Showing papers by "Ghent University 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 School of Sport Sciences12, Norwegian Institute of Public Health13, 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 Amsterdam1, Ghent University2, University of Chicago3, University of Pennsylvania4, Lund University5, Auckland City Hospital6, University of Antwerp7, University of New South Wales8, Katholieke Universiteit Leuven9, Guy's and St Thomas' NHS Foundation Trust10, Queen's University11, University of Zagreb12, Northwestern University13, Medical University of Łódź14, University of Aberdeen15, Medical University of South Carolina16, University of North Carolina at Chapel Hill17, University of Southampton18, University of São Paulo19, National University of Singapore20, Flinders University21
TL;DR: The European Position Paper on Rhinosinusitis and Nasal Polyps 2020 is the update of similar evidence based position papers published in 2005 and 2007 and 2012 and addresses areas not extensively covered in EPOS2012 such as paediatric CRS and sinus surgery.
Abstract: The European Position Paper on Rhinosinusitis and Nasal Polyps 2020 is the update of similar evidence based position papers published in 2005 and 2007 and 2012. The core objective of the EPOS2020 guideline is to provide revised, up-to-date and clear evidence-based recommendations and integrated care pathways in ARS and CRS. EPOS2020 provides an update on the literature published and studies undertaken in the eight years since the EPOS2012 position paper was published and addresses areas not extensively covered in EPOS2012 such as paediatric CRS and sinus surgery. EPOS2020 also involves new stakeholders, including pharmacists and patients, and addresses new target users who have become more involved in the management and treatment of rhinosinusitis since the publication of the last EPOS document, including pharmacists, nurses, specialised care givers and indeed patients themselves, who employ increasing self-management of their condition using over the counter treatments. The document provides suggestions for future research in this area and offers updated guidance for definitions and outcome measurements in research in different settings. EPOS2020 contains chapters on definitions and classification where we have defined a large number of terms and indicated preferred terms. A new classification of CRS into primary and secondary CRS and further division into localized and diffuse disease, based on anatomic distribution is proposed. There are extensive chapters on epidemiology and predisposing factors, inflammatory mechanisms, (differential) diagnosis of facial pain, allergic rhinitis, genetics, cystic fibrosis, aspirin exacerbated respiratory disease, immunodeficiencies, allergic fungal rhinosinusitis and the relationship between upper and lower airways. The chapters on paediatric acute and chronic rhinosinusitis are totally rewritten. All available evidence for the management of acute rhinosinusitis and chronic rhinosinusitis with or without nasal polyps in adults and children is systematically reviewed and integrated care pathways based on the evidence are proposed. Despite considerable increases in the amount of quality publications in recent years, a large number of practical clinical questions remain. It was agreed that the best way to address these was to conduct a Delphi exercise . The results have been integrated into the respective sections. Last but not least, advice for patients and pharmacists and a new list of research needs are included. The full document can be downloaded for free on the website of this journal: http://www.rhinologyjournal.com.
2,853 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: This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences and proposed reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties.
Abstract: The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).
1,496 citations
University of California, San Diego1, University of Arizona2, Ghent University3, Université libre de Bruxelles4, University of Erlangen-Nuremberg5, California Institute of Technology6, University of Sheffield7, Spanish National Research Council8, University of Basel9, University of British Columbia10, University of California, San Francisco11, Anschutz Medical Campus12, Karolinska University Hospital13, Pompeu Fabra University14, University of South Australia15, Memorial Sloan Kettering Cancer Center16, National Taiwan University17, Hebrew University of Jerusalem18, University of Texas MD Anderson Cancer Center19, Princeton University20, Northeastern University21, Washington University in St. Louis22, University College London23, Duke University24, Royal Children's Hospital25, PSL Research University26, Claude Bernard University Lyon 127, Université Paris-Saclay28, University of Pennsylvania29, Kyoto University30, University of Toulouse31, Queensland University of Technology32, Massachusetts Institute of Technology33, University of Pittsburgh34, University of Kentucky35, Kumamoto University36
TL;DR: This Consensus Statement is the outcome of a 2-year-long discussion among EMT researchers and aims to both clarify the nomenclature and provide definitions and guidelines for EMT research in future publications to reduce misunderstanding and misinterpretation of research data generated in various experimental models.
