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- Bakker, D. C. E., et al.
(author)
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An update to the surface ocean CO2 atlas (SOCAT version 2)
- 2014
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In: Earth System Science Data. - : Copernicus GmbH. - 1866-3508 .- 1866-3516. ; 6:1, s. 69-90
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Journal article (peer-reviewed)abstract
- The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO 2 values) and extended data coverage (from 1968-2007 to 1968-2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models. © Author(s) 2014. CC Attribution 3.0 License.
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- Brownstein, Catherine A., et al.
(author)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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In: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Journal article (peer-reviewed)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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- Butterworth, J., et al.
(author)
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Les Houches 2013: Physics at TeV Colliders: Standard Model Working Group Report
- 2014
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Conference paper (peer-reviewed)abstract
- This Report summarizes the proceedings of the 2013 Les Houches workshop on Physics at TeV Colliders. Session 1 dealt primarily with (1) the techniques for calculating standard model multi-leg NLO and NNLO QCD and NLO EW cross sections and (2) the comparison of those cross sections with LHC data from Run 1, and projections for future measurements in Run 2.
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- Hervas, A, et al.
(author)
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Efficacy and safety of extended-release guanfacine hydrochloride in children and adolescents with attention-deficit/hyperactivity disorder: A randomized, controlled, Phase III trial
- 2014
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In: European Neuropsychopharmacology. - : Elsevier BV. - 0924-977X. ; 24:12, s. 1861-72
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Journal article (peer-reviewed)abstract
- Abstract: Guanfacine extended-release (GXR), a selective α2A-adrenergic agonist, is a non-stimulant treatment for attention-deficit/hyperactivity disorder (ADHD). This study assessed the efficacy (symptoms and function) and safety of dose-optimized GXR compared with placebo in children and adolescents with ADHD. An atomoxetine (ATX) arm was included to provide reference data against placebo. Patients (6-17 years) were randomized at baseline to dose-optimized GXR (0.05 mg/kg/day- 0.12 mg/kg/day: 6-12 years: 1-4 mg/day; 13-17 years: 1-7 mg/day), ATX (10-100 mg/day) or placebo for 4 or 7 weeks. The primary efficacy measure was change from baseline in ADHD Rating Scale version IV (ADHD-RS-IV). Key secondary measures were Clinical Global Impressions-Improvement (CGI-I) and the Weiss Functional Impairment Rating Scale-Parent Report (WFIRS-P; learning and school, and family domains). Safety assessments included treatment-emergent adverse events (TEAEs), electrocardiograms and vital signs. A total of 272 (80.5%) patients from Europe, the USA and Canada completed the study. Significant differences were observed in least squares mean change from baseline in ADHD-RS-IV total score (placebo-adjusted differences) (GXR: [−8.9, p<0.001]; ATX: [−3.8, p<0.05]), the difference from placebo in the percentage of patients showing improvement (1 ['very much improved'] or 2 ['much improved']) for CGI-I (GXR: [23.7, p<0.001]; ATX: [12.1 p<0.05]), WFIRS-P learning and school domain (GXR: [−0.22, p<0.01]; ATX: [−0.16, p<0.05]) and family domain (GXR: [−0.21, p<0.01]; ATX: [−0.09, p=0.242]). Most common TEAEs for GXR were somnolence, headache and fatigue; 70.1% of GXR subjects reported mild-to-moderate TEAEs. GXR was effective and well tolerated in children and adolescents with ADHD.
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- Huss, Magnus, 1979-, et al.
(author)
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Experimental evidence for emergent facilitation : promoting the existence of an invertebrate predator by killing its prey
- 2011
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In: Journal of Animal Ecology. - : John Wiley & Sons. - 0021-8790 .- 1365-2656. ; 80:3, s. 615-621
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Journal article (peer-reviewed)abstract
- 1. Recent theoretical insights have shown that predator species may help each other to persist by size-selective foraging on a shared prey. By feeding on a certain prey stage, a predator may induce a compensatory response in another stage of the same prey species, thereby favouring other predators; a phenomenon referred to as emergent facilitation. 2. To test whether emergent facilitation may occur in a natural system, we performed an enclosure experiment where we mimicked fish predation by selectively removing large zooplankton and subsequently following the response of the invertebrate predator Bythotrephes longimanus. 3. Positive responses to harvest were observed in the biomass of juvenile individuals of the dominant zooplankton Holopedium gibberum and in Bythotrephes densities. Hence, by removing large prey, we increased the biomass of small prey, i.e. stage-specific biomass overcompensation was present in the juvenile stage of Holopedium. This favoured Bythotrephes, which preferentially feed on small Holopedium. 4. We argue that the stage-specific overcompensation occurred as a result of increased per capita fecundity of adult Holopedium and as a result of competitive release following harvest. If shown to be common, emergent facilitation may be a major mechanism behind observed predator extinctions and patterns of predator invasions.
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- Song, Lingyun, et al.
(author)
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Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
- 2011
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In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 21:10, s. 1757-1767
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Journal article (peer-reviewed)abstract
- The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq (Formaldehyde Assisted Isolation of Regulatory Elements) to map open chromatin.'' Over 870,000 DNaseI or FAIRE sites, which correspond tightly to nucleosome-depleted regions, were identified across the seven cell lines, covering nearly 9% of the genome. The combination of DNaseI and FAIRE is more effective than either assay alone in identifying likely regulatory elements, as judged by coincidence with transcription factor binding locations determined in the same cells. Open chromatin common to all seven cell types tended to be at or near transcription start sites and to be coincident with CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start sites and contained DNA motifs recognized by regulators of cell-type identity. We show that open chromatin regions bound by CTCF are potent insulators. We identified clusters of open regulatory elements (COREs) that were physically near each other and whose appearance was coordinated among one or more cell types. Gene expression and RNA Pol II binding data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity. This publicly available atlas of regulatory elements may prove valuable in identifying noncoding DNA sequence variants that are causally linked to human disease.
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| 23. |
- Zemp, M., et al.
(author)
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Reanalysing glacier mass balance measurement series
- 2013
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In: The Cryosphere. - : Copernicus GmbH. - 1994-0416 .- 1994-0424. ; 7:4, s. 1227-1245
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Journal article (peer-reviewed)abstract
- Glacier-wide mass balance has been measured for more than sixty years and is widely used as an indicator of climate change and to assess the glacier contribution to runoff and sea level rise. Until recently, comprehensive uncertainty assessments have rarely been carried out and mass balance data have often been applied using rough error estimation or without consideration of errors. In this study, we propose a framework for reanalysing glacier mass balance series that includes conceptual and statistical toolsets for assessment of random and systematic errors, as well as for validation and calibration (if necessary) of the glaciological with the geodetic balance results. We demonstrate the usefulness and limitations of the proposed scheme, drawing on an analysis that comprises over 50 recording periods for a dozen glaciers, and we make recommendations to investigators and users of glacier mass balance data. Reanalysing glacier mass balance series needs to become a standard procedure for every monitoring programme to improve data quality, including reliable uncertainty estimates.
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