Showing papers by "University of St Andrews published in 2015"
TL;DR: Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes, is introduced, making construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results.
Abstract: Summary: A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors.
Availability and implementation: Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary
Contact: ku.ca.regnas@yraor
Supplementary information: Supplementary data are available at Bioinformatics online.
3,147 citations
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
TL;DR: An approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes is presented.
Abstract: The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
1,988 citations
TL;DR: Roary is introduced, a tool that rapidly builds large-scale pan genomes, identifying the core and dispensable accessory genes and making construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results.
Abstract: A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and dispensable accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors.
955 citations
TL;DR: The purpose of this article is to describe the fundamental stimulation paradigms for steady-state visual evoked potentials and to illustrate these principles through research findings across a range of applications in vision science.
Abstract: Periodic visual stimulation and analysis of the resulting steady-state visual evoked potentials were first introduced over 80 years ago as a means to study visual sensation and perception. From the first single-channel recording of responses to modulated light to the present use of sophisticated digital displays composed of complex visual stimuli and high-density recording arrays, steady-state methods have been applied in a broad range of scientific and applied settings.The purpose of this article is to describe the fundamental stimulation paradigms for steady-state visual evoked potentials and to illustrate these principles through research findings across a range of applications in vision science.
875 citations
TL;DR: The structure, core assumptions and novel predictions of the extended evolutionary synthesis (EES) are spelled out, and it is shown how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.
Abstract: Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.
790 citations
TL;DR: It is indicated that risk variants for psychiatric disorders aggregate in particular biological pathways and that these pathways are frequently shared between disorders.
Abstract: Genome-wide association studies (GWAS) of psychiatric disorders have identified multiple genetic associations with such disorders, but better methods are needed to derive the underlying biological mechanisms that these signals indicate. We sought to identify biological pathways in GWAS data from over 60,000 participants from the Psychiatric Genomics Consortium. We developed an analysis framework to rank pathways that requires only summary statistics. We combined this score across disorders to find common pathways across three adult psychiatric disorders: schizophrenia, major depression and bipolar disorder. Histone methylation processes showed the strongest association, and we also found statistically significant evidence for associations with multiple immune and neuronal signaling pathways and with the postsynaptic density. Our study indicates that risk variants for psychiatric disorders aggregate in particular biological pathways and that these pathways are frequently shared between disorders. Our results confirm known mechanisms and suggest several novel insights into the etiology of psychiatric disorders.
630 citations
TL;DR: Good redox stability with tolerance to coking and sulphur contamination from hydrocarbon fuels is demonstrated for the layered perovskite anode PrBaMn2O5+δ (PBMO).
Abstract: Different layered perovskite-related oxides are known to exhibit important electronic, magnetic and electrochemical properties. Owing to their excellent mixed-ionic and electronic conductivity and fast oxygen kinetics, cation layered double perovskite oxides such as PrBaCo2O5 in particular have exhibited excellent properties as solid oxide fuel cell oxygen electrodes. Here, we show for the first time that related layered materials can be used as high-performance fuel electrodes. Good redox stability with tolerance to coking and sulphur contamination from hydrocarbon fuels is demonstrated for the layered perovskite anode PrBaMn2O5+δ (PBMO). The PBMO anode is fabricated by in situ annealing of Pr0.5Ba0.5MnO3-δ in fuel conditions and actual fuel cell operation is demonstrated. At 800 °C, layered PBMO shows high electrical conductivity of 8.16 S cm(-1) in 5% H2 and demonstrates peak power densities of 1.7 and 1.3 W cm(-2) at 850 °C using humidified hydrogen and propane fuels, respectively.
573 citations
TL;DR: It is shown that unlike nickel particles deposited on perovskite oxides, exsolved analogues are socketed into the parent perovkite, leading to enhanced stability and a significant decrease in the propensity for hydrocarbon coking, indicative of a stronger metal–oxide interface.
