Exploring massive, genome scale datasets with the GenometriCorr package

We have created a statistically grounded tool for determining the correlation of genomewide data with other datasets or known biological features, intended to guide biological exploration of high-dimensional datasets, rather than providing immediate answers. The software enables several biologically motivated approaches to these data and here we describe the rationale and implementation for each approach. Our models and statistics are implemented in an R package that efficiently calculates the spatial correlation between two sets of genomic intervals (data and/or annotated features), for use as a metric of functional interaction. The software handles any type of pointwise or interval data and instead of running analyses with predefined metrics, it computes the significance and direction of several types of spatial association; this is intended to suggest potentially relevant relationships between the datasets. AVAILABILITY AND IMPLEMENTATION: The package, GenometriCorr, can be freely downloaded at http://genometricorr.sourceforge.net/. Installation guidelines and examples are available from the sourceforge repository. The package is pending submission to Bioconductor.     

Land use impacts on biodiversity from kiwifruit production in New Zealand assessed with global and national datasets

Purpose

Habitat loss is a significant cause of biodiversity loss, but while its importance is widely recognized, there is no generally accepted method on how to include impacts on biodiversity from land use and land use changes in cycle assessment (LCA), and existing methods are suffering from data gaps. This paper proposes a methodology for assessing the impact of land use on biodiversity using ecological structures as opposed to information on number of species.

Methods

Two forms of the model (global and local scales) were used to assess environmental quality, combining ecosystem scarcity, vulnerability, and conditions for maintaining biodiversity. A case study for New Zealand kiwifruit production is presented. As part of the sensitivity analysis, model parameters (area and vulnerability) were altered and New Zealand datasets were also used.

Results and discussion

When the biodiversity assessment was implemented using a global dataset, the importance of productivity values was shown to depend on the area the results were normalized against. While the area parameter played an important role in the results, the proposed alternative vulnerability scale had little influence on the final outcome.

Conclusions

Overall, the paper successfully implements a model to assess biodiversity impacts in LCA using easily accessible, free-of-charge data and software. Comparing the model using global vs. national datasets showed that there is a potential loss of regional significance when using the generalized model with the global dataset. However, as a guide to assessing biodiversity impact, the model allows for consistent comparison of product systems on an international basis.     

基于改进生态足迹三维模型的自然资本利用特征分析-选取11个国家为数据源

自然资本利用评估是可持续发展量化领域的重要课题。生态足迹三维模型首次实现了流量资本与存量资本的分类测度,为更全面、准确地反映人类利用自然资本的状况提供了可行的途径。从探讨模型缺陷入手,通过细致追踪各地类载体上的流量资本与存量资本变化,克服了地类间赤字转移问题,明确了适用于区域尺度和地类尺度的足迹广度、足迹深度和三维足迹等指标的计算方法。运用改进后的模型,分析了1999—2008年全球11个国家自然资本利用的时空变化特征。结果表明:在过去10年自然资本利用的国际格局中,美国、法国和德国(后6年)为流量资本与存量资本双高型;印度(前2年)为双低型;英国、德国(前4年)、意大利、日本、印度(后8年)和中国为流量资本低、存量资本高型;加拿大、巴西和俄罗斯为流量资本高、存量资本低型。研究表明:各国的自然资本利用状况是自然资源禀赋与社会经济发展水平共同作用的结果,发达国家的自然资本利用强度总体仍显著高于发展中国家;流量资本占用与存量资本消耗之间存在负相关性,资源富足型国家的人均区域足迹广度一般较高,区域足迹深度相对较低,资源贫乏型国家则相反。针对研究存在的局限性提出了进一步改进的优先方向。     

Regional material flow accounts for China: Examining China's natural resource use at the provincial and national level

Over the last three decades, China has experienced the most dynamic economic development lifting living standards and resulting in fast‐growing use of natural resources. In the past, the focus has been on national MFA accounts which do not do justice to the second largest economy, home to 19% of the world population and having 30% of global material use. In this research, we calculate material extraction for China at the regional level during 1995–2015 using the most recent available statistical data and applying the most up‐to‐date international calculation methods. In particular, we combine a bottom‐up and top‐down approach for constructing the dataset of China's economically used Domestic Extraction (DEU) in an integrated way. This approach also improves the Chinese national material flow accounts and allows us to present a reliable database of DE of materials for China to date. Our new dataset provides the basis for calculating material footprints and environmental impacts of China's regions. The dataset enables us to evaluate regional resource efficiency trends in China. We find that during the past two decades, China's material use has grown strongly from 11.7 billion tonnes in 1995 to 35.4 billion tonnes in 2015. Material use has accelerated between 2000 and 2010 but slowed down between 2010 and 2015 reflecting the economic contraction caused by the Global Financial Crisis which reduced the global demand for China's manufacturing and a reorientation of China's economic policy settings toward quality of growth. Unsurprisingly, different regions play different roles in the supply chain of materials, achieving different economic performances resulting in very diverse material efficiency outcomes. This information is important to allow for a targeted policy approach to increase resource efficiency, reduce environmental impacts of resource use, and grow wellbeing in China with large positive implications for global sustainability. This study provides the basis for the development of relevant resource management policies for different regions in the future.     

