Showing papers by "University of California, Santa Cruz published in 2015"
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TL;DR: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations, and has reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-generation sequencing, deep exome sequencing, and dense microarray genotyping.
Abstract: The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.
12,661 citations
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Massachusetts Institute of Technology1, Broad Institute2, University of California, Los Angeles3, University of British Columbia4, Baylor College of Medicine5, Howard Hughes Medical Institute6, University of Washington7, Ludwig Institute for Cancer Research8, University of California, San Francisco9, University of Connecticut10, University of Zagreb11, University of Texas at Austin12, Washington University in St. Louis13, University of Queensland14, Harvard University15, Cold Spring Harbor Laboratory16, University of Southern California17, University of California, Santa Cruz18, Simon Fraser University19, Morgridge Institute for Research20, University of Texas at Dallas21, National Institutes of Health22
TL;DR: It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.
Abstract: The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.
5,037 citations
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Michael S. Lawrence1, Carrie Sougnez1, Lee Lichtenstein1, Kristian Cibulskis1 +306 more•Institutions (26)
TL;DR: It is shown that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1.
Abstract: The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1 Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22 A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53 Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours Therapeutic candidate alterations were identified in most HNSCCs
2,997 citations
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Shadab Alam1, Franco D. Albareti2, Carlos Allende Prieto3, Carlos Allende Prieto4 +360 more•Institutions (102)
TL;DR: The third generation of the Sloan Digital Sky Survey (SDSS-III) took data from 2008 to 2014 using the original SDSS wide-field imager, the original and an upgraded multi-object fiber-fed optical spectrograph, a new near-infrared high-resolution spectrogram, and a novel optical interferometer.
Abstract: The third generation of the Sloan Digital Sky Survey (SDSS-III) took data from 2008 to 2014 using the original SDSS wide-field imager, the original and an upgraded multi-object fiber-fed optical spectrograph, a new near-infrared high-resolution spectrograph, and a novel optical interferometer. All the data from SDSS-III are now made public. In particular, this paper describes Data Release 11 (DR11) including all data acquired through 2013 July, and Data Release 12 (DR12) adding data acquired through 2014 July (including all data included in previous data releases), marking the end of SDSS-III observing. Relative to our previous public release (DR10), DR12 adds one million new spectra of galaxies and quasars from the Baryon Oscillation Spectroscopic Survey (BOSS) over an additional 3000 sq. deg of sky, more than triples the number of H-band spectra of stars as part of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE), and includes repeated accurate radial velocity measurements of 5500 stars from the Multi-Object APO Radial Velocity Exoplanet Large-area Survey (MARVELS). The APOGEE outputs now include measured abundances of 15 different elements for each star. In total, SDSS-III added 2350 sq. deg of ugriz imaging; 155,520 spectra of 138,099 stars as part of the Sloan Exploration of Galactic Understanding and Evolution 2 (SEGUE-2) survey; 2,497,484 BOSS spectra of 1,372,737 galaxies, 294,512 quasars, and 247,216 stars over 9376 sq. deg; 618,080 APOGEE spectra of 156,593 stars; and 197,040 MARVELS spectra of 5,513 stars. Since its first light in 1998, SDSS has imaged over 1/3 of the Celestial sphere in five bands and obtained over five million astronomical spectra.
2,471 citations
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TL;DR: In this paper, the authors argue that the issues about naming relevant to the Anthropocene, Plantationocene, or Capitalocene have to do with scale, rate/speed, synchronicity, and complexity.
Abstract: There is no question that anthropogenic processes have had planetary effects, in inter/intraaction with other processes and species, for as long as our species can be identified (a few tens of thousand years); and agriculture has been huge (a few thousand years). Of course, from the start the greatest planetary terraformers (and reformers) of all have been and still are bacteria and their kin, also in inter/intra-action of myriad kinds (including with people and their practices, technological and otherwise). 1 The spread of seed-dispersing plants millions of years before human agriculture was a planet-changing development, and so were many other revolutionary evolutionary ecological developmental historical events. People joined the bumptious fray early and dynamically, even before they/we were critters who were later named Homo sapiens. But I think the issues about naming relevant to the Anthropocene, Plantationocene, or Capitalocene have to do with scale, rate/speed, synchronicity, and complexity. The constant question when considering systemic phenomena has to be, when do changes in degree become changes in kind, and what are the effects of bioculturally, biotechnically, biopolitically, historically situated people (not Man) relative to, and combined with, the effects of other species assemblages and other biotic/abiotic forces? No species, not even our own arrogant one pretending to be good individuals in so-called modern Western scripts, acts alone; assemblages of organic species and of abiotic actors make history, the evolutionary kind and the other kinds too. But, is there an inflection point of consequence that changes the name of the “game” of life on earth for everybody and everything? It's more than climate change; it's also extraordinary burdens of toxic chemistry, mining, depletion of lakes and rivers under and above ground, ecosystem simplification, vast genocides of people and other critters, etc, etc, in systemically linked patterns that threaten major system collapse after major system collapse after major system collapse. Recursion can be a drag. Anna Tsing in a recent paper called “Feral Biologies” suggests that the inflection point between the Holocene and the Anthropocene might be the wiping out of most of the refugia from which diverse species assemblages (with or without people) can be reconstituted after major events (like desertification, or clear cutting, or, or, …). 2 This is kin to the World-Ecology
1,294 citations
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TL;DR: In this paper, the evolution of the rest-frame UV luminosity function (LF) from to was mapped using the HST data sets from optical, near-IR, and mid-IR observations.
