Showing papers by "University of Exeter published in 2016"

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Principal component analysis: a review and recent developments

Abstract: Large datasets are increasingly common and are often difficult to interpret. Principal component analysis (PCA) is a technique for reducing the dimensionality of such datasets, increasing interpretability but at the same time minimizing information loss. It does so by creating new uncorrelated variables that successively maximize variance. Finding such new variables, the principal components, reduces to solving an eigenvalue/eigenvector problem, and the new variables are defined by the dataset at hand, not a priori , hence making PCA an adaptive data analysis technique. It is adaptive in another sense too, since variants of the technique have been developed that are tailored to various different data types and structures. This article will begin by introducing the basic ideas of PCA, discussing what it can and cannot do. It will then describe some variants of PCA and their application.

A reference panel of 64,976 haplotypes for genotype imputation

Abstract: We describe a reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry. Using this resource leads to accurate genotype imputation at minor allele frequencies as low as 0.1% and a large increase in the number of SNPs tested in association studies, and it can help to discover and refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.

The Scenario Model Intercomparison Project (ScenarioMIP) for CMIP6

Abstract: . Projections of future climate change play a fundamental role in improving understanding of the climate system as well as characterizing societal risks and response options. The Scenario Model Intercomparison Project (ScenarioMIP) is the primary activity within Phase 6 of the Coupled Model Intercomparison Project (CMIP6) that will provide multi-model climate projections based on alternative scenarios of future emissions and land use changes produced with integrated assessment models. In this paper, we describe ScenarioMIP's objectives, experimental design, and its relation to other activities within CMIP6. The ScenarioMIP design is one component of a larger scenario process that aims to facilitate a wide range of integrated studies across the climate science, integrated assessment modeling, and impacts, adaptation, and vulnerability communities, and will form an important part of the evidence base in the forthcoming Intergovernmental Panel on Climate Change (IPCC) assessments. At the same time, it will provide the basis for investigating a number of targeted science and policy questions that are especially relevant to scenario-based analysis, including the role of specific forcings such as land use and aerosols, the effect of a peak and decline in forcing, the consequences of scenarios that limit warming to below 2 °C, the relative contributions to uncertainty from scenarios, climate models, and internal variability, and long-term climate system outcomes beyond the 21st century. To serve this wide range of scientific communities and address these questions, a design has been identified consisting of eight alternative 21st century scenarios plus one large initial condition ensemble and a set of long-term extensions, divided into two tiers defined by relative priority. Some of these scenarios will also provide a basis for variants planned to be run in other CMIP6-Endorsed MIPs to investigate questions related to specific forcings. Harmonized, spatially explicit emissions and land use scenarios generated with integrated assessment models will be provided to participating climate modeling groups by late 2016, with the climate model simulations run within the 2017–2018 time frame, and output from the climate model projections made available and analyses performed over the 2018–2020 period.

Greening of the Earth and its drivers

Abstract: Global environmental change is rapidly altering the dynamics of terrestrial vegetation, with consequences for the functioning of the Earth system and provision of ecosystem services(1,2). Yet how global vegetation is responding to the changing environment is not well established. Here we use three long-term satellite leaf area index (LAI) records and ten global ecosystem models to investigate four key drivers of LAI trends during 1982-2009. We show a persistent and widespread increase of growing season integrated LAI (greening) over 25% to 50% of the global vegetated area, whereas less than 4% of the globe shows decreasing LAI (browning). Factorial simulations with multiple global ecosystem models suggest that CO2 fertilization effects explain 70% of the observed greening trend, followed by nitrogen deposition (9%), climate change (8%) and land cover change (LCC) (4%). CO2 fertilization effects explain most of the greening trends in the tropics, whereas climate change resulted in greening of the high latitudes and the Tibetan Plateau. LCC contributed most to the regional greening observed in southeast China and the eastern United States. The regional effects of unexplained factors suggest that the next generation of ecosystem models will need to explore the impacts of forest demography, differences in regional management intensities for cropland and pastures, and other emerging productivity constraints such as phosphorus availability.

