11. |
- Hudson, Lawrence N., et al.
(author)
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The PREDICTS database : a global database of how local terrestrial biodiversity responds to human impacts
- 2014
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In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:24, s. 4701-4735
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Journal article (peer-reviewed)abstract
- Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
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12. |
- Baumgardner, D., et al.
(author)
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Soot reference materials for instrument calibration and intercomparisons: a workshop summary with recommendations
- 2012
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In: Atmospheric Measurement Techniques. - : Copernicus GmbH. - 1867-1381 .- 1867-8548. ; 5:8, s. 1869-1887
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Journal article (peer-reviewed)abstract
- Soot, which is produced from biomass burning and the incomplete combustion of fossil and biomass fuels, has been linked to regional and global climate change and to negative health problems. Scientists measure the properties of soot using a variety of methods in order to quantify source emissions and understand its atmospheric chemistry, reactivity under emission conditions, interaction with solar radiation, influence on clouds, and health impacts. A major obstacle currently limiting progress is the absence of established standards or reference materials for calibrating the many instruments used to measure the various properties of soot. The current state of availability and practicability of soot standard reference materials (SRMs) was reviewed by a group of 50 international experts during a workshop in June of 2011. The workshop was convened to summarize the current knowledge on soot measurement techniques, identify the measurement uncertainties and limitations related to the lack of soot SRMs, and identify attributes of SRMs that, if developed, would reduce measurement uncertainties. The workshop established that suitable SRMs are available for calibrating some, but not all, measurement methods. The community of users of the single-particle soot-photometer (SP2), an instrument using laser-induced incandescence, identified a suitable SRM, fullerene soot, but users of instruments that measure light absorption by soot collected on filters did not. Similarly, those who use thermal optical analysis (TOA) to analyze the organic and elemental carbon components of soot were not satisfied with current SRMs. The workshop, and subsequent, interactive discussions, produced a number of recommendations for the development of new SRMs, and their implementation, that would be suitable for the different soot measurement methods.
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13. |
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14. |
- Killela, Patrick J., et al.
(author)
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TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal
- 2013
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In: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 110:15, s. 6021-6026
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Journal article (peer-reviewed)abstract
- Malignant cells, like all actively growing cells, must maintain their telomeres, but genetic mechanisms responsible for telomere maintenance in tumors have only recently been discovered. In particular, mutations of the telomere binding proteins alpha thalassemia/mental retardation syndrome X-linked (ATRX) or death-domain associated protein (DAXX) have been shown to underlie a telomere maintenance mechanism not involving telomerase (alternative lengthening of telomeres), and point mutations in the promoter of the telomerase reverse transcriptase (TERT) gene increase telomerase expression and have been shown to occur in melanomas and a small number of other tumors. To further define the tumor types in which this latter mechanism plays a role, we surveyed 1,230 tumors of 60 different types. We found that tumors could be divided into types with low (<15%) and high (>= 15%) frequencies of TERT promoter mutations. The nine TERT-high tumor types almost always originated in tissues with relatively low rates of self renewal, including melanomas, liposarcomas, hepatocellular carcinomas, urothelial carcinomas, squamous cell carcinomas of the tongue, medulloblastomas, and subtypes of gliomas (including 83% of primary glioblastoma, the most common brain tumor type). TERT and ATRX mutations were mutually exclusive, suggesting that these two genetic mechanisms confer equivalent selective growth advantages. In addition to their implications for understanding the relationship between telomeres and tumorigenesis, TERT mutations provide a biomarker that may be useful for the early detection of urinary tract and liver tumors and aid in the classification and prognostication of brain tumors.
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15. |
- Knote, C., et al.
(author)
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Towards an online-coupled chemistry-climate model: evaluation of trace gases and aerosols in COSMO-ART
- 2011
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In: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 4:4, s. 1077-1102
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Journal article (peer-reviewed)abstract
- The online-coupled, regional chemistry transport model COSMO-ART is evaluated for periods in all seasons against several measurement datasets to assess its ability to represent gaseous pollutants and ambient aerosol characteristics over the European domain. Measurements used in the comparison include long-term station observations, satellite and ground-based remote sensing products, and complex datasets of aerosol chemical composition and number size distribution from recent field campaigns. This is the first time these comprehensive measurements of aerosol characteristics in Europe are used to evaluate a regional chemistry transport model. We show a detailed analysis of the simulated size-resolved chemical composition under different meteorological conditions. Mean, variability and spatial distribution of the concentrations of O-3 and NOx are well reproduced. SO2 is found to be overestimated, simulated PM2.5 and PM10 levels are on average underestimated, as is AOD. We find indications of an overestimation of shipping emissions. Time evolution of aerosol chemical composition is captured, although some biases are found in relative composition. Nitrate aerosol components are on average overestimated, and sulfates underestimated. The accuracy of simulated organics depends strongly on season and location. While strongly underestimated during summer, organic mass is comparable in spring and autumn. We see indications for an overestimated fractional contribution of primary organic matter in urban areas and an underestimation of SOA at many locations. Aerosol number concentrations compare well with measurements for larger size ranges, but overestimations of particle number concentration with factors of 2-5 are found for particles smaller than 50 nm. Size distribution characteristics are often close to measurements, but show discrepancies at polluted sites. Suggestions for further improvement of the modeling system consist of the inclusion of a revised secondary organic aerosols scheme, aqueous-phase chemistry and improved aerosol boundary conditions. Our work sets the basis for subsequent studies of aerosol characteristics and climate impacts with COSMO-ART, and highlights areas where improvements are necessary for current regional modeling systems in general.