Abstract: The remarkable Hubble Space Telescope?(HST) data sets from the CANDELS, HUDF09, HUDF12, ERS, and BoRG/HIPPIES programs have allowed us to map the evolution of the rest-frame UV luminosity function (LF) from to . We develop new color criteria that more optimally utilize the full wavelength coverage from the optical, near-IR, and mid-IR observations over our search fields, while simultaneously minimizing the incompleteness and eliminating redshift gaps. We have identified 5859, 3001, 857, 481, 217, and 6 galaxy candidates at , , , , , and , respectively, from the ?1000 arcmin2 area covered by these data sets. This sample of >10,000 galaxy candidates at is by far the largest assembled to date with HST. The selection of 4?8 candidates over the five CANDELS fields allows us to assess the cosmic variance; the largest variations are at . Our new LF determinations at and span a 6 mag baseline and reach to ?16 AB mag. These determinations agree well with previous estimates, but the larger samples and volumes probed here result in a more reliable sampling of galaxies and allow us to reassess the form of the UV LFs. Our new LF results strengthen our earlier findings to significance for a steeper faint-end slope of the UV LF at , with ? evolving from at to at (and at ), consistent with that expected from the evolution of the halo mass function. We find less evolution in the characteristic magnitude M* from to the observed evolution in the LF is now largely represented by changes in . No evidence for a non-Schechter-like form to the z ? 4?8 LFs is found. A simple conditional LF model based on halo growth and evolution in the M/L ratio of halos provides a good representation of the observed evolution.
1,143 citations
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TL;DR: A unified framework to learn latent representations of sub-structures for graphs, inspired by latest advancements in language modeling and deep learning, which achieves significant improvements in classification accuracy over state-of-the-art graph kernels.
Abstract: In this paper, we present Deep Graph Kernels, a unified framework to learn latent representations of sub-structures for graphs, inspired by latest advancements in language modeling and deep learning. Our framework leverages the dependency information between sub-structures by learning their latent representations. We demonstrate instances of our framework on three popular graph kernels, namely Graphlet kernels, Weisfeiler-Lehman subtree kernels, and Shortest-Path graph kernels. Our experiments on several benchmark datasets show that Deep Graph Kernels achieve significant improvements in classification accuracy over state-of-the-art graph kernels.
1,074 citations
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TL;DR: A browser for the first new human genome reference assembly in 4 years in December 2013, a watershed comparative genomics annotation (100-species multiple alignment and conservation), and a novel distribution mechanism for the browser are among the highlights of the past year.
Abstract: Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.
984 citations
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TL;DR: Today’s low rates of marine extinction may be the prelude to a major extinction pulse, similar to that observed on land during the industrial revolution, as the footprint of human ocean use widens.
Abstract: BACKGROUND: Comparing patterns of ter- restrial and marine defaunation helps to place human impacts on marine fauna in context and to navigate toward recovery. De- faunation began in ear- nest tens of thousands of years later in the oceans than it did on land. Al- though defaunation has been less severe in the oceans than on land, our effects on marine animals are increasing in pace and impact. Humans have caused few complete extinctions in the sea, but we are responsible for many ecological, commercial, and local extinctions. Despite our late start, humans have already powerfully changed virtually all major marine ecosystems. ADVANCES: Humans have profoundly de- creased the abundance of both large (e.g., whales) and small (e.g., anchovies) marine fauna. Such declines can generate waves of ecological change that travel both up and down marine food webs and can alter ocean ecosystem functioning. Human harvesters have also been a major force of evolutionary change in the oceans and have reshaped the genetic structure of marine animal popula- tions. Climate change threatens toaccelerate marine defaunation over the next century. The high mobility of many marine animals offers some increased, though limited, ca- pacity for marine species to respond to cli- mate stress, but it also exposes many species to increased risk from other stressors. Be- cause humans are intensely reliant on ocean ecosystems for food and other ecosystem ser- vices, we are deeply affected by all of these forecasted changes. Three lessons emerge when comparing the marine and terrestrial defaunation ex-
898 citations
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TL;DR: It is shown that YS MFs are the main precursors of microglia, while most other MFs derive from fetal monocytes (MOs), which arise from erythro-myeloid progenitors (EMPs) generated in the YS.
814 citations
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TL;DR: In this paper, the authors present an analysis of the deep Herschel images in four major extragalactic fields Goodfellow-Herschel, CANDELS, UDS, and COSMOS.
