Showing papers by "Lawrence Berkeley National Laboratory published in 2011"
TL;DR: It is reported that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1,BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes.
Abstract: A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.
5,878 citations
University of Zurich1, University of California, Berkeley2, Lawrence Berkeley National Laboratory3, University of Oldenburg4, Max Planck Society5, Leibniz University of Hanover6, University of Antwerp7, Oregon State University8, Technische Universität München9, Cornell University10, Newcastle University11, University of Florence12, Weizmann Institute of Science13
TL;DR: In this article, a new generation of experiments and soil carbon models were proposed to predict the SOM response to global warming, and they showed that molecular structure alone alone does not control SOM stability.
Abstract: Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily—and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.
4,219 citations
TL;DR: In this paper, the topological semimetal, a three-dimensional phase of a magnetic solid, is described and it may be realized in a class of pyrochlore iridates based on calculations using the LDA+U$ method.
Abstract: We investigate novel phases that emerge from the interplay of electron correlations and strong spin-orbit interactions. We focus on describing the topological semimetal, a three-dimensional phase of a magnetic solid, and argue that it may be realized in a class of pyrochlore iridates (such as ${\mathrm{Y}}_{2}$Ir${}_{2}$O${}_{7}$) based on calculations using the $\text{LDA}+U$ method. This state is a three-dimensional analog of graphene with linearly dispersing excitations and provides a condensed-matter realization of Weyl fermions that obeys a two-component Dirac equation. It also exhibits remarkable topological properties manifested by surface states in the form of Fermi arcs, which are impossible to realize in purely two-dimensional band structures. For intermediate correlation strengths, we find this to be the ground state of the pyrochlore iridates, coexisting with noncollinear magnetic order. A narrow window of magnetic ``axion'' insulator may also be present. An applied magnetic field is found to induce a metallic ground state.
3,865 citations
TL;DR: Graphene-based optical modulation mechanism, with combined advantages of compact footprint, low operation voltage and ultrafast modulation speed across a broad range of wavelengths, can enable novel architectures for on-chip optical communications.
Abstract: Graphene, the single-atom-thick form of carbon, holds promise for many applications, notably in electronics where it can complement or be integrated with silicon-based devices. Intense efforts have been devoted to develop a key enabling device, a broadband, fast optical modulator with a small device footprint. Now Liu et al. demonstrate an exciting new possibility for graphene in the area of on-chip optical communication: a graphene-based optical modulator integrated with a silicon chip. This new device relies on the electrical tuning of the Fermi level of the graphene sheet, and achieves modulation of guided light at frequencies over 1 gigahertz, together with a broad operating spectrum. At just 25 square micrometres in area, it is one of the smallest of its type. Integrated optical modulators with high modulation speed, small footprint and large optical bandwidth are poised to be the enabling devices for on-chip optical interconnects1,2. Semiconductor modulators have therefore been heavily researched over the past few years. However, the device footprint of silicon-based modulators is of the order of millimetres, owing to its weak electro-optical properties3. Germanium and compound semiconductors, on the other hand, face the major challenge of integration with existing silicon electronics and photonics platforms4,5,6. Integrating silicon modulators with high-quality-factor optical resonators increases the modulation strength, but these devices suffer from intrinsic narrow bandwidth and require sophisticated optical design; they also have stringent fabrication requirements and limited temperature tolerances7. Finding a complementary metal-oxide-semiconductor (CMOS)-compatible material with adequate modulation speed and strength has therefore become a task of not only scientific interest, but also industrial importance. Here we experimentally demonstrate a broadband, high-speed, waveguide-integrated electroabsorption modulator based on monolayer graphene. By electrically tuning the Fermi level of the graphene sheet, we demonstrate modulation of the guided light at frequencies over 1 GHz, together with a broad operation spectrum that ranges from 1.35 to 1.6 µm under ambient conditions. The high modulation efficiency of graphene results in an active device area of merely 25 µm2, which is among the smallest to date. This graphene-based optical modulation mechanism, with combined advantages of compact footprint, low operation voltage and ultrafast modulation speed across a broad range of wavelengths, can enable novel architectures for on-chip optical communications.