Abstract: Metal particles supported on oxide surfaces are used as catalysts for a wide variety of processes in the chemical and energy conversion industries. For catalytic applications, metal particles are generally formed on an oxide support by physical or chemical deposition, or less commonly by exsolution from it. Although fundamentally different, both methods might be assumed to produce morphologically and functionally similar particles. Here we show that unlike nickel particles deposited on perovskite oxides, exsolved analogues are socketed into the parent perovskite, leading to enhanced stability and a significant decrease in the propensity for hydrocarbon coking, indicative of a stronger metal-oxide interface. In addition, we reveal key surface effects and defect interactions critical for future design of exsolution-based perovskite materials for catalytic and other functionalities. This study provides a new dimension for tailoring particle-substrate interactions in the context of increasing interest for emergent interfacial phenomena.
552 citations
TL;DR: It is argued that the understanding of biodiversity trends in the Anthropocene is impeded by a failure to consider different types of biodiversity measured at different spatial scales, and it is proposed that ecologists should recognize and assess 15 distinct categories of biodiversity trend.
Abstract: Humans are transforming the biosphere in unprecedented ways, raising the important question of how these impacts are changing biodiversity. Here we argue that our understanding of biodiversity trends in the Anthropocene, and our ability to protect the natural world, is impeded by a failure to consider different types of biodiversity measured at different spatial scales. We propose that ecologists should recognize and assess 15 distinct categories of biodiversity trend. We summarize what is known about each of these 15 categories, identify major gaps in our current knowledge, and recommend the next steps required for better understanding of trends in biodiversity.
526 citations
TL;DR: It is demonstrated that non-Hermiticity dramatically modifies the structure of modes and spectral degeneracies in exciton-polariton systems, and, therefore, will affect their quantum transport, localization and dynamical properties.
Abstract: Exciton-polaritons are hybrid light-matter quasiparticles formed by strongly interacting photons and excitons (electron-hole pairs) in semiconductor microcavities. They have emerged as a robust solid-state platform for next-generation optoelectronic applications as well as for fundamental studies of quantum many-body physics. Importantly, exciton-polaritons are a profoundly open (that is, non-Hermitian) quantum system, which requires constant pumping of energy and continuously decays, releasing coherent radiation. Thus, the exciton-polaritons always exist in a balanced potential landscape of gain and loss. However, the inherent non-Hermitian nature of this potential has so far been largely ignored in exciton-polariton physics. Here we demonstrate that non-Hermiticity dramatically modifies the structure of modes and spectral degeneracies in exciton-polariton systems, and, therefore, will affect their quantum transport, localization and dynamical properties. Using a spatially structured optical pump, we create a chaotic exciton-polariton billiard--a two-dimensional area enclosed by a curved potential barrier. Eigenmodes of this billiard exhibit multiple non-Hermitian spectral degeneracies, known as exceptional points. Such points can cause remarkable wave phenomena, such as unidirectional transport, anomalous lasing/absorption and chiral modes. By varying parameters of the billiard, we observe crossing and anti-crossing of energy levels and reveal the non-trivial topological modal structure exclusive to non-Hermitian systems. We also observe mode switching and a topological Berry phase for a parameter loop encircling the exceptional point. Our findings pave the way to studies of non-Hermitian quantum dynamics of exciton-polaritons, which may uncover novel operating principles for polariton-based devices.
European Southern Observatory1, Liverpool John Moores University2, University of Western Australia3, University of St Andrews4, Max Planck Society5, Ames Research Center6, Australian Astronomical Observatory7, University of the Western Cape8, Durham University9, University of Sussex10, University of Melbourne11, University of Nottingham12, University of Sydney13, Monash University, Clayton campus14, University of Queensland15, University of Edinburgh16, University of Central Lancashire17, Australian National University18, University of Turku19, University of Canterbury20, University of Oxford21, University of Hertfordshire22, Leiden University23, Institute of Cosmology and Gravitation, University of Portsmouth24, National Institute of Astrophysics, Optics and Electronics25, Macquarie University26, National Autonomous University of Mexico27, Carnegie Institution for Science28, University of Bristol29, University of Hull30, Romanian Academy31, Queen Mary University of London32, University of Innsbruck33
TL;DR: The Galaxy And Mass Assembly (GAMA) survey as mentioned in this paper is one of the largest contemporary spectroscopic surveys of low redshift galaxies, covering an area of ∼286 deg2 (split among five survey regions) down to a limiting magnitude of r < 19.8 mag, and collecting spectra and reliable redshifts for 238'000 objects using the AAOmega spectrograph on the Anglo-Australian Telescope.
