| 1. |
- Jackson, N., et al.
(författare)
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LBCS: The LOFAR Long-Baseline Calibrator Survey
- 2016
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 595, s. Art no A86-
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Tidskriftsartikel (refereegranskat)abstract
- We outline the LOFAR Long-Baseline Calibrator Survey (LBCS), whose aim is to identify sources suitable for calibrating the highest-resolution observations made with the International LOFAR Telescope, which include baselines > 1000 km. Suitable sources must contain significant correlated flux density (greater than or similar to 50 - 100 mJy) at frequencies around 110-190 MHz on scales of a few hundred milliarcseconds. At least for the 200-300-km international baselines, we find around 1 suitable calibrator source per square degree over a large part of the northern sky, in agreement with previous work. This should allow a randomly selected target to be successfully phase calibrated on the international baselines in over 50% of cases. Products of the survey include calibrator source lists and fringe-rate and delay maps of wide areas-typically a few degrees-around each source. The density of sources with significant correlated flux declines noticeably with baseline length over the range 200-600 km, with good calibrators on the longest baselines appearing only at the rate of 0.5 per sq. deg. Coherence times decrease from 1-3 min on 200-km baselines to about 1 min on 600-km baselines, suggesting that ionospheric phase variations contain components with scales of a few hundred kilometres. The longest median coherence time, at just over 3 min, is seen on the DE609 baseline, which at 227 km is close to being the shortest. We see median coherence times of between 80 and 110 s on the four longest baselines (580-600 km), and about 2 min for the other baselines. The success of phase transfer from calibrator to target is shown to be influenced by distance, in a manner that suggests a coherence patch at 150-MHz of the order of 1 deg. Although source structures cannot be measured in these observations, we deduce that phase transfer is affected if the calibrator source structure is not known. We give suggestions for calibration strategies and choice of calibrator sources, and describe the access to the online catalogue and data products.
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| 2. |
- van Cappellen, W., et al.
(författare)
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Apertif: Phased array feeds for the Westerbork Synthesis Radio Telescope: System overview and performance characteristics
- 2022
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 658
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Tidskriftsartikel (refereegranskat)abstract
- We describe the APERture Tile In Focus (Apertif) system, a phased array feed (PAF) upgrade of the Westerbork Synthesis Radio Telescope that transforms this telescope into a high-sensitivity, wide-field-of-view L-band imaging and transient survey instrument. Using novel PAF technology, up to 40 partially overlapping beams are formed on the sky simultaneously, significantly increasing the survey speed of the telescope. With this upgraded instrument, an imaging survey covering an area of 2300 deg2 is being performed that will deliver both continuum and spectral line datasets, of which the first data have been publicly released. In addition, a time domain transient and pulsar survey covering 15 000 deg2 is in progress. An overview of the Apertif science drivers, hardware, and software of the upgraded telescope is presented, along with its key performance characteristics.
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| 3. |
- Andersen, M. R., et al.
(författare)
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Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88
- 2011
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 21:6, s. 885-897
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Tidskriftsartikel (refereegranskat)abstract
- The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook wholegenome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi
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| 4. |
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| 5. |
- Schaap, M., et al.