Spatial modelling of nitrous oxide emissions at the national scale using soil, climate and land use information

Nitrous oxide (N₂O) is a powerful greenhouse gas. The UK government is committed to reducing all greenhouse gas emissions and is required to make an inventory of the sources and emissions of these gases. Here, we extend work from a pilot study at the catchment scale reported in an earlier paper. This paper reports on the upscaling measurements of emissions to derive annual emission rates for specific combinations of soil type, land management and fertiliser practices to the national scale. Digital soil, climate and land use maps were combined within Geographic Information Systems (GIS) software. Upscaling of field emissions measurements involves adjusting measured annual N₂O emissions to fit combinations of crop growth cycles, soil wetness and the amount and timing of fertiliser applications. We have also taken account of the differences in emission rates from grazed pasture land due to differences in land management between land utilised for dairy production and land utilised for beef production. Calculated annual emission rates were then spatially scaled to derive national figures through the use of a GIS modelling framework, termed NitOx. The annual emission of N₂O from Scotland was determined as approximately 6 000 000 kg N yr⁻¹ (2.8 Mt carbon dioxide (CO₂) equivalents) and compares favourably with other national scale estimates such as the IPCC (1997) . The combination of animal grazing, high N inputs, climatic warmth and poorly drained soils means that the south west contributes significantly to the national total N₂O emissions. Localised areas of high emission can also be identified, but identification could be improved by applying this modelling approach at a larger scale. It would be beneficial to target these areas with mitigation strategies.     

Resource requirements for ecosystem conservation: A combined industrial and natural ecology approach to quantifying natural capital use in nature

Socioeconomic demand for natural capital is causing catastrophic losses of biodiversity and ecosystem functionality, most notably in regions where socioeconomic‐and eco‐systems compete for natural capital, e.g., energy (animal or plant matter). However, a poor quantitative understanding of what natural capital is needed to support biodiversity in ecosystems, while at the same time satisfy human development needs—those associated with human development within socioeconomic systems—undermines our ability to sustainably manage global stocks of natural capital. Here we describe a novel concept and accompanying methodology (relating the adult body mass of terrestrial species to their requirements for land area, water, and energy) to quantify the natural capital needed to support terrestrial species within ecosystems, analogous to how natural capital use by humans is quantified in a socioeconomic context. We apply this methodology to quantify the amount of natural capital needed to support species observed using a specific surveyed site in Scotland. We find that the site can support a larger assemblage of species than those observed using the site; a primary aim of the rewilding project taking place there. This method conceptualises, for the first time, a comprehensive “dual‐system” approach: modelling natural capital use in socioeconomic‐and eco‐systems simultaneously. It can facilitate the management of natural capital at the global scale, and in both the conservation and creation (e.g., rewilding) of biodiversity within managed ecosystems, representing an advancement in determining what socioeconomic trade‐offs are needed to achieve contemporary conservation targets alongside ongoing human development.     

生态系统服务与自然资本价值评估

生态系统服务是生态系统提供的商品和服务,是人类生态和发展的物质基础和基本条件,是人类拥有的关键自然资本。概述了生态系统服务的内涵及类型,介绍了当前国内外有关生态系统服务及自然资本的价值理论、价值评估的各种方法及其类型;评述了研究的主要进展,存在的主要问题、难点和研究的主要趋向。认为生态系统服务及自然资本的价值评估研究是建立生态－环境－经济综合核算体系（可持续发展核算体系）的重要内容和关键环节,完善价值评估的理论与经济技术方法是生态系统服务价值评估研究亟待解决的问题。     

The isolation of primary hepatocytes from human tissue: optimising the use of small non-encapsulated liver resection surplus