3,105 citations
TL;DR: It is demonstrated that graphene plasmon resonances can be tuned over a broad terahertz frequency range by changing micro-ribbon width and in situ electrostatic doping and the results represent a first look at light-plasmon coupling in graphene and point to potential graphene-based terAhertz metamaterials.
Abstract: Plasmons describe collective oscillations of electrons. They have a fundamental role in the dynamic responses of electron systems and form the basis of research into optical metamaterials 1–3 . Plasmons of two-dimensional massless electrons, as present in graphene, show unusual behaviour 4–7 that enables new tunable plasmonic metamaterials 8–10 and, potentially, optoelectronic applications in the terahertz frequency range 8,9,11,12 .H ere we explore plasmon excitations in engineered graphene microribbon arrays. We demonstrate that graphene plasmon resonances can be tuned over a broad terahertz frequency range by changing micro-ribbon width and in situ electrostatic doping. The ribbon width and carrier doping dependences of graphene plasmon frequency demonstrate power-law behaviour characteristic of two-dimensional massless Dirac electrons 4–6 . The plasmon resonances have remarkably large oscillator strengths, resulting
2,701 citations
TL;DR: This work focuses on the interplay between the mechanisms that individually contribute to strength and toughness, noting that these phenomena can originate from very different lengthscales in a material's structural architecture.
Abstract: The attainment of both strength and toughness is a vital requirement for most structural materials; unfortunately these properties are generally mutually exclusive. Although the quest continues for stronger and harder materials, these have little to no use as bulk structural materials without appropriate fracture resistance. It is the lower-strength, and hence higher-toughness, materials that find use for most safety-critical applications where premature or, worse still, catastrophic fracture is unacceptable. For these reasons, the development of strong and tough (damage-tolerant) materials has traditionally been an exercise in compromise between hardness versus ductility. Drawing examples from metallic glasses, natural and biological materials, and structural and biomimetic ceramics, we examine some of the newer strategies in dealing with this conflict. Specifically, we focus on the interplay between the mechanisms that individually contribute to strength and toughness, noting that these phenomena can originate from very different lengthscales in a material's structural architecture. We show how these new and natural materials can defeat the conflict of strength versus toughness and achieve unprecedented levels of damage tolerance within their respective material classes.
2,350 citations
Daniel J. Eisenstein1, Daniel J. Eisenstein2, David H. Weinberg3, Eric Agol4 +260 more•Institutions (62)
TL;DR: SDSS-III as mentioned in this paper is a program of four spectroscopic surveys on three scientific themes: dark energy and cosmological parameters, the history and structure of the Milky Way, and the population of giant planets around other stars.
Abstract: Building on the legacy of the Sloan Digital Sky Survey (SDSS-I and II), SDSS-III is a program of four spectroscopic surveys on three scientific themes: dark energy and cosmological parameters, the history and structure of the Milky Way, and the population of giant planets around other stars. In keeping with SDSS tradition, SDSS-III will provide regular public releases of all its data, beginning with SDSS DR8 (which occurred in Jan 2011). This paper presents an overview of the four SDSS-III surveys. BOSS will measure redshifts of 1.5 million massive galaxies and Lya forest spectra of 150,000 quasars, using the BAO feature of large scale structure to obtain percent-level determinations of the distance scale and Hubble expansion rate at z 100 per resolution element), H-band (1.51-1.70 micron) spectra of 10^5 evolved, late-type stars, measuring separate abundances for ~15 elements per star and creating the first high-precision spectroscopic survey of all Galactic stellar populations (bulge, bar, disks, halo) with a uniform set of stellar tracers and spectral diagnostics. MARVELS will monitor radial velocities of more than 8000 FGK stars with the sensitivity and cadence (10-40 m/s, ~24 visits per star) needed to detect giant planets with periods up to two years, providing an unprecedented data set for understanding the formation and dynamical evolution of giant planet systems. (Abridged)
2,265 citations