(författare)
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Performance of European chemistry transport models as function of horizontal resolution
- 2015
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Ingår i: Atmospheric Environment. - : Elsevier BV. - 1873-2844 .- 1352-2310. ; 112, s. 90-105
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Tidskriftsartikel (refereegranskat)abstract
- Air pollution causes adverse effects on human health as well as ecosystems and crop yield and also has an impact on climate change trough short-lived climate forcers. To design mitigation strategies for air pollution, 3D Chemistry Transport Models (CTMs) have been developed to support the decision process. Increases in model resolution may provide more accurate and detailed information, but will cubically increase computational costs and pose additional challenges concerning high resolution input data. The motivation for the present study was therefore to explore the impact of using finer horizontal grid resolution for policy support applications of the European Monitoring and Evaluation Programme (EMEP) model within the Long Range Transboundary Air Pollution (LRTAP) convention. The goal was to determine the "optimum resolution" at which additional computational efforts do not provide increased model performance using presently available input data. Five regional CTMs performed four runs for 2009 over Europe at different horizontal resolutions. The models' responses to an increase in resolution are broadly consistent for all models. The largest response was found for NO2 followed by PM10 and O-3. Model resolution does not impact model performance for rural background conditions. However, increasing model resolution improves the model performance at stations in and near large conglomerations. The statistical evaluation showed that the increased resolution better reproduces the spatial gradients in pollution regimes, but does not help to improve significantly the model performance for reproducing observed temporal variability. This study clearly shows that increasing model resolution is advantageous, and that leaving a resolution of 50 km in favour of a resolution between 10 and 20 km is practical and worthwhile. As about 70% of the model response to grid resolution is determined by the difference in the spatial emission distribution, improved emission allocation procedures at high spatial and temporal resolution are a crucial factor for further model resolution improvements. (C) 2015 Elsevier Ltd. All rights reserved.
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| 6. |
- Ciarelli, Giancarlo, et al.
(författare)
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Trends of inorganic and organic aerosols and precursor gases in Europe: Insights from the EURODELTA multi-model experiment over the 1990-2010 period
- 2019
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Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 12:12, s. 4923-4954
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Tidskriftsartikel (refereegranskat)abstract
- In the framework of the EURODELTA-Trends (EDT) modeling experiment, several chemical transport models (CTMs) were applied for the 1990-2010 period to investigate air quality changes in Europe as well as the capability of the models to reproduce observed long-term air quality trends. Five CTMs have provided modeled air quality data for 21 continuous years in Europe using emission scenarios prepared by the International Institute for Applied Systems Analysis/Greenhouse Gas - Air Pollution Interactions and Synergies (IIASA/GAINS) and corresponding year-by-year meteorology derived from ERA-Interim global reanalysis. For this study, long-term observations of particle sulfate (SO2 4-), total nitrate (TNO3), total ammonium (TNHx) as well as sulfur dioxide (SO2) and nitrogen dioxide (NO2) for multiple sites in Europe were used to evaluate the model results. The trend analysis was performed for the full 21 years (referred to as PT) but also for two 11-year subperiods: 1990-2000 (referred to as P1) and 2000-2010 (referred to as P2). The experiment revealed that the models were able to reproduce the faster decline in observed SO2 concentrations during the first decade, i.e., 1990-2000, with a 64%-76% mean relative reduction in SO2 concentrations indicated by the EDT experiment (range of all the models) versus an 82% mean relative reduction in observed concentrations. During the second decade (P2), the models estimated a mean relative reduction in SO2 concentrations of about 34%-54%, which was also in line with that observed (47%). Comparisons of observed and modeled NO2 trends revealed a mean relative decrease of 25% and between 19% and 23% (range of all the models) during the P1 period, and 12% and between 22% and 26% (range of all the models) during the P2 period, respectively. Comparisons of observed and modeled trends in SO4 2- concentrations during the P1 period indicated that the models were able to reproduce the observed trends at most of the sites, with a 42%-54% mean relative reduction indicated by the EDT experiment (range of all models) versus a 57% mean relative reduction in observed concentrations and with good performance also