Showing papers by "University of St Andrews published in 2019"
TL;DR: The DESI Legacy Imaging Surveys (http://legacysurvey.org/) as mentioned in this paper is a combination of three public projects (the Dark Energy Camera Legacy Survey, the Beijing-Arizona Sky Survey, and the Mayall z-band Legacy Survey) that will jointly image ≈14,000 deg2 of the extragalactic sky visible from the northern hemisphere in three optical bands (g, r, and z) using telescopes at the Kitt Peak National Observatory and the Cerro Tololo Inter-American Observatory.
Abstract: The DESI Legacy Imaging Surveys (http://legacysurvey.org/) are a combination of three public projects (the Dark Energy Camera Legacy Survey, the Beijing–Arizona Sky Survey, and the Mayall z-band Legacy Survey) that will jointly image ≈14,000 deg2 of the extragalactic sky visible from the northern hemisphere in three optical bands (g, r, and z) using telescopes at the Kitt Peak National Observatory and the Cerro Tololo Inter-American Observatory. The combined survey footprint is split into two contiguous areas by the Galactic plane. The optical imaging is conducted using a unique strategy of dynamically adjusting the exposure times and pointing selection during observing that results in a survey of nearly uniform depth. In addition to calibrated images, the project is delivering a catalog, constructed by using a probabilistic inference-based approach to estimate source shapes and brightnesses. The catalog includes photometry from the grz optical bands and from four mid-infrared bands (at 3.4, 4.6, 12, and 22 μm) observed by the Wide-field Infrared Survey Explorer satellite during its full operational lifetime. The project plans two public data releases each year. All the software used to generate the catalogs is also released with the data. This paper provides an overview of the Legacy Surveys project.
517 citations
TL;DR: An extension to two popular approaches to modeling complex structures in ecological data: the generalized additive model (GAM) and the hierarchical model (HGLM), which allows modeling of nonlinear functional relationships between covariates and outcomes where the shape of the function itself varies between different grouping levels.
Abstract: In this paper, we discuss an extension to two popular approaches to modeling complex structures in ecological data: the generalized additive model (GAM) and the hierarchical model (HGLM). The hierarchical GAM (HGAM), allows modeling of nonlinear functional relationships between covariates and outcomes where the shape of the function itself varies between different grouping levels. We describe the theoretical connection between HGAMs, HGLMs, and GAMs, explain how to model different assumptions about the degree of intergroup variability in functional response, and show how HGAMs can be readily fitted using existing GAM software, the mgcv package in R. We also discuss computational and statistical issues with fitting these models, and demonstrate how to fit HGAMs on example data. All code and data used to generate this paper are available at: github.com/eric-pedersen/mixed-effect-gams.
425 citations
Centre national de la recherche scientifique1, IFREMER2, ETH Zurich3, University of Bern4, Cardiff University5, Université Paris-Saclay6, University of Bordeaux7, Federal Fluminense University8, Leibniz Institute for Baltic Sea Research9, University of St Andrews10, University of New Hampshire11, Oregon State University12, École pratique des hautes études13, Royal Holloway, University of London14, University of Nantes15, Hofstra University16, Lamont–Doherty Earth Observatory17, Uppsala University18, Woods Hole Oceanographic Institution19, University of Edinburgh20, Geological Survey of Denmark and Greenland21, Instituto Geológico y Minero de España22, University of Connecticut23, Georgia Institute of Technology24, University of Colorado Boulder25, University of the Algarve26, British Antarctic Survey27, VU University Amsterdam28, University of Bremen29, Max Planck Society30, Thermo Fisher Scientific31, University of Cambridge32, University of Paris33, University College London34, Ghent University35, Aix-Marseille University36, Autonomous University of Barcelona37, University of California, Santa Barbara38, Utrecht University39
TL;DR: This is the first set of consistently dated marine sediment cores enabling paleoclimate scientists to evaluate leads/lags between circulation and climate changes over vast regions of the Atlantic Ocean.
