Showing papers by "University of East Anglia published in 2020"
University of Coimbra1, University of Southern Queensland2, National Institute for Health and Welfare3, Arizona State University4, Ghent University5, Institute of Technology, Tralee6, University of Ottawa7, Glasgow Caledonian University8, Oregon Health & Science University9, Cambridge University Hospitals NHS Foundation Trust10, George Washington University11, Norwegian Institute of Public Health12, Norwegian School of Sport Sciences13, University of Sydney14, Alberta Health Services15, Queen's University Belfast16, University of Bristol17, Pennington Biomedical Research Center18, University of Cape Town19, University of Regensburg20, University of East Anglia21, University of Granada22, University of Colombo23, National Institutes of Health24, World Health Organization25
TL;DR: New WHO 2020 guidelines on physical activity and sedentary behaviour reaffirm messages that some physical activity is better than none, that more physical Activity is better for optimal health outcomes and provide a new recommendation on reducing sedentary behaviours.
Abstract: Objectives To describe new WHO 2020 guidelines on physical activity and sedentary behaviour. Methods The guidelines were developed in accordance with WHO protocols. An expert Guideline Development Group reviewed evidence to assess associations between physical activity and sedentary behaviour for an agreed set of health outcomes and population groups. The assessment used and systematically updated recent relevant systematic reviews; new primary reviews addressed additional health outcomes or subpopulations. Results The new guidelines address children, adolescents, adults, older adults and include new specific recommendations for pregnant and postpartum women and people living with chronic conditions or disability. All adults should undertake 150-300 min of moderate-intensity, or 75-150 min of vigorous-intensity physical activity, or some equivalent combination of moderate-intensity and vigorous-intensity aerobic physical activity, per week. Among children and adolescents, an average of 60 min/day of moderate-to-vigorous intensity aerobic physical activity across the week provides health benefits. The guidelines recommend regular muscle-strengthening activity for all age groups. Additionally, reducing sedentary behaviours is recommended across all age groups and abilities, although evidence was insufficient to quantify a sedentary behaviour threshold. Conclusion These 2020 WHO guidelines update previous WHO recommendations released in 2010. They reaffirm messages that some physical activity is better than none, that more physical activity is better for optimal health outcomes and provide a new recommendation on reducing sedentary behaviours. These guidelines highlight the importance of regularly undertaking both aerobic and muscle strengthening activities and for the first time, there are specific recommendations for specific populations including for pregnant and postpartum women and people living with chronic conditions or disability. These guidelines should be used to inform national health policies aligned with the WHO Global Action Plan on Physical Activity 2018-2030 and to strengthen surveillance systems that track progress towards national and global targets.
3,218 citations
University of Exeter1, École Normale Supérieure2, Norwich Research Park3, Wageningen University and Research Centre4, University of Groningen5, Max Planck Society6, Ludwig Maximilian University of Munich7, Commonwealth Scientific and Industrial Research Organisation8, Université Paris-Saclay9, Stanford University10, National Oceanic and Atmospheric Administration11, National Institute for Space Research12, University of Southampton13, Bermuda Institute of Ocean Sciences14, PSL Research University15, Japan Agency for Marine-Earth Science and Technology16, National Institute for Environmental Studies17, University of Maryland, College Park18, University of Leeds19, International Institute of Minnesota20, Flanders Marine Institute21, ETH Zurich22, University of East Anglia23, German Aerospace Center24, Woods Hole Research Center25, University of Illinois at Urbana–Champaign26, University of Toulouse27, Japan Meteorological Agency28, Plymouth Marine Laboratory29, University of Paris30, Hobart Corporation31, Oeschger Centre for Climate Change Research32, Tsinghua University33, National Center for Atmospheric Research34, Appalachian State University35, University of Colorado Boulder36, University of Washington37, Atlantic Oceanographic and Meteorological Laboratory38, Princeton University39, Met Office40, Leibniz Institute of Marine Sciences41, Auburn University42, University of Tasmania43, VU University Amsterdam44, Oak Ridge National Laboratory45, Sun Yat-sen University46, Nanjing University47
TL;DR: In this paper, the authors describe and synthesize data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties, including emissions from land use and land-use change data and bookkeeping models.