Abstract: We present an analysis of the deepest Herschel images in four major extragalactic fields GOODS–North, GOODS–South, UDS, and COSMOS obtained within the GOODS–Herschel and CANDELS–Herschel key programs. The star formation picture provided by a total of 10 497 individual far-infrared detections is supplemented by the stacking analysis of a mass complete sample of 62 361 star-forming galaxies from the Hubble Space Telescope (HST) H band-selected catalogs of the CANDELS survey and from two deep ground-based Ks band-selected catalogs in the GOODS–North and the COSMOS-wide field to obtain one of the most accurate and unbiased understanding to date of the stellar mass growth over the cosmic history. We show, for the first time, that stacking also provides a powerful tool to determine the dispersion of a physical correlation and describe our method called “scatter stacking”, which may be easily generalized to other experiments. The combination of direct UV and far-infrared UV-reprocessed light provides a complete census on the star formation rates (SFRs), allowing us to demonstrate that galaxies at z = 4 to 0 of all stellar masses (M∗) follow a universal scaling law, the so-called main sequence of star-forming galaxies. We find a universal close-to-linear slope of the log 10(SFR)–log 10(M∗) relation, with evidence for a flattening of the main sequence at high masses (log 10(M∗/M⊙) > 10.5) that becomesless prominent with increasing redshift and almost vanishes by z ≃ 2. This flattening may be due to the parallel stellar growth of quiescent bulges in star-forming galaxies, which mostly happens over the same redshift range. Within the main sequence, we measure a nonvarying SFR dispersion of 0.3 dex: at a fixed redshift and stellar mass, about 68% of star-forming galaxies form stars at a universal rate within a factor 2. The specific SFR (sSFR = SFR/M∗) of star-forming galaxies is found to continuously increase from z = 0 to 4. Finally we discuss the implications of our findings on the cosmic SFR history and on the origin of present-day stars: more than two-thirds of present-day stars must have formed in a regime dominated by the “main sequence” mode. As a consequence we conclude that, although omnipresent in the distant Universe, galaxy mergers had little impact in shaping the global star formation history over the last 12.5 billion years.
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University of Texas at Austin1, Space Telescope Science Institute2, Texas A&M University3, Rutgers University4, University of Massachusetts Amherst5, Harvard University6, University of Edinburgh7, University of California, Santa Cruz8, Aix-Marseille University9, Colby College10, University of California, Riverside11, University of Pittsburgh12, Goddard Space Flight Center13
TL;DR: In this article, a robust measurement and analysis of the rest-frame ultraviolet (UV) luminosity function at z = 4 to 8.5 was presented, with more than 1000 galaxies at z of approximately 6 - 8.4.
Abstract: We present a robust measurement and analysis of the rest-frame ultraviolet (UV) luminosity function at z = 4 to 8. We use deep Hubble Space Telescope imaging over the CANDELS/GOODS fields, the Hubble Ultra Deep Field and the Hubble Frontier Field deep parallel observations near the Abell 2744 and MACS J0416.1- 2403 clusters. The combination of these surveys provides an effective volume of 0.6-1.2 ×10(exp 6) Mpc(exp 3) over this epoch, allowing us to perform a robust search for bright (M(sub UV) less than −21) and faint (M(sub UV) = −18) galaxies. We select galaxies using a well-tested photometric redshift technique with careful screening of contaminants, finding a sample of 7446 galaxies at 3.5 less than z less than 8.5, with more than 1000 galaxies at z of approximately 6 - 8. We measure both a stepwise luminosity function for galaxies in our redshift samples, as well as a Schechter function, using a Markov Chain Monte Carlo analysis to measure robust uncertainties. At the faint end our UV luminosity functions agree with previous studies, yet we find a higher abundance of UV-bright galaxies at z of greater than or equal to 6. Our bestfit value of the characteristic magnitude M* is consistent with −21 at z of greater than or equal to 5, different than that inferred based on previous trends at lower redshift. At z = 8, a single power-law provides an equally good fit to the UV luminosity function, while at z = 6 and 7, an exponential cutoff at the bright-end is moderately preferred. We compare our luminosity functions to semi-analytical models, and find that the lack of evolution in M* is consistent with models where the impact of dust attenuation on the bright-end of the luminosity function decreases at higher redshift, though a decreasing impact of feedback may also be possible. We measure the evolution of the cosmic star-formation rate (SFR) density by integrating our observed luminosity functions to M(sub UV) = −17, correcting for dust attenuation, and find that the SFR density declines proportionally to (1 + z)((exp −4.3)(+/-)(0.5)) at z greater than 4, consistent with observations at z greater than or equal to 9. Our observed luminosity functions are consistent with a reionization history that starts at redshift of approximately greater than 10, completes at z greater than 6, and reaches a midpoint (x(sub HII) = 0.5) at 6.7 less than z less than 9.4. Finally, using a constant cumulative number density selection and an empirically derived rising star-formation history, our observations predict that the abundance of bright z = 9 galaxies is likely higher than previous constraints, though consistent with recent estimates of bright z similar to 10 galaxies.
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TL;DR: In this article, the authors proposed a confidence interval that does not require equal variances or equal covariances and demonstrated that the proposed method performed better than alternative methods, and also presented some sample size formulas that approximate the sample size requirements for desired power or desired confidence interval precision.