Abstract: Rapid changes in ocean circulation and climate have been observed in marine-sediment and ice cores over the last glacial period and deglaciation, highlighting the non-linear character of the climate system and underlining the possibility of rapid climate shifts in response to anthropogenic greenhouse gas forcing. To date, these rapid changes in climate and ocean circulation are still not fully explained. One obstacle hindering progress in our understanding of the interactions between past ocean circulation and climate changes is the difficulty of accurately dating marine cores. Here, we present a set of 92 marine sediment cores from the Atlantic Ocean for which we have established age-depth models that are consistent with the Greenland GICC05 ice core chronology, and computed the associated dating uncertainties, using a new deposition modeling technique. This is the first set of consistently dated marine sediment cores enabling paleoclimate scientists to evaluate leads/lags between circulation and climate changes over vast regions of the Atlantic Ocean. Moreover, this data set is of direct use in paleoclimate modeling studies.
399 citations
TL;DR: Solid-state sources of highly efficient, pure, and indistinguishable single photons and 3D integration of ultralow-loss optical circuits are developed and the Boson sampling regime enters into a genuine sampling regime where it becomes impossible to exhaust all possible output combinations.
Abstract: Quantum computing experiments are moving into a new realm of increasing size and complexity, with the short-term goal of demonstrating an advantage over classical computers. Boson sampling is a promising platform for such a goal; however, the number of detected single photons is up to five so far, limiting these small-scale implementations to a proof-of-principle stage. Here, we develop solid-state sources of highly efficient, pure, and indistinguishable single photons and 3D integration of ultralow-loss optical circuits. We perform experiments with 20 pure single photons fed into a 60-mode interferometer. In the output, we detect up to 14 photons and sample over Hilbert spaces with a size up to 3.7×10^{14}, over 10 orders of magnitude larger than all previous experiments, which for the first time enters into a genuine sampling regime where it becomes impossible to exhaust all possible output combinations. The results are validated against distinguishable samplers and uniform samplers with a confidence level of 99.9%.
370 citations
TL;DR: A Perspective discussing the factors that have contributed to the success and failure of point-of-care tests for resource-limited settings and the challenges and opportunities that exist for developing new infectious disease diagnostics.
Abstract: Copyright: 2018. Due to copyright restrictions, the attached PDF file only contains the abstract version of the full-text item. For access to the full-text item, please consult the publisher's website. The definitive version of the work is published in Nature Microbiology, vol 4, pp. 46-54
336 citations
Martin Luther University of Halle-Wittenberg1, Denison University2, University of St Andrews3, University of Aveiro4, University of Helsinki5, Memorial University of Newfoundland6, University of Maine7, University of Edinburgh8, University of Massachusetts Boston9, McGill University10, Leipzig University11, University of Minnesota12, Northern Illinois University13, University of British Columbia14, Université de Sherbrooke15, National Oceanography Centre16
TL;DR: Examining spatial variation in species richness and composition change using more than 50,000 biodiversity time series from 239 studies found clear geographic variation in biodiversity change, suggesting that biodiversity change may be spatially structured.
Abstract: Human activities are fundamentally altering biodiversity. Projections of declines at the global scale are contrasted by highly variable trends at local scales, suggesting that biodiversity change may be spatially structured. Here, we examined spatial variation in species richness and composition change using more than 50,000 biodiversity time series from 239 studies and found clear geographic variation in biodiversity change. Rapid compositional change is prevalent, with marine biomes exceeding and terrestrial biomes trailing the overall trend. Assemblage richness is not changing on average, although locations exhibiting increasing and decreasing trends of up to about 20% per year were found in some marine studies. At local scales, widespread compositional reorganization is most often decoupled from richness change, and biodiversity change is strongest and most variable in the oceans.
318 citations
TL;DR: In this article, a polarization-orthogonal excitation collection scheme is designed to minimize the polarization filtering loss under resonant excitation, achieving a single-photon efficiency of 0.60.