Abstract: Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere in a changing climate – the “global carbon budget” – is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe and synthesize data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. Fossil CO2 emissions (EFOS) are based on energy statistics and cement production data, while emissions from land-use change (ELUC), mainly deforestation, are based on land use and land-use change data and bookkeeping models. Atmospheric CO2 concentration is measured directly and its growth rate (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1σ. For the last decade available (2010–2019), EFOS was 9.6 ± 0.5 GtC yr−1 excluding the cement carbonation sink (9.4 ± 0.5 GtC yr−1 when the cement carbonation sink is included), and ELUC was 1.6 ± 0.7 GtC yr−1. For the same decade, GATM was 5.1 ± 0.02 GtC yr−1 (2.4 ± 0.01 ppm yr−1), SOCEAN 2.5 ± 0.6 GtC yr−1, and SLAND 3.4 ± 0.9 GtC yr−1, with a budget imbalance BIM of −0.1 GtC yr−1 indicating a near balance between estimated sources and sinks over the last decade. For the year 2019 alone, the growth in EFOS was only about 0.1 % with fossil emissions increasing to 9.9 ± 0.5 GtC yr−1 excluding the cement carbonation sink (9.7 ± 0.5 GtC yr−1 when cement carbonation sink is included), and ELUC was 1.8 ± 0.7 GtC yr−1, for total anthropogenic CO2 emissions of 11.5 ± 0.9 GtC yr−1 (42.2 ± 3.3 GtCO2). Also for 2019, GATM was 5.4 ± 0.2 GtC yr−1 (2.5 ± 0.1 ppm yr−1), SOCEAN was 2.6 ± 0.6 GtC yr−1, and SLAND was 3.1 ± 1.2 GtC yr−1, with a BIM of 0.3 GtC. The global atmospheric CO2 concentration reached 409.85 ± 0.1 ppm averaged over 2019. Preliminary data for 2020, accounting for the COVID-19-induced changes in emissions, suggest a decrease in EFOS relative to 2019 of about −7 % (median estimate) based on individual estimates from four studies of −6 %, −7 %, −7 % (−3 % to −11 %), and −13 %. Overall, the mean and trend in the components of the global carbon budget are consistently estimated over the period 1959–2019, but discrepancies of up to 1 GtC yr−1 persist for the representation of semi-decadal variability in CO2 fluxes. Comparison of estimates from diverse approaches and observations shows (1) no consensus in the mean and trend in land-use change emissions over the last decade, (2) a persistent low agreement between the different methods on the magnitude of the land CO2 flux in the northern extra-tropics, and (3) an apparent discrepancy between the different methods for the ocean sink outside the tropics, particularly in the Southern Ocean. This living data update documents changes in the methods and data sets used in this new global carbon budget and the progress in understanding of the global carbon cycle compared with previous publications of this data set (Friedlingstein et al., 2019; Le Quere et al., 2018b, a, 2016, 2015b, a, 2014, 2013). The data presented in this work are available at https://doi.org/10.18160/gcp-2020 (Friedlingstein et al., 2020).
1,764 citations
TL;DR: The construction of a major new version of CRU TS (Climatic Research Unit gridded Time Series), updated to span 1901–2018 by the inclusion of additional station observations, and it will be updated annually.
Abstract: CRU TS (Climatic Research Unit gridded Time Series) is a widely used climate dataset on a 0.5° latitude by 0.5° longitude grid over all land domains of the world except Antarctica. It is derived by the interpolation of monthly climate anomalies from extensive networks of weather station observations. Here we describe the construction of a major new version, CRU TS v4. It is updated to span 1901-2018 by the inclusion of additional station observations, and it will be updated annually. The interpolation process has been changed to use angular-distance weighting (ADW), and the production of secondary variables has been revised to better suit this approach. This implementation of ADW provides improved traceability between each gridded value and the input observations, and allows more informative diagnostics that dataset users can utilise to assess how dataset quality might vary geographically.
1,689 citations
TL;DR: The flagship paper of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium describes the generation of the integrative analyses of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types, the structures for international data sharing and standardized analyses, and the main scientific findings from across the consortium studies.
Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10,11,12,13,14,15,16,17,18.
1,600 citations
TL;DR: In this paper, the authors compile government policies and activity data to estimate the decrease in CO2 emissions during forced confinements during the COVID-19 pandemic, which drastically altered patterns of energy demand around the world.
Abstract: Government policies during the COVID-19 pandemic have drastically altered patterns of energy demand around the world. Many international borders were closed and populations were confined to their homes, which reduced transport and changed consumption patterns. Here we compile government policies and activity data to estimate the decrease in CO2 emissions during forced confinements. Daily global CO2 emissions decreased by –17% (–11 to –25% for ±1σ) by early April 2020 compared with the mean 2019 levels, just under half from changes in surface transport. At their peak, emissions in individual countries decreased by –26% on average. The impact on 2020 annual emissions depends on the duration of the confinement, with a low estimate of –4% (–2 to –7%) if prepandemic conditions return by mid-June, and a high estimate of –7% (–3 to –13%) if some restrictions remain worldwide until the end of 2020. Government actions and economic incentives postcrisis will likely influence the global CO2 emissions path for decades.
1,461 citations
University of Virginia1, McGill University2, National Radio Astronomy Observatory3, Goddard Space Flight Center4, West Virginia University5, Lafayette College6, Hillsdale College7, Durham University8, University of East Anglia9, University of Maryland, College Park10, First Green Bank11, University of British Columbia12, University of Toronto13, Hungarian Academy of Sciences14, Swinburne University of Technology15, University of Wisconsin–Milwaukee16, Chinese Academy of Sciences17
TL;DR: In this article, the authors measured the mass of the MSP J0740+6620 to be ${\mathbf{2.14} + 2.09} + 0.10% credibility interval.