Abstract: Summary
Cronbach's alpha is one of the most widely used measures of reliability in the social and organizational sciences. Current practice is to report the sample value of Cronbach's alpha reliability, but a confidence interval for the population reliability value also should be reported. The traditional confidence interval for the population value of Cronbach's alpha makes an unnecessarily restrictive assumption that the multiple measurements have equal variances and equal covariances. We propose a confidence interval that does not require equal variances or equal covariances. The results of a simulation study demonstrated that the proposed method performed better than alternative methods. We also present some sample size formulas that approximate the sample size requirements for desired power or desired confidence interval precision. R functions are provided that can be used to implement the proposed confidence interval and sample size methods. Copyright © 2014 John Wiley & Sons, Ltd.
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TL;DR: This work presents a single-nucleotide-variant detection tool that uses maximum-likelihood parameter estimates and marginalization over many possible read alignments to achieve precision and recall of up to 99% by pairing the authors' high-confidence alignment strategy with long MinION reads.
Abstract: Speed, single-base sensitivity and long read lengths make nanopores a promising technology for high-throughput sequencing. We evaluated and optimized the performance of the MinION nanopore sequencer using M13 genomic DNA and used expectation maximization to obtain robust maximum-likelihood estimates for insertion, deletion and substitution error rates (4.9%, 7.8% and 5.1%, respectively). Over 99% of high-quality 2D MinION reads mapped to the reference at a mean identity of 85%. We present a single-nucleotide-variant detection tool that uses maximum-likelihood parameter estimates and marginalization over many possible read alignments to achieve precision and recall of up to 99%. By pairing our high-confidence alignment strategy with long MinION reads, we resolved the copy number for a cancer-testis gene family (CT47) within an unresolved region of human chromosome Xq24.
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Lawrence Livermore National Laboratory1, Stanford University2, University of California, Berkeley3, University of Arizona4, University of California, San Diego5, Ames Research Center6, Herzberg Institute of Astrophysics7, University of Victoria8, Space Telescope Science Institute9, Arizona State University10, Université de Montréal11, Los Alamos National Laboratory12, University of California, Los Angeles13, University of Western Ontario14, Subaru15, University of Hertfordshire16, Princeton University17, University of Toronto18, Centre national de la recherche scientifique19, University of Chicago20, University of California, Santa Cruz21, Durham University22, University of Exeter23, University of Georgia24, Stony Brook University25, University of California, Santa Barbara26, American Museum of Natural History27, University of Chile28, Universities Space Research Association29, Cornell University30, University of Toledo31, California Institute of Technology32
TL;DR: Using the Gemini Planet Imager, a Jupiter-like planet is discovered orbiting the ~20-million-year-old star 51 Eridani at a projected separation of 13 astronomical units and has a methane signature and is probably the smallest exoplanet that has been directly imaged.
Abstract: Directly detecting thermal emission from young extrasolar planets allows measurement of their atmospheric compositions and luminosities, which are influenced by their formation mechanisms. Using the Gemini Planet Imager, we discovered a planet orbiting the ~20-million-year-old star 51 Eridani at a projected separation of 13 astronomical units. Near-infrared observations show a spectrum with strong methane and water-vapor absorption. Modeling of the spectra and photometry yields a luminosity (normalized by the luminosity of the Sun) of 1.6 to 4.0 × 10(-6) and an effective temperature of 600 to 750 kelvin. For this age and luminosity, "hot-start" formation models indicate a mass twice that of Jupiter. This planet also has a sufficiently low luminosity to be consistent with the "cold-start" core-accretion process that may have formed Jupiter.
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TL;DR: The diverse range of polysaccharide structures, properties, and roles highlight the importance of this matrix constituent to the successful adaptation of bacteria to nearly every niche.
Abstract: Microbes produce a biofilm matrix consisting of proteins, extracellular DNA, and polysaccharides that is integral in the formation of bacterial communities. Historical studies of polysaccharides revealed that their overproduction often alters the colony morphology and can be diagnostic in identifying certain species. The polysaccharide component of the matrix can provide many diverse benefits to the cells in the biofilm, including adhesion, protection, and structure. Aggregative polysaccharides act as molecular glue, allowing the bacterial cells to adhere to each other as well as surfaces. Adhesion facilitates the colonization of both biotic and abiotic surfaces by allowing the bacteria to resist physical stresses imposed by fluid movement that could separate the cells from a nutrient source. Polysaccharides can also provide protection from a wide range of stresses, such as desiccation, immune effectors, and predators such as phagocytic cells and amoebae. Finally, polysaccharides can provide structure to biofilms, allowing stratification of the bacterial community and establishing gradients of nutrients and waste products. This can be advantageous for the bacteria by establishing a heterogeneous population that is prepared to endure stresses created by the rapidly changing environments that many bacteria encounter. The diverse range of polysaccharide structures, properties, and roles highlight the importance of this matrix constituent to the successful adaptation of bacteria to nearly every niche. Here, we present an overview of the current knowledge regarding the diversity and benefits that polysaccharide production provides to bacterial communities within biofilms.