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16. |
- Michalczuk, Jerzy, et al.
(author)
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Tests of multiple molecular markers for the identification of Great Spotted and Syrian Woodpeckers and their hybrids
- 2014
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In: Journal of Ornithology. - : Springer Science and Business Media LLC. - 2193-7206 .- 2193-7192. ; 155:3, s. 591-600
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Journal article (peer-reviewed)abstract
- Great Spotted and Syrian Woodpeckers (Dendrocopos major and D. syriacus) are known to hybridize in nature; however, the extent of this phenomenon is not known due to difficulties in hybrid detection based on plumage analyses. Here, we tested five markers (one mitochondrial and four nuclear) and a set of six microsatellite loci for the identification of these two Woodpeckers and their hybrids. Sequencing of DNA from 26 individuals of both Woodpeckers from different parts of their ranges: one allopatric (D. major; Norway) and two sympatric (Poland and Bulgaria) showed that both species can be clearly separated based on all sequence markers. The highest number of fixed nucleotide sites were found in the mtDNA control region and intron 5 of the transforming growth factor. Analyses of microsatellite data distinguished the two species, but all loci showed a large number of common alleles and their utility in identifying hybrids is therefore doubtful. According to the DNA sequence analyses, 2 out of 18 specimens within the sympatric range in Poland were identified as possible hybrids, most probably paternal backcrosses. Moreover, both hybrids are from synantropic populations (settled in cities), whereas none of the D. major sampled in forests and in its allopatric range (Norway) showed signs of an intermixed genotype. Further research on hybridization and introgression in woodpeckers is undoubtedly needed and could be useful for understanding ecological and ethological interactions among these species, particularly for D. syriacus, which is relatively rare in Europe.
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17. |
- Anton, Christian, et al.
(author)
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Research needs for incorporating the ecosystem service approach into EU biodiversity conservation policy
- 2010
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In: Biodiversity and Conservation. - : Springer Science and Business Media LLC. - 0960-3115 .- 1572-9710. ; 19:10, s. 2979-2994
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Journal article (peer-reviewed)abstract
- Using a range of different methods including extensive reviews, workshops and an electronic conference, 70 key research recommendations and 12 priority research needs to integrate the ecosystem services approach into biodiversity conservation policy and funding were identified by a cross-disciplinary group of over 100 scientists and 50 stakeholders, including research funders and policy-makers. These recommendations focus on the ecological underpinning of ecosystem services, drivers that affect ecosystems and their services, biological traits and ecosystem services, the valuation of ecosystem services, spatial and temporal scales in ecosystem service assessment, indicators of ecosystem services, and habitat management, conservation policy and ecosystem services. The recommendations in this paper help steer the research agenda on ecosystem services into policy-relevant areas, agreed upon by funders, researchers and policy-makers. This research agenda will only succeed with increased collaboration between researchers across disciplines, thereby providing a challenge to the research community and research funders to work in new, interdisciplinary ways.
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18. |
- Bolton, Kelly L., et al.
(author)
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Association Between BRCA1 and BRCA2 Mutations and Survival in Women With Invasive Epithelial Ovarian Cancer
- 2012
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In: JAMA: The Journal of the American Medical Association. - : American Medical Association (AMA). - 1538-3598. ; 307:4, s. 382-390
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Journal article (peer-reviewed)abstract
- Context Approximately 10% of women with invasive epithelial ovarian cancer (EOC) carry deleterious germline mutations in BRCA1 or BRCA2. A recent article suggested that BRCA2-related EOC was associated with an improved prognosis, but the effect of BRCA1 remains unclear. Objective To characterize the survival of BRCA carriers with EOC compared with noncarriers and to determine whether BRCA1 and BRCA2 carriers show similar survival patterns. Design, Setting, and Participants A pooled analysis of 26 observational studies on the survival of women with ovarian cancer, which included data from 1213 EOC cases with pathogenic germline mutations in BRCA1 (n=909) or BRCA2 (n=304) and from 2666 noncarriers recruited and followed up at variable times between 1987 and 2010 (the median year of diagnosis was 1998). Main Outcome Measure Five-year overall mortality. Results The 5-year overall survival was 36% (95% CI, 34%-38%) for noncarriers, 44% (95% CI, 40%-48%) for BRCA1 carriers, and 52% (95% CI, 46%-58%) for BRCA2 carriers. After adjusting for study and year of diagnosis, BRCA1 and BRCA2 mutation carriers showed a more favorable survival than noncarriers (for BRCA1: hazard ratio [HR], 0.78; 95% CI, 0.68-0.89; P<.001; and for BRCA2: HR, 0.61; 95% CI, 0.50-0.76; P<.001). These survival differences remained after additional adjustment for stage, grade, histology, and age at diagnosis (for BRCA1: HR, 0.73; 95% CI, 0.64-0.84; P<.001; and for BRCA2: HR, 0.49; 95% CI, 0.39-0.61; P<.001). The BRCA1 HR estimate was significantly different from the HR estimated in the adjusted model (P for heterogeneity=.003). Conclusion Among patients with invasive EOC, having a germline mutation in BRCA1 or BRCA2 was associated with improved 5-year overall survival. BRCA2 carriers had the best prognosis. JAMA. 2012;307(4):382-390
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19. |
- Engelen, Lian, et al.