Abstract: The Galaxy And Mass Assembly (GAMA) survey is one of the largest contemporary spectroscopic surveys of low redshift galaxies. Covering an area of ∼286 deg2 (split among five survey regions) down to a limiting magnitude of r < 19.8 mag, we have collected spectra and reliable redshifts for 238 000 objects using the AAOmega spectrograph on the Anglo-Australian Telescope. In addition, we have assembled imaging data from a number of independent surveys in order to generate photometry spanning the wavelength range 1 nm–1 m. Here, we report on the recently completed spectroscopic survey and present a series of diagnostics to assess its final state and the quality of the redshift data. We also describe a number of survey aspects and procedures, or updates thereof, including changes to the input catalogue, redshifting and re-redshifting, and the derivation of ultraviolet, optical and near-infrared photometry. Finally, we present the second public release of GAMA data. In this release, we provide input catalogue and targeting information, spectra, redshifts, ultraviolet, optical and near-infrared photometry, single-component Sersic fits, stellar masses, Hα-derived star formation rates, environment information, and group properties for all galaxies with r < 19.0 mag in two of our survey regions, and for all galaxies with r < 19.4 mag in a third region (72 225 objects in total). The data base serving these data is available at http://www.gama-survey.org/.
TL;DR: In this paper, the 3D structure of graphitic carbon nitride (g-C3N4) is solved by means of X-ray diffraction and of neutron scattering, and parallel chains of tri-s-triazine units organized in layers with an A-B stacking motif are found to describe the structure of the synthesized graphitic C3N 4 well.
Abstract: Graphitic carbon nitride (g-C3N4) has, since 2009, attracted great attention for its activity as a visible-light-active photocatalyst for hydrogen evolution. Since it was synthesized in 1834, g-C3N4 has been extensively studied both catalytically and structurally. Although its 2D structure seems to have been solved, its 3D crystal structure has not yet been confirmed. This study attempts to solve the 3D structure of graphitic carbon nitride by means of X-ray diffraction and of neutron scattering. Initially, various structural models are considered and their XRD patterns compared to the measured one. After selecting possible candidates as g-C3N4 structure, neutron scattering is employed to identify the best model that describes the 3D structure of graphitic carbon nitride. Parallel chains of tri-s-triazine units organized in layers with an A–B stacking motif are found to describe the structure of the synthesized graphitic carbon nitride well. A misalignment of the layers is favorable because of the decreas...
TL;DR: New strategies that markedly suppress such undesired pathways to result in diverse aromatic compounds previously not systematically targeted from lignin are described, indicating that the aldehyde intermediates play a significant role in these processes.
Abstract: Conversion of lignin into well-defined aromatic chemicals is a highly attractive goal but is often hampered by recondensation of the formed fragments, especially in acidolysis. Here, we describe new strategies that markedly suppress such undesired pathways to result in diverse aromatic compounds previously not systematically targeted from lignin. Model studies established that a catalytic amount of triflic acid is very effective in cleaving the β-O-4 linkage, most abundant in lignin. An aldehyde product was identified as the main cause of side reactions under cleavage conditions. Capturing this unstable compound by reaction with diols and by in situ catalytic hydrogenation or decarbonylation lead to three distinct groups of aromatic compounds in high yields acetals, ethanol and ethyl aromatics, and methyl aromatics. Notably, the same product groups were obtained when these approaches were successfully extended to lignin. In addition, the formation of higher molecular weight side products was markedly supp...