Abstract: An optimal single-photon source should deterministically deliver one, and only one, photon at a time, with no trade-off between the source’s efficiency and the photon indistinguishability. However, all reported solid-state sources of indistinguishable single photons had to rely on polarization filtering, which reduced the efficiency by 50%, fundamentally limiting the scaling of photonic quantum technologies. Here, we overcome this long-standing challenge by coherently driving quantum dots deterministically coupled to polarization-selective Purcell microcavities. We present two examples: narrowband, elliptical micropillars and broadband, elliptical Bragg gratings. A polarization-orthogonal excitation–collection scheme is designed to minimize the polarization filtering loss under resonant excitation. We demonstrate a polarized single-photon efficiency of 0.60 ± 0.02 (0.56 ± 0.02), a single-photon purity of 0.975 ± 0.005 (0.991 ± 0.003) and an indistinguishability of 0.975 ± 0.006 (0.951 ± 0.005) for the micropillar (Bragg grating) device. Our work provides promising solutions for truly optimal single-photon sources combining near-unity indistinguishability and near-unity system efficiency simultaneously. Single-photon sources with a single-photon efficiency of 0.60, a single-photon purity of 0.975 and an indistinguishability of 0.975 are demonstrated. This is achieved by fabricating elliptical resonators around site-registered quantum dots.
309 citations
TL;DR: The Sloan Digital Sky Survey (SDSS) as discussed by the authors released data taken by the fourth phase of SDSS-IV across its first three years of operation (2014 July-2017 July).
Abstract: Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 July–2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGA—we release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020–2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.
305 citations
TL;DR: NMR spectroscopy of oxygen-17 reveals a drop of the Knight shift in the superconducting state, contradicting previous work and imposing tight constraints on the order parameter symmetry of the system.
Abstract: Phases of matter are usually identified through spontaneous symmetry breaking, especially regarding unconventional superconductivity and the interactions from which it originates. In that context, the superconducting state of the quasi-two-dimensional and strongly correlated perovskite Sr2RuO4 is considered to be the only solid-state analogue to the superfluid 3He-A phase1,2, with an odd-parity order parameter that is unidirectional in spin space for all electron momenta and breaks time-reversal symmetry. This characterization was recently called into question by a search for an expected 'split' transition in a Sr2RuO4 crystal under in-plane uniaxial pressure, which failed to find any such evidence; instead, a dramatic rise and a peak in a single-transition temperature were observed3,4. Here we use nuclear magnetic resonance (NMR) spectroscopy of oxygen-17, which is directly sensitive to the order parameter via hyperfine coupling to the electronic spin degrees of freedom, to probe the nature of superconductivity in Sr2RuO4 and its evolution under strain. A reduction of the Knight shift is observed for all strain values and at temperatures below the critical temperature, consistent with a drop in spin polarization in the superconducting state. In unstrained samples, our results contradict a body of previous NMR work reporting no change in the Knight shift5 and the most prevalent theoretical interpretation of the order parameter as a chiral p-wave state. Sr2RuO4 is an extremely clean layered perovskite and its superconductivity emerges from a strongly correlated Fermi liquid, and our work imposes tight constraints on the order parameter symmetry of this archetypal system.
261 citations
TL;DR: This work generates entangled photon pairs with a state fidelity of 0.90(1), pair generation rate, pair extraction efficiency, and photon indistinguishability simultaneously, and will open up many applications in high-efficiency multiphoton experiments and solid-state quantum repeaters.
Abstract: An outstanding goal in quantum optics and scalable photonic quantum technology is to develop a source that each time emits one and only one entangled photon pair with simultaneously high entanglement fidelity, extraction efficiency, and photon indistinguishability. By coherent two-photon excitation of a single InGaAs quantum dot coupled to a circular Bragg grating bull's-eye cavity with a broadband high Purcell factor of up to 11.3, we generate entangled photon pairs with a state fidelity of 0.90(1), pair generation rate of 0.59(1), pair extraction efficiency of 0.62(6), and photon indistinguishability of 0.90(1) simultaneously. Our work will open up many applications in high-efficiency multiphoton experiments and solid-state quantum repeaters.
246 citations
TL;DR: In the last few decades the Circular economy has increasingly been advertised as an economic model that can replace the current linear economy whilst addressing the issues of environmental deterioration, social equity and long-term economic growth with the explicit suggestion that it can serve as a tool for sustainable development as mentioned in this paper.