(author)
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Improved glycemic control induced by both metformin and repaglinide is associated with a reduction in blood levels of 3-deoxyglucosone in nonobese patients with type 2 diabetes
- 2011
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In: European Journal of Endocrinology. - 1479-683X. ; 164:3, s. 371-379
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Journal article (peer-reviewed)abstract
- Objective: Metformin has been reported to reduce alpha-dicarbonyls, which are known to contribute to diabetic complications. It is unclear whether this is due to direct quenching of alpha-dicarbonyls or to an improvement in glycemic control. We therefore compared the effects of metformin versus repaglinide, an antihyperglycemic agent with an insulin-secreting mechanism, on the levels of the alpha-dicarbonyl 3-deoxyglucosone (3DG). Methods: We conducted a single-center, double-masked, double-dummy, crossover study involving 96 nonobese patients with type 2 diabetes. After a 1-month run-in on diet-only treatment, patients were randomized to either repaglinide (6 mg daily) followed by metformin (2 g daily) or vice versa each during 4 months with a 1-month washout between interventions. Results: 3DG levels decreased after both metformin (-19.3% (95% confidence interval (CI): -23.5, -14.8)) and repaglinide (-20.8% (95% CI: -24.9, -16.3)) treatments, but no difference was found between treatments (1.8% (95% CI: -3.8, 7.8)). Regardless of the treatment, changes in glycemic variables were associated with changes in 3DG. Specifically, 3DG decreased by 22.7% (95% CI: 19.0, 26.5) per S. D. decrease in fasting plasma glucose (PG), by 20.0% (95% CI: 16.2, 23.9) per S. D. decrease in seven-point mean plasma glucose, by 22.5% (95% CI: 18.6, 26.6) per S. D. decrease in area under the curve for PG, by 17.2% (95% CI: 13.8, 20.6) per S. D. decrease in HbAlc, and by 10.9% (95% CI: 6.4, 15.5) per S. D. decrease in Amadori albumin. In addition, decreases in 3DG were associated with decreases in advanced glycation endproducts and endothelial markers. Conclusion: Improved glycemic control induced by both metformin and repaglinide is associated with a reduction in 3DG levels in nonobese individuals with type 2 diabetes. This may constitute a shared metabolic pathway through which both treatments have a beneficial impact on the cardiovascular risk.
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20. |
- Fountoukis, C., et al.
(author)
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Organic aerosol concentration and composition over Europe: insights from comparison of regional model predictions with aerosol mass spectrometer factor analysis
- 2014
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In: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7324. ; 14:17, s. 9061-9076
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Journal article (peer-reviewed)abstract
- A detailed three-dimensional regional chemical transport model (Particulate Matter Comprehensive Air Quality Model with Extensions, PMCAMx) was applied over Europe, focusing on the formation and chemical transformation of organic matter. Three periods representative of different seasons were simulated, corresponding to intensive field campaigns. An extensive set of AMS measurements was used to evaluate the model and, using factor-analysis results, gain more insight into the sources and transformations of organic aerosol (OA). Overall, the agreement be-tween predictions and measurements for OA concentration is encouraging, with the model reproducing two-thirds of the data (daily average mass concentrations) within a factor of 2. Oxygenated OA (OOA) is predicted to contribute 93% to total OA during May, 87% during winter and 96% during autumn, with the rest consisting of fresh primary OA (POA). Predicted OOA concentrations compare well with the observed OOA values for all periods, with an average fractional error of 0.53 and a bias equal to -0.07 (mean error = 0.9 mu g m(-3), mean bias =-0.2 mu g m(-3)). The model systematically underpredicts fresh POA at most sites during late spring and autumn (mean bias up to -0.8 mu g m(-3)). Based on results from a source apportionment algorithm running in parallel with PMCAMx, most of the POA originates from biomass burning (fires and residential wood combustion), and therefore biomass burning OA is most likely underestimated in the emission inventory. The sensitivity of POA predictions to the corresponding emissions' volatility distribution is discussed. The model performs well at all sites when the Positive Matrix Factorization (PMF)-estimated low-volatility OOA is compared against the OA with saturation concentrations of the OA surrogate species C* <= 0.1 mu g m(-3) and semivolatile OOA against the OA with C* > 0.1 mu g m(-3).
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