections between these techniques and more classical (empirical) Bayesian approaches. The proposed framework is used to arrive at new insights and methods, both practical and theoretical. In particular, several novel optimality properties of algorithms in wide use such as block-matching and three-dimensional (3-D) filtering (BM3D), and methods for their iterative improvement (or nonexistence thereof) are discussed. A general approach is laid out to enable the performance analysis and subsequent improvement of many existing filtering algorithms. While much of the material discussed is applicable to the wider class of linear degradation models beyond noise (e.g., blur,) to keep matters focused, we consider the problem of denoising here.

Why Don't the Poor Save More? Evidence from Health Savings Experiments

Abstract: Using data from a field experiment in Kenya, we document that providing individuals with simple informal savings technologies can substantially increase investment in preventative health and reduce vulnerability to health shocks. Simply providing a safe place to keep money was sufficient to increase health savings by 66 percent. Adding an earmarking feature was only helpful when funds were put toward emergencies, or for individuals that are frequently taxed by friends and relatives. Group-based savings and credit schemes had very large effects.

CANDELS multi-wavelength catalogs: source detection and photometry in the GOODS-South field

Abstract: We present a UV to mid-infrared multi-wavelength catalog in the CANDELS/GOODS-S field, combining the newly obtained CANDELS HST/WFC3 F105W, F125W, and F160W data with existing public data. The catalog is based on source detection in the WFC3 F160W band. The F160W mosaic includes the data from CANDELS deep and wide observations as well as previous ERS and HUDF09 programs. The mosaic reaches a 5? limiting depth (within an aperture of radius 0.''17) of 27.4, 28.2, and 29.7?AB for CANDELS wide, deep, and HUDF regions, respectively. The catalog contains 34,930 sources with the representative 50% completeness reaching 25.9, 26.6, and 28.1?AB in the F160W band for the three regions. In addition to WFC3 bands, the catalog also includes data from UV (U band from both CTIO/MOSAIC and VLT/VIMOS), optical (HST/ACS F435W, F606W, F775W, F814W, and F850LP), and infrared (HST/WFC3 F098M, VLT/ISAAC Ks, VLT/HAWK-I Ks, and Spitzer/IRAC 3.6, 4.5, 5.8, 8.0 ?m) observations. The catalog is validated via stellar colors, comparison with other published catalogs, zero-point offsets determined from the best-fit templates of the spectral energy distribution of spectroscopically observed objects, and the accuracy of photometric redshifts. The catalog is able to detect unreddened star-forming (passive) galaxies with stellar mass of 1010 M ? at a 50% completeness level to z ~ 3.4 (2.8), 4.6 (3.2), and 7.0 (4.2) in the three regions. As an example of application, the catalog is used to select both star-forming and passive galaxies at z ~ 2-4 via the Balmer break. It is also used to study the color-magnitude diagram of galaxies at 0 < z < 4.