Abstract: Despite its importance to our understanding of physics at supranuclear densities, the equation of state (EoS) of matter deep within neutron stars remains poorly understood. Millisecond pulsars (MSPs) are among the most useful astrophysical objects in the Universe for testing fundamental physics, and place some of the most stringent constraints on this high-density EoS. Pulsar timing—the process of accounting for every rotation of a pulsar over long time periods—can precisely measure a wide variety of physical phenomena, including those that allow the measurement of the masses of the components of a pulsar binary system1. One of these, called relativistic Shapiro delay2, can yield precise masses for both an MSP and its companion; however, it is only easily observed in a small subset of high-precision, highly inclined (nearly edge-on) binary pulsar systems. By combining data from the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) 12.5-yr data set with recent orbital-phase-specific observations using the Green Bank Telescope, we have measured the mass of the MSP J0740+6620 to be $${\mathbf{2}}{\mathbf{.14}}_{ - {\mathbf{0}}{\mathbf{.09}}}^{ + {\mathbf{0}}{\mathbf{.10}}}$$ M⊙ (68.3% credibility interval; the 95.4% credibility interval is $${\mathbf{2}}{\mathbf{.14}}_{ - {\mathbf{0}}{\mathbf{.18}}}^{ + {\mathbf{0}}{\mathbf{.20}}}$$ M⊙). It is highly likely to be the most massive neutron star yet observed, and serves as a strong constraint on the neutron star interior EoS. Cromartie et al. have probably found the most massive neutron star discovered so far by combining NANOGrav 12.5-yr data with radio data from the Green Bank Telescope. Millisecond pulsar J0740+6620 has a mass of 2.14 M⊙, ~0.1 M⊙ more massive than the previous record holder, and very close to the upper limit on neutron star masses from Laser Interferometer Gravitational-Wave Observatory measurements.
770 citations
Posted Content•
TL;DR: A powerful AGW baseline is designed, achieving state-of-the-art or at least comparable performance on twelve datasets for four different Re-ID tasks, and a new evaluation metric (mINP) is introduced, indicating the cost for finding all the correct matches, which provides an additional criteria to evaluate the Re- ID system for real applications.
Abstract: Person re-identification (Re-ID) aims at retrieving a person of interest across multiple non-overlapping cameras. With the advancement of deep neural networks and increasing demand of intelligent video surveillance, it has gained significantly increased interest in the computer vision community. By dissecting the involved components in developing a person Re-ID system, we categorize it into the closed-world and open-world settings. The widely studied closed-world setting is usually applied under various research-oriented assumptions, and has achieved inspiring success using deep learning techniques on a number of datasets. We first conduct a comprehensive overview with in-depth analysis for closed-world person Re-ID from three different perspectives, including deep feature representation learning, deep metric learning and ranking optimization. With the performance saturation under closed-world setting, the research focus for person Re-ID has recently shifted to the open-world setting, facing more challenging issues. This setting is closer to practical applications under specific scenarios. We summarize the open-world Re-ID in terms of five different aspects. By analyzing the advantages of existing methods, we design a powerful AGW baseline, achieving state-of-the-art or at least comparable performance on twelve datasets for FOUR different Re-ID tasks. Meanwhile, we introduce a new evaluation metric (mINP) for person Re-ID, indicating the cost for finding all the correct matches, which provides an additional criteria to evaluate the Re-ID system for real applications. Finally, some important yet under-investigated open issues are discussed.
737 citations
Auburn University1, Commonwealth Scientific and Industrial Research Organisation2, Norwegian Institute for Air Research3, International Institute for Applied Systems Analysis4, University of Zielona Góra5, University of East Anglia6, University of Maryland Center for Environmental Science7, Centre national de la recherche scientifique8, Stanford University9, Ghent University10, University of California, Irvine11, Université libre de Bruxelles12, Food and Agriculture Organization13, Max Planck Society14, Peking University15, Karlsruhe Institute of Technology16, University of Bern17, University of Toulouse18, École Normale Supérieure19, Netherlands Environmental Assessment Agency20, Utrecht University21, Ocean University of China22, Zhejiang University23, University of Leeds24, Woods Hole Research Center25, National Oceanic and Atmospheric Administration26, Southern Cross University27, Chinese Academy of Sciences28, Beijing Normal University29, National Institute for Environmental Studies30, Leibniz Institute of Marine Sciences31, Université Paris-Saclay32, Tsinghua University33, Oeschger Centre for Climate Change Research34, Yale University35, Scotland's Rural College36, University of Minnesota37, Lund University38, Japan Agency for Marine-Earth Science and Technology39, Chiba University40, Massachusetts Institute of Technology41, VU University Amsterdam42, University of California, San Diego43, Mississippi State University44
TL;DR: A global N2O inventory is presented that incorporates both natural and anthropogenic sources and accounts for the interaction between nitrogen additions and the biochemical processes that control N 2O emissions, using bottom-up, top-down and process-based model approaches.
Abstract: Nitrous oxide (N2O), like carbon dioxide, is a long-lived greenhouse gas that accumulates in the atmosphere. Over the past 150 years, increasing atmospheric N2O concentrations have contributed to stratospheric ozone depletion1 and climate change2, with the current rate of increase estimated at 2 per cent per decade. Existing national inventories do not provide a full picture of N2O emissions, owing to their omission of natural sources and limitations in methodology for attributing anthropogenic sources. Here we present a global N2O inventory that incorporates both natural and anthropogenic sources and accounts for the interaction between nitrogen additions and the biochemical processes that control N2O emissions. We use bottom-up (inventory, statistical extrapolation of flux measurements, process-based land and ocean modelling) and top-down (atmospheric inversion) approaches to provide a comprehensive quantification of global N2O sources and sinks resulting from 21 natural and human sectors between 1980 and 2016. Global N2O emissions were 17.0 (minimum-maximum estimates: 12.2-23.5) teragrams of nitrogen per year (bottom-up) and 16.9 (15.9-17.7) teragrams of nitrogen per year (top-down) between 2007 and 2016. Global human-induced emissions, which are dominated by nitrogen additions to croplands, increased by 30% over the past four decades to 7.3 (4.2-11.4) teragrams of nitrogen per year. This increase was mainly responsible for the growth in the atmospheric burden. Our findings point to growing N2O emissions in emerging economies-particularly Brazil, China and India. Analysis of process-based model estimates reveals an emerging N2O-climate feedback resulting from interactions between nitrogen additions and climate change. The recent growth in N2O emissions exceeds some of the highest projected emission scenarios3,4, underscoring the urgency to mitigate N2O emissions.