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TL;DR: The challenges of understanding the role protists play in geochemical cycling in the oceans are reviewed, and researchers must bring the conceptual framework of systems biology into bigger “ecosystems biology” models that broadly capture the geochemical activities of interacting plankton networks.
Abstract: BACKGROUND Marine ecosystems are composed of a diverse array of life forms, the majority of which are unicellular—archaea, bacteria, and eukaryotes. The power of these microbes to process carbon, shape Earth’s atmosphere, and fuel marine food webs has been established over the past 40 years. The marine biosphere is responsible for approximately half of global primary production, rivaling that of land plants. Unicellular eukaryotes (protists) are major contributors to this ocean productivity. In addition to photosynthetic growth, protists exhibit a range of other trophic modes, including predation, mixotrophy (a combination of photosynthetic and predatory-based nutrition), parasitism, symbiosis, osmotrophy, and saprotrophy (wherein extracellular enzymes break down organic matter to smaller compounds that are then transported into the cell by osmotrophy). ADVANCES Sensitive field approaches have illuminated the enormous diversity of protistan life (much of it uncultured) and, coupled with activity measurements, are leading to hypotheses about their ecological roles. In parallel, large-scale sequencing projects are providing fundamental advances in knowledge of genome/gene composition, especially among photosynthetic lineages, many of which are complex amalgams derived from multiple endosymbiotic mergers. Marine protists have yielded insight into basic biology, evolution, and molecular machineries that control organismal responses to the environment. These studies reveal tightly controlled signaling and transcriptional regulation as well as responses to limitation of resources such as iron, nitrogen, and vitamins, and offer understanding of animal and plant evolution. With the formulation of better computational approaches, hypotheses about interactions and trophic exchanges are becoming more exact and modelers more assertive at integrating different data types. At the same time, the impacts of climate change are being reported in multiple systems, of which polar environments are the touchstone of change. OUTLOOK Driven by the need to translate the biology of cells into processes at global scales, researchers must bring the conceptual framework of systems biology into bigger “ecosystems biology” models that broadly capture the geochemical activities of interacting plankton networks. Existing data show that protists are major components of marine food webs, but deducing and quantifying their ecosystem linkages and the resulting influences on carbon cycling is difficult. Genome-based functional predictions are complicated by the importance of cellular structures and flexible behaviors in protists, which are inherently more difficult to infer than the biochemical pathways typically studied in prokaryotes. Alongside the plethora of genes of unknown function, manipulable genetic systems are rare for marine protists. The development of genetic systems and gene editing for diverse, ecologically important lineages, as well as innovative tools for preserving microbe-microbe interactions during sampling, for visual observation, and for quantifying biogeochemical transformations, are critical but attainable goals. These must be implemented in both field work and laboratory physiology studies that examine multiple environmental factors. Expanding genome functional predictions to identify the molecular underpinnings of protistan trophic modes and realistically constrain metabolism will position the field to build reliable cell systems biology models and link these to field studies. By factoring in true complexities, we can capture key elements of protistan interactions for assimilation into more predictive global carbon cycle models.
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California Institute of Technology1, Imperial College London2, University of California, Santa Cruz3, Indiana University4, University of California, Davis5, Washington University in St. Louis6, United States Geological Survey7, Smithsonian Institution8, University of Tennessee9, Johns Hopkins University10, University of Nantes11, Planetary Science Institute12, Western Washington University13, Ames Research Center14, Goddard Space Flight Center15, University of California, Berkeley16, University of Lyon17, Texas A&M University18, University of Guelph19, Stony Brook University20, University of Texas at Austin21, Brown University22, University of New Mexico23, Los Alamos National Laboratory24
TL;DR: The observations suggest that individual lakes were stable on the ancient surface of Mars for 100 to 10,000 years, a minimum duration when each lake was stable both thermally (as liquid water) and in terms of mass balance (with inputs effectively matching evaporation and loss of water to colder regions).
Abstract: The landforms of northern Gale crater on Mars expose thick sequences of sedimentary rocks. Based on images obtained by the Curiosity rover, we interpret these outcrops as evidence for past fluvial, deltaic, and lacustrine environments. Degradation of the crater wall and rim probably supplied these sediments, which advanced inward from the wall, infilling both the crater and an internal lake basin to a thickness of at least 75 meters. This intracrater lake system probably existed intermittently for thousands to millions of years, implying a relatively wet climate that supplied moisture to the crater rim and transported sediment via streams into the lake basin. The deposits in Gale crater were then exhumed, probably by wind-driven erosion, creating Aeolis Mons (Mount Sharp).
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University of Maine1, National Oceanic and Atmospheric Administration2, University of Rhode Island3, University of Western Ontario4, University of California, Santa Cruz5, Mie University6, Council of Scientific and Industrial Research7, University of Gothenburg8, Woods Hole Oceanographic Institution9, San Francisco State University10
TL;DR: Forecasting changes in HAB patterns over the next few decades will depend critically upon considering harmful algal blooms within the competitive context of plankton communities, and linking these insights to ecosystem, oceanographic and climate models.
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TL;DR: In this article, the authors used cosmological simulations to study a characteristic evolution pattern of high-redshift galaxies, which is consistent with the way galaxies populate the SFR-size-mass space, and with gradients and scatter across the main sequence.