Lamont–Doherty Earth Observatory1, University of East Anglia2, University of Freiburg3, Royal Netherlands Meteorological Institute4, Queen's University Belfast5, University of Padua6, University of Ljubljana7, University of Mainz8, Cornell University9, Stockholm University10, Dresden University of Technology11, University of Barcelona12, United States Department of State13, Deutsches Archäologisches Institut14, Czech University of Life Sciences Prague15, Istanbul University16, University of Gothenburg17, University of Oxford18, University of Pavia19, University of Forestry, Sofia20, Norwegian University of Science and Technology21, University of Arizona22, Nicolaus Copernicus University in Toruń23, University of St Andrews24, Technische Universität München25
TL;DR: Megadroughts reconstructed over north-central Europe in the 11th and mid-15th centuries reinforce other evidence from North America and Asia that droughts were more severe, extensive, and prolonged over Northern Hemisphere land areas before the 20th century, with an inadequate understanding of their causes.
Abstract: Climate model projections suggest widespread drying in the Mediterranean Basin and wetting in Fennoscandia in the coming decades largely as a consequence of greenhouse gas forcing of climate. To place these and other “Old World” climate projections into historical perspective based on more complete estimates of natural hydroclimatic variability, we have developed the “Old World Drought Atlas” (OWDA), a set of year-to-year maps of tree-ring reconstructed summer wetness and dryness over Europe and the Mediterranean Basin during the Common Era. The OWDA matches historical accounts of severe drought and wetness with a spatial completeness not previously available. In addition, megadroughts reconstructed over north-central Europe in the 11th and mid-15th centuries reinforce other evidence from North America and Asia that droughts were more severe, extensive, and prolonged over Northern Hemisphere land areas before the 20th century, with an inadequate understanding of their causes. The OWDA provides new data to determine the causes of Old World drought and wetness and attribute past climate variability to forced and/or internal variability.
Australian Astronomical Observatory1, University of Sydney2, University of Western Australia3, University of St Andrews4, University of Queensland5, Swinburne University of Technology6, Australian National University7, University of Melbourne8, Liverpool John Moores University9, Rutgers University10, University of North Carolina at Chapel Hill11, University of Oxford12, Durham University13, University of Hawaii14, European Southern Observatory15, Macquarie University16, Indian Institute of Science Education and Research, Mohali17, Leibniz Institute for Astrophysics Potsdam18
TL;DR: The SAMI Galaxy Survey as discussed by the authors is a 3-year survey of 3400 galaxies with the Sydney-AAO Multi-Object Integral Field Spectrograph (SAMI) on the Anglo-Australian Telescope (AAT).
Abstract: The SAMI Galaxy Survey will observe 3400 galaxies with the Sydney-AAO Multi- object Integral-field spectrograph (SAMI) on the Anglo-Australian Telescope (AAT) in a 3-year survey which began in 2013. We present the throughput of the SAMI system, the science basis and specifications for the target selection, the survey observation plan and the combined properties of the selected galaxies. The survey includes four volume-limited galaxy samples based on cuts in a proxy for stellar mass, along with low-stellar-mass dwarf galaxies all selected from the Galaxy And Mass Assembly (GAMA) survey. The GAMA regions were selected because of the vast array of ancillary data available, including ultraviolet through to radio bands. These fields are on the celestial equator at 9, 12, and 14.5 hours, and cover a total of 144 square degrees (in GAMA-I). Higher density environments are also included with the addition of eight clusters. The clusters have spectroscopy from 2dFGRS and SDSS and photometry in regions covered by the Sloan Digital Sky Survey (SDSS) and/or VLT Survey Telescope/ATLAS. The aim is to cover a broad range in stellar mass and environment, and therefore the primary survey targets cover redshifts 0.004 < z < 0.095, magnitudes rpet < 19.4, stellar masses 107– 1012M⊙, and environments from isolated field galaxies through groups to clusters of _ 1015M⊙.
Macquarie University1, Australian Astronomical Observatory2, California Institute of Technology3, University of California, Berkeley4, Paris Diderot University5, University of Oxford6, University of Toledo7, University of Hertfordshire8, European Southern Observatory9, Leiden University10, École normale supérieure de Lyon11, University of Edinburgh12, Leibniz Institute for Astrophysics Potsdam13, Kapteyn Astronomical Institute14, Max Planck Society15, University of Sydney16, ASTRON17, Commonwealth Scientific and Industrial Research Organisation18, University of St Andrews19, New Mexico Institute of Mining and Technology20, Academia Sinica Institute of Astronomy and Astrophysics21
TL;DR: In this article, the stellar population content of early-type galaxies from the ATLAS^(3D) survey is analyzed using spectra integrated within apertures covering up to one effective radius.