TL;DR: In this paper, a band inversion between manifolds of surface states is proposed to stabilize topological and symmetry-protected states in solids, by aliovalent substitution of Nb for Zr and Sb for S in the ZrSiS family of nonsymmorphic semimetals.
Abstract: Band inversions are key to stabilising a variety of novel electronic states in solids, from topological surface states to the formation of symmetry-protected three-dimensional Dirac and Weyl points and nodal-line semimetals. Here, we create a band inversion not of bulk states, but rather between manifolds of surface states. We realise this by aliovalent substitution of Nb for Zr and Sb for S in the ZrSiS family of nonsymmorphic semimetals. Using angle-resolved photoemission and density-functional theory, we show how two pairs of surface states, known from ZrSiS, are driven to intersect each other near the Fermi level in NbGeSb, and to develop pronounced spin splittings. We demonstrate how mirror symmetry leads to protected crossing points in the resulting spin-orbital entangled surface band structure, thereby stabilising surface state analogues of three-dimensional Weyl points. More generally, our observations suggest new opportunities for engineering topologically and symmetry-protected states via band inversions of surface states.
TL;DR: A series of π-extended boron- and nitrogen-doped nanographenes are designed as promising candidates for efficient thermally activated delayed fluorescence emitters with concomitantly decreased singlet-triplet energy gaps, improved oscillator strengths and core rigidity compared to previously reported structures, permitting both emission color purity and tunability across the visible spectrum.
Abstract: The work was supported by the European Union’s Horizon 2020 research and innovation program under Grant Agreement N°. 646176 (EXTMOS project). A.P. acknowledges the financial support from the Marie Curie Fellowship (MILORD project, N°. 748042). Computational resources have been provided by the Consortium des Equipements de Calcul Intensif (CECI), funded by the Fonds de la Recherche Scientifiques de Belgique (F.R.S.-FNRS) under Grant No. 2.5020.11, as well as the Tier-1 supercomputer of the Federation Wallonie-Bruxelles, infrastructure funded by the Walloon Region under the grant agreement n1117545. The St Andrews team would like to thank the Leverhulme Trust (RPG-2016-047) and EPSRC (EP/P010482/1) for financial support.
TL;DR: In this paper, an energy justice framework is outlined to account for distributional, procedural and recognition inequalities, as well as emerging themes such as cosmopolitan and non-western understandings of justice, in decision-making relating to energy systems.
TL;DR: This review provides an account of the development of the Chan-Lam amination, highlighting progress and notable examples of application since 2011 and focusing on evolution in mechanistic understanding and selected applications of the methodology within medicinal and process chemistry.
Abstract: Transition metal-mediated formation of C-N bonds is an essential synthetic methodology. The discovery of the Chan-Lam amination provided a C-N bond forming process that was mild, convenient, and inexpensive, offering an alternative to complementary methods using other transition metals (TMs). Over the past 20 years, this reaction has seen considerable development in its scope of application, uptake into industry, and understanding of its mechanism. This review provides an account of the development of the Chan-Lam amination, highlighting progress and notable examples of application since 2011. Focus is given to evolution in mechanistic understanding and selected applications of the methodology within medicinal and process chemistry.
University of Oxford1, University of Wisconsin-Madison2, University of California, Santa Cruz3, European Southern Observatory4, Tsinghua University5, Space Telescope Science Institute6, University of Kentucky7, University of Pittsburgh8, University of Utah9, Johns Hopkins University10, University of Texas at Austin11, University of Washington12, University of St Andrews13, National Autonomous University of Mexico14, Chinese Academy of Sciences15
TL;DR: The data analysis pipeline (DAP) as discussed by the authors provides higher-level data products, such as stellar kinematics (velocity and velocity dispersion), emission-line properties (kinematics, fluxes, and equivalent widths), and spectral indices (e.g., D4000 and the Lick indices).