Exercise-based cardiac rehabilitation for coronary heart disease

Abstract: Background Coronary heart disease (CHD) is the most common cause of death globally. However, with falling CHD mortality rates, an increasing number of people living with CHD may need support to manage their symptoms and prognosis. Exercise‐based cardiac rehabilitation (CR) aims to improve the health and outcomes of people with CHD. This is an update of a Cochrane Review previously published in 2016. Objectives To assess the clinical effectiveness and cost‐effectiveness of exercise‐based CR (exercise training alone or in combination with psychosocial or educational interventions) compared with 'no exercise' control, on mortality, morbidity and health‐related quality of life (HRQoL) in people with CHD. Search methods We updated searches from the previous Cochrane Review, by searching CENTRAL, MEDLINE, Embase, and two other databases in September 2020. We also searched two clinical trials registers in June 2021. Selection criteria We included randomised controlled trials (RCTs) of exercise‐based interventions with at least six months’ follow‐up, compared with 'no exercise' control. The study population comprised adult men and women who have had a myocardial infarction (MI), coronary artery bypass graft (CABG) or percutaneous coronary intervention (PCI), or have angina pectoris, or coronary artery disease. Data collection and analysis We screened all identified references, extracted data and assessed risk of bias according to Cochrane methods. We stratified meta‐analysis by duration of follow‐up: short‐term (6 to 12 months); medium‐term (> 12 to 36 months); and long‐term ( > 3 years), and used meta‐regression to explore potential treatment effect modifiers. We used GRADE for primary outcomes at 6 to 12 months (the most common follow‐up time point). Main results This review included 85 trials which randomised 23,430 people with CHD. This latest update identified 22 new trials (7795 participants). The population included predominantly post‐MI and post‐revascularisation patients, with a mean age ranging from 47 to 77 years. In the last decade, the median percentage of women with CHD has increased from 11% to 17%, but females still account for a similarly small percentage of participants recruited overall ( < 15%). Twenty‐one of the included trials were performed in low‐ and middle‐income countries (LMICs). Overall trial reporting was poor, although there was evidence of an improvement in quality over the last decade. The median longest follow‐up time was 12 months (range 6 months to 19 years). At short‐term follow‐up (6 to 12 months), exercise‐based CR likely results in a slight reduction in all‐cause mortality (risk ratio (RR) 0.87, 95% confidence interval (CI) 0.73 to 1.04; 25 trials; moderate certainty evidence), a large reduction in MI (RR 0.72, 95% CI 0.55 to 0.93; 22 trials; number needed to treat for an additional beneficial outcome (NNTB) 75, 95% CI 47 to 298; high certainty evidence), and a large reduction in all‐cause hospitalisation (RR 0.58, 95% CI 0.43 to 0.77; 14 trials; NNTB 12, 95% CI 9 to 21; moderate certainty evidence). Exercise‐based CR likely results in little to no difference in risk of cardiovascular mortality (RR 0.88, 95% CI 0.68 to 1.14; 15 trials; moderate certainty evidence), CABG (RR 0.99, 95% CI 0.78 to 1.27; 20 trials; high certainty evidence), and PCI (RR 0.86, 95% CI 0.63 to 1.19; 13 trials; moderate certainty evidence) up to 12 months' follow‐up. We are uncertain about the effects of exercise‐based CR on cardiovascular hospitalisation, with a wide confidence interval including considerable benefit as well as harm (RR 0.80, 95% CI 0.41 to 1.59; low certainty evidence). There was evidence of substantial heterogeneity across trials for cardiovascular hospitalisations (I2 = 53%), and of small study bias for all‐cause hospitalisation, but not for all other outcomes. At medium‐term follow‐up, although there may be little to no difference in all‐cause mortality (RR 0.90, 95% CI 0.80 to 1.02; 15 trials), MI (RR 1.07, 95% CI 0.91 to 1.27; 12 trials), PCI (RR 0.96, 95% CI 0.69 to 1.35; 6 trials), CABG (RR 0.97, 95% CI 0.77 to 1.23; 9 trials), and all‐cause hospitalisation (RR 0.92, 95% CI 0.82 to 1.03; 9 trials), a large reduction in cardiovascular mortality was found (RR 0.77, 95% CI 0.63 to 0.93; 5 trials). Evidence is uncertain for difference in risk of cardiovascular hospitalisation (RR 0.92, 95% CI 0.76 to 1.12; 3 trials). At long‐term follow‐up, although there may be little to no difference in all‐cause mortality (RR 0.91, 95% CI 0.75 to 1.10), exercise‐based CR may result in a large reduction in cardiovascular mortality (RR 0.58, 95% CI 0.43 to 0.78; 8 trials) and MI (RR 0.67, 95% CI 0.50 to 0.90; 10 trials). Evidence is uncertain for CABG (RR 0.66, 95% CI 0.34 to 1.27; 4 trials), and PCI (RR 0.76, 95% CI 0.48 to 1.20; 3 trials). Meta‐regression showed benefits in outcomes were independent of CHD case mix, type of CR, exercise dose, follow‐up length, publication year, CR setting, study location, sample size or risk of bias. There was evidence that exercise‐based CR may slightly increase HRQoL across several subscales (SF‐36 mental component, physical functioning, physical performance, general health, vitality, social functioning and mental health scores) up to 12 months' follow‐up; however, these may not be clinically important differences. The eight trial‐based economic evaluation studies showed exercise‐based CR to be a potentially cost‐effective use of resources in terms of gain in quality‐adjusted life years (QALYs). Authors' conclusions This updated Cochrane Review supports the conclusions of the previous version, that exercise‐based CR provides important benefits to people with CHD, including reduced risk of MI, a likely small reduction in all‐cause mortality, and a large reduction in all‐cause hospitalisation, along with associated healthcare costs, and improved HRQoL up to 12 months' follow‐up. Over longer‐term follow‐up, benefits may include reductions in cardiovascular mortality and MI. In the last decade, trials were more likely to include females, and be undertaken in LMICs, increasing the generalisability of findings. Well‐designed, adequately‐reported RCTs of CR in people with CHD more representative of usual clinical practice are still needed. Trials should explicitly report clinical outcomes, including mortality and hospital admissions, and include validated HRQoL outcome measures, especially over longer‐term follow‐up, and assess costs and cost‐effectiveness.