Max Planck Society1, National University of Cordoba2, Centre national de la recherche scientifique3, Macquarie University4, University of Paris-Sud5, University of Minnesota6, University of Western Sydney7, VU University Amsterdam8, University of Arizona9, University of California, Berkeley10, University of Guelph11, Australian National University12, University of Innsbruck13, University of Leeds14, University of Groningen15, Universidade Federal do Rio Grande do Sul16, University of Cape Town17, University of Wollongong18, New Jersey Institute of Technology19, Centro Agronómico Tropical de Investigación y Enseñanza20, Lawrence Berkeley National Laboratory21, University of Alaska Fairbanks22, University of Cambridge23, Kansas State University24, Helmholtz Centre for Environmental Research - UFZ25, Arizona State University26, University of Giessen27, Autonomous University of Barcelona28, University of Maryland, College Park29, Universidad del Tolima30, University of São Paulo31, University of La Réunion32, University of York33, University of Sydney34, Harvard University35, Goethe University Frankfurt36, University of Sheffield37, University of Ulm38, State University of Campinas39, Kenyon College40, Royal Botanic Gardens41, University of Florida42, University of Oldenburg43, University of Nebraska–Lincoln44, Tohoku University45, Northern Arizona University46, University of Wisconsin–Eau Claire47, Naturalis48, James Cook University49, Institut national de la recherche agronomique50, Newcastle University51, University of New South Wales52, Leipzig University53, Columbia University54, Estonian University of Life Sciences55, Polish Academy of Sciences56, Moscow State University57, Kyushu University58, Wageningen University and Research Centre59, Spanish National Research Council60, University of Regensburg61, University of Rennes62, Université du Québec à Trois-Rivières63, Potsdam Institute for Climate Impact Research64, Technical University of Denmark65, University of California, Los Angeles66, Hokkaido University67, Université de Sherbrooke68, Syracuse University69, Empresa Brasileira de Pesquisa Agropecuária70, University of Aberdeen71, Michigan State University72, Oak Ridge National Laboratory73, University of Leicester74, Utah State University75, Smithsonian Institution76, University of Missouri77
TL;DR: TRY as discussed by the authors is a global database of plant traits, including morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs, which can be used for a wide range of research from evolutionary biology, community and functional ecology to biogeography.
Abstract: Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.
2,017 citations
TL;DR: It is indicated that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.
Abstract: Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.
1,948 citations
TL;DR: The challenge now is to understand the senescence response well enough to harness its benefits while suppressing its drawbacks.
Abstract: Cellular senescence is an important mechanism for preventing the proliferation of potential cancer cells. Recently, however, it has become apparent that this process entails more than a simple cessation of cell growth. In addition to suppressing tumorigenesis, cellular senescence might also promote tissue repair and fuel inflammation associated with aging and cancer progression. Thus, cellular senescence might participate in four complex biological processes (tumor suppression, tumor promotion, aging, and tissue repair), some of which have apparently opposing effects. The challenge now is to understand the senescence response well enough to harness its benefits while suppressing its drawbacks.
1,723 citations
University of Hamburg1, Arizona State University2, Uppsala University3, Max Planck Society4, European XFEL5, SLAC National Accelerator Laboratory6, Forschungszentrum Jülich7, Lawrence Livermore National Laboratory8, Lawrence Berkeley National Laboratory9, University of Gothenburg10, Technical University of Berlin11, Swedish University of Agricultural Sciences12
TL;DR: This work offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage, by using pulses briefer than the timescale of most damage processes.
Abstract: X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded(1-3). It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source(4). We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes(5). More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (similar to 200 nm to 2 mm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes(6). This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
TL;DR: In this article, the components of RFBs with a focus on understanding the underlying physical processes are examined and various transport and kinetic phenomena are discussed along with the most common redox couples.
Abstract: Redox flow batteries (RFBs) are enjoying a renaissance due to their ability to store large amounts of electrical energy relatively cheaply and efficiently. In this review, we examine the components of RFBs with a focus on understanding the underlying physical processes. The various transport and kinetic phenomena are discussed along with the most common redox couples.
Hiroaki Aihara1, Carlos Allende Prieto2, Carlos Allende Prieto3, Deokkeun An4 +191 more•Institutions (58)
TL;DR: The first data release of SDSS-III is described in this article, which includes five-band imaging of roughly 5200 deg2 in the southern Galactic cap, bringing the total footprint of the Sloan Digital Sky Survey imaging to 14,555 deg2, or over a third of the Celestial Sphere.