Two-step perfusion is considered the gold standard method for isolating hepatocytes from human liver tissue. As perfusion may require a large tissue specimen, which is encapsulated and has accessible vessels for cannulation, only a limited number of tissue samples may be suitable. Therefore, the aim of this work was to develop an alternative method to isolate hepatocytes from non-encapsulated and small samples of human liver tissue. Healthy tissue from 44 human liver resections were graded for steatosis and tissue weights between 7.8 and 600 g were used for hepatocyte isolations. Tissue was diced and underwent a two-step digestion (EDTA and collagenase). Red cell lysis buffer was used to prevent red blood cell contamination and toxicity. Isolated hepatocyte viability was determined by trypan blue exclusion. Western blot and biochemical analyses were undertaken to ascertain cellular phenotype and function. Liver tissue that weighed ≥50 g yielded significantly higher (P < 0.01) cell viability than tissue <50 g. Viable cells secreted urea and displayed the phenotypic hepatocyte markers albumin and cytochrome P450. Presence of steatosis in liver tissue or intra-hepatocellular triglyceride content had no effect on cell viability. This methodology allows for the isolation of viable primary human hepatocytes from small amounts of “healthy” resected liver tissue which are not suitable for perfusion. This work provides the opportunity to increase the utilisation of resection surplus tissue, and may ultimately lead to an increased number of in vitro cellular studies being undertaken using the gold-standard model of human primary hepatocytes.     

Stocks and flows of natural capital: Implications for Ecological Footprint

Over the past decade, Ecological Footprint has become one of the most popular and widespread indicators for sustainability assessment and resource management. However, its popularity has been coupled, especially in recent years, by the emergence of critical views on the indicator’s rationale, methodology and policy usefulness. Most of these criticisms commonly point to the inability of the Ecological Footprint to track the human-induced depletion of natural capital stocks as one of the main shortcomings of the methodology. Fully addressing this issue will require research efforts and, most likely, further methodological refinements. The aim of this paper is therefore to outline the basis of a new area of investigation in Ecological Footprint research, primarily aimed at implementing the distinction between the use of stocks and the use of flows in Ecological Footprint Accounting and debating its implications.     

Mapping biomedical terminologies using natural language processing tools and UMLS: Mapping the Orphanet thesaurus to the MeSH

BackgroundOrphanet aims to provide rare disease information to healthcare professionals, patients, and their relatives.ObjectiveThe objective of this work is to evaluate two methodologies (Unified Medical Languages Systems [UMLS] and manual Orphanet-ICD-10 link-based mapping & string-based matching) used to map Orphanet thesaurus to the MeSH thesaurus.ResultsOn a corpus of 375 mappings, the string-based matching provides significantly better results than the UMLS and manual Orphanet-ICD-10 link-based mapping.ConclusionString-based matching could be applied to any biomedical terminology in French not yet included into UMLS.     

Exploring the convergence of natural flows for the generation of natural capital stocks in marine ecosystems

Marine ecosystems are open, complex, adaptive, and hierarchical systems highly integrated through the exchange of matter and energy flows. This flows exchange allows marine ecosystems to operate at different scales acting as dissipative structures, building natural capital stocks capable of generating several ecosystem services vital for human well-being. Humans derive a wide range of goods and services from marine ecosystems while, at the same time, generate several impacts causing biodiversity loss and seriously affecting their capacity to provide benefits to humans. Effective management strategies are crucial to conserve healthy and diverse marine and coastal ecosystems, maintain the valuable functions and services they provide, and allow for sustainable human activities. In recent years, Marine Protected Areas (MPAs) have been increasingly acknowledged worldwide as important tools to conserve biodiversity and achieve human well-being and sustainable development goals. Assessing the value of natural capital and ecosystem services is crucial to raise awareness on their importance, support conservation strategies, and ensure the sustainable management of marine ecosystems. This study aimed at calculating biomass and emergy-based indicators to assess the value of natural capital stocks in a Mediterranean MPA. The assessment was performed through a biophysical and trophodynamic environmental accounting model fed with field biomass data collected through ad hoc sampling campaigns performed in the MPA. Four main macro-habitats were investigated: sciaphilic hard bottom (coralligenous bioconstructions), photophilic hard bottom, soft bottom, and Posidonia oceanica seagrass beds. The biomass density of the main autotrophic and heterotrophic taxonomic groups identified in the four macro-habitats of the MPA was evaluated. Based on this biomass matrix, the emergy value of natural capital stocks was assessed. The Posidonia oceanica seagrass beds habitat showed the highest biophysical value (2.32·10¹⁹ sej) at MPA scale, while coralligenous bioconstructions resulted the habitat with the highest biophysical value per unit area (2.72·10¹² sej m⁻²). In addition, to complement the biophysical assessment with an economic perspective, the emergy-based indicators were converted into monetary units. The total value of natural capital of the whole MPA resulted in about 46 M€. The results of this study can support local managers and policy makers in the development of management strategies to ensure nature conservation and sustainable human activities. They can be also used as a benchmark for the assessment of natural capital value at larger scales in support of a proper consideration and inclusion of nature value into processes of policy making.     