Abstract: Epithelial-mesenchymal transition (EMT) encompasses dynamic changes in cellular organization from epithelial to mesenchymal phenotypes, which leads to functional changes in cell migration and invasion. EMT occurs in a diverse range of physiological and pathological conditions and is driven by a conserved set of inducing signals, transcriptional regulators and downstream effectors. With over 5,700 publications indexed by Web of Science in 2019 alone, research on EMT is expanding rapidly. This growing interest warrants the need for a consensus among researchers when referring to and undertaking research on EMT. This Consensus Statement, mediated by 'the EMT International Association' (TEMTIA), is the outcome of a 2-year-long discussion among EMT researchers and aims to both clarify the nomenclature and provide definitions and guidelines for EMT research in future publications. We trust that these guidelines will help to reduce misunderstanding and misinterpretation of research data generated in various experimental models and to promote cross-disciplinary collaboration to identify and address key open questions in this research field. While recognizing the importance of maintaining diversity in experimental approaches and conceptual frameworks, we emphasize that lasting contributions of EMT research to increasing our understanding of developmental processes and combatting cancer and other diseases depend on the adoption of a unified terminology to describe EMT.
931 citations
TL;DR: The extent of the trait data compiled in TRY is evaluated and emerging patterns of data coverage and representativeness are analyzed to conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements.
Abstract: Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
882 citations
TL;DR: It is suggested that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.
Abstract: Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A key question is whether SARS-CoV-2 (CoV-2) - the causal agent in COVID-19 - affects olfaction directly, by infecting olfactory sensory neurons or their targets in the olfactory bulb, or indirectly, through perturbation of supporting cells. Here we identify cell types in the olfactory epithelium and olfactory bulb that express SARS-CoV-2 cell entry molecules. Bulk sequencing demonstrated that mouse, non-human primate and human olfactory mucosa expresses two key genes involved in CoV-2 entry, ACE2 and TMPRSS2. However, single cell sequencing revealed that ACE2 is expressed in support cells, stem cells, and perivascular cells, rather than in neurons. Immunostaining confirmed these results and revealed pervasive expression of ACE2 protein in dorsally-located olfactory epithelial sustentacular cells and olfactory bulb pericytes in the mouse. These findings suggest that CoV-2 infection of non-neuronal cell types leads to anosmia and related disturbances in odor perception in COVID-19 patients.
727 citations
TL;DR: NicheNet is presented, a method that predicts ligand–target links between interacting cells by combining their expression data with prior knowledge on signaling and gene regulatory networks, and can infer active ligands and their gene regulatory effects on interacting cells.
Abstract: Computational methods that model how gene expression of a cell is influenced by interacting cells are lacking. We present NicheNet (https://github.com/saeyslab/nichenetr), a method that predicts ligand-target links between interacting cells by combining their expression data with prior knowledge on signaling and gene regulatory networks. We applied NicheNet to tumor and immune cell microenvironment data and demonstrate that NicheNet can infer active ligands and their gene regulatory effects on interacting cells.
681 citations
Université de Sherbrooke1, World Health Organization2, McMaster University3, University of Indonesia4, Geneva College5, University of California, San Francisco6, Peking Union Medical College Hospital7, Royal Melbourne Hospital8, Ziauddin University9, St Thomas' Hospital10, All India Institute of Medical Sciences11, Aga Khan University12, Guy's and St Thomas' NHS Foundation Trust13, St. George's University14, University of Colombo15, University of São Paulo16, Charité17, Ghent University18, Andrés Bello National University19, King's College London20, Hanoi Medical University21, Stellenbosch University22, University of Oxford23, Lanzhou University24, University of Liverpool25
TL;DR: A standing international panel of content experts, patients, clinicians, and methodologists, free from relevant conflicts of interest, produce recommendations for clinical practice, containing a strong recommendation for systemic corticosteroids in patients with severe and critical covid-19, and a weak or conditional recommendation against systemic cortiosteroids for non-severe patients.