during the P2 and PT periods, even though all the models overpredicted the number of statistically significant decreasing trends during the P2 period. Moreover, especially during the P1 period, both modeled and observational data indicated smaller reductions in SO42- concentrations compared with their gas-phase precursor (i.e., SO2), which could be mainly attributed to increased oxidant levels and pH-dependent cloud chemistry. An analysis of the trends in TNO3 concentrations indicated a 28%-39% and 29% mean relative reduction in TNO3 concentrations for the full period for model data (range of all the models) and observations, respectively. Further analysis of the trends in modeled HNO3 and particle nitrate (NO-3 ) concentrations revealed that the relative reduction in HNO3 was larger than that for NO-3 during the P1 period, which was mainly attributed to an increased availability of "free ammonia". By contrast, trends in modeled HNO3 and NO-3 concentrations were more comparable during the P2 period. Also, trends of TNHx concentrations were, in general, underpredicted by all models, with worse performance for the P1 period than for P2. Trends in modeled anthropogenic and biogenic secondary organic aerosol (ASOA and BSOA) concentrations together with the trends in available emissions of biogenic volatile organic compounds (BVOCs) were also investigated. A strong decrease in ASOA was indicated by all the models, following the reduction in anthropogenic non-methane VOC (NMVOC) precursors. Biogenic emission data provided by the modeling teams indicated a few areas with statistically significant increase in isoprene emissions and monoterpene emissions during the 1990-2010 period over Fennoscandia and eastern European regions (i.e., around 14 %-27 %), which was mainly attributed to the increase of surface temperature. However, the modeled BSOA concentrations did not linearly follow the increase in biogenic emissions. Finally, a comprehensive evaluation against positive matrix factorization (PMF) data, available during the second period (P2) at various European sites, revealed a systematic underestimation of the modeled SOA fractions of a factor of 3 to 11, on average, most likely because of missing SOA precursors and formation pathways, with reduced biases for the models that accounted for chemical aging of semi-volatile SOA components in the atmosphere.
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| 7. |
- Otero, Noelia, et al.
(författare)
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A multi-model comparison of meteorological drivers of surface ozone over Europe
- 2018
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 18:16, s. 12269-12288
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Tidskriftsartikel (refereegranskat)abstract
- The implementation of European emission abatement strategies has led to a significant reduction in the emissions of ozone precursors during the last decade. Ground-level ozone is also influenced by meteorological factors such as temperature, which exhibit interannual variability and are expected to change in the future. The impacts of climate change on air quality are usually investigated through air-quality models that simulate interactions between emissions, meteorology and chemistry. Within a multi-model assessment, this study aims to better understand how air-quality models represent the relationship between meteorological variables and surface ozone concentrations over Europe. A multiple linear regression (MLR) approach is applied to observed and modelled time series across 10 European regions in springtime and summertime for the period of 2000-2010 for both models and observations. Overall, the air-quality models are in better agreement with observations in summertime than in springtime and particularly in certain regions, such as France, central Europe or eastern Europe, where local meteorological variables show a strong influence on surface ozone concentrations. Larger discrepancies are found for the southern regions, such as the Balkans, the Iberian Peninsula and the Mediterranean basin, especially in springtime. We show that the air-quality models do not properly reproduce the sensitivity of surface ozone to some of the main meteorological drivers, such as maximum temperature, relative humidity and surface solar radiation. Specifically, all air-quality models show more limitations in capturing the strength of the ozone-relative-humidity relationship detected in the observed time series in most of the regions, for both seasons. Here, we speculate that dry-deposition schemes in the air-quality models might play an essential role in capturing this relationship. We further quantify the relationship between ozone and maximum temperature (m(o3-T), climate penalty) in observations and air-quality models. In summertime, most of the air-quality models are able to reproduce the observed climate penalty reasonably well in certain regions such as France, central Europe and northern Italy. However, larger discrepancies are found in springtime, where air-quality models tend to overestimate the magnitude of the observed climate penalty.
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| 8. |
- Grinberg, Marianna, et al.