650 citations
TL;DR: It is proposed that there is a potential association between mean levels of vitamin D in various countries with cases and mortality caused by COVID-19 and vitamin D levels are severely low in the aging population especially in Spain, Italy and Switzerland.
Abstract: WHO declared SARS-CoV-2 a global pandemic. The present aim was to propose an hypothesis that there is a potential association between mean levels of vitamin D in various countries with cases and mortality caused by COVID-19. The mean levels of vitamin D for 20 European countries and morbidity and mortality caused by COVID-19 were acquired. Negative correlations between mean levels of vitamin D (average 56 mmol/L, STDEV 10.61) in each country and the number of COVID-19 cases/1 M (mean 295.95, STDEV 298.7, and mortality/1 M (mean 5.96, STDEV 15.13) were observed. Vitamin D levels are severely low in the aging population especially in Spain, Italy and Switzerland. This is also the most vulnerable group of the population in relation to COVID-19. It should be advisable to perform dedicated studies about vitamin D levels in COVID-19 patients with different degrees of disease severity.
595 citations
Queen Mary University of London1, University of Bath2, University of Leeds3, Bocconi University4, London School of Economics and Political Science5, European Society of Cardiology6, Intermountain Medical Center7, Ghent University8, University of East Anglia9, University of Cape Town10, University of Adelaide11, Leipzig University12, Leiden University Medical Center13, John Radcliffe Hospital14, University of Erlangen-Nuremberg15, University of Oxford16
TL;DR: A seemingly inexorable rise in the prevalence of obesity and diabetes currently provides the greatest challenge to achieving further reductions in CVD burden across ESC member countries.
Abstract: Aims: The 2019 report from the European Society of Cardiology (ESC) Atlas provides a contemporary analysis of cardiovascular disease (CVD) statistics across 56 member countries, with particular emphasis on international inequalities in disease burden and healthcare delivery together with estimates of progress towards meeting 2025 World Health Organization (WHO) non-communicable disease targets.
Methods and results: In this report, contemporary CVD statistics are presented for member countries of the ESC. The statistics are drawn from the ESC Atlas which is a repository of CVD data from a variety of sources including the WHO, the Institute for Health Metrics and Evaluation, and the World Bank. The Atlas also includes novel ESC sponsored data on human and capital infrastructure and cardiovascular healthcare delivery obtained by annual survey of the national societies of ESC member countries. Across ESC member countries, the prevalence of obesity (body mass index >= 30 kg/m(2)) and diabetes has increased two- to three-fold during the last 30years making the WHO 2025 target to halt rises in these risk factors unlikely to be achieved. More encouraging have been variable declines in hypertension, smoking, and alcohol consumption but on current trends only the reduction in smoking from 28% to 21% during the last 20years appears sufficient for the WHO target to be achieved. The median age-standardized prevalence of major risk factors was higher in middle-income compared with high-income ESC member countries for hypertension {23.8% [interquartile range (IQR) 22.5-23.1%] vs. 15.7% (IQR 14.5-21.1%)}, diabetes [7.7% (IQR 7.1-10.1%) vs. 5.6% (IQR 4.8-7.0%)], and among males smoking [43.8% (IQR 37.4-48.0%) vs. 26.0% (IQR 20.9-31.7%)] although among females smoking was less common in middle-income countries [8.7% (IQR 3.0-10.8) vs. 16.7% (IQR 13.9-19.7%)]. There were associated inequalities in disease burden with disability-adjusted life years per 100 000 people due to CVD over three times as high in middle-income [7160 (IQR 5655-8115)] compared with high-income [2235 (IQR 1896-3602)] countries. Cardiovascular disease mortality was also higher in middle-income countries where it accounted for a greater proportion of potential years of life lost compared with high-income countries in both females (43% vs. 28%) and males (39% vs. 28%). Despite the inequalities in disease burden across ESC member countries, survey data from the National Cardiac Societies of the ESC showed that middle-income member countries remain severely under-resourced compared with high-income countries in terms of cardiological person-power and technological infrastructure. Under-resourcing in middle-income countries is associated with a severe procedural deficit compared with high-income countries in terms of coronary intervention, device implantation and cardiac surgical procedures.
Conclusion: A seemingly inexorable rise in the prevalence of obesity and diabetes currently provides the greatest challenge to achieving further reductions in CVD burden across ESC member countries. Additional challenges are provided by inequalities in disease burden that now require intensification of policy initiatives in order to reduce population risk and prioritize cardiovascular healthcare delivery, particularly in the middle-income countries of the ESC where need is greatest.