Abstract: We use cosmological simulations to study a characteristic evolution pattern of high-redshift galaxies. Early, stream-fed, highly perturbed, gas-rich discs undergo phases of dissipative contraction into compact, star-forming systems (‘blue’ nuggets) at z ∼ 4–2. The peak of gas compaction marks the onset of central gas depletion and inside-out quenching into compact ellipticals (red nuggets) by z ∼ 2. These are sometimes surrounded by gas rings or grow extended dry stellar envelopes. The compaction occurs at a roughly constant specific star formation rate (SFR), and the quenching occurs at a constant stellar surface density within the inner kpc (Σ
1
). Massive galaxies quench earlier, faster, and at a higher Σ
1 than lower mass galaxies, which compactify and attempt to quench more than once. This evolution pattern is consistent with the way galaxies populate the SFR-size–mass space, and with gradients and scatter across the main sequence. The compaction is triggered by an intense inflow episode, involving (mostly minor) mergers, counter-rotating streams or recycled gas, and is commonly associated with violent disc instability. The contraction is dissipative, with the inflow rate >SFR, and the maximum Σ
1 anticorrelated with the initial spin parameter. The central quenching is triggered by the high SFR and stellar/supernova feedback (maybe also active galactic nucleus feedback) due to the high central gas density, while the central inflow weakens as the disc vanishes. Suppression of fresh gas supply by a hot halo allows the long-term maintenance of quenching once above a threshold halo mass, inducing the quenching downsizing.
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Smithsonian Conservation Biology Institute1, Smithsonian Tropical Research Institute2, National Museum of Natural History3, University of Alabama4, Stanford University5, Wilfrid Laurier University6, Mahidol University7, Department of National Parks, Wildlife and Plant Conservation8, University of Aberdeen9, University of Queensland10, Environmental Change Institute11, Xishuangbanna Tropical Botanical Garden12, University of Buea13, Indiana University14, United States Forest Service15, Indian Institute of Science16, Chinese Academy of Sciences17, National University of Colombia18, Forest Research Institute Malaysia19, University of California, Santa Cruz20, University of Peradeniya21, University of Hong Kong22, University of Alberta23, Oak Ridge National Laboratory24, University of Wisconsin–Green Bay25, University of California, Los Angeles26, College of Tropical Agriculture and Human Resources27, Wageningen University and Research Centre28, Kyoto University29, University of Nairobi30, Wildlife Conservation Society31, University of Montana32, Nanyang Technological University33, Utah State University34, Smithsonian Environmental Research Center35, Centre national de la recherche scientifique36, Natural England37, Washington University in St. Louis38, Academy of Sciences of the Czech Republic39, University of São Paulo40, University of the Philippines Diliman41, Harvard University42, University of Hawaii at Hilo43, Maejo University44, National Dong Hwa University45, University of Toronto46, Washington State University Vancouver47, University of Puerto Rico, Río Piedras48, Columbia University49, Pontificia Universidad Católica del Ecuador50, National Institute of Amazonian Research51, East China Normal University52, University of Minnesota53
TL;DR: The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.
Abstract: Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25ha), all stems 1cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 degrees S-61 degrees N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 degrees C), changes in precipitation (up to +/- 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8g Nm(-2)yr(-1) and 3.1g Sm(-2)yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.
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TL;DR: It is shown that MPP2 and MPP3 are distinct myeloid-biased MPP subsets that work together with lymphoid-primed MPP4 cells to control blood production, and these results support a dynamic model of blood development in which HSCs convey lineage specification through independent production of distinct lineage-biased MPs that, in turn, support lineage expansion and differentiation.
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TL;DR: In this paper, a grid of supernovae resulting from massive stars with solar metallicity and masses from 9.0 to 120 solar masses are calculated for nucleosynthesis, light curves, explosion energies, and remnant masses.
Abstract: Nucleosynthesis, light curves, explosion energies, and remnant masses are calculated for a grid of supernovae resulting from massive stars with solar metallicity and masses from 9.0 to 120 solar masses. The full evolution is followed using an adaptive reaction network of up to 2000 nuclei. A novel aspect of the survey is the use of a one-dimensional neutrino transport model for the explosion. This explosion model has been calibrated to give the observed energy for SN 1987A, using several standard progenitors, and for the Crab supernova using a 9.6 solar mass progenitor. As a result of using a calibrated central engine, the final kinetic energy of the supernova is variable and sensitive to the structure of the presupernova star. Many progenitors with extended core structures do not explode, but become black holes, and the masses of exploding stars do not form a simply connected set. The resulting nucleosynthesis agrees reasonably well with the sun provided that a reasonable contribution from Type Ia supernovae is also allowed, but with a deficiency of light s-process isotopes. The resulting neutron star IMF has a mean gravitational mass near 1.4 solar masses. The average black hole mass is about 9 solar masses if only the helium core implodes, and 14 solar masses if the entire presupernova star collapses. Only ~10% of supernovae come from stars over 20 solar masses and some of these are Type Ib or Ic. Some useful systematics of Type IIp light curves are explored.
