| 1. |
- Byrne, Myles, et al.
(författare)
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VarioML framework for comprehensive variation data representation and exchange
- 2012
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 13:254
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Tidskriftsartikel (refereegranskat)abstract
- Background: Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. Results: The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e. g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. Conclusions: VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.
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| 2. |
- Cornell, Sarah E.
(författare)
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Assessment and Characterisation of the Organic Component of Atmospheric Nitrogen Deposition
- 2014
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Ingår i: Nitrogen Deposition, Critical Loads and Biodiversity. - Dordrecht : Springer Science+Business Media B.V.. - 9789400779389 - 9789400779396 ; , s. 107-116
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The organic component of atmospheric reactive nitrogen is known to be important for biogeochemical cycles, climate and ecosystems, but it is still not routinely assessed in atmospheric deposition studies, and most worldwide air quality monitoring networks disregard it. The available jigsaw puzzle pieces of knowledge from diverse sources can now give a richer picture of global patterns of organic nitrogen deposition. This effort at data synthesis highlights the need for more data, but also suggests where those data gathering efforts should be focused. The development of new analytical techniques allows long-standing conjectures about the nature and sources of the organic matter to be investigated, with tantalising indications of the complex interplay between natural and anthropogenic sources, and links between the nitrogen and carbon cycles. Atmospheric emission and deposition models are needed, along with new chemical process models, to let us explore questions about the role and dynamics of organic nitrogen.
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| 3. |
- Dearing, John A., et al.
(författare)
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Safe and just operating spaces for regional social-ecological systems
- 2014
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Ingår i: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 28, s. 227-238
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Tidskriftsartikel (refereegranskat)abstract
- Humanity faces a major global challenge in achieving wellbeing for all, while simultaneously ensuring that the biophysical processes and ecosystem services that underpin wellbeing are exploited within scientifically informed boundaries of sustainability. We propose a framework for defining the safe and just operating space for humanity that integrates social wellbeing into the original planetary boundaries concept (Rockstrom et al., 2009a,b) for application at regional scales. We argue that such a framework can: (1) increase the policy impact of the boundaries concept as most governance takes place at the regional rather than planetary scale; (2) contribute to the understanding and dissemination of complexity thinking throughout governance and policy-making; (3) act as a powerful metaphor and communication tool for regional equity and sustainability. We demonstrate the approach in two rural Chinese localities where we define the safe and just operating space that lies between an environmental ceiling and a social foundation from analysis of time series drawn from monitored and palaeoecological data, and from social survey statistics respectively. Agricultural intensification has led to poverty reduction, though not eradicated it, but at the expense of environmental degradation. Currently, the environmental ceiling is exceeded for degraded water quality at both localities even though the least well-met social standards are for available piped water and sanitation. The conjunction of these social needs and environmental constraints around the issue of water access and quality illustrates the broader value of the safe and just operating space approach for sustainable development.
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| 4. |
- Jickells, T., et al.
(författare)
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The cycling of organic nitrogen through the atmosphere
- 2013
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Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 368:1621
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Forskningsöversikt (refereegranskat)abstract
- Atmospheric organic nitrogen (ON) appears to be a ubiquitous but poorly understood component of the atmospheric nitrogen deposition flux. Here, we focus on the ON components that dominate deposition and do not consider reactive atmospheric gases containing ON such as peroxyacyl nitrates that are important in atmospheric nitrogen transport, but are probably not particularly important in deposition. We first review the approaches to the analysis and characterization of atmospheric ON. We then briefly summarize the available data on the concentrations of ON in both aerosols and rainwater from around the world, and the limited information available on its chemical characterization. This evidence clearly shows that atmospheric aerosol and rainwater ON is a complex mixture of material from multiple sources. This synthesis of available information is then used to try and identify some of the important sources of this material, in particular, if it is of predominantly natural or anthropogenic origin. Finally, we suggest that the flux of ON is about 25 per cent of the total nitrogen deposition flux.
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| 5. |
- Mace, Georgina M., et al.
(författare)
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Approaches to defining a planetary boundary for biodiversity
- 2014
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Ingår i: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 28, s. 289-297
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Tidskriftsartikel (refereegranskat)abstract
- The idea that there is an identifiable set of boundaries, beyond which anthropogenic change will put the Earth system outside a safe operating space for humanity, is attracting interest in the scientific community and gaining support in the environmental policy world. Rockstrom et al. (2009) identify nine such boundaries and highlight biodiversity loss as being the single boundary where current rates of extinction put the Earth system furthest outside the safe operating space. Here we review the evidence to support a boundary based on extinction rates and identify weaknesses with this metric and its bearing on humanity's needs. While changes to biodiversity are of undisputed importance, we show that both extinction rate and species richness are weak metrics for this purpose, and they do not scale well from local to regional or global levels. We develop alternative approaches to determine biodiversity loss boundaries and extend our analysis to consider large-scale responses in the Earth system that could affect its suitability for complex human societies which in turn are mediated by the biosphere. We suggest three facets of biodiversity on which a boundary could be based: the genetic library of life; functional type diversity; and biome condition and extent. For each of these we explore the science needed to indicate how it might be measured and how changes would affect human societies. In addition to these three facets, we show how biodiversity's role in supporting a safe operating space for humanity may lie primarily in its interactions with other boundaries, suggesting an immediate area of focus for scientists and policymakers.
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| 6. |
- Sjöqvist, Axel S.L. 1990, et al.
(författare)
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Geochronology of the Norra Kärr alkaline complex, southern Sweden
- 2014
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Ingår i: 31st Nordic Geological Winter Meeting.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The Norra Kärr alkaline complex is a small intrusion of agpaitic nepheline syenite, located approximately 10 km north of Grän- na, southern Sweden, that is being explored for REE and Zr. Agpaitic nepheline syenites per definition do not contain simple Zr minerals like zircon and baddeleyite, despite generally high Zr contents (up to 1–2 wt.% ZrO2). Instead, Zr is mainly hosted in rock-forming complex Na-Ca-Zr silicate minerals such as members of the catapleiite, eudialyte, rosenbuschite, and wöhlerite groups. U-Pb zircon geochronology is thus highly impeded by the agpaitic nature. We established a new, reliable igneous age for the Norra Kärr alkaline complex at 1489±8 Ma (MSWD = 0.95) by dating zircons (U-Pb) in the country rocks that were affected by the magmatism-related alkaline alteration (fenitisation) by LA-MC-ICP-MS. Zircons from a satellite body of non-agpaitic syenite gave intercept ages within error of the age of fenitisation. This is an improvement upon an imprecise whole-rock Rb-Sr age of 1545±61 Ma (Blaxland 1977; Welin 1980). The non-fenitised country granite itself is dated at 1781±8 Ma (MSWD = 0.59), and thus belongs to the TIB1 (1.81–1.76 Ga) episode of the Transscandinavian Igneous Belt (TIB). Rare zircon xenocrysts extracted from the nepheline syenite show ages corresponding to 1.5 Ga lower crustal intrusives (rapakivi?), TIB, Svecofennian, and one Archaean zircon, which suggests the possibility for a remnant of Archaean basement below the TIB. There has historically been a vivid discussion about wheth- er or not Norra Kärr has been deformed and metamorphosed. New Ar-Ar step heating ages on sodic amphibole from Norra Kärr and muscovite and biotite from the country rocks give plateau ages at 1.1 Ga and 0.94 Ga, which correspond to ages derived for Sveconorwegian shear zones in the area. Together with textural and crystal chemical evidence, these ages make a compelling argument for some form of Sveconorwegian overprint of the Norra Kärr alkaline complex.
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