Abstract: Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) is acquiring integral-field spectroscopy for the largest sample of galaxies to date. By 2020, the MaNGA Survey --- one of three core programs in the fourth-generation Sloan Digital Sky Survey (SDSS-IV) --- will have observed a statistically representative sample of 10$^4$ galaxies in the local Universe ($z\lesssim0.15$). In addition to a robust data-reduction pipeline (DRP), MaNGA has developed a data-analysis pipeline (DAP) that provides higher-level data products. To accompany the first public release of its code base and data products, we provide an overview of the MaNGA DAP, including its software design, workflow, measurement procedures and algorithms, performance, and output data model. In conjunction with our companion paper Belfiore et al., we also assess the DAP output provided for 4718 observations of 4648 unique galaxies in the recent SDSS Data Release 15 (DR15). These analysis products focus on measurements that are close to the data and require minimal model-based assumptions. Namely, we provide stellar kinematics (velocity and velocity dispersion), emission-line properties (kinematics, fluxes, and equivalent widths), and spectral indices (e.g., D4000 and the Lick indices). We find that the DAP provides robust measurements and errors for the vast majority ($>$99%) of analyzed spectra. We summarize assessments of the precision and accuracy of our measurements as a function of signal-to-noise, and provide specific guidance to users regarding the limitations of the data. The MaNGA DAP software is publicly available and we encourage community involvement in its development.
TL;DR: It is shown that this system remains localized in the presence of interactions and exhibits physics analogous to models of conventional many-body localization (MBL), and that a quench experiment starting from a charge-density wave state would show results similar to those of Schreiber et al.
Abstract: We consider spinless fermions on a finite one-dimensional lattice, interacting via nearest-neighbor repulsion and subject to a strong electric field. In the noninteracting case, due to Wannier-Stark localization, the single-particle wave functions are exponentially localized even though the model has no quenched disorder. We show that this system remains localized in the presence of interactions and exhibits physics analogous to models of conventional many-body localization (MBL). In particular, the entanglement entropy grows logarithmically with time after a quench, albeit with a slightly different functional form from the MBL case, and the level statistics of the many-body energy spectrum are Poissonian. We moreover predict that a quench experiment starting from a charge-density wave state would show results similar to those of Schreiber et al. [Science 349, 842 (2015)SCIEAS0036-807510.1126/science.aaa7432].
Chinese Academy of Sciences1, Institute of Cosmology and Gravitation, University of Portsmouth2, Max Planck Society3, University of Paris4, Stanford University5, Leibniz Institute for Astrophysics Potsdam6, Yale University7, Ohio State University8, University of St Andrews9, Centre national de la recherche scientifique10, University of Wyoming11, New York University12, Lawrence Berkeley National Laboratory13, Humboldt University of Berlin14, University of Utah15, Ohio University16, Ludwig Maximilian University of Munich17, National Autonomous University of Mexico18, Sejong University19, University of Edinburgh20, Korea Astronomy and Space Science Institute21, Pennsylvania State University22, Tsinghua University23
TL;DR: In this paper, a new method based on the optimal redshift weighting scheme was developed to extract the maximal tomographic information of baryonic acoustic oscillations (BAO) and redshift space distortions (RSD) from the extended Baryon Oscillation Spectroscopic Survey (eBOSS) Data Release 14 quasar (DR14Q) survey.
Abstract: We develop a new method, which is based on the optimal redshift weighting scheme, to extract the maximal tomographic information of baryonic acoustic oscillations (BAO) and redshift space distortions (RSD) from the extended Baryon Oscillation Spectroscopic Survey (eBOSS) Data Release 14 quasar (DR14Q) survey. We validate our method using the Extended Zel'dovich mocks, and apply our pipeline to the eBOSS DR14Q sample in the redshift range of 0.8 < z < 2.2. We report a joint measurement of fσ and two-dimensional BAO parameters D and H at four effective redshifts of zeff = 0.98, 1.23, 1.52, and 1.94, and provide the full data covariance matrix. Using our measurement combined with BOSS DR12, Main Galaxy Sample (MGS), and 6 degree Field Galaxy Survey (6dFGS) BAO measurements, we find that the existence of dark energy is supported by observations at a 7.4σ significance level. Combining our measurement with BOSS DR12 and Planck observations, we constrain the gravitational growth index to be γ = 0.580 ± 0.082, which is fully consistent with the prediction of general relativity. This paper is part of a set that analyses the eBOSS DR14 quasar sample.