Abstract: We present the stellar population content of early-type galaxies from the ATLAS^(3D) survey. Using spectra integrated within apertures covering up to one effective radius, we apply two methods: one based on measuring line-strength indices and applying single stellar population (SSP) models to derive SSP-equivalent values of stellar age, metallicity, and alpha enhancement; and one based on spectral fitting to derive non-parametric star formation histories, mass-weighted average values of age, metallicity, and half-mass formation time-scales. Using homogeneously derived effective radii and dynamically determined galaxy masses, we present the distribution of stellar population parameters on the Mass Plane (M_(JAM), σ_e, R^(maj)_e), showing that at fixed mass, compact early-type galaxies are on average older, more metal-rich, and more alpha-enhanced than their larger counterparts. From non-parametric star formation histories, we find that the duration of star formation is systematically more extended in lower mass objects. Assuming that our sample represents most of the stellar content of today's local Universe, approximately 50 per cent of all stars formed within the first 2 Gyr following the big bang. Most of these stars reside today in the most massive galaxies (>10^(10.5) M⊙), which themselves formed 90 per cent of their stars by z ∼ 2. The lower mass objects, in contrast, have formed barely half their stars in this time interval. Stellar population properties are independent of environment over two orders of magnitude in local density, varying only with galaxy mass. In the highest density regions of our volume (dominated by the Virgo cluster), galaxies are older, alpha-enhanced, and have shorter star formation histories with respect to lower density regions.
TL;DR: It is found that differentially expressed mRNAs correlate significantly better with their protein product than non-differentially expressed MNCs, providing optimism for the usefulness of inferences from mRNA expression in general.
Abstract: Differential mRNA expression studies implicitly assume that changes in mRNA expression have biological meaning, most likely mediated by corresponding changes in protein levels. Yet studies into mRNA-protein correspondence have shown notoriously poor correlation between mRNA and protein expression levels, creating concern for inferences from only mRNA expression data. However, none of these studies have examined in particular differentially expressed mRNA. Here, we examined this question in an ovarian cancer xenograft model. We measured protein and mRNA expression for twenty-nine genes in four drug-treatment conditions and in untreated controls. We identified mRNAs differentially expressed between drug-treated xenografts and controls, then analysed mRNA-protein expression correlation across a five-point time-course within each of the four experimental conditions. We evaluated correlations between mRNAs and their protein products for mRNAs differentially expressed within an experimental condition compared to those that are not. We found that differentially expressed mRNAs correlate significantly better with their protein product than non-differentially expressed mRNAs. This result increases confidence for the use of differential mRNA expression for biological discovery in this system, as well as providing optimism for the usefulness of inferences from mRNA expression in general.
TL;DR: In this paper, a frequency analysis of EBM principles was conducted to identify the Key Principles that currently define EBM, from a list of twenty-six principles extracted from a subset of the EBM theoretical/conceptual literature (covering a range of published sources across disciplines and application types).
TL;DR: Functionalized phenolic monomers have been generated and isolated from an organosolv lignin through a two-step depolymerization process, giving rise to a simple mixture of products that can be readily purified to give pure compounds.
Abstract: Functionalized phenolic monomers have been generated and isolated from an organosolv lignin through a two-step depolymerization process. Chemoselective catalytic oxidation of β-O-4 linkages promoted by the DDQ/tBuONO/O2 system was achieved in model compounds, including polymeric models and in real lignin. The oxidized β-O-4 linkages were then cleaved on reaction with zinc. Compared to many existing methods, this protocol, which can be achieved in one pot, is highly selective, giving rise to a simple mixture of products that can be readily purified to give pure compounds. The functionality present in these products makes them potentially valuable building blocks.
TL;DR: In this article, a single-site and single-atom-resolved fluorescence imaging of fermionic potassium-40 atoms in a quantum-gas microscope set-up, using electromagnetically-induced-transparency cooling, was demonstrated.