Mapping of natural anti-factor VIII antibodies in plasma pools from healthy donors: use of rationally designed synthetic peptides.

Inhibitor antibodies of blood coagulation factor VIII (FVIII) impair FVIII replacement therapy, constituting a serious complication in haemophilic patients. anti-FVIII antibodies may also develop in a variety of disease-associated autoimmunity. Mapping of human FVIII inhibitors in haemophilia A or autoantibody origin have delineated three major clusters of B-cell inhibitory epitopes (domain A2, A3 and C2). Inhibitory and non-inhibitory FVIII antibodies have also been described in plasma of healthy donors and pools of immunoglobulins. The purpose of this study was to use synthetic FVIII-peptides to more closely define regions of the molecule targeted by natural anti-FVIII antibodies. Predictive algorithms were used for defining the positions of potential continuous epitopes. To investigate the presence of peptide-reactive antibodies in normal plasma pools of healthy donors, a plasma fraction (Cohn fraction II+III) containing all IgG subclasses was purified by affinity chromatography on peptide-Sepharose columns. The results of ELISAs and Western blotting experiments (with the selected peptides and well-defined recombinant FVIII thrombin fragments) confirmed the reaction specificities of the affinity-purified human antibodies. For each IgG preparation, the isotopic subclass was also determined. In the clotting assay, several IgG preparations showed neutralising activity in a dose-dependent manner. Our observations support the recent hypothesis that FVIII inhibitors in haemophilia A and autoimmune disease may originate from the proliferation of natural FVIII-specific B-cell clones.     

Mapping of Ebola virus spillover: Suitability and seasonal variability at the landscape scale

The unexpected Ebola virus outbreak in West Africa in 2014 involving the Zaire ebolavirus made clear that other regions outside Central Africa, its previously documented niche, were at risk of future epidemics. The complex transmission cycle and a lack of epidemiological data make mapping areas at risk of the disease challenging. We used a Geographic Information System-based multicriteria evaluation (GIS-MCE), a knowledge-based approach, to identify areas suitable for Ebola virus spillover to humans in regions of Guinea, Congo and Gabon where Ebola viruses already emerged. We identified environmental, climatic and anthropogenic risk factors and potential hosts from a literature review. Geographical data layers, representing risk factors, were combined to produce suitability maps of Ebola virus spillover at the landscape scale. Our maps show high spatial and temporal variability in the suitability for Ebola virus spillover at a fine regional scale. Reported spillover events fell in areas of intermediate to high suitability in our maps, and a sensitivity analysis showed that the maps produced were robust. There are still important gaps in our knowledge about what factors are associated with the risk of Ebola virus spillover. As more information becomes available, maps produced using the GIS-MCE approach can be easily updated to improve surveillance and the prevention of future outbreaks.     

Mapping of sample collection data: GIS tools for the natural product researcher

Scientists engaged in the research of natural products often either conduct field collections themselves or collaborate with partners who do, such as botanists, mycologists, or SCUBA divers. The information gleaned from such collecting trips (e.g. longitude/latitude coordinates, geography, elevation, and a multitude of other field observations) have provided valuable data to the scientific community (e.g., biodiversity), even if it is tangential to the direct aims of the natural products research, which are often focused on drug discovery and/or chemical ecology. Geographic Information Systems (GIS) have been used to display, manage, and analyze geographic data, including collection sites for natural products. However, to the uninitiated, these tools are often beyond the financial and/or computational means of the natural product scientist. With new, free, and easy-to-use geospatial visualization tools, such as Google Earth, mapping and geographic imaging of sampling data are now within the reach of natural products scientists. The goals of the present study were to develop simple tools that are tailored for the natural products setting, thereby presenting a means to map such information, particularly via open source software like Google Earth.     