Abstract: Clinical question What is the role of drug interventions in the treatment of patients with covid-19? New recommendation Increased attention on ivermectin as a potential treatment for covid-19 triggered this recommendation. The panel made a recommendation against ivermectin in patients with covid-19 regardless of disease severity, except in the context of a clinical trial. Prior recommendations (a) a strong recommendation against the use of hydroxychloroquine in patients with covid-19, regardless of disease severity; (b) a strong recommendation against the use of lopinavir-ritonavir in patients with covid-19, regardless of disease severity; (c) a strong recommendation for systemic corticosteroids in patients with severe and critical covid-19; (d) a conditional recommendation against systemic corticosteroids in patients with non-severe covid-19, and (e) a conditional recommendation against remdesivir in hospitalised patients with covid-19. How this guideline was created This living guideline is from the World Health Organization (WHO) and provides up to date covid-19 guidance to inform policy and practice worldwide. Magic Evidence Ecosystem Foundation (MAGIC) provided methodological support. A living systematic review with network analysis informed the recommendations. An international guideline development group (GDG) of content experts, clinicians, patients, an ethicist and methodologists produced recommendations following standards for trustworthy guideline development using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. Understanding the new recommendation There is insufficient evidence to be clear to what extent, if any, ivermectin is helpful or harmful in treating covid-19. There was a large degree of uncertainty in the evidence about ivermectin on mortality, need for mechanical ventilation, need for hospital admission, time to clinical improvement, and other patient-important outcomes. There is potential for harm with an increased risk of adverse events leading to study drug discontinuation. Applying pre-determined values and preferences, the panel inferred that almost all well informed patients would want to receive ivermectin only in the context of a randomised trial, given that the evidence left a very high degree of uncertainty on important effects. Updates This is a living guideline. It replaces earlier versions (4 September, 20 November, and 17 December 2020) and supersedes the BMJ Rapid Recommendations on remdesivir published on 2 July 2020. The previous versions can be found as data supplements. New recommendations will be published as updates to this guideline. Readers note This is the fourth version (update 3) of the living guideline (BMJ 2020;370:m3379). When citing this article, please consider adding the update number and date of access for clarity.
660 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, Chiba University39, Japan Agency for Marine-Earth Science and Technology40, 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
Harvard University1, University of Salamanca2, McGill University Health Centre3, University of Toronto4, Northeastern University5, Ghent University6, Flanders Institute for Biotechnology7, Ben-Gurion University of the Negev8, University of Cambridge9, University of Perugia10, Centre national de la recherche scientifique11, Paris Diderot University12, Genentech13, University of Liège14, McGill University15, Catalan Institution for Research and Advanced Studies16
TL;DR: The utility of HuRI is demonstrated in identifying the specific subcellular roles of protein–protein interactions and in identifying potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases.
Abstract: Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype–phenotype relationships1,2. Here we present a human ‘all-by-all’ reference interactome map of human binary protein interactions, or ‘HuRI’. With approximately 53,000 protein–protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome3, transcriptome4 and proteome5 data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein–protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes. A human binary protein interactome map that includes around 53,000 protein–protein interactions involving more than 8,000 proteins provides a reference for the study of human cellular function in health and disease.
TL;DR: The COVID-19 pandemic and lockdown seems particularly stressful for younger adults (<35 years), women, people without work, and low income and highest mental health problems in adults under 35 years,Women, people with no work,and low income.
14 May 2020
TL;DR: The proposed ECAPA-TDNN architecture significantly outperforms state-of-the-art TDNN based systems on the Voxceleb test sets and the 2019 VoxCeleb Speaker Recognition Challenge.
Abstract: Current speaker verification techniques rely on a neural network to extract speaker representations. The successful x-vector architecture is a Time Delay Neural Network (TDNN) that applies statistics pooling to project variable-length utterances into fixed-length speaker characterizing embeddings. In this paper, we propose multiple enhancements to this architecture based on recent trends in the related fields of face verification and computer vision. Firstly, the initial frame layers can be restructured into 1-dimensional Res2Net modules with impactful skip connections. Similarly to SE-ResNet, we introduce Squeeze-and-Excitation blocks in these modules to explicitly model channel interdependencies. The SE block expands the temporal context of the frame layer by rescaling the channels according to global properties of the recording. Secondly, neural networks are known to learn hierarchical features, with each layer operating on a different level of complexity. To leverage this complementary information, we aggregate and propagate features of different hierarchical levels. Finally, we improve the statistics pooling module with channel-dependent frame attention. This enables the network to focus on different subsets of frames during each of the channel’s statistics estimation. The proposed ECAPA-TDNN architecture significantly outperforms state-of-the-art TDNN based systems on the VoxCeleb test sets and the 2019 VoxCeleb Speaker Recognition Challenge.
