| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 5. |
- Campbell, PJ, et al.
(författare)
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Pan-cancer analysis of whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Tidskriftsartikel (refereegranskat)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 scale1–3. 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 genomes8,10–18.
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| 6. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
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Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 7. |
- van Bragt, JJMH, et al.
(författare)
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Characteristics and treatment regimens across ERS SHARP severe asthma registries
- 2020
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Ingår i: The European respiratory journal. - : European Respiratory Society (ERS). - 1399-3003 .- 0903-1936. ; 55:1
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Tidskriftsartikel (refereegranskat)abstract
- Little is known about the characteristics and treatments of patients with severe asthma across Europe, but both are likely to vary. This is the first study in the European Respiratory Society Severe Heterogeneous Asthma Research collaboration, Patient-centred (SHARP) Clinical Research Collaboration and it is designed to explore these variations. Therefore, we aimed to compare characteristics of patients in European severe asthma registries and treatments before starting biologicals.This was a cross-sectional retrospective analysis of aggregated data from 11 national severe asthma registries that joined SHARP with established patient databases.Analysis of data from 3236 patients showed many differences in characteristics and lifestyle factors. Current smokers ranged from 0% (Poland and Sweden) to 9.5% (Belgium), mean body mass index ranged from 26.2 (Italy) to 30.6 kg·m−2 (the UK) and the largest difference in mean pre-bronchodilator forced expiratory volume in 1 s % predicted was 20.9% (the Netherlands versus Hungary). Before starting biologicals patients were treated differently between countries: mean inhaled corticosteroid dose ranged from 700 to 1335 µg·day−1 between those from Slovenia versus Poland when starting anti-interleukin (IL)-5 antibody and from 772 to 1344 µg·day−1 in those starting anti-IgE (Slovenia versus Spain). Maintenance oral corticosteroid use ranged from 21.0% (Belgium) to 63.0% (Sweden) and from 9.1% (Denmark) to 56.1% (the UK) in patients starting anti-IL-5 and anti-IgE, respectively.The severe asthmatic population in Europe is heterogeneous and differs in both clinical characteristics and treatment, often appearing not to comply with the current European Respiratory Society/American Thoracic Society guidelines definition of severe asthma. Treatment regimens before starting biologicals were different from inclusion criteria in clinical trials and varied between countries.
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| 8. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 9. |
- Wade, G. A., et al.
(författare)
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The MiMeS survey of magnetism in massive stars : introduction and overview
- 2016
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 456:1, s. 2-22
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The MiMeS (Magnetism in Massive Stars) project is a large-scale, high-resolution, sensitive spectropolarimetric investigation of the magnetic properties of O- and early B-type stars. Initiated in 2008 and completed in 2013, the project was supported by three Large Program allocations, as well as various programmes initiated by independent principal investigators, and archival resources. Ultimately, over 4800 circularly polarized spectra of 560 O and B stars were collected with the instruments ESPaDOnS (Echelle SpectroPolarimetric Device for the Observation of Stars) at the Canada-France-Hawaii Telescope, Narval at the Telescope Bernard Lyot and HARPSpol at the European Southern Observatory La Silla 3.6 m telescope, making MiMeS by far the largest systematic investigation of massive star magnetism ever undertaken. In this paper, the first in a series reporting the general results of the survey, we introduce the scientific motivation and goals, describe the sample of targets, review the instrumentation and observational techniques used, explain the exposure time calculation designed to provide sensitivity to surface dipole fields above approximately 100 G, discuss the polarimetric performance, stability and uncertainty of the instrumentation, and summarize the previous and forthcoming publications.
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| 10. |
- Grunhut, H, et al.