Global Carbon Budget 2016

Abstract: . Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere – 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 data sets and methodology to quantify all major components of the global carbon budget, including their uncertainties, based on the combination of a range of data, algorithms, statistics, and model estimates and their interpretation by a broad scientific community. We discuss changes compared to previous estimates and consistency within and among components, alongside methodology and data limitations. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, respectively, while emissions from land-use change (ELUC), mainly deforestation, are based on combined evidence from land-cover change data, fire activity associated with deforestation, and models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The mean ocean CO2 sink (SOCEAN) is based on observations from the 1990s, while the annual anomalies and trends are estimated with ocean models. The variability in SOCEAN is evaluated with data products based on surveys of ocean CO2 measurements. The global residual terrestrial CO2 sink (SLAND) is estimated by the difference of the other terms of the global carbon budget and compared to results of independent dynamic global vegetation models. We compare the mean land and ocean fluxes and their variability to estimates from three atmospheric inverse methods for three broad latitude bands. All uncertainties are reported as ±1σ, reflecting the current capacity to characterise the annual estimates of each component of the global carbon budget. For the last decade available (2006–2015), EFF was 9.3 ± 0.5 GtC yr−1, ELUC 1.0 ± 0.5 GtC yr−1, GATM 4.5 ± 0.1 GtC yr−1, SOCEAN 2.6 ± 0.5 GtC yr−1, and SLAND 3.1 ± 0.9 GtC yr−1. For year 2015 alone, the growth in EFF was approximately zero and emissions remained at 9.9 ± 0.5 GtC yr−1, showing a slowdown in growth of these emissions compared to the average growth of 1.8 % yr−1 that took place during 2006–2015. Also, for 2015, ELUC was 1.3 ± 0.5 GtC yr−1, GATM was 6.3 ± 0.2 GtC yr−1, SOCEAN was 3.0 ± 0.5 GtC yr−1, and SLAND was 1.9 ± 0.9 GtC yr−1. GATM was higher in 2015 compared to the past decade (2006–2015), reflecting a smaller SLAND for that year. The global atmospheric CO2 concentration reached 399.4 ± 0.1 ppm averaged over 2015. For 2016, preliminary data indicate the continuation of low growth in EFF with +0.2 % (range of −1.0 to +1.8 %) based on national emissions projections for China and USA, and projections of gross domestic product corrected for recent changes in the carbon intensity of the economy for the rest of the world. In spite of the low growth of EFF in 2016, the growth rate in atmospheric CO2 concentration is expected to be relatively high because of the persistence of the smaller residual terrestrial sink (SLAND) in response to El Nino conditions of 2015–2016. From this projection of EFF and assumed constant ELUC for 2016, cumulative emissions of CO2 will reach 565 ± 55 GtC (2075 ± 205 GtCO2) for 1870–2016, about 75 % from EFF and 25 % from ELUC. This living data update documents changes in the methods and data sets used in this new carbon budget compared with previous publications of this data set (Le Quere et al., 2015b, a, 2014, 2013). All observations presented here can be downloaded from the Carbon Dioxide Information Analysis Center ( doi:10.3334/CDIAC/GCP_2016 ).