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.
Rotem Botvinik-Nezer1, Rotem Botvinik-Nezer2, Felix Holzmeister3, Colin F. Camerer4 +217 more•Institutions (78)
TL;DR: The results obtained by seventy different teams analysing the same functional magnetic resonance imaging dataset show substantial variation, highlighting the influence of analytical choices and the importance of sharing workflows publicly and performing multiple analyses.
Abstract: Data analysis workflows in many scientific domains have become increasingly complex and flexible. Here we assess the effect of this flexibility on the results of functional magnetic resonance imaging by asking 70 independent teams to analyse the same dataset, testing the same 9 ex-ante hypotheses1. The flexibility of analytical approaches is exemplified by the fact that no two teams chose identical workflows to analyse the data. This flexibility resulted in sizeable variation in the results of hypothesis tests, even for teams whose statistical maps were highly correlated at intermediate stages of the analysis pipeline. Variation in reported results was related to several aspects of analysis methodology. Notably, a meta-analytical approach that aggregated information across teams yielded a significant consensus in activated regions. Furthermore, prediction markets of researchers in the field revealed an overestimation of the likelihood of significant findings, even by researchers with direct knowledge of the dataset2-5. Our findings show that analytical flexibility can have substantial effects on scientific conclusions, and identify factors that may be related to variability in the analysis of functional magnetic resonance imaging. The results emphasize the importance of validating and sharing complex analysis workflows, and demonstrate the need for performing and reporting multiple analyses of the same data. Potential approaches that could be used to mitigate issues related to analytical variability are discussed.
NanoString Technologies1, Ghent University2, Katholieke Universiteit Leuven3, Cornell University4, Memorial Sloan Kettering Cancer Center5, Ludwig Institute for Cancer Research6, Charles University in Prague7, Istituto Superiore di Sanità8, National Institutes of Health9, Institute of Cancer Research10, Merck & Co.11, University of Manchester12, University of California, San Diego13, Harvard University14, University of Navarra15, University of Pittsburgh16, McMaster University17, University of Tromsø18, Humanitas University19, University of Turin20, QIMR Berghofer Medical Research Institute21, Université de Montréal22, University of São Paulo23, University of Texas Southwestern Medical Center24, Yale University25
TL;DR: An updated operational definition of immunogenic cell death is provided, the key factors that dictate the ability of dying cells to drive an adaptive immune response are discussed, and experimental assays that are currently available for the assessment of ICD in vitro and in vivo are summarized.
Abstract: Cells succumbing to stress via regulated cell death (RCD) can initiate an adaptive immune response associated with immunological memory, provided they display sufficient antigenicity and adjuvanticity. Moreover, multiple intracellular and microenvironmental features determine the propensity of RCD to drive adaptive immunity. Here, we provide an updated operational definition of immunogenic cell death (ICD), discuss the key factors that dictate the ability of dying cells to drive an adaptive immune response, summarize experimental assays that are currently available for the assessment of ICD in vitro and in vivo, and formulate guidelines for their interpretation.
TL;DR: The isolation of single-domain antibodies (VHHs) from a llama immunized with prefusion-stabilized coronavirus spikes provide a molecular basis for the neutralization of pathogenic betacoronaviruses by VHHs and suggest that these molecules may serve as useful therapeutics during coronav virus outbreaks.
TL;DR: Generic chips can accelerate the development of future photonic circuits by providing a higher-level platform for prototyping novel optical functionalities without the need for custom chip fabrication.