(författare)
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Discovery of a magnetic field in the O9 sub-giant star HD 57682 by the MiMeS Collaboration
- 2009
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966 .- 1745-3925 .- 1745-3933. ; 400:1, s. L94-L98
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Tidskriftsartikel (refereegranskat)abstract
- We report the detection of a strong, organized magnetic field in the O9IV star HD 57682, using spectropolarimetric observations obtained with ESPaDOnS at the 3.6-m Canada-France-Hawaii Telescope within the context of the Magnetism in Massive Stars (MiMeS) Large Programme. From the fitting of our spectra using non-local thermodynamic equilibrium model atmospheres, we determined that HD 57682 is a 17(-9)(+19)M(circle dot) star with a radius of 7.0(-1.8)(+2.4)R(circle dot) and a relatively low mass-loss rate of 1.4(-0.95)(+3.1) x 10(-9) M-circle dot yr(-1). The photospheric absorption lines are narrow, and we use the Fourier transform technique to infer v sin i = 15 +/- 3 km s(-1). This v sin i implies a maximum rotational period of 31.5 d, a value qualitatively consistent with the observed variability of the optical absorption and emission lines, as well as the Stokes V profiles and longitudinal field. Using a Bayesian analysis of the velocity-resolved Stokes V profiles to infer the magnetic field characteristics, we tentatively derive a dipole field strength of 1680(-356)(+134)G. The derived field strength and wind characteristics imply a wind that is strongly confined by the magnetic field.
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| 11. |
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| 12. |
- Pahl-Wostl, Claudia, et al.
(författare)
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Environmental flows and water governance : managing sustainable water uses
- 2013
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Ingår i: Current Opinion in Environmental Sustainability. - : Elsevier BV. - 1877-3435 .- 1877-3443. ; 5:3-4, s. 341-351
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Forskningsöversikt (refereegranskat)abstract
- Human water security is often achieved with little consideration of environmental consequences and, even when these are acknowledged, the trade-offs between human and environmental water needs are increasing in frequency and amplitude on the increase. The environmental flows concept has continued to evolve in response to these challenges. However, the field is characterized by a limited transferability of insights, due to the prevalence of specific case-study analyses and a lack of research on the governance of environmental flows. Building on recent advances in environmental flow science, water governance and management, we identify a clear need for a more systematic approach to the determination of environmental flow requirements (EFRs) on both the natural and social science fronts and, in particular, on the interaction between social/political and environmental systems. We suggest a framework that details as to how these advances and interactions can be achieved. The framework supports scientific analysis and practical implementation of EFRs involving systematic compilation, sharing and evaluation of experiences from different riverine ecosystems and governance systems around the globe. The concept of ecosystem services is introduced into the framework to raise awareness for the importance of ecosystem functions for the resilience of social-ecological systems, to support negotiation of trade-offs and development of strategies for adaptive implementation. Experience in implementation of environmental flow policies reveals the need for an engaged, transdisciplinary research approach where research is closely linked to implementation initiatives on the ground. We advocate that this is more effective at building the foundations for sustainable water management.
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| 13. |
- Soerensen, Anne L., et al.
(författare)
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A mass budget for mercury and methylmercury in the Arctic Ocean
- 2016
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Ingår i: Global Biogeochemical Cycles. - 0886-6236 .- 1944-9224. ; 30:4, s. 560-575
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Tidskriftsartikel (refereegranskat)abstract
- Elevated biological concentrations of methylmercury (MeHg), a bioaccumulative neurotoxin, are observed throughout the Arctic Ocean, but major sources and degradation pathways in seawater are not well understood. We develop a mass budget for mercury species in the Arctic Ocean based on available data since 2004 and discuss implications and uncertainties. Our calculations show that high total mercury (Hg) in Arctic seawater relative to other basins reflect large freshwater inputs and sea ice cover that inhibits losses through evasion. We find that most net MeHg production (20Mga(-1)) occurs in the subsurface ocean (20-200m). There it is converted to dimethylmercury (Me2Hg: 17Mga(-1)), which diffuses to the polar mixed layer and evades to the atmosphere (14Mga(-1)). Me2Hg has a short atmospheric lifetime and rapidly degrades back to MeHg. We postulate that most evaded Me2Hg is redeposited as MeHg and that atmospheric deposition is the largest net MeHg source (8Mga(-1)) to the biologically productive surface ocean. MeHg concentrations in Arctic Ocean seawater are elevated compared to lower latitudes. Riverine MeHg inputs account for approximately 15% of inputs to the surface ocean (2.5Mga(-1)) but greater importance in the future is likely given increasing freshwater discharges and permafrost melt. This may offset potential declines driven by increasing evasion from ice-free surface waters. Geochemical model simulations illustrate that for the most biologically relevant regions of the ocean, regulatory actions that decrease Hg inputs have the capacity to rapidly affect aquatic Hg concentrations.
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