TL;DR: In this paper, a critical review focusses on Earth-abundant metal complexes as potential replacement photocatalysts and summarizes the use of photoactive Cu(I), Zn(II), Ni(0), V(V), Zr(IV), W(0, W(VI), Mo( 0), Cr(III), Co(III) and Fe(II) complexes in photoredox reactions.
TL;DR: Psychological interventions for FCR revealed a small but robust effect at postintervention, which was largely maintained at follow-up, and future trials could investigate how to further optimize and tailor interventions to individual patients’ FCR presentation.
Abstract: PURPOSEFear of cancer recurrence (FCR) is a significantly distressing problem that affects a substantial number of patients with and survivors of cancer; however, the overall efficacy of available ...
TL;DR: In this paper, it was shown that careful tuning of the coupled system can lead to a modest reduction of simultaneous two-polariton generation probability by 5% in the presence of a photon blockade effect.
Abstract: Cavity–polaritons in semiconductor microstructures have emerged as a promising system for exploring non-equilibrium dynamics of many-body systems1. Key advances in this field, including the observation of polariton condensation2, superfluidity3, realization of topological photonic bands4, and dissipative phase transitions5–7, generically allow for a description based on a mean-field Gross–Pitaevskii formalism. Observation of polariton intensity squeezing8,9 and decoherence of a polarization entangled photon pair by a polariton condensate10, on the other hand, demonstrate quantum effects that show up at high polariton occupancy. Going beyond and into the regime of strongly correlated polaritons requires the observation of a photon blockade effect11,12 where interactions are strong enough to suppress double occupancy of a photonic lattice site. Here, we report evidence of quantum correlations between polaritons spatially confined in a fibre cavity. Photon correlation measurements show that careful tuning of the coupled system can lead to a modest reduction of simultaneous two-polariton generation probability by 5%. Concurrently, our experiments allow us to measure the polariton interaction strength, thereby resolving the controversy stemming from recent experimental reports13. Our findings constitute an essential step towards the realization of strongly interacting photonic systems. Confined exciton–polaritons in semiconductor-based quantum wells can give rise to correlations slightly below the level of classical coincidence counts under resonant excitation, such that single or few polariton excitations are sufficient to modify the statistics of the radiation going through the system.
TL;DR: The Jiangnan Orogen has been interpreted as an intra-oceanic terrane based on the juvenile radiogenic isotopic signature of the igneous rocks, the absence of older detritus and inherited xenocrysts, and the presence of ophiolites along its southwestern and western margins.
University of Western Australia1, University of Gothenburg2, Australian Institute of Marine Science3, University of Sydney4, Dalhousie University5, James Cook University6, University of Tasmania7, University of California, Santa Cruz8, Stanford University9, National Oceanic and Atmospheric Administration10, Office of Naval Research11, University of St Andrews12, École Normale Supérieure13, University of Paris14, Carleton University15, South African Institute for Aquatic Biodiversity16, University of Pretoria17, Fisheries and Oceans Canada18, King Abdullah University of Science and Technology19, Spanish National Research Council20, Commonwealth Scientific and Industrial Research Organisation21, National Institute of Water and Atmospheric Research22, University of Tokyo23, University of La Rochelle24, Deakin University25, Flinders University26, Universiti Malaysia Terengganu27, Norwegian Polar Institute28, Japan Aerospace Exploration Agency29, University of British Columbia30
TL;DR: The use of animal telemetry is a powerful tool for observing marine animals and the physical environments that they inhabit, from coastal and continental shelf ecosystems to polar seas and open oceans.