Abstract: Imaging individual atoms in an optical lattice with single-site resolution has so far only been possible for bosonic species, but thanks to electromagnetically-induced-transparency cooling fermionic species can now also be imaged. Single-atom-resolved detection in optical lattices using quantum-gas microscopes1,2 has enabled a new generation of experiments in the field of quantum simulation. Although such devices have been realized with bosonic species, a fermionic quantum-gas microscope has remained elusive. Here we demonstrate single-site- and single-atom-resolved fluorescence imaging of fermionic potassium-40 atoms in a quantum-gas microscope set-up, using electromagnetically-induced-transparency cooling3,4. We detected on average 1,000 fluorescence photons from a single atom within 1.5 s, while keeping it close to the vibrational ground state of the optical lattice. A quantum simulator for fermions with single-particle access will be an excellent test bed to investigate phenomena and properties of strongly correlated fermionic quantum systems, allowing direct measurement of ordered quantum phases5,6,7,8,9 and out-of-equilibrium dynamics10,11, with access to quantities ranging from spin–spin correlation functions to many-particle entanglement12.
TL;DR: Socioeconomic inequality has increased in many domains of adolescent health and these trends coincide with unequal distribution of income between rich and poor people.
University of Aberdeen1, Scottish Association for Marine Science2, Bangor University3, University of Brighton4, University of Dundee5, James Hutton Institute6, Birmingham City University7, Aberystwyth University8, University of Edinburgh9, University of the Highlands and Islands10, Anglia Ruskin University11, University of St Andrews12, University of Exeter13, Edge Hill University14, Marine Conservation Society15, Natural Resources Wales16
TL;DR: In this article, a framework of shared/social values across five dimensions: value concept, provider, intention, scale, and elicitation process is proposed for valuation of ecosystem services.
TL;DR: It is proposed that the slowdown of the Indian plate at ca.
Abstract: New geochronological and geochemical data on magmatic activity from the India-Asia collision zone enables recognition of a distinct magmatic flare-up event that we ascribe to slab breakoff. This tie-point in the collisional record can be used to back-date to the time of initial impingement of the Indian continent with the Asian margin. Continental arc magmatism in southern Tibet during 80–40 Ma migrated from south to north and then back to south with significant mantle input at 70–43 Ma. A pronounced flare up in magmatic intensity (including ignimbrite and mafic rock) at ca. 52–51 Ma corresponds to a sudden decrease in the India-Asia convergence rate. Geological and geochemical data are consistent with mantle input controlled by slab rollback from ca. 70 Ma and slab breakoff at ca. 53 Ma. We propose that the slowdown of the Indian plate at ca. 51 Ma is largely the consequence of slab breakoff of the subducting Neo-Tethyan oceanic lithosphere, rather than the onset of the India-Asia collision as traditionally interpreted, implying that the initial India-Asia collision commenced earlier, likely at ca. 55 Ma.
TL;DR: The results support the hypothesis that hominin reliance on stone tool-making generated selection for teaching and language and imply that teaching or proto-language may have been pre-requisites for the appearance of Acheulean technology.
Abstract: Hominin reliance on Oldowan stone tools—which appear from 2.5 mya and are believed to have been socially transmitted—has been hypothesized to have led to the evolution of teaching and language. Here we present an experiment investigating the efficacy of transmission of Oldowan tool-making skills along chains of adult human participants (N ¼ 184) using five different transmission mechanisms. Across six measures, transmission improves with teaching, and particularly with language, but not with imitation or emulation. Our results support the hypothesis that hominin reliance on stone tool-making generated selection for teaching and language, and imply that (i) low-fidelity social transmission, such as imitation/emulation, may have contributed to the B700,000 year stasis of the Oldowan technocomplex, and (ii) teaching or proto-language may have been pre-requisites for the appearance of Acheulean technology. This work supports a gradual evolution of language, with simple symbolic communication preceding behavioural modernity by hundreds of thousands of years.