Biophysical and economic limits to negative CO2 emissions

Abstract: To have a >50% chance of limiting warming below 2 °C, most recent scenarios from integrated assessment models (IAMs) require large-scale deployment of negative emissions technologies (NETs). These are technologies that result in the net removal of greenhouse gases from the atmosphere. We quantify potential global impacts of the different NETs on various factors (such as land, greenhouse gas emissions, water, albedo, nutrients and energy) to determine the biophysical limits to, and economic costs of, their widespread application. Resource implications vary between technologies and need to be satisfactorily addressed if NETs are to have a significant role in achieving climate goals.

A continuum from clear to cloudy hot-Jupiter exoplanets without primordial water depletion

Abstract: Thousands of transiting exoplanets have been discovered, but spectral analysis of their atmospheres has so far been dominated by a small number of exoplanets and data spanning relatively narrow wavelength ranges (such as 1.1-1.7 micrometres). Recent studies show that some hot-Jupiter exoplanets have much weaker water absorption features in their near-infrared spectra than predicted. The low amplitude of water signatures could be explained by very low water abundances, which may be a sign that water was depleted in the protoplanetary disk at the planet's formation location, but it is unclear whether this level of depletion can actually occur. Alternatively, these weak signals could be the result of obscuration by clouds or hazes, as found in some optical spectra. Here we report results from a comparative study of ten hot Jupiters covering the wavelength range 0.3-5 micrometres, which allows us to resolve both the optical scattering and infrared molecular absorption spectroscopically. Our results reveal a diverse group of hot Jupiters that exhibit a continuum from clear to cloudy atmospheres. We find that the difference between the planetary radius measured at optical and infrared wavelengths is an effective metric for distinguishing different atmosphere types. The difference correlates with the spectral strength of water, so that strong water absorption lines are seen in clear-atmosphere planets and the weakest features are associated with clouds and hazes. This result strongly suggests that primordial water depletion during formation is unlikely and that clouds and hazes are the cause of weaker spectral signatures.

Sensitivity analysis of environmental models

Abstract: Sensitivity Analysis (SA) investigates how the variation in the output of a numerical model can be attributed to variations of its input factors. SA is increasingly being used in environmental modelling for a variety of purposes, including uncertainty assessment, model calibration and diagnostic evaluation, dominant control analysis and robust decision-making. In this paper we review the SA literature with the goal of providing: (i) a comprehensive view of SA approaches also in relation to other methodologies for model identification and application; (ii) a systematic classification of the most commonly used SA methods; (iii) practical guidelines for the application of SA. The paper aims at delivering an introduction to SA for non-specialist readers, as well as practical advice with best practice examples from the literature; and at stimulating the discussion within the community of SA developers and users regarding the setting of good practices and on defining priorities for future research. We present an overview of SA and its link to uncertainty analysis, model calibration and evaluation, robust decision-making.We provide a systematic review of existing approaches, which can support users in the choice of an SA method.We provide practical guidelines by developing a workflow for the application of SA and discuss critical choices.We give best practice examples from the literature and highlight trends and gaps for future research.

The genetic architecture of type 2 diabetes

Abstract: The genetic architecture of common traits, including the number, frequency, and effect sizes of inherited variants that contribute to individual risk, has been long debated. Genome-wide association studies have identified scores of common variants associated with type 2 diabetes, but in aggregate, these explain only a fraction of the heritability of this disease. Here, to test the hypothesis that lower-frequency variants explain much of the remainder, the GoT2D and T2D-GENES consortia performed whole-genome sequencing in 2,657 European individuals with and without diabetes, and exome sequencing in 12,940 individuals from five ancestry groups. To increase statistical power, we expanded the sample size via genotyping and imputation in a further 111,548 subjects. Variants associated with type 2 diabetes after sequencing were overwhelmingly common and most fell within regions previously identified by genome-wide association studies. Comprehensive enumeration of sequence variation is necessary to identify functional alleles that provide important clues to disease pathophysiology, but large-scale sequencing does not support the idea that lower-frequency variants have a major role in predisposition to type 2 diabetes.