591 citations
National Institutes of Health1, Wellcome Trust Sanger Institute2, Rockefeller University3, University of California, Davis4, European Bioinformatics Institute5, Seoul National University6, Max Planck Society7, Durham University8, University of Massachusetts Amherst9, University of Adelaide10, University of Missouri11, East Carolina University12, University of Queensland13, Queen Mary University of London14, Wellington Management Company15, University of Arizona16, Natural History Museum17, Bangor University18, University of Konstanz19, Northeastern University20, Naturalis21, University of Graz22, Florida Museum of Natural History23, University of California, Santa Cruz24, Pacific Biosciences25, University of Maryland, College Park26, Harbin Institute of Technology27, University of Chicago28, Oregon Health & Science University29, Monash University Malaysia Campus30, University of Milan31, University of Copenhagen32, Pennsylvania State University33, University of Los Andes34, Agency for Science, Technology and Research35, Royal Ontario Museum36, Smithsonian Conservation Biology Institute37, University of East Anglia38, Pompeu Fabra University39, University College Dublin40, University of Illinois at Urbana–Champaign41, La Trobe University42, University of California, San Diego43, UPRRP College of Natural Sciences44, Dresden University of Technology45
TL;DR: The Vertebrate Genomes Project is embarked on, an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species. To address this issue, the international Genome 10K (G10K) consortium has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.
University of Tübingen1, University of Pavia2, Charité3, University of Leicester4, University of Barcelona5, University of Graz6, Istanbul University7, Paris Diderot University8, University of Birmingham9, Norfolk and Norwich University Hospital10, Instituto de Medicina Molecular11, Peking Union Medical College Hospital12, University of Iceland13, University of East Anglia14, University of Oxford15
TL;DR: The recommendations for the management of LVV have been updated to facilitate the translation of current scientific evidence and expert opinion into better management and improved outcome of patients in clinical practice.
Abstract: BACKGROUND
Since the publication of the European League Against Rheumatism (EULAR) recommendations for the management of large vessel vasculitis (LVV) in 2009, several relevant randomised clinical trials and cohort analyses have been published, which have the potential to change clinical care and therefore supporting the need to update the original recommendations.
METHODS
Using EULAR standardised operating procedures for EULAR-endorsed recommendations, the EULAR task force undertook a systematic literature review and sought opinion from 20 experts from 13 countries. We modified existing recommendations and created new recommendations.
RESULTS
Three overarching principles and 10 recommendations were formulated. We recommend that a suspected diagnosis of LVV should be confirmed by imaging or histology. High dose glucocorticoid therapy (40-60 mg/day prednisone-equivalent) should be initiated immediately for induction of remission in active giant cell arteritis (GCA) or Takayasu arteritis (TAK). We recommend adjunctive therapy in selected patients with GCA (refractory or relapsing disease, presence of an increased risk for glucocorticoid-related adverse events or complications) using tocilizumab. Methotrexate may be used as an alternative. Non-biological glucocorticoid-sparing agents should be given in combination with glucocorticoids in all patients with TAK and biological agents may be used in refractory or relapsing patients. We no longer recommend the routine use of antiplatelet or anticoagulant therapy for treatment of LVV unless it is indicated for other reasons.
CONCLUSIONS
We have updated the recommendations for the management of LVV to facilitate the translation of current scientific evidence and expert opinion into better management and improved outcome of patients in clinical practice.
TL;DR: In this paper, the authors estimate that the direct effect of the pandemic-driven response will be negligible, with a cooling of around 0.01 ± 0.005°C by 2030 compared to a baseline scenario that follows current national policies.
Abstract: The global response to the COVID-19 pandemic has led to a sudden reduction of both GHG emissions and air pollutants. Here, using national mobility data, we estimate global emission reductions for ten species during the period February to June 2020. We estimate that global NOx emissions declined by as much as 30% in April, contributing a short-term cooling since the start of the year. This cooling trend is offset by ~20% reduction in global SO2 emissions that weakens the aerosol cooling effect, causing short-term warming. As a result, we estimate that the direct effect of the pandemic-driven response will be negligible, with a cooling of around 0.01 ± 0.005 °C by 2030 compared to a baseline scenario that follows current national policies. In contrast, with an economic recovery tilted towards green stimulus and reductions in fossil fuel investments, it is possible to avoid future warming of 0.3 °C by 2050.
TL;DR: This study constructs the most up-to-date CO2 emission inventories for China and its 30 provinces, as well as their energy inventories, for the years 2016 and 2017 and provides key updates and supplements to the previous emission dataset for 1997–2015.
Abstract: Despite China's emissions having plateaued in 2013, it is still the world's leading energy consumer and CO2 emitter, accounting for approximately 30% of global emissions. Detailed CO2 emission inventories by energy and sector have great significance to China's carbon policies as well as to achieving global climate change mitigation targets. This study constructs the most up-to-date CO2 emission inventories for China and its 30 provinces, as well as their energy inventories for the years 2016 and 2017. The newly compiled inventories provide key updates and supplements to our previous emission dataset for 1997-2015. Emissions are calculated based on IPCC (Intergovernmental Panel on Climate Change) administrative territorial scope that covers all anthropogenic emissions generated within an administrative boundary due to energy consumption (i.e. energy-related emissions from 17 fossil fuel types) and industrial production (i.e. process-related emissions from cement production). The inventories are constructed for 47 economic sectors consistent with the national economic accounting system. The data can be used as inputs to climate and integrated assessment models and for analysis of emission patterns of China and its regions.