TL;DR: A multitude of methods aimed towards solvent modelling and solubility prediction are discussed, aiming to inform the reader of the options available, and outlining the various advantages and disadvantages of each approach.
Abstract: Over the past decade, pharmaceutical companies have seen a decline in the number of drug candidates successfully passing through clinical trials, though billions are still spent on drug development. Poor aqueous solubility leads to low bio-availability, reducing pharmaceutical effectiveness. The human cost of inefficient drug candidate testing is of great medical concern, with fewer drugs making it to the production line, slowing the development of new treatments. In biochemistry and biophysics, water mediated reactions and interactions within active sites and protein pockets are an active area of research, in which methods for modelling solvated systems are continually pushed to their limits. Here, we discuss a multitude of methods aimed towards solvent modelling and solubility prediction, aiming to inform the reader of the options available, and outlining the various advantages and disadvantages of each approach.
TL;DR: In this paper, the authors describe the design, manufacture, and performance of bare-fiber integral field units (IFUs) for the SDSS-IV survey Mapping Nearby Galaxies at Apache Point Observatory (MaNGA).
Abstract: We describe the design, manufacture, and performance of bare-fiber integral field units (IFUs) for the SDSS-IV survey Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) on the the Sloan 2.5 m telescope at Apache Point Observatory. MaNGA is a luminosity-selected integral-field spectroscopic survey of 104 local galaxies covering 360–1030 nm at R ~ 2200. The IFUs have hexagonal dense packing of fibers with packing regularity of 3 μm (rms), and throughput of 96 ± 0.5% from 350 nm to 1 μm in the lab. Their sizes range from 19 to 127 fibers (3–7 hexagonal layers) using Polymicro FBP 120:132:150 μm core:clad:buffer fibers to reach a fill fraction of 56%. High throughput (and low focal-ratio degradation (FRD)) is achieved by maintaining the fiber cladding and buffer intact, ensuring excellent surface polish, and applying a multi-layer anti-reflection (AR) coating of the input and output surfaces. In operations on-sky, the IFUs show only an additional 2.3% FRD-related variability in throughput despite repeated mechanical stressing during plate plugging (however other losses are present). The IFUs achieve on-sky throughput 5% above the single-fiber feeds used in SDSS-III/BOSS, attributable to equivalent performance compared to single fibers and additional gains from the AR coating. The manufacturing process is geared toward mass-production of high-multiplex systems. The low-stress process involves a precision ferrule with a hexagonal inner shape designed to lead inserted fibers to settle in a dense hexagonal pattern. The ferrule ID is tapered at progressively shallower angles toward its tip and the final 2 mm are straight and only a few microns larger than necessary to hold the desired number of fibers. Our IFU manufacturing process scales easily to accommodate other fiber sizes and can produce IFUs with substantially larger fiber counts. To assure quality, automated testing in a simple and inexpensive system enables complete characterization of throughput and fiber metrology. Future applications include larger IFUs, higher fill factors with stripped buffer, de-cladding, and lenslet coupling.
TL;DR: The signal processing techniques needed to produce calibrated measurements of terrestrial and aquatic acoustic habitats are reviewed and a supplemental tutorial and template computer codes in matlab and r are included, which give detailed guidance on how to production calibrated spectrograms and statistical analyses of sound levels.
Abstract: Summary 1. Many organisms depend on sound for communication, predator/prey detection and navigation. The acoustic environment can therefore play an important role in ecosystem dynamics and evolution. A growing number of studies are documenting acoustic habitats and their influences on animal development, behaviour, physiology and spatial ecology, which has led to increasing demand for passive acoustic monitoring (PAM) expertise in the life sciences. However, as yet, there has been no synthesis of data processing methods for acoustic habitat monitoring, which presents an unnecessary obstacle to would-be PAM analysts. 2. Here, we review the signal processing techniques needed to produce calibrated measurements of terrestrial and aquatic acoustic habitats. We include a supplemental tutorial and template computer codes in MATLAB and R, which give detailed guidance on how to produce calibrated spectrograms and statistical analyses of sound levels. Key metrics and terminology for the characterisation of biotic, abiotic and anthropogenic sound are covered, and their application to relevant monitoring scenarios is illustrated through example data sets. To inform study design and hardware selection, we also include an up-to-date overview of terrestrial and aquatic PAM instruments. 3. Monitoring of acoustic habitats at large spatiotemporal scales is becoming possible through recent advances in PAM technology. This will enhance our understanding of the role of sound in the spatial ecology of acoustically sensitive species and inform spatial planning to mitigate the rising influence of anthropogenic noise in these ecosystems. As we demonstrate in this work, progress in these areas will depend upon the application of consistent and appropriate PAM methodologies.