Extinction of experience: the loss of human–nature interactions

Abstract: Increasingly, people are becoming less likely to have direct contact with nature (natural environments and their associated wildlife) in their everyday lives. Over 20 years ago, Robert M Pyle termed this ongoing alienation the “extinction of experience”, but the phenomenon has continued to receive surprisingly limited attention. Here, we present current understanding of the extinction of experience, with particular emphasis on its causes and consequences, and suggest future research directions. Our review illustrates that the loss of interaction with nature not only diminishes a wide range of benefits relating to health and well-being, but also discourages positive emotions, attitudes, and behavior with regard to the environment, implying a cycle of disaffection toward nature. Such serious implications highlight the importance of reconnecting people with nature, as well as focusing research and public policy on addressing and improving awareness of the extinction of experience.

Sustainability‐oriented Innovation: A Systematic Review

Abstract: This article is intended as a contribution to the ongoing conceptual development of Sustainability-Oriented Innovation (SOI) and provides initial guidance on becoming and being sustainable. We organize and integrate the diverse body of empirical literature relating to SOI and, in doing so, develop a synthesized conceptual framework onto which SOI practices and processes can be mapped. SOI involves making intentional changes to an organization’s philosophy and values, as well as to its products, processes or practices to serve the specific purpose of creating and realising social and environmental value in addition to economic returns. A critical reading of previous literature relating to environmental management and sustainability reveals how little attention has been paid to SOI and what exists is only partial. In a review of 100 scholarly articles and 27 grey sources drawn from the period of the three Earth Summits (1992, 2002 and 2012), we address four specific deficiencies that have given rise to these limitations: the meaning of SOI, how it has been conceptualised, its treatment as a dichotomous phenomenon and a general failure to reflect more contemporary practices. We adopt a framework synthesis approach involving first constructing an initial architecture of the landscape grounded in previous studies which is subsequently iteratively tested, shaped, refined and reinforced into a model of SOI with data drawn from included studies: so advancing theoretical development in the field of SOI.

Using Raman spectroscopy to characterize biological materials

Abstract: Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and polymer science fields. The application of Raman spectroscopy and microscopy within biology is rapidly increasing because it can provide chemical and compositional information, but it does not typically suffer from interference from water molecules. Analysis does not conventionally require extensive sample preparation; biochemical and structural information can usually be obtained without labeling. In this protocol, we aim to standardize and bring together multiple experimental approaches from key leaders in the field for obtaining Raman spectra using a microspectrometer. As examples of the range of biological samples that can be analyzed, we provide instructions for acquiring Raman spectra, maps and images for fresh plant tissue, formalin-fixed and fresh frozen mammalian tissue, fixed cells and biofluids. We explore a robust approach for sample preparation, instrumentation, acquisition parameters and data processing. By using this approach, we expect that a typical Raman experiment can be performed by a nonspecialist user to generate high-quality data for biological materials analysis.

DNA methylation-based measures of biological age: meta-analysis predicting time to death

Abstract: Estimates of biological age based on DNA methylation patterns, often referred to as "epigenetic age", "DNAm age", have been shown to be robust biomarkers of age in humans. We previously demonstrated that independent of chronological age, epigenetic age assessed in blood predicted all-cause mortality in four human cohorts. Here, we expanded our original observation to 13 different cohorts for a total sample size of 13,089 individuals, including three racial/ethnic groups. In addition, we examined whether incorporating information on blood cell composition into the epigenetic age metrics improves their predictive power for mortality. All considered measures of epigenetic age acceleration were predictive of mortality (p≤8.2x10-9), independent of chronological age, even after adjusting for additional risk factors (p<5.4x10-4), and within the racial/ethnic groups that we examined (non-Hispanic whites, Hispanics, African Americans). Epigenetic age estimates that incorporated information on blood cell composition led to the smallest p-values for time to death (p=7.5x10-43). Overall, this study a) strengthens the evidence that epigenetic age predicts all-cause mortality above and beyond chronological age and traditional risk factors, and b) demonstrates that epigenetic age estimates that incorporate information on blood cell counts lead to highly significant associations with all-cause mortality.