TL;DR: The findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.
Abstract: Objective Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty. Design We profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet). Results Adherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks. Conclusion Collectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.
TL;DR: A failure to recognize the factors behind continued emissions growth could limit the world's ability to shift to a pathway consistent with 1.5 °C or 2 °C of global warming as mentioned in this paper.
Abstract: A failure to recognize the factors behind continued emissions growth could limit the world’s ability to shift to a pathway consistent with 1.5 °C or 2 °C of global warming. Continued support for low-carbon technologies needs to be combined with policies directed at phasing out the use of fossil fuels.
Research Triangle Park1, Foundation for Research & Technology – Hellas2, University of Washington3, University of Michigan4, National Center for Atmospheric Research5, University of East Anglia6, Colorado State University7, University of Maryland, Baltimore County8, Leibniz Association9, University of Crete10, Columbia University11, University of Illinois at Urbana–Champaign12, Nankai University13, Georgia Institute of Technology14, Tsinghua University15, Pacific Northwest National Laboratory16, McGill University17
TL;DR: This paper reviews and synthesizes the current state of knowledge on the acidity of atmospheric condensed phases, specifically particles and cloud droplets, including recommendations for estimating acidity and pH, standard nomenclature, a synthesis of current pH estimates based on observations, and new model calculations on the local and global scale.
Abstract: . Acidity, defined as pH, is a central component of aqueous
chemistry. In the atmosphere, the acidity of condensed phases (aerosol
particles, cloud water, and fog droplets) governs the phase partitioning of
semivolatile gases such as HNO3 , NH3 , HCl, and organic acids and
bases as well as chemical reaction rates. It has implications for the
atmospheric lifetime of pollutants, deposition, and human health. Despite
its fundamental role in atmospheric processes, only recently has this field
seen a growth in the number of studies on particle acidity. Even with this
growth, many fine-particle pH estimates must be based on thermodynamic model
calculations since no operational techniques exist for direct measurements.
Current information indicates acidic fine particles are ubiquitous, but
observationally constrained pH estimates are limited in spatial and temporal
coverage. Clouds and fogs are also generally acidic, but to a lesser degree
than particles, and have a range of pH that is quite sensitive to
anthropogenic emissions of sulfur and nitrogen oxides, as well as ambient
ammonia. Historical measurements indicate that cloud and fog droplet pH has
changed in recent decades in response to controls on anthropogenic
emissions, while the limited trend data for aerosol particles indicate
acidity may be relatively constant due to the semivolatile nature of the
key acids and bases and buffering in particles. This paper reviews and
synthesizes the current state of knowledge on the acidity of atmospheric
condensed phases, specifically particles and cloud droplets. It includes
recommendations for estimating acidity and pH, standard nomenclature, a
synthesis of current pH estimates based on observations, and new model
calculations on the local and global scale.
TL;DR: To assess current trajectories towards the GPW13 UHC billion target—1 billion more people benefiting from UHC by 2023—the authors estimated additional population equivalents with UHC effective coverage from 2018 to 2023, and quantified frontiers of U HC effective coverage performance on the basis of pooled health spending per capita.
TL;DR: The affordance theory is contributed to by providing an understanding of the substitution of affordances for team collaboration during COVID-19 as various affordances of technology were perceived and actualised to sustain “business as usual”.
Abstract: COVID-19 has caused unprecedented challenges to our lives. Many governments have forced people to stay at home, leading to a radical shift from on-site to virtual collaboration for many knowledge workers. Existing remote working literature does not provide a thorough explanation of government-enforced working from home situations. Using an affordance lens, this study explores the sudden and enforced issues that COVID-19 has presented, and the technological means knowledge workers use to achieve their team collaboration goals. We interviewed 29 knowledge workers about their experiences of being required to work from home and introduced the term “enforced work from home”. This paper contributes to the affordance theory by providing an understanding of the substitution of affordances for team collaboration during COVID-19. The shifting of affordances results in positive and negative effects on team collaboration as various affordances of technology were perceived and actualised to sustain “business as usual”.
TL;DR: This work highlights recent work to give a full picture of how NPR proteins support the role of SA in plant immunity and discusses challenges and potential opportunities for future research and application related to the functions ofSA in plants.
01 May 2020
TL;DR: To accurately diagnose and study co-infection in COVID-19, patients should be recruited on admission to intensive care units and sampled longitudinally throughout the disease course using cultureindependent techniques capable of identifying complex mixed infections without previous target selection, such as whole-genome metagenomics.