Abstract: The growing maturity of integrated photonic technology makes it possible to build increasingly large and complex photonic circuits on the surface of a chip. Today, most of these circuits are designed for a specific application, but the increase in complexity has introduced a generation of photonic circuits that can be programmed using software for a wide variety of functions through a mesh of on-chip waveguides, tunable beam couplers and optical phase shifters. Here we discuss the state of this emerging technology, including recent developments in photonic building blocks and circuit architectures, as well as electronic control and programming strategies. We cover possible applications in linear matrix operations, quantum information processing and microwave photonics, and examine how these generic chips can accelerate the development of future photonic circuits by providing a higher-level platform for prototyping novel optical functionalities without the need for custom chip fabrication. The current state of programmable photonic integrated circuits is discussed, including recent developments in their building blocks, circuit architectures, electronic control and programming strategies, as well as different application spaces.
TL;DR: The study of basic psychological needs has witnessed a strong revival, in part spurred by Basic Psychological Need Theory (BPNT), one of the six mini-theories within Self-Determination Theory.
Abstract: The study of basic psychological needs has witnessed a strong revival, in part spurred by Basic Psychological Need Theory (BPNT), one of the six mini-theories within Self-Determination Theory. Empirical studies on BPNT have increased exponentially since the millennium turn, leading to refinements and extensions in theory. In this contribution we review these two decades of research in order to introduce two special issues on BPNT. We first discuss key criteria that define and identify a basic need within BPNT. We then review several need-relevant themes, highlighting advancements and trends that characterize contemporary research on BPNT. Specifically, we address potential extensions of the shortlist of basic psychological needs, the role of psychological need frustration in increasing vulnerability to maladjustment, the study of the interface between individuals’ psychological and physical needs (e.g., sleep, sex, hunger), novel insights into critical need-supportive and need-thwarting practices, and the universality (versus variability) of effects of need satisfactions and supports across demographics, psychological characteristics, and cultural contexts. We also situate each of the 19 contributions that appear in this special double-issue on BPNT within these themes, while suggesting avenues for further research on the role of basic psychological needs in motivation, adjustment, and wellness.
TL;DR: The updated recommendations provide stakeholders with an updated consensus on the pharmacological management of PsA, based on a combination of evidence and expert opinion.
Abstract: Objective To update the European League Against Rheumatism (EULAR) recommendations for the pharmacological treatment of psoriatic arthritis (PsA). Methods According to the EULAR standardised operating procedures, a systematic literature review was followed by a consensus meeting to develop this update involving 28 international taskforce members in May 2019. Levels of evidence and strengths of recommendations were determined. Results The updated recommendations comprise 6 overarching principles and 12 recommendations. The overarching principles address the nature of PsA and diversity of both musculoskeletal and non-musculoskeletal manifestations; the need for collaborative management and shared decision-making is highlighted. The recommendations provide a treatment strategy for pharmacological therapies. Non-steroidal anti-inflammatory drugs and local glucocorticoid injections are proposed as initial therapy; for patients with arthritis and poor prognostic factors, such as polyarthritis or monoarthritis/oligoarthritis accompanied by factors such as dactylitis or joint damage, rapid initiation of conventional synthetic disease-modifying antirheumatic drugs is recommended. If the treatment target is not achieved with this strategy, a biological disease-modifying antirheumatic drugs (bDMARDs) targeting tumour necrosis factor (TNF), interleukin (IL)-17A or IL-12/23 should be initiated, taking into account skin involvement if relevant. If axial disease predominates, a TNF inhibitor or IL-17A inhibitor should be started as first-line disease-modifying antirheumatic drug. Use of Janus kinase inhibitors is addressed primarily after bDMARD failure. Phosphodiesterase-4 inhibition is proposed for patients in whom these other drugs are inappropriate, generally in the context of mild disease. Drug switches and tapering in sustained remission are addressed. Conclusion These recommendations provide stakeholders with an updated consensus on the pharmacological management of PsA, based on a combination of evidence and expert opinion.
TL;DR: Recent progress toward understanding theBR pathway is summarized, including BR perception and the molecular mechanisms of BR signaling, and how knowledge of the BR pathway is being applied to manipulate the growth and stress responses of crops is shown.