Global threats from invasive alien species in the twenty-first century and national response capacities

Abstract: Invasive alien species (IAS) threaten human livelihoods and biodiversity globally. Increasing globalization facilitates IAS arrival, and environmental changes, including climate change, facilitate IAS establishment. Here we provide the first global, spatial analysis of the terrestrial threat from IAS in light of twenty-first century globalization and environmental change, and evaluate national capacities to prevent and manage species invasions. We find that one-sixth of the global land surface is highly vulnerable to invasion, including substantial areas in developing economies and biodiversity hotspots. The dominant invasion vectors differ between high-income countries (imports, particularly of plants and pets) and low-income countries (air travel). Uniting data on the causes of introduction and establishment can improve early-warning and eradication schemes. Most countries have limited capacity to act against invasions. In particular, we reveal a clear need for proactive invasion strategies in areas with high poverty levels, high biodiversity and low historical levels of invasion.

Anthropogenic disturbance in tropical forests can double biodiversity loss from deforestation

Abstract: Concerted political attention has focused on reducing deforestation, and this remains the cornerstone of most biodiversity conservation strategies. However, maintaining forest cover may not reduce anthropogenic forest disturbances, which are rarely considered in conservation programmes. These disturbances occur both within forests, including selective logging and wildfires, and at the landscape level, through edge, area and isolation effects. Until now, the combined effect of anthropogenic disturbance on the conservation value of remnant primary forests has remained unknown, making it impossible to assess the relative importance of forest disturbance and forest loss. Here we address these knowledge gaps using a large data set of plants, birds and dung beetles (1,538, 460 and 156 species, respectively) sampled in 36 catchments in the Brazilian state of Para. Catchments retaining more than 69–80% forest cover lost more conservation value from disturbance than from forest loss. For example, a 20% loss of primary forest, the maximum level of deforestation allowed on Amazonian properties under Brazil’s Forest Code, resulted in a 39–54% loss of conservation value: 96–171% more than expected without considering disturbance effects. We extrapolated the disturbance-mediated loss of conservation value throughout Para, which covers 25% of the Brazilian Amazon. Although disturbed forests retained considerable conservation value compared with deforested areas, the toll of disturbance outside Para’s strictly protected areas is equivalent to the loss of 92,000–139,000 km2 of primary forest. Even this lowest estimate is greater than the area deforested across the entire Brazilian Amazon between 2006 and 2015 (ref. 10). Species distribution models showed that both landscape and within-forest disturbances contributed to biodiversity loss, with the greatest negative effects on species of high conservation and functional value. These results demonstrate an urgent need for policy interventions that go beyond the maintenance of forest cover to safeguard the hyper-diversity of tropical forest ecosystems.

Epigenetic Signatures of Cigarette Smoking

Abstract: Background —DNA methylation leaves a long-term signature of smoking exposure and is one potential mechanism by which tobacco exposure predisposes to adverse health outcomes, such as cancers, osteoporosis, lung, and cardiovascular disorders. Methods and Results —To comprehensively determine the association between cigarette smoking and DNA methylation, we conducted a meta-analysis of genome-wide DNA methylation assessed using the Illumina BeadChip 450K array on 15,907 blood derived DNA samples from participants in 16 cohorts (including 2,433 current, 6,518 former, and 6,956 never smokers). Comparing current versus never smokers, 2,623 CpG sites (CpGs), annotated to 1,405 genes, were statistically significantly differentially methylated at Bonferroni threshold of p<1×10-7 (18,760 CpGs at False Discovery Rate (FDR)<0.05). Genes annotated to these CpGs were enriched for associations with several smoking-related traits in genome-wide studies including pulmonary function, cancers, inflammatory diseases and heart disease. Comparing former versus never smokers, 185 of the CpGs that differed between current and never smokers were significant p<1×10-7 (2,623 CpGs at FDR<0.05), indicating a pattern of persistent altered methylation, with attenuation, after smoking cessation. Transcriptomic integration identified effects on gene expression at many differentially methylated CpGs. Conclusions —Cigarette smoking has a broad impact on genome-wide methylation that, at many loci, persists many years after smoking cessation. Many of the differentially methylated genes were novel genes with respect to biologic effects of smoking, and might represent therapeutic targets for prevention or treatment of tobacco-related diseases. Methylation at these sites could also serve as sensitive and stable biomarkers of lifetime exposure to tobacco smoke.

Global change pressures on soils from land use and management.