Paris Diderot University1, PSL Research University2, European Southern Observatory3, University of Oxford4, California Institute of Technology5, University of California, Berkeley6, University of Toledo7, Leiden University8, École normale supérieure de Lyon9, University of Edinburgh10, Leibniz Institute for Astrophysics Potsdam11, Macquarie University12, Australian Astronomical Observatory13, ASTRON14, Kapteyn Astronomical Institute15, Max Planck Society16, University of Hertfordshire17, University of Sydney18, Australia Telescope National Facility19, University of St Andrews20, New Mexico Institute of Mining and Technology21, Academia Sinica Institute of Astronomy and Astrophysics22
TL;DR: In this article, the authors presented a catalogue of 92 galaxies from the ATLAS^(3D) sample, which are located in low- to medium-density environments, which achieved a gain of several magnitudes in the limiting surface brightness with respect to classical imaging surveys.
Abstract: Galactic archaeology based on star counts is instrumental to reconstruct the past mass assembly of Local Group galaxies. The development of new observing techniques and data reduction, coupled with the use of sensitive large field of view cameras, now allows us to pursue this technique in more distant galaxies exploiting their diffuse low surface brightness (LSB) light. As part of the ATLAS^(3D) project, we have obtained with the MegaCam camera at the Canada–France–Hawaii Telescope extremely deep, multiband images of nearby early-type galaxies (ETGs). We present here a catalogue of 92 galaxies from the ATLAS^(3D) sample, which are located in low- to medium-density environments. The observing strategy and data reduction pipeline, which achieve a gain of several magnitudes in the limiting surface brightness with respect to classical imaging surveys, are presented. The size and depth of the survey are compared to other recent deep imaging projects. The paper highlights the capability of LSB-optimized surveys at detecting new prominent structures that change the apparent morphology of galaxies. The intrinsic limitations of deep imaging observations are also discussed, among those, the contamination of the stellar haloes of galaxies by extended ghost reflections, and the cirrus emission from Galactic dust. The detection and systematic census of fine structures that trace the present and past mass assembly of ETGs are one of the prime goals of the project. We provide specific examples of each type of observed structures – tidal tails, stellar streams and shells – and explain how they were identified and classified. We give an overview of the initial results. The detailed statistical analysis will be presented in future papers.
University of Tartu1, Estonian Biocentre2, University of Cambridge3, Arizona State University4, University of California, Berkeley5, Armenian National Academy of Sciences6, Russian Academy of Sciences7, University of Auckland8, Pennsylvania State University9, University of Winchester10, Wellcome Trust Sanger Institute11, University of Copenhagen12, Bashkir State University13, Kazan Federal University14, University of Pennsylvania15, Georgia Institute of Technology16, Centre national de la recherche scientifique17, Eijkman Institute for Molecular Biology18, Massey University19, University of Dhaka20, Aarhus University21, Griffith University22, Josip Juraj Strossmayer University of Osijek23, Academy of Sciences of Uzbekistan24, Kuban State Medical University25, L.N.Gumilyov Eurasian National University26, Nazarbayev University27, North-Eastern Federal University28, Academy of Medical Sciences, United Kingdom29, Anthony Nolan30, University College London31, University of St Andrews32, University of Kharkiv33, International Burch University34, National Academy of Sciences of Belarus35, Radboud University Nijmegen36, King Abdullah University of Science and Technology37, Stanford University38, University of Arizona39, Stony Brook University40, University Hospital of North Norway41, Estonian Academy of Sciences42
TL;DR: A study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples, infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky, and hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.
Abstract: It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.