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TL;DR: The New Horizons encounter revealed that Pluto displays a surprisingly wide variety of geological landforms, including those resulting from glaciological and surface-atmosphere interactions as well as impact, tectonic, possible cryovolcanic, and mass-wasting processes.
Abstract: The Pluto system was recently explored by NASA's New Horizons spacecraft, making closest approach on 14 July 2015. Pluto's surface displays diverse landforms, terrain ages, albedos, colors, and composition gradients. Evidence is found for a water-ice crust, geologically young surface units, surface ice convection, wind streaks, volatile transport, and glacial flow. Pluto's atmosphere is highly extended, with trace hydrocarbons, a global haze layer, and a surface pressure near 10 microbars. Pluto's diverse surface geology and long-term activity raise fundamental questions about how small planets remain active many billions of years after formation. Pluto's large moon Charon displays tectonics and evidence for a heterogeneous crustal composition; its north pole displays puzzling dark terrain. Small satellites Hydra and Nix have higher albedos than expected.
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TL;DR: How ecologists are using miniature sensors to answer new questions about the physiological performance, energetics, foraging, migration, habitat selection, and sociality of wild animals, as well as collect data on the environments in which they live is explored.
Abstract: Great leaps forward in scientific understanding are often spurred by innovations in technology. The explosion of miniature sensors that are driving the boom in consumer electronics, such as smart phones, gaming platforms, and wearable fitness devices, are now becoming available to ecologists for remotely monitoring the activities of wild animals. While half a century ago researchers were attaching balloons to the backs of seals to measure their movement, today ecologists have access to an arsenal of sensors that can continuously measure most aspects of an animal's state (e.g., location, behavior, caloric expenditure, interactions with other animals) and external environment (e.g., temperature, salinity, depth). This technology is advancing our ability to study animal ecology by allowing researchers to (1) answer questions about the physiology, behavior, and ecology of wild animals in situ that would have previously been limited to tests on model organisms in highly controlled settings, (2) study cryptic or wide-ranging animals that have previously evaded investigation, and (3) develop and test entirely new theories. Here we explore how ecologists are using these tools to answer new questions about the physiological performance, energetics, foraging, migration, habitat selection, and sociality of wild animals, as well as collect data on the environments in which they live.
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Brigham and Women's Hospital1, Broad Institute2, Harvard University3, University of Leicester4, Boston Children's Hospital5, University of Toronto6, Maastricht University7, Radboud University Nijmegen8, Google9, McGill University10, Leiden University Medical Center11, Cambridge University Hospitals NHS Foundation Trust12, Baylor College of Medicine13, Oregon Health & Science University14, Johns Hopkins University15, Children's Hospital of Eastern Ontario16, Wellcome Trust Sanger Institute17, Lawrence Berkeley National Laboratory18, European Bioinformatics Institute19, University of California, Santa Cruz20, University of Applied Sciences Leiden21, Genetic Alliance22, University of Miami23
TL;DR: The Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API).
Abstract: There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.
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University of California, Berkeley1, University of California, Los Angeles2, University of California, Riverside3, University of California, San Diego4, Space Telescope Science Institute5, Yale University6, University of Cambridge7, W.M. Keck Observatory8, University of California, Irvine9, Harvard University10, University of California, Santa Cruz11, University of the Western Cape12
TL;DR: The MOSFIRE Deep Evolution Field (MOSDEF) survey as discussed by the authors was the first large-scale deep evolution field (DEDF) survey, which aims to obtain moderate-resolution (R = 3000-3650) rest-frame optical spectra (∼3700-7000 Å) for ∼1500 galaxies at in three well-studied CANDELS fields: AEGIS, COSMOS, and GOODS-N. In addition, 55 additional galaxies were serendipitously detected.
Abstract: In this paper we present the MOSFIRE Deep Evolution Field (MOSDEF) survey. The MOSDEF survey aims to obtain moderate-resolution (R = 3000–3650) rest-frame optical spectra (∼3700–7000 Å) for ∼1500 galaxies at in three well-studied CANDELS fields: AEGIS, COSMOS, and GOODS-N. Targets are selected in three redshift intervals: , , and , down to fixed (F160W) magnitudes of 24.0, 24.5, and 25.0, respectively, using the photometric and spectroscopic catalogs from the 3D-HST survey. We target both strong nebular emission lines (e.g., [O ii] , Hβ, [O iii] , Hα, [N ii] , and [S ii] ) and stellar continuum and absorption features (e.g., Balmer lines, Ca-ii H and K, Mgb, 4000 Å break). Here we present an overview of our survey, the observational strategy, the data reduction and analysis, and the sample characteristics based on spectra obtained during the first 24 nights. To date, we have completed 21 masks, obtaining spectra for 591 galaxies. For ∼80% of the targets we derive a robust redshift from either emission or absorption lines. In addition, we confirm 55 additional galaxies, which were serendipitously detected. The MOSDEF galaxy sample includes unobscured star-forming, dusty star-forming, and quiescent galaxies and spans a wide range in stellar mass () and star formation rate (). The spectroscopically confirmed sample is roughly representative of an H-band limited galaxy sample at these redshifts. With its large sample size, broad diversity in galaxy properties, and wealth of available ancillary data, MOSDEF will transform our understanding of the stellar, gaseous, metal, dust, and black hole content of galaxies during the time when the universe was most active.