Abstract: The Sloan Digital Sky Survey (SDSS) started a new phase in 2008 August, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Lyα forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg2 in the southern Galactic cap, bringing the total footprint of the SDSS imaging to 14,555 deg2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Exploration (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameter pipeline, which has better determination of metallicity for high-metallicity stars.
TL;DR: The principles learned from studies of various natural antenna complexes are described and how to elucidate strategies for designing light-harvesting systems are suggested to be used for solar fuel production, to direct and regulate excitation energy flow using molecular organizations that facilitate feedback and control, or to transfer excitons over long distances.
Abstract: Solar fuel production often starts with the energy from light being absorbed by an assembly of molecules; this electronic excitation is subsequently transferred to a suitable acceptor. For example, in photosynthesis, antenna complexes capture sunlight and direct the energy to reaction centres that then carry out the associated chemistry. In this Review, we describe the principles learned from studies of various natural antenna complexes and suggest how to elucidate strategies for designing light-harvesting systems. We envisage that such systems will be used for solar fuel production, to direct and regulate excitation energy flow using molecular organizations that facilitate feedback and control, or to transfer excitons over long distances. Also described are the notable properties of light-harvesting chromophores, spatial-energetic landscapes, the roles of excitonic states and quantum coherence, as well as how antennas are regulated and photoprotected.
TL;DR: In this article, the authors describe localized surface plasmon resonances arising from p-type carriers in vacancy-doped semiconductor quantum dots (QDs) and demonstrate that doped QDs allow realization of LSPRs and quantum-confined excitons within the same nanostructure.
Abstract: Localized surface plasmon resonances (LSPRs) typically arise in nanostructures of noble metals resulting in enhanced and geometrically tunable absorption and scattering resonances. LSPRs, however, are not limited to nanostructures of metals and can also be achieved in semiconductor nanocrystals with appreciable free carrier concentrations. Here, we describe well-defined LSPRs arising from p-type carriers in vacancy-doped semiconductor quantum dots (QDs). Achievement of LSPRs by free carrier doping of a semiconductor nanocrystal would allow active on-chip control of LSPR responses. Plasmonic sensing and manipulation of solid-state processes in single nanocrystals constitutes another interesting possibility. We also demonstrate that doped semiconductor QDs allow realization of LSPRs and quantum-confined excitons within the same nanostructure, opening up the possibility of strong coupling of photonic and electronic modes, with implications for light harvesting, nonlinear optics, and quantum information processing.
University of Connecticut Health Center1, University of California, Berkeley2, Lawrence Berkeley National Laboratory3, National Institutes of Health4, Washington University in St. Louis5, Indiana University6, Cold Spring Harbor Laboratory7, Life Technologies8, Amgen9, Stowers Institute for Medical Research10, University of Kansas11, University of California, Santa Cruz12, Howard Hughes Medical Institute13, Affymetrix14
TL;DR: 111,195 new elements are identified, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches.
Abstract: Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.
TL;DR: Recent work has shown the ability of bioactive glass to promote angiogenesis, which is critical to numerous applications in tissue regeneration, such as neovascularization for bone regeneration and the healing of soft tissue wounds.
Washington University in St. Louis1, Argonne National Laboratory2, Polytechnic University of Turin3, Imperial College London4, Yale University5, Lawrence Berkeley National Laboratory6, University of California, Berkeley7, National Renewable Energy Laboratory8, City University of New York9, University of Osnabrück10, Michigan State University11, Arizona State University12, University of Pennsylvania13, Massachusetts Institute of Technology14, University of Colorado Boulder15, University of Illinois at Urbana–Champaign16, University of Washington17, ExxonMobil18, Donald Danforth Plant Science Center19
TL;DR: Natural photosynthesis is compared with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen and opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency are considered.
Abstract: Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chemical fuels in the case of natural photosynthesis and nonstored electrical current in the case of photovoltaics. In order to find common ground for evaluating energy-conversion efficiency, we compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. We consider opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency.
TL;DR: Three PDA subtypes are defined: classical, quasimesenchymal and exocrine-like, and evidence for clinical outcome and therapeutic response differences between them is presented, and gene signatures for these subtypes that may have utility in stratifying patients for treatment are defined.