Abstract: Soils are subject to varying degrees of direct or indirect human disturbance, constituting a major global change driver. Factoring out natural from direct and indirect human influence is not always straightforward, but some human activities have clear impacts. These include land-use change, land management and land degradation (erosion, compaction, sealing and salinization). The intensity of land use also exerts a great impact on soils, and soils are also subject to indirect impacts arising from human activity, such as acid deposition (sulphur and nitrogen) and heavy metal pollution. In this critical review, we report the state-of-the-art understanding of these global change pressures on soils, identify knowledge gaps and research challenges and highlight actions and policies to minimize adverse environmental impacts arising from these global change drivers. Soils are central to considerations of what constitutes sustainable intensification. Therefore, ensuring that vulnerable and high environmental value soils are considered when protecting important habitats and ecosystems, will help to reduce the pressure on land from global change drivers. To ensure that soils are protected as part of wider environmental efforts, a global soil resilience programme should be considered, to monitor, recover or sustain soil fertility and function, and to enhance the ecosystem services provided by soils. Soils cannot, and should not, be considered in isolation of the ecosystems that they underpin and vice versa. The role of soils in supporting ecosystems and natural capital needs greater recognition. The lasting legacy of the International Year of Soils in 2015 should be to put soils at the centre of policy supporting environmental protection and sustainable development.

Environmental and Social Disclosures: Link with Corporate Financial Performance

Abstract: Environmental and social disclosures entail costs, yet increasingly, large listed firms are making higher and better quality disclosures. In this paper we examine the link between a firm's environmental and social disclosures and its profitability and market value. We find that past profitability drives current social disclosures. However, consistent with the existing evidence, we do not find any relation between environmental disclosures and profitability. Further, while prior literature has largely focussed on environmental disclosure, we find that it is the social disclosures that matter to investors. We find that firms that make higher social disclosures have higher market values. Further analysis reveals that this link is driven by higher expected growth rates in the cash flows of such companies. Overall our findings are consistent with the resource based view of the firm and the voluntary disclosure theory, suggesting that firms with greater economic resources make more extensive disclosures which yield net positive economic benefits.

Anti-Inflammatory Effects of Metformin Irrespective of Diabetes Status

Abstract: Rationale:The diabetes mellitus drug metformin is under investigation in cardiovascular disease, but the molecular mechanisms underlying possible benefits are poorly understood. Objective:Here, we have studied anti-inflammatory effects of the drug and their relationship to antihyperglycemic properties. Methods and Results:In primary hepatocytes from healthy animals, metformin and the IKKβ (inhibitor of kappa B kinase) inhibitor BI605906 both inhibited tumor necrosis factor-α–dependent IκB degradation and expression of proinflammatory mediators interleukin-6, interleukin-1β, and CXCL1/2 (C-X-C motif ligand 1/2). Metformin suppressed IKKα/β activation, an effect that could be separated from some metabolic actions, in that BI605906 did not mimic effects of metformin on lipogenic gene expression, glucose production, and AMP-activated protein kinase activation. Equally AMP-activated protein kinase was not required either for mitochondrial suppression of IκB degradation. Consistent with discrete anti-inflammato...

How climate change affects extreme weather events

Abstract: Human-induced climate change has led to an increase in the frequency and intensity of daily temperature extremes and has contributed to a widespread intensification of daily precipitation extremes ( 1 , 2 ). But has it also made specific extreme weather and climate events—such as floods, droughts, and heat waves—more likely? Although it has been said that individual climate events cannot be attributed to anthropogenic climate change ( 3 ), a recent assessment by the National Academies of Science concludes that “this is no longer true as an unqualified blanket statement” ( 4 ). Robust event attribution can support decisions such as how to rebuild after a disaster and how to price insurance by quantifying the current risk of such events.

Health Benefits from Nature Experiences Depend on Dose

Abstract: Nature within cities will have a central role in helping address key global public health challenges associated with urbanization. However, there is almost no guidance on how much or how frequently people need to engage with nature, and what types or characteristics of nature need to be incorporated in cities for the best health outcomes. Here we use a nature dose framework to examine the associations between the duration, frequency and intensity of exposure to nature and health in an urban population. We show that people who made long visits to green spaces had lower rates of depression and high blood pressure, and those who visited more frequently had greater social cohesion. Higher levels of physical activity were linked to both duration and frequency of green space visits. A dose-response analysis for depression and high blood pressure suggest that visits to outdoor green spaces of 30 minutes or more during the course of a week could reduce the population prevalence of these illnesses by up to 7% and 9% respectively. Given that the societal costs of depression alone in Australia are estimated at AUD$12.6 billion per annum, savings to public health budgets across all health outcomes could be immense.