Abstract: Animal telemetry is a powerful tool for observing marine animals and the physical environments that they inhabit, from coastal and continental shelf ecosystems to polar seas and open oceans. Satellite-linked biologgers and networks of acoustic receivers allow animals to be reliably monitored over scales of tens of meters to thousands of kilometers, giving insight into their habitat use, home range size, the phenology of migratory patterns and the biotic and abiotic factors that drive their distributions. Furthermore, physical environmental variables can be collected using animals as autonomous sampling platforms, increasing spatial and temporal coverage of global oceanographic observation systems. The use of animal telemetry, therefore, has the capacity to provide measures from a suite of essential ocean variables (EOVs) for improved monitoring of Earth's oceans. Here we outline the design features of animal telemetry systems, describe current applications and their benefits and challenges, and discuss future directions. We describe new analytical techniques that improve our ability to not only quantify animal movements but to also provide a powerful framework for comparative studies across taxa. We discuss the application of animal telemetry and its capacity to collect biotic and abiotic data, how the data collected can be incorporated into ocean observing systems, and the role these data can play in improved ocean management.
TL;DR: A multi-omics survey of progressive compared to regressive carcinoma in situ lesions provides a molecular map of early lung cancer development and is expected to improve early detection, reduce overtreatment, and foster preventative therapies targeting early clonal events in lung cancer.
Abstract: The molecular alterations that occur in cells before cancer is manifest are largely uncharted. Lung carcinoma in situ (CIS) lesions are the pre-invasive precursor to squamous cell carcinoma. Although microscopically identical, their future is in equipoise, with half progressing to invasive cancer and half regressing or remaining static. The cellular basis of this clinical observation is unknown. Here, we profile the genomic, transcriptomic, and epigenomic landscape of CIS in a unique patient cohort with longitudinally monitored pre-invasive disease. Predictive modeling identifies which lesions will progress with remarkable accuracy. We identify progression-specific methylation changes on a background of widespread heterogeneity, alongside a strong chromosomal instability signature. We observed mutations and copy number changes characteristic of cancer and chart their emergence, offering a window into early carcinogenesis. We anticipate that this new understanding of cancer precursor biology will improve early detection, reduce overtreatment, and foster preventative therapies targeting early clonal events in lung cancer.
TL;DR: How FFAs are altered in T2DM is reviewed and the likely downstream physiological and pathological implications of such changes are explored.
Abstract: Type 2 diabetes mellitus (T2DM) is associated with increased total plasma free fatty acid (FFA) concentrations and an elevated risk of cardiovascular disease. The exact mechanisms by which the plasma FFA profile of subjects with T2DM changes is unclear, but it is thought that dietary fats and changes to lipid metabolism are likely to contribute. Therefore, establishing the changes in concentrations of specific FFAs in an individual’s plasma is important. Each type of FFA has different effects on physiological processes, including the regulation of lipolysis and lipogenesis in adipose tissue, inflammation, endocrine signalling and the composition and properties of cellular membranes. Alterations in such processes due to altered plasma FFA concentrations/profiles can potentially result in the development of insulin resistance and coagulatory defects. Finally, fibrates and statins, lipid-regulating drugs prescribed to subjects with T2DM, are also thought to exert part of their beneficial effects by impacting on plasma FFA concentrations. Thus, it is also interesting to consider their effects on the concentration of FFAs in plasma. Collectively, we review how FFAs are altered in T2DM and explore the likely downstream physiological and pathological implications of such changes.
TL;DR: This paper reviews work on the interdisciplinary attempt of training deep neural networks using whole slide images, and highlights the different ideas underlying these methodologies.
Abstract: The widespread adoption of whole slide imaging has increased the demand for effective and efficient gigapixel image analysis. Deep learning is at the forefront of computer vision, showcasing significant improvements over previous methodologies on visual understanding. However, whole slide images have billions of pixels and suffer from high morphological heterogeneity as well as from different types of artifacts. Collectively, these impede the conventional use of deep learning. For the clinical translation of deep learning solutions to become a reality, these challenges need to be addressed. In this paper, we review work on the interdisciplinary attempt of training deep neural networks using whole slide images, and highlight the different ideas underlying these methodologies.