Abstract: Pancreatic ductal adenocarcinoma (PDA) is a lethal disease. Overall survival is typically 6 months from diagnosis. Numerous phase 3 trials of agents effective in other malignancies have failed to benefit unselected PDA populations, although patients do occasionally respond. Studies in other solid tumors have shown that heterogeneity in response is determined, in part, by molecular differences between tumors. Furthermore, treatment outcomes are improved by targeting drugs to tumor subtypes in which they are selectively effective, with breast and lung cancers providing recent examples. Identification of PDA molecular subtypes has been frustrated by a paucity of tumor specimens available for study. We have overcome this problem by combined analysis of transcriptional profiles of primary PDA samples from several studies, along with human and mouse PDA cell lines. We define three PDA subtypes: classical, quasimesenchymal and exocrine-like, and we present evidence for clinical outcome and therapeutic response differences between them. We further define gene signatures for these subtypes that may have utility in stratifying patients for treatment and present preclinical model systems that may be used to identify new subtype specific therapies.
Technische Universität München1, Novosibirsk State University2, Cornell University3, Lawrence Livermore National Laboratory4, University of California, Davis5, Argonne National Laboratory6, Fermilab7, Florida State University8, Indiana University9, Brookhaven National Laboratory10, Wayne State University11, University of Paris-Sud12, GSI Helmholtz Centre for Heavy Ion Research13, Ohio State University14, University of Regensburg15, University of Ferrara16, Polish Academy of Sciences17, University of Bari18, Max Planck Society19, Lancaster University20, Peking University21, Thomas Jefferson National Accelerator Facility22, University of Auvergne23, University of Cincinnati24, Stanford University25, University of Alberta26, Forschungszentrum Jülich27, University of Hawaii28, Illinois Institute of Technology29, Lawrence Berkeley National Laboratory30, École Polytechnique31, Budker Institute of Nuclear Physics32, CERN33, Université catholique de Louvain34, Pratt Institute35, University of São Paulo36, Seoul National University37, Tsinghua University38, Stony Brook University39, University of Valencia40, University of Milan41, Tohoku University42, University of Minnesota43
TL;DR: The early years of this period were chronicled in the Quarkonium Working Group (QWG) CERN Yellow Report (YR) in 2004, which presented a comprehensive review of the status of the field at that time and provided specific recommendations for further progress as mentioned in this paper.
Abstract: A golden age for heavy-quarkonium physics dawned a decade ago, initiated by the confluence of exciting advances in quantum chromodynamics (QCD) and an explosion of related experimental activity. The early years of this period were chronicled in the Quarkonium Working Group (QWG) CERN Yellow Report (YR) in 2004, which presented a comprehensive review of the status of the field at that time and provided specific recommendations for further progress. However, the broad spectrum of subsequent breakthroughs, surprises, and continuing puzzles could only be partially anticipated. Since the release of the YR, the BESII program concluded only to give birth to BESIII; the B-factories and CLEO-c flourished; quarkonium production and polarization measurements at HERA and the Tevatron matured; and heavy-ion collisions at RHIC have opened a window on the deconfinement regime. All these experiments leave legacies of quality, precision, and unsolved mysteries for quarkonium physics, and therefore beg for continuing investigations at BESIII, the LHC, RHIC, FAIR, the Super Flavor and/or Tau-Charm factories, JLab, the ILC, and beyond. The list of newly found conventional states expanded to include h(c)(1P), chi(c2)(2P), B-c(+), and eta(b)(1S). In addition, the unexpected and still-fascinating X(3872) has been joined by more than a dozen other charmonium- and bottomonium-like "XYZ" states that appear to lie outside the quark model. Many of these still need experimental confirmation. The plethora of new states unleashed a flood of theoretical investigations into new forms of matter such as quark-gluon hybrids, mesonic molecules, and tetraquarks. Measurements of the spectroscopy, decays, production, and in-medium behavior of c (c) over bar, b (b) over bar, and b (c) over bar bound states have been shown to validate some theoretical approaches to QCD and highlight lack of quantitative success for others. Lattice QCD has grown from a tool with computational possibilities to an industrial-strength effort now dependent more on insight and innovation than pure computational power. New effective field theories for the description of quarkonium in different regimes have been developed and brought to a high degree of sophistication, thus enabling precise and solid theoretical predictions. Many expected decays and transitions have either been measured with precision or for the first time, but the confusing patterns of decays, both above and below open-flavor thresholds, endure and have deepened. The intriguing details of quarkonium suppression in heavy-ion collisions that have emerged from RHIC have elevated the importance of separating hot- and cold-nuclear-matter effects in quark-gluon plasma studies. This review systematically addresses all these matters and concludes by prioritizing directions for ongoing and future efforts.