Abstract: Respiratory viral infections predispose patients to co-infections and these lead to increased disease severity and mortality. Most fatalities in the 1918 influenza outbreak were due to subsequent bacterial infection, particularly with Streptococcus pneumoniae. Poor outcomes in the 2009 H1N1 influenza pandemic were also associated with bacterial co-infections, although few studies captured these data. Despite the proven importance of co-infections in the severity of respiratory diseases, they are understudied during large outbreaks of respiratory infections. Zhou and colleagues showed that in the current coronavirus disease 2019 (COVID-19) pandemic, 50% of patients with COVID-19 who have died had secondary bacterial infections, and Chen and colleagues have recorded both bacterial and fungal co-infections. Although 71% of the admitted patients with COVID-19 received antibiotic drugs, no information is available on the antimicrobial sensitivities of the organisms that were identified, or on the type and duration of antimicrobial treatment. Chronic obstructive pulmonary disease (COPD) is a risk factor for severe COVID-19 disease and many patients with COPD will have underlying chronic bacterial infections before severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but this important information is not being reported. More data on co-infections are urgently required to establish their importance in COVID-19 severity and mortality. Diagnosing co-infections is complex. The organism itself might be carried by the patient before the viral infection, might be part of an underlying chronic infection, or might be picked up nosocomially. In the UK, National Institute for Health and Care Excellence (NICE) treatment guidance for severe acquired pneumonia is broadspectrum antibiotic co-amoxiclav plus a macrolide to cover atypical organisms. Currently, antibiotic use is high (74·5%) among patients with COVID-19 who are admitted to intensive care units, rendering culture-based microbiological testing less sensitive. Patients with COVID-19 are kept on invasive mechanical ventilation for a long time (mean 9·1 days [SD 5·5]), increasing chances of hospital and ventilator acquired infections. Hence, early diagnosis of co-infection is required, preferably using methods capable of detecting a broad range of potential pathogens and antimicrobial resistances, with subsequent monitoring for infection development. To accurately diagnose and study co-infection in COVID-19, patients should be recruited on admission to intensive care units and sampled longitudinally throughout the disease course using cultureindependent techniques capable of identifying complex mixed infections without previous target selection, such as whole-genome metagenomics. Such a study would provide valuable surveillance data on the pathogens causing co-infections and antimicrobial resistance in the intensive care setting, thereby helping inform antibiotic prescribing policy. Rapid characterisation of coinfection is essential in the management and treatment of the most severe COVID-19 cases, could help to save lives, and will improve antimicrobial stewardship throughout the course of the pandemic.
TL;DR: This perspective reviews the biological and medicinal chemistry advances over the last three decades with an emphasis on the design of selective inhibitors that discriminate between the eleven human HDAC isoforms.
Abstract: It is now 30 years since the first report of a potent zinc-dependent histone deacetylase (HDAC) inhibitor appeared Since then, five HDAC inhibitors have received regulatory approval for cancer chemotherapy while many others are in clinical development for oncology as well as other therapeutic indications This Perspective reviews the biological and medicinal chemistry advances over the past 3 decades with an emphasis on the design of selective inhibitors that discriminate between the 11 human HDAC isoforms
TL;DR: A semi-systematic review of studies investigating the number of microplastic found in commercially important organisms of different trophic levels suggests that microplastics do not biomagnify, and that organisms at lower troPHic levels are more likely to contaminated by micropl Plastic pollution than apex predators.
TL;DR: A global expert group on older people might be useful to help improve knowledge and understanding of how to care for older people.
Abstract: A global expert group on older people might be useful
TL;DR: Current evidence of the impact gut microbes and their metabolites have on blood-brain barrier integrity and brain function is summarized, and the communication networks between the gastrointestinal tract and brain, which they may modulate are summarized.
Abstract: The human gastrointestinal (gut) microbiota comprises diverse and dynamic populations of bacteria, archaea, viruses, fungi, and protozoa, coexisting in a mutualistic relationship with the host. When intestinal homeostasis is perturbed, the function of the gastrointestinal tract and other organ systems, including the brain, can be compromised. The gut microbiota is proposed to contribute to blood-brain barrier disruption and the pathogenesis of neurodegenerative diseases. While progress is being made, a better understanding of interactions between gut microbes and host cells, and the impact these have on signaling from gut to brain is now required. In this review, we summarise current evidence of the impact gut microbes and their metabolites have on blood-brain barrier integrity and brain function, and the communication networks between the gastrointestinal tract and brain, which they may modulate. We also discuss the potential of microbiota modulation strategies as therapeutic tools for promoting and restoring brain health.
TL;DR: The relationship between the activation of intracellular receptors in the absence of surface receptor-mediated immunity is dissected and mutual potentiation between these two recognition-dependent defense pathways is revealed.
Abstract: The plant immune system involves cell-surface receptors that detect intercellular pathogen-derived molecules, and intracellular receptors that activate immunity upon detection of pathogen-secreted effectors that act inside the plant cell. Surface receptor-mediated immunity has been extensively studied but in authentic interactions between plants and microbial pathogens, its presence impedes study of intracellular receptor-mediated immunity alone. How these two immune pathways interact is poorly understood. Here, we reveal mutual potentiation between these two recognition-dependent defense pathways. Recognition by surface receptors activates multiple protein kinases and NADPH oxidases, whereas intracellular receptors primarily elevate abundance of these proteins. Reciprocally, the intracellular receptor-dependent hypersensitive cell death response is strongly enhanced by activation of surface receptors. Activation of either immune system alone is insufficient to provide effective resistance against Pseudomonas syringae. Thus, immune pathways activated by cell-surface and intracellular receptors mutually potentiate to activate strong defense that thwarts pathogens. By studying the activation of intracellular receptors in the absence of surface receptor-mediated immunity, we have dissected the relationship between the two distinct immune systems. These findings reshape our understanding of plant immunity and have broad implications for crop improvement.
TL;DR: Global “hotspots” where there is projected to be a significant change in episodic flooding by the end of the century are identified and found to be mostly concentrated in north western Europe and Asia.