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Lawrence Livermore National Laboratory1, Stanford University2, University of California, Berkeley3, University of Arizona4, University of California, San Diego5, Ames Research Center6, University of Victoria7, Herzberg Institute of Astrophysics8, Space Telescope Science Institute9, Arizona State University10, Université de Montréal11, Los Alamos National Laboratory12, University of California, Los Angeles13, University of Western Ontario14, Subaru15, University of Hertfordshire16, Princeton University17, University of Toronto18, Centre national de la recherche scientifique19, University of Chicago20, University of California, Santa Cruz21, Durham University22, University of Exeter23, University of Georgia24, Stony Brook University25, University of California, Santa Barbara26, American Museum of Natural History27, University of Chile28, Universities Space Research Association29, Cornell University30, University of Toledo31, California Institute of Technology32
TL;DR: In this paper, the Gemini Planet Imager was used to detect a planet orbiting the star 51 Eridani at a projected separation of 13 astronomical units, with a spectrum with strong methane and water vapor absorption.
Abstract: Directly detecting thermal emission from young extrasolar planets allows measurement of their atmospheric composition and luminosity, which is influenced by their formation mechanism. Using the Gemini Planet Imager, we discovered a planet orbiting the \$sim$20 Myr-old star 51 Eridani at a projected separation of 13 astronomical units. Near-infrared observations show a spectrum with strong methane and water vapor absorption. Modeling of the spectra and photometry yields a luminosity of L/LS=1.6-4.0 x 10-6 and an effective temperature of 600-750 K. For this age and luminosity, "hot-start" formation models indicate a mass twice that of Jupiter. This planet also has a sufficiently low luminosity to be consistent with the "cold- start" core accretion process that may have formed Jupiter.
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TL;DR: Madau et al. as discussed by the authors assess a model of late cosmic reionization in which the ionizing background radiation arises entirely from highredshift quasars and other active galactic nuclei (AGNs).
Abstract: Author(s): Madau, P; Haardt, F | Abstract: We assess a model of late cosmic reionization in which the ionizing background radiation arises entirely from highredshift quasars and other active galactic nuclei (AGNs). The low optical depth to Thomson scattering reported by the Planck Collaboration pushes the redshift of instantaneous reionization down to z = 8.8-1.4+1.7and greatly reduces the need for significant Lyman-continuum emission at very early times. We show that if recent claims of a numerous population of faint AGNs at z = 4-6 are upheld and the high inferred AGN comoving emissivity at these epochs persists to higher, z ≳ 10, redshifts, then active galaxies may drive the reionization of hydrogen and helium with little contribution from normal star-forming galaxies. We discuss an AGN-dominated scenario that satisfies a number of observational constraints: the H I photoionization rate is relatively flat over the range 2 l z l 5, hydrogen gets fully reionized by z ; 5.7, and the integrated Thomson scattering optical depth is τ ; 0.056, in agreement with measurements based on the Lyα opacity of the intergalactic medium (IGM) and cosmic microwave background polarization. It is a prediction of the model that helium gets doubly reionized before redshift 4, the heat input from helium reionization dominates the thermal balance of the IGM after hydrogen reionization, and z g 5 AGNs provide a significant fraction of the unresolved X-ray background at 2 keV. Singly and doubly ionized helium contribute about 13% to τ, and the He III volume fraction is already 50% when hydrogen becomes fully reionized.
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TL;DR: In this article, the authors report the discovery of an extremely long (∼110 Mpc/h) and dark (τeff≳7) Lyα trough extending down to z≃5.5 towards the zem≃6.0 quasar ULAS J0148+0600.
Abstract: We report the discovery of an extremely long (∼110 Mpc/h) and dark (τeff≳7) Lyα trough extending down to z≃5.5 towards the zem≃6.0 quasar ULAS J0148+0600. We use these new data in combination with Lyα forest measurements from 42 quasars at 4.5≤zem≤6.4 to conduct an updated analysis of the line-of-sight variance in the intergalactic Lyα opacity over 4≤z≤6. We find that the scatter in transmission among lines of sight near z∼6 significantly exceeds theoretical expectations for either a uniform ultraviolet background (UVB) or simple fluctuating UVB models in which the mean free path to ionizing photons is spatially invariant. The data, particularly near z≃5.6-5.8, instead require fluctuations in the volume-weighted hydrogen neutral fraction that are a factor of 3 or more beyond those expected from density variations alone. We argue that these fluctuations are most likely driven by large-scale variations in the mean free path, consistent with expectations for the final stages of inhomogeneous hydrogen reionization. Even by z≃5.6, however, a large fraction of the data are consistent with a uniform UVB, and by z∼5 the data are fully consistent with opacity fluctuations arising solely from the density field. This suggests that while reionization may be ongoing at z∼6, it has fully completed by z∼5.