TL;DR: How normal tissue homeostasis and architecture inhibit progression of cancer and how changes in the microenvironment can shift the balance of these signals to the procancerous state are reviewed.
Abstract: Tumors are like new organs and are made of multiple cell types and components. The tumor competes with the normal microenvironment to overcome antitumorigenic pressures. Before that battle is won, the tumor may exist within the organ unnoticed by the host, referred to as 'occult cancer'. We review how normal tissue homeostasis and architecture inhibit progression of cancer and how changes in the microenvironment can shift the balance of these signals to the procancerous state. We also include a discussion of how this information is being tailored for clinical use.
TL;DR: Investigation of the electrochemical oxygen evolution reaction (OER) occurring on cobalt oxide films deposited on Au and other metal substrates revealed that the as-deposited cobALT oxide is present as Co(3)O(4) but undergoes progressive oxidation to CoO(OH) with increasing anodic potential.
Abstract: Scanning electron microscopy, linear sweep voltammetry, chronoamperometry, and in situ surface-enhanced Raman spectroscopy were used to investigate the electrochemical oxygen evolution reaction (OER) occurring on cobalt oxide films deposited on Au and other metal substrates. All experiments were carried out in 0.1 M KOH. A remarkable finding is that the turnover frequency for the OER exhibited by ∼0.4 ML of cobalt oxide deposited on Au is 40 times higher than that of bulk cobalt oxide. The activity of small amounts of cobalt oxide deposited on Pt, Pd, Cu, and Co decreased monotonically in the order Au > Pt > Pd > Cu > Co, paralleling the decreasing electronegativity of the substrate metal. Another notable finding is that the OER turnover frequency for ∼0.4 ML of cobalt oxide deposited on Au is nearly three times higher than that for bulk Ir. Raman spectroscopy revealed that the as-deposited cobalt oxide is present as Co3O4 but undergoes progressive oxidation to CoO(OH) with increasing anodic potential. Th...
TL;DR: This Review summarizes the recent developments in transcriptome assembly approaches — reference-based, de novo and combined strategies — along with some perspectives on transcriptomeAssembly in the near future.
Abstract: Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalog of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies-along with some perspectives on transcriptome assembly in the near future.
TL;DR: To characterize biomass-degrading genes and genomes, this work sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen and identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates.
Abstract: The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and genomes, we sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.
TL;DR: This work places a single palladium nanoparticle near the tip region of a gold nanoantenna and detects the changing optical properties of the system upon hydrogen exposure, demonstrating antenna-enhanced hydrogen sensing at the single-particle level.
Abstract: Plasmonic resonances are widely used for sensing applications. The plasmon resonance of a single nanoantenna structure is now used to detect changes in the dielectric properties of a nearby palladium nanoparticle exposed to hydrogen gas, enabling highly sensitive sensing in ultrasmall volumes. The approach can be easily extended to other sensing and catalysis schemes.
University of Colorado Boulder1, University of Toronto2, Pierre-and-Marie-Curie University3, University of Oxford4, University of Paris5, Centre national de la recherche scientifique6, Aix-Marseille University7, INAF8, Las Cumbres Observatory Global Telescope Network9, University of California, Santa Barbara10, Defence Research and Development Canada11, University of Victoria12, California Institute of Technology13, Centra14, Lawrence Berkeley National Laboratory15, University of Waterloo16, Australian Astronomical Observatory17, University of California, Berkeley18
TL;DR: In this article, the authors combine high redshift Type Ia supernovae from the first 3 years of the Supernova Legacy Survey (SNLS) with other supernova (SN) samples, primarily at lower redshifts, to form a high-quality joint sample of 472 SNe (123 low-$z, 93 SDSS, 242 SNLS, and 14 {\it Hubble Space Telescope}).