Microplastics Alter the Properties and Sinking Rates of Zooplankton Faecal Pellets

Abstract: Plastic debris is a widespread contaminant, prevalent in aquatic ecosystems across the globe. Zooplankton readily ingest microscopic plastic (microplastic, < 1 mm), which are later egested within their faecal pellets. These pellets are a source of food for marine organisms, and contribute to the oceanic vertical flux of particulate organic matter as part of the biological pump. The effects of microplastics on faecal pellet properties are currently unknown. Here we test the hypotheses that (1) faecal pellets are a vector for transport of microplastics, (2) polystyrene microplastics can alter the properties and sinking rates of zooplankton egests and, (3) faecal pellets can facilitate the transfer of plastics to coprophagous biota. Following exposure to 20.6 μm polystyrene microplastics (1000 microplastics mL–1) and natural prey (∼1650 algae mL–1) the copepod Calanus helgolandicus egested faecal pellets with significantly (P < 0.001) reduced densities, a 2.25-fold reduction in sinking rates, and a higher pr...

Conceptualising cultural ecosystem services: A novel framework for research and critical engagement

Abstract: The construction of culture as a class of ecosystem service presents a significant test of the holistic ambitions of an ecosystems approach to decision making. In this paper we explore the theoretical challenges arising from efforts to understand ecosystems as objects of cultural concern and consider the operational complexities associated with understanding how, and with what consequences, knowledge about cultural ecosystem services are created, communicated and accounted for in real world decision making. We specifically forward and develop a conceptual framework for understanding cultural ecosystem services and related benefits in terms of the environmental spaces and cultural practices that arise from interactions between humans and ecosystems. The types of knowledge, and approaches to knowledge production, presumed by this relational, non-linear and place-based perspective on cultural ecosystem services are discussed and reviewed. The framework not only helps navigate more fully the challenge of operationalising ‘cultural ecosystem services’ but points to a more relational understanding of the ecosystem services framework as a whole. Extending and refining understanding through more ambitious engagements in interdisciplinarity remains important.

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function

Abstract: Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.

A multi-decade record of high-quality fCO2 data in version 3 of the Surface Ocean CO2 Atlas (SOCAT)

Abstract: . The Surface Ocean CO2 Atlas (SOCAT) is a synthesis of quality-controlled fCO2 (fugacity of carbon dioxide) values for the global surface oceans and coastal seas with regular updates. Version 3 of SOCAT has 14.7 million fCO2 values from 3646 data sets covering the years 1957 to 2014. This latest version has an additional 4.6 million fCO2 values relative to version 2 and extends the record from 2011 to 2014. Version 3 also significantly increases the data availability for 2005 to 2013. SOCAT has an average of approximately 1.2 million surface water fCO2 values per year for the years 2006 to 2012. Quality and documentation of the data has improved. A new feature is the data set quality control (QC) flag of E for data from alternative sensors and platforms. The accuracy of surface water fCO2 has been defined for all data set QC flags. Automated range checking has been carried out for all data sets during their upload into SOCAT. The upgrade of the interactive Data Set Viewer (previously known as the Cruise Data Viewer) allows better interrogation of the SOCAT data collection and rapid creation of high-quality figures for scientific presentations. Automated data upload has been launched for version 4 and will enable more frequent SOCAT releases in the future. High-profile scientific applications of SOCAT include quantification of the ocean sink for atmospheric carbon dioxide and its long-term variation, detection of ocean acidification, as well as evaluation of coupled-climate and ocean-only biogeochemical models. Users of SOCAT data products are urged to acknowledge the contribution of data providers, as stated in the SOCAT Fair Data Use Statement. This ESSD (Earth System Science Data) "living data" publication documents the methods and data sets used for the assembly of this new version of the SOCAT data collection and compares these with those used for earlier versions of the data collection (Pfeil et al., 2013; Sabine et al., 2013; Bakker et al., 2014). Individual data set files, included in the synthesis product, can be downloaded here: doi:10.1594/PANGAEA.849770 . The gridded products are available here: doi:10.3334/CDIAC/OTG.SOCAT_V3_GRID .