Abstract: Global models of tide, storm surge, and wave setup are used to obtain projections of episodic coastal flooding over the coming century. The models are extensively validated against tide gauge data and the impact of uncertainties and assumptions on projections estimated in detail. Global “hotspots” where there is projected to be a significant change in episodic flooding by the end of the century are identified and found to be mostly concentrated in north western Europe and Asia. Results show that for the case of, no coastal protection or adaptation, and a mean RCP8.5 scenario, there will be an increase of 48% of the world’s land area, 52% of the global population and 46% of global assets at risk of flooding by 2100. A total of 68% of the global coastal area flooded will be caused by tide and storm events with 32% due to projected regional sea level rise.
Met Office1, University of New South Wales2, Barcelona Supercomputing Center3, VU University Amsterdam4, University of East Anglia5, University of Grenoble6, National Oceanic and Atmospheric Administration7, Ontario Ministry of Transportation8, South African Weather Service9, University of Pretoria10, Hokkaido University11, University of Reading12, Bureau of Meteorology13, University of Cape Coast14, National University of Colombia15, University of Florence16, China Meteorological Administration17, Royal Netherlands Meteorological Institute18, Universidad Veracruzana19
TL;DR: In this article, the authors presented the results of the second workshop on ASEAN Regional Climate Data, Analysis and Projections (ARCDAP•2), which was held at the University of Singapore and was jointly funded by Meteorological Service Singapore and WMO through the Canada Climate Risk and Early Warning Systems (CREWS) initiative.
Abstract: Robert Dunn was supported by the Met Office Hadley Centre Climate Programme funded by BEIS and Defra (GA01101) and thanks Nick Rayner and Lizzie Good for helpful comments on the manuscript Lisa Alexander is supported by the Australian Research Council (ARC) Grants DP160103439 and CE170100023 Markus Donat acknowledges funding by the Spanish Ministry for the Economy, Industry and Competitiveness Ramon y Cajal 2017 Grant Reference RYC‐2017‐22964 Mohd Noor'Arifin Bin Hj Yussof and Muhammad Khairul Izzat Bin Ibrahim thank the Brunei Darussalam Meteorological Department (BDMD) Ying Sun was supported by China funding agencies 2018YFA0605604 and 2018YFC1507702 Fatemeh Rahimzadeh and Mahbobeh Khoshkam thank IR of Iranian Meteorological Organization (IRIMO) and the Atmospheric Science and Meteorological Organization Research Center (ASMERC) for Data and also sharing their experiences, especially Abbas Rangbar Jose Marengo was supported by the National Institute of Science and Technology for Climate Change Phase 2 under CNPq Grant 465501/2014‐1, FAPESP Grants 2014/50848‐9 and 2015/03804‐9, and the National Coordination for High Level Education and Training (CAPES) Grant 88887136402‐00INCT The team that worked on the data in West Africa received funding from the UK's National Environment Research Council (NERC)/Department for International Development DFID) Future Climate For Africa programme, under the AMMA‐2050 project (Grants NE/M020428/1 and NE/M019969/1) Data from Southeast Asia (excl Indonesia) was supported by work on using ClimPACT2 during the Second Workshop on ASEAN Regional Climate Data, Analysis and Projections (ARCDAP‐2), 25–29 March 2019, Singapore, jointly funded by Meteorological Service Singapore and WMO through the Canada‐Climate Risk and Early Warning Systems (CREWS) initiative This research was supported by Thai Meteorological Department (TMD) and Thailand Science Research and Innovation (TSRI) under Grant RDG6030003 Daily data for Mexico were provided by the Servicio Meteorologico Nacional (SMN) of Comision Nacional del Agua (CONAGUA) We acknowledge the data providers in the ECA&D project (https://wwwecadeu), the SACA&D project (https://saca-bmkgknminl), and the LACA&D project (https://ciifenknminl) We thank the three anonymous reviewers for their detailed comments which improved the manuscript
German Cancer Research Center1, Ontario Institute for Cancer Research2, Norwich University3, University of East Anglia4, Heinrich Pette Institute5, University of Hamburg6, Francis Crick Institute7, University College London8, University of Zurich9, Institute of Cancer Research10, Heidelberg University11, Charité12, Université de Montréal13
TL;DR: The study revealed significant exclusivity of HPV and driver mutations in head-and-neck cancer and the association of HPV with APOBEC mutational signatures, which suggests that impaired antiviral defense is a driving force in cervical, bladder and head- and-neck carcinoma.
Abstract: Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, for which whole-genome and-for a subset-whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using a consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found a high prevalence of known tumor-associated viruses such as Epstein-Barr virus (EBV), hepatitis B virus (HBV) and human papilloma virus (HPV; for example, HPV16 or HPV18). The study revealed significant exclusivity of HPV and driver mutations in head-and-neck cancer and the association of HPV with APOBEC mutational signatures, which suggests that impaired antiviral defense is a driving force in cervical, bladder and head-and-neck carcinoma. For HBV, HPV16, HPV18 and adeno-associated virus-2 (AAV2), viral integration was associated with local variations in genomic copy numbers. Integrations at the TERT promoter were associated with high telomerase expression evidently activating this tumor-driving process. High levels of endogenous retrovirus (ERV1) expression were linked to a worse survival outcome in patients with kidney cancer.
TL;DR: The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA.
Abstract: Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.