Abstract: We combine high redshift Type Ia supernovae from the first 3 years of the Supernova Legacy Survey (SNLS) with other supernova (SN) samples, primarily at lower redshifts, to form a high-quality joint sample of 472 SNe (123 low-$z$, 93 SDSS, 242 SNLS, and 14 {\it Hubble Space Telescope}). SN data alone require cosmic acceleration at >99.9% confidence, including systematic effects. For the dark energy equation of state parameter (assumed constant out to at least $z=1.4$) in a flat universe, we find $w = -0.91^{+0.16}_{-0.20}(\mathrm{stat}) ^{+0.07}_{-0.14} (\mathrm{sys})$ from SNe only, consistent with a cosmological constant. Our fits include a correction for the recently discovered relationship between host-galaxy mass and SN absolute brightness. We pay particular attention to systematic uncertainties, characterizing them using a systematics covariance matrix that incorporates the redshift dependence of these effects, as well as the shape-luminosity and color-luminosity relationships. Unlike previous work, we include the effects of systematic terms on the empirical light-curve models. The total systematic uncertainty is dominated by calibration terms. We describe how the systematic uncertainties can be reduced with soon to be available improved nearby and intermediate-redshift samples, particularly those calibrated onto USNO/SDSS-like systems.
TL;DR: In this article, the performance of two metal-organic frameworks, Zn4O(BTB)2 (BTB3− = 1,3,5-benzenetribenzoate; MOF-177) and Mg2(dobdc) were evaluated in detail for their potential use in post-combustion CO2 capture via temperature swing adsorption.
Abstract: Two representative metal–organic frameworks, Zn4O(BTB)2 (BTB3− = 1,3,5-benzenetribenzoate; MOF-177) and Mg2(dobdc) (dobdc4− = 1,4-dioxido-2,5-benzenedicarboxylate; Mg-MOF-74, CPO-27-Mg), are evaluated in detail for their potential use in post-combustion CO2 capture via temperature swing adsorption (TSA). Low-pressure single-component CO2 and N2 adsorption isotherms were measured every 10 °C from 20 to 200 °C, allowing the performance of each material to be analyzed precisely. In order to gain a more complete understanding of the separation phenomena and the thermodynamics of CO2 adsorption, the isotherms were analyzed using a variety of methods. With regard to the isosteric heat of CO2 adsorption, Mg2(dobdc) exhibits an abrupt drop at loadings approaching the saturation of the Mg2+ sites, which has significant implications for regeneration in different industrial applications. The CO2/N2 selectivities were calculated using ideal adsorbed solution theory (IAST) for MOF-177, Mg2(dobdc), and zeolite NaX, and working capacities were estimated using a simplified TSA model. Significantly, MOF-177 fails to exhibit a positive working capacity even at regeneration temperatures as high as 200 °C, while Mg2(dobdc) reaches a working capacity of 17.6 wt % at this temperature. Breakthrough simulations were also performed for the three materials, demonstrating the superior performance of Mg2(dobdc) over MOF-177 and zeolite NaX. These results show that the presence of strong CO2 adsorption sites is essential for a metal–organic framework to be of utility in post-combustion CO2 capture via a TSA process, and present a methodology for the evaluation of new metal–organic frameworks via analysis of single-component gas adsorption isotherms.
TL;DR: A number of intriguing phenomena and applications associated with metamaterials are discussed, including negative refraction, sub-diffraction-limited imaging, strong optical activities in chiral metamMaterials, interaction of meta-atoms and transformation optics.
Abstract: Metamaterials, artificial composite structures with exotic material properties, have emerged as a new frontier of science involving physics, material science, engineering and chemistry. This critical review focuses on the fundamentals, recent progresses and future directions in the research of electromagnetic metamaterials. An introduction to metamaterials followed by a detailed elaboration on how to design unprecedented electromagnetic properties of metamaterials is presented. A number of intriguing phenomena and applications associated with metamaterials are discussed, including negative refraction, sub-diffraction-limited imaging, strong optical activities in chiral metamaterials, interaction of meta-atoms and transformation optics. Finally, we offer an outlook on future directions of metamaterials research including but not limited to three-dimensional optical metamaterials, nonlinear metamaterials and “quantum” perspectives of metamaterials (142 references).