基于生态资产的生态系统风险分析模型及应用实例

生态学将在生态系统的管理和生命支持系统的可持续发展上发挥核心作用.对生态系统的定量研究是生态系统管理研究的核心和前沿.研究借助于金融资产风险管理方法,结合生态资产价值化和生态系统风险研究建立了基于生态资产的生态系统风险分析方法,给出了对区域(流域)生态系统总体风险进行度量的分析模型和计算公式,并以民勤绿洲生态系统为例进行了实证研究.实证研究结果表明:未来3a内民勤绿洲生态资产价值损失在95%置信水平下不会超过1.92亿元.所建立的生态资产风险分析模型对区域生态系统管理具有一定的意义.     

People and mammals in Mexico: conservation conflicts at a national scale

Contrary to much supposition, recent studies, typically at global and continent-wide scales, have documented a positive relationship between spatial variations in human density and species richness of selected groups of vertebrates. How widely this pattern generalises remains unknown, and particularly how well it extends to analyses at the extent of a country and at reasonably fine spatial resolution, and to regions with well-developed mechanised agricultural infrastructure. Here, we demonstrate that there is a positive relationship between human density and mammal species richness across Mexico, and that this appears to follow from similar patterns between spatial environmental variation (particularly net primary productivity, precipitation and temperature) and both human density and mammal species richness. These results have some potentially important implications for conservation planning in the region, particularly given that optimal complementary sets of areas to represent all mammal species in Mexico tend to lie in areas of disproportionately high human density.     

No specimen left behind: industrial scale digitization of natural history collections

Traditional approaches for digitizing natural history collections, which include both imaging and metadata capture, are both labour- and time-intensive. Mass-digitization can only be completed if the resource-intensive steps, such as specimen selection and databasing of associated information, are minimized. Digitization of larger collections should employ an “industrial” approach, using the principles of automation and crowd sourcing, with minimal initial metadata collection including a mandatory persistent identifier. A new workflow for the mass-digitization of natural history museum collections based on these principles, and using SatScan® tray scanning system, is described.     

Household factors influencing participation in bird feeding activity: a national scale analysis

Ameliorating pressures on the ecological condition of the wider landscape outside of protected areas is a key focus of conservation initiatives in the developed world. In highly urbanized nations, domestic gardens can play a significant role in maintaining biodiversity and facilitating human-wildlife interactions, which benefit personal and societal health and well-being. The extent to which sociodemographic and socioeconomic factors are associated with engagement in wildlife gardening activities remain largely unresolved. Using two household-level survey datasets gathered from across Britain, we determine whether and how the socioeconomic background of a household influences participation in food provision for wild birds, the most popular and widespread form of human-wildlife interaction. A majority of households feed birds (64% across rural and urban areas in England, and 53% within five British study cities). House type, household size and the age of the head of the household were all important predictors of bird feeding, whereas gross annual household income, the occupation of the head of the household, and whether the house is owned or rented were not. In both surveys, the prevalence of bird feeding rose as house type became more detached and as the age of the head of the household increased. A clear, consistent pattern between households of varying size was less evident. When regularity of food provision was examined in the study cities, just 29% of households provided food at least once a week. The proportion of households regularly feeding birds was positively related to the age of the head of the household, but declined with gross annual income. As concerns grow about the lack of engagement between people and the natural environment, such findings are important if conservation organizations are successfully to promote public participation in wildlife gardening specifically and environmentally beneficial behaviour in society more generally.     

Neighborhood linking social capital as a predictor of lung cancer: A Swedish national cohort study

BackgroundThe aim of this nationwide follow-up study was to examine whether neighborhood linking social capital is associated with lung cancer, including incident and mortality cases, after adjustment for individual- and familial-level factors.MethodsThis follow-up study comprised 2,123,707 men and 2,046,174 women aged 25 years or older in Sweden. The follow-up period started on January 1, 2002 and proceeded until first incident of lung cancer, mortality of lung cancer, death from any other cause, emigration or the end of the study period on December 31, 2010. Multilevel logistic regression models (individual-level factors at the first level and neighborhood-level factors at the second level) were used to calculate odds ratios (ORs) with 95% confidence intervals (95% CIs).ResultsWe identified 16,561 lung cancer cases (8422 men and 8139 women) during the follow-up period. Higher ORs of lung cancer, including incident and mortality cases, were observed in individuals who lived in neighborhoods with low social capital (men: OR = 1.37, 95% CI = 1.27–1.47; women: OR = 1.32, 95% CI = 1.23–1.42) than in those living in neighborhoods with high social capital, after adjustment for potential confounding factors.ConclusionThe results of this large national cohort study suggest that neighborhood linking social capital has important independent effects on lung cancer, including incident and mortality cases. These findings indicate that decision-makers must consider the effect of neighborhood-level factors as well as individual- and familial-level factors.