01 Feb 2019
TL;DR: In this article, the critical properties of the super-radiant phase transition and the distinction between equilibrium and none-quilibrium conditions are reviewed, as well as some aspects of real-time dynamics, including superconducting qubits, trapped ions, and using spin-orbit coupling for cold atoms.
Abstract: The Dicke model describes the coupling between a quantized cavity field and a large ensemble of two-level atoms. When the number of atoms tends to infinity, this model can undergo a transition to a superradiant phase, belonging to the mean-field Ising universality class. The superradiant transition was first predicted for atoms in thermal equilibrium and was recently realized with a quantum simulator made of atoms in an optical cavity, subject to both dissipation and driving. In this Progress Report, we offer an introduction to some theoretical concepts relevant to the Dicke model, reviewing the critical properties of the superradiant phase transition, and the distinction between equilibrium and nonequilibrium conditions. In addition, we explain the fundamental difference between the superradiant phase transition and the more common lasing transition. Our report mostly focuses on the steady states of atoms in single-mode optical cavities, but we also mention some aspects of real-time dynamics, as well as other quantum simulators, including superconducting qubits, trapped ions, and using spin-orbit coupling for cold atoms. These realizations differ in regard to whether they describe equilibrium or non-equilibrium systems.
TL;DR: In this article, the authors show that the crystal structure defines the dimensionality and connectivity of interstitial sites, thus determining lithium ion diffusion kinetics, and they identify a crucial property that has previously been overlooked and provides guidelines for designing and engineering cation-disordered cathode materials.
Abstract: Structure plays a vital role in determining materials properties. In lithium ion cathode materials, the crystal structure defines the dimensionality and connectivity of interstitial sites, thus determining lithium ion diffusion kinetics. In most conventional cathode materials that are well-ordered, the average structure as seen in diffraction dictates the lithium ion diffusion pathways. Here, we show that this is not the case in a class of recently discovered high-capacity lithium-excess rocksalts. An average structure picture is no longer satisfactory to understand the performance of such disordered materials. Cation short-range order, hidden in diffraction, is not only ubiquitous in these long-range disordered materials, but fully controls the local and macroscopic environments for lithium ion transport. Our discovery identifies a crucial property that has previously been overlooked and provides guidelines for designing and engineering cation-disordered cathode materials.
TL;DR: Analysis of demographic data from 121 species shows that animal life history strategies vary across two axes of variation defined by the pace of life and the distribution of a species’ mortality and reproduction over their life course.
Abstract: Animals exhibit an extraordinary diversity of life history strategies. These realized combinations of survival, development and reproduction are predicted to be constrained by physiological limitations and by trade-offs in resource allocation. However, our understanding of these patterns is restricted to a few taxonomic groups. Using demographic data from 121 species, ranging from humans to sponges, we test whether such trade-offs universally shape animal life history strategies. We show that, after accounting for body mass and phylogenetic relatedness, 71% of the variation in animal life history strategies can be explained by life history traits associated with the fast-slow continuum (pace of life) and with a second axis defined by the distribution of age-specific mortality hazards and the spread of reproduction. While we found that life history strategies are associated with metabolic rate and ecological modes of life, surprisingly similar life history strategies can be found across the phylogenetic and physiological diversity of animals.
TL;DR: For a set of 23 241 populations, 16 009 species, in 158 assemblages, significantly accelerating extinction and colonisation rates were detected, with both rates being approximately balanced.
Abstract: Scientists disagree about the nature of biodiversity change. While there is evidence for widespread declines from population surveys, assemblage surveys reveal a mix of declines and increases. These conflicting conclusions may be caused by the use of different metrics: assemblage metrics may average out drastic changes in individual populations. Alternatively, differences may arise from data sources: populations monitored individually, versus whole assemblage monitoring. To test these hypotheses, we estimated population change metrics using assemblage data. For a set of 23,241 populations, 16,009 species, in 158 assemblages, we detected significantly accelerating extinction and colonisation rates, with both rates being approximately balanced. Most populations (85%) did not show significant trends in abundance, and those that did were balanced between winners (8%) and losers (7%). Thus, population metrics estimated with assemblage data are commensurate with assemblage metrics and reveal sustained and increasing species turnover.