Uppsala University1, University of Hamburg2, Aix-Marseille University3, Stanford University4, Swedish University of Agricultural Sciences5, Arizona State University6, Lawrence Berkeley National Laboratory7, Lawrence Livermore National Laboratory8, Max Planck Society9, Technical University of Berlin10
TL;DR: This work shows that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source.
Abstract: The start-up of the Linac Coherent Light Source (LCLS), the new femtosecond hard X-ray laser facility in Stanford, California, has brought high expectations of a new era for biological imaging. The intense, ultrashort X-ray pulses allow diffraction imaging of small structures before radiation damage occurs. Two papers in this issue of Nature present proof-of-concept experiments showing the LCLS in action. Chapman et al. tackle structure determination from nanocrystals of macromolecules that cannot be grown in large crystals. They obtain more than three million diffraction patterns from a stream of nanocrystals of the membrane protein photosystem I, and assemble a three-dimensional data set for this protein. Seibert et al. obtain images of a non-crystalline biological sample, mimivirus, by injecting a beam of cooled mimivirus particles into the X-ray beam. The start-up of the new femtosecond hard X-ray laser facility in Stanford, the Linac Coherent Light Source, has brought high expectations for a new era for biological imaging. The intense, ultrashort X-ray pulses allow diffraction imaging of small structures before radiation damage occurs. This new capability is tested for the problem of imaging a non-crystalline biological sample. Images of mimivirus are obtained, the largest known virus with a total diameter of about 0.75 micrometres, by injecting a beam of cooled mimivirus particles into the X-ray beam. The measurements indicate no damage during imaging and prove the concept of this imaging technique. X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions1,2,3,4. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma1. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval2. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source5. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
TL;DR: In this article, the observed luminosity functions (LFs) of supernovae are derived from the Lick Observatory Supernova Search (LOSS) data, and a complete sample is constructed, and the observed (uncorrected for host-galaxy extinction) luminosity function (LF) of SNe are derived.
Abstract: This is the second paper of a series in which we present new measurements of the observed rates of supernovae (SNe) in the local Universe, determined from the Lick Observatory Supernova Search (LOSS). In this paper, a complete SN sample is constructed, and the observed (uncorrected for host-galaxy extinction) luminosity functions (LFs) of SNe are derived. These LFs solve two issues that have plagued previous rate calculations for nearby SNe: the luminosity distribution of SNe and the host-galaxy extinction. We select a volume-limited sample of 175 SNe, collect photometry for every object, and fit a family of light curves to constrain the peak magnitudes and light-curve shapes. The volume-limited LFs show that they are not well represented by a Gaussian distribution. There are notable differences in the LFs for galaxies of different Hubble types (especially for SNe Ia). We derive the observed fractions for the different subclasses in a complete SN sample, and find significant fractions of SNe II-L (10%), IIb (12%), and IIn (9%) in the SN II sample. Furthermore, we derive the LFs and the observed fractions of different SN subclasses in a magnitudelimited survey with different observation intervals, and find that the LFs are enhanced at the high-luminosity end and appear more “standard” with smaller scatter, and that the LFs and fractions of SNe do not change significantly when the observation interval is shorter than 10 d. We also discuss the LFs in different galaxy sizes and inclinations, and for different SN subclasses. Some notable results are that there is not a strong correlation between the SN LFs and the host-galaxy size, but there might be a preference for SNe IIn to occur in small, late-type spiral galaxies. The LFs in different inclination bins do not provide strong evidence for extreme extinction in highly inclined galaxies, though the sample is still small. The LFs of different SN subclasses show significant differences. We also find that SNe Ibc and IIb come from more luminous galaxies than SNe II-P, while SNe IIn come from less luminous galaxies, suggesting a possible metallicity effect. The limitations and applications of our LFs are also discussed.