Abstract: Brassinosteroids (BRs) are a group of polyhydroxylated plant steroid hormones crucial for many aspects of plant life. BRs were originally characterized for their function in cell elongation, but it is becoming clear that they play major roles in plant growth, development and responses to several stresses such as temperature and drought. A BR signaling pathway from cell surface receptors to central transcription factors has been well characterized. Here we summarize recent progress towards understanding the BR pathway including BR perception and the molecular mechanisms of BR signaling. Next, we discuss the roles of BRs in development and stress responses. Finally, we show how knowledge of the BR pathway is being applied to manipulate the growth and stress responses in crops. These studies highlight the complex regulation of BR signaling, multiple points of crosstalk between BRs and other hormones or stress responses, and finely tuned spatiotemporal regulation of BR signaling.
University of Haifa1, Fudan University2, Federal University of Bahia3, Israel Ministry of Health4, University of Melbourne5, Christian Michelsen Institute6, University of Zambia7, University of Bergen8, Chulalongkorn University9, Umeå University10, American University of Armenia11, Johns Hopkins University12, Bar-Ilan University13, Monash University14, Thailand Ministry of Public Health15, Ghent University16
TL;DR: To address the challenges to health equity and describe some of the approaches taken by governments and local organizations, 13 country case studies from various regions around the world are compiled.
Abstract: The COVID-19 is disproportionally affecting the poor, minorities and a broad range of vulnerable populations, due to its inequitable spread in areas of dense population and limited mitigation capacity due to high prevalence of chronic conditions or poor access to high quality public health and medical care. Moreover, the collateral effects of the pandemic due to the global economic downturn, and social isolation and movement restriction measures, are unequally affecting those in the lowest power strata of societies. To address the challenges to health equity and describe some of the approaches taken by governments and local organizations, we have compiled 13 country case studies from various regions around the world: China, Brazil, Thailand, Sub Saharan Africa, Nicaragua, Armenia, India, Guatemala, United States of America (USA), Israel, Australia, Colombia, and Belgium. This compilation is by no-means representative or all inclusive, and we encourage researchers to continue advancing global knowledge on COVID-19 health equity related issues, through rigorous research and generation of a strong evidence base of new empirical studies in this field.
Royal Museum for Central Africa1, University of Leeds2, Ghent University3, University College London4, Forestry Commission5, University of York6, Wildlife Conservation Society7, University of Kisangani8, University of Plymouth9, World Wide Fund for Nature10, Norwegian University of Life Sciences11, University of Yaoundé I12, Manchester Metropolitan University13, Center for International Forestry Research14, University of British Columbia15, Bioversity International16, University of Toronto17, University of Stirling18, Forestry Research Institute of Ghana19, Centre de coopération internationale en recherche agronomique pour le développement20, University of Montpellier21, Mbarara University of Science and Technology22, Marien Ngouabi University23, University of Buea24, Duke University25, University of Edinburgh26, Smithsonian Institution27, National Park Service28, University of Cambridge29, Gembloux Agro-Bio Tech30, University of Birmingham31, University of Exeter32, Smithsonian Tropical Research Institute33, Chinese Academy of Sciences34, Royal Botanic Garden Edinburgh35, American Museum of Natural History36, African Wildlife Foundation37, University of Bristol38, University of Hong Kong39, Royal Society for the Protection of Birds40, Royal Botanic Gardens41, Environmental Change Institute42, University of the Sunshine Coast43, Fleming College44, Sokoine University of Agriculture45, University of Southampton46, University of Lincoln47, University of Florence48, University of Aberdeen49, Innovate UK50, National University of Singapore51, Washington State University Vancouver52, Yale University53, University of Nottingham54, Université libre de Bruxelles55, Florida International University56, Bangor University57, University of Liberia58
TL;DR: Overall, the uptake of carbon into Earth’s intact tropical forests peaked in the 1990s and independent observations indicating greater recent carbon uptake into the Northern Hemisphere landmass reinforce the conclusion that the intact tropical forest carbon sink has already peaked.
Abstract: Structurally intact tropical forests sequestered about half of the global terrestrial carbon uptake over the 1990s and early 2000s, removing about 15 per cent of anthropogenic carbon dioxide emissions. Climate-driven vegetation models typically predict that this tropical forest ‘carbon sink’ will continue for decades. Here we assess trends in the carbon sink using 244 structurally intact African tropical forests spanning 11 countries, compare them with 321 published plots from Amazonia and investigate the underlying drivers of the trends. The carbon sink in live aboveground biomass in intact African tropical forests has been stable for the three decades to 2015, at 0.66 tonnes of carbon per hectare per year (95 per cent confidence interval 0.53–0.79), in contrast to the long-term decline in Amazonian forests. Therefore the carbon sink responses of Earth’s two largest expanses of tropical forest have diverged. The difference is largely driven by carbon losses from tree mortality, with no detectable multi-decadal trend in Africa and a long-term increase in Amazonia. Both continents show increasing tree growth, consistent with the expected net effect of rising atmospheric carbon dioxide and air temperature. Despite the past stability of the African carbon sink, our most intensively monitored plots suggest a post-2010 increase in carbon losses, delayed compared to Amazonia, indicating asynchronous carbon sink saturation on the two continents. A statistical model including carbon dioxide, temperature, drought and forest dynamics accounts for the observed trends and indicates a long-term future decline in the African sink, whereas the Amazonian sink continues to weaken rapidly. Overall, the uptake of carbon into Earth’s intact tropical forests peaked in the 1990s. Given that the global terrestrial carbon sink is increasing in size, independent observations indicating greater recent carbon uptake into the Northern Hemisphere landmass reinforce our conclusion that the intact tropical forest carbon sink has already peaked. This saturation and ongoing decline of the tropical forest carbon sink has consequences for policies intended to stabilize Earth’s climate.
TL;DR: A detailed protocol for pySCENIC: a faster, container-based implementation in Python, resulting in a tenfold increase in speed, and has been packaged into containers for ease of use is described.
Abstract: This protocol explains how to perform a fast SCENIC analysis alongside standard best practices steps on single-cell RNA-sequencing data using software containers and Nextflow pipelines. SCENIC reconstructs regulons (i.e., transcription factors and their target genes) assesses the activity of these discovered regulons in individual cells and uses these cellular activity patterns to find meaningful clusters of cells. Here we present an improved version of SCENIC with several advances. SCENIC has been refactored and reimplemented in Python (pySCENIC), resulting in a tenfold increase in speed, and has been packaged into containers for ease of use. It is now also possible to use epigenomic track databases, as well as motifs, to refine regulons. In this protocol, we explain the different steps of SCENIC: the workflow starts from the count matrix depicting the gene abundances for all cells and consists of three stages. First, coexpression modules are inferred using a regression per-target approach (GRNBoost2). Next, the indirect targets are pruned from these modules using cis-regulatory motif discovery (cisTarget). Lastly, the activity of these regulons is quantified via an enrichment score for the regulon's target genes (AUCell). Nonlinear projection methods can be used to display visual groupings of cells based on the cellular activity patterns of these regulons. The results can be exported as a loom file and visualized in the SCope web application. This protocol is illustrated on two use cases: a peripheral blood mononuclear cell data set and a panel of single-cell RNA-sequencing cancer experiments. For a data set of 10,000 genes and 50,000 cells, the pipeline runs in <2 h.
TL;DR: Through discussing the role of NHC ligands in promoting challenging C-H activation methods, the reader is provided with an overview of this important area and its crucial role in forging carbon-carbon and carbon-heteroatom bonds by directly engaging ubiquitous C- H bonds.
Abstract: In this contribution, we provide a comprehensive overview of C-H activation methods promoted by NHC-transition metal complexes, covering the literature since 2002 (the year of the first report on metal-NHC-catalyzed C-H activation) through June 2019, focusing on both NHC ligands and C-H activation methods. This review covers C-H activation reactions catalyzed by group 8 to 11 NHC-metal complexes. Through discussing the role of NHC ligands in promoting challenging C-H activation methods, the reader is provided with an overview of this important area and its crucial role in forging carbon-carbon and carbon-heteroatom bonds by directly engaging ubiquitous C-H bonds.
TL;DR: In this article, the authors provide an extensive overview of the current state-of-the-art in the field by outlining the challenges and opportunities of distributed machine learning over conventional (centralized) machine learning.
Abstract: The demand for artificial intelligence has grown significantly over the past decade, and this growth has been fueled by advances in machine learning techniques and the ability to leverage hardware acceleration. However, to increase the quality of predictions and render machine learning solutions feasible for more complex applications, a substantial amount of training data is required. Although small machine learning models can be trained with modest amounts of data, the input for training larger models such as neural networks grows exponentially with the number of parameters. Since the demand for processing training data has outpaced the increase in computation power of computing machinery, there is a need for distributing the machine learning workload across multiple machines, and turning the centralized into a distributed system. These distributed systems present new challenges: first and foremost, the efficient parallelization of the training process and the creation of a coherent model. This article provides an extensive overview of the current state-of-the-art in the field by outlining the challenges and opportunities of distributed machine learning over conventional (centralized) machine learning, discussing the techniques used for distributed machine learning, and providing an overview of the systems that are available.
Paul M. Thompson1, Neda Jahanshad1, Christopher R.K. Ching1, Lauren E. Salminen1 +210 more•Institutions (99)
TL;DR: This review summarizes the last decade of work by the ENIGMA Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease, and highlights the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings.
Abstract: This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors.
Université catholique de Louvain1, Université du Québec à Trois-Rivières2, University of Paris3, Université Paris-Saclay4, University of Liège5, Université de Montréal6, Ghent University7, Rutgers University8, Wake Forest University9, Martin Luther University of Halle-Wittenberg10, University of California, Berkeley11, Lawrence Berkeley National Laboratory12, University of Cantabria13, West Virginia University14, Katholieke Universiteit Leuven15, Dalhousie University16
TL;DR: An analysis of the impact that Abinit has had, through for example the bibliometric indicators of the 2009 publication, and the new capabilities of abinit that have been implemented during the last three years are covered, complementing a recent update of the2009 article published in 2016.
TL;DR: A thorough understanding of the pathophysiological determinants of respiratory drive and hypoxemia may promote a more complete comprehension of a patient’s clinical presentation and management in COVID-19 patients.
Abstract: The novel coronavirus disease 2019 (COVID-19) pandemic is a global crisis, challenging healthcare systems worldwide. Many patients present with a remarkable disconnect in rest between profound hypoxemia yet without proportional signs of respiratory distress (i.e. happy hypoxemia) and rapid deterioration can occur. This particular clinical presentation in COVID-19 patients contrasts with the experience of physicians usually treating critically ill patients in respiratory failure and ensuring timely referral to the intensive care unit can, therefore, be challenging. A thorough understanding of the pathophysiological determinants of respiratory drive and hypoxemia may promote a more complete comprehension of a patient’s clinical presentation and management. Preserved oxygen saturation despite low partial pressure of oxygen in arterial blood samples occur, due to leftward shift of the oxyhemoglobin dissociation curve induced by hypoxemia-driven hyperventilation as well as possible direct viral interactions with hemoglobin. Ventilation-perfusion mismatch, ranging from shunts to alveolar dead space ventilation, is the central hallmark and offers various therapeutic targets.
Wellcome Trust Sanger Institute1, Newcastle University2, Ghent University3, University of Cambridge4, Wellcome Trust/Cancer Research UK Gurdon Institute5, University College London6, Francis Crick Institute7, Laboratory of Molecular Biology8, Freeman Hospital9, Cambridge University Hospitals NHS Foundation Trust10
TL;DR: The authors' single-cell transcriptome profile of the thymus across the human lifetime and across species provides a high-resolution census of T cell development within the native tissue microenvironment, and identifies novel subpopulations of human thymic fibroblasts and epithelial cells and located them in situ.
Abstract: The thymus provides a nurturing environment for the differentiation and selection of T cells, a process orchestrated by their interaction with multiple thymic cell types. We used single-cell RNA sequencing to create a cell census of the human thymus across the life span and to reconstruct T cell differentiation trajectories and T cell receptor (TCR) recombination kinetics. Using this approach, we identified and located in situ CD8αα+ T cell populations, thymic fibroblast subtypes, and activated dendritic cell states. In addition, we reveal a bias in TCR recombination and selection, which is attributed to genomic position and the kinetics of lineage commitment. Taken together, our data provide a comprehensive atlas of the human thymus across the life span with new insights into human T cell development.