(författare)
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Toxicogenomics directory of chemically exposed human hepatocytes
- 2014
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Ingår i: Archives of Toxicology. - : Springer Science and Business Media LLC. - 1432-0738 .- 0340-5761. ; 88:12, s. 2261-2287
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Tidskriftsartikel (refereegranskat)abstract
- A long-term goal of numerous research projects is to identify biomarkers for in vitro systems predicting toxicity in vivo. Often, transcriptomics data are used to identify candidates for further evaluation. However, a systematic directory summarizing key features of chemically influenced genes in human hepatocytes is not yet available. To bridge this gap, we used the Open TG-GATES database with Affymetrix files of cultivated human hepatocytes incubated with chemicals, further sets of gene array data with hepatocytes from human donors generated in this study, and publicly available genome-wide datasets of human liver tissue from patients with non-alcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular cancer (HCC). After a curation procedure, expression data of 143 chemicals were included into a comprehensive biostatistical analysis. The results are summarized in the publicly available toxicotranscriptomics directory (http://wiki.toxbank.net/toxicogenomics-map/) which provides information for all genes whether they are up- or downregulated by chemicals and, if yes, by which compounds. The directory also informs about the following key features of chemically influenced genes: (1) Stereotypical stress response. When chemicals induce strong expression alterations, this usually includes a complex but highly reproducible pattern named 'stereotypical response.' On the other hand, more specific expression responses exist that are induced only by individual compounds or small numbers of compounds. The directory differentiates if the gene is part of the stereotypical stress response or if it represents a more specific reaction. (2) Liver disease-associated genes. Approximately 20 % of the genes influenced by chemicals are up- or downregulated, also in liver disease. Liver disease genes deregulated in cirrhosis, HCC, and NASH that overlap with genes of the aforementioned stereotypical chemical stress response include CYP3A7, normally expressed in fetal liver; the phase II metabolizing enzyme SULT1C2; ALDH8A1, known to generate the ligand of RXR, one of the master regulators of gene expression in the liver; and several genes involved in normal liver functions: CPS1, PCK1, SLC2A2, CYP8B1, CYP4A11, ABCA8, and ADH4. (3) Unstable baseline genes. The process of isolating and the cultivation of hepatocytes was sufficient to induce some stress leading to alterations in the expression of genes, the so-called unstable baseline genes. (4) Biological function. Although more than 2,000 genes are transcriptionally influenced by chemicals, they can be assigned to a relatively small group of biological functions, including energy and lipid metabolism, inflammation and immune response, protein modification, endogenous and xenobiotic metabolism, cytoskeletal organization, stress response, and DNA repair. In conclusion, the introduced toxicotranscriptomics directory offers a basis for a rationale choice of candidate genes for biomarker evaluation studies and represents an easy to use source of background information on chemically influenced genes.
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| 9. |
- Theobald, M. R., et al.
(författare)
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An evaluation of European nitrogen and sulfur wet deposition and their trends estimated by six chemistry transport models for the period 1990–2010
- 2019
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Ingår i: Atmospheric Chemistry and Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 19:1, s. 379-405
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Tidskriftsartikel (refereegranskat)abstract
- The wet deposition of nitrogen and sulfur in Europe for the period 1990–2010 was estimated by six atmospheric chemistry transport models (CHIMERE, CMAQ, EMEP MSC-W, LOTOS-EUROS, MATCH and MINNI) within the framework of the EURODELTA-Trends model intercomparison. The simulated wet deposition and its trends for two 11-year periods (1990–2000 and 2000–2010) were evaluated using data from observations from the EMEP European monitoring network. For annual wet deposition of oxidised nitrogen (WNOx), model bias was within 30 % of the average of the observations for most models. There was a tendency for most models to underestimate annual wet deposition of reduced nitrogen (WNHx), although the model bias was within 40 % of the average of the observations. Model bias for WNHx was inversely correlated with model bias for atmospheric concentrations of NH3 + NH4+, suggesting that an underestimation of wet deposition partially contributed to an overestimation of atmospheric concentrations. Model bias was also within about 40 % of the average of the observations for the annual wet deposition of sulfur (WSOx) for most models. Decreasing trends in WNOx were observed at most sites for both 11-year periods, with larger trends, on average, for the second period. The models also estimated predominantly decreasing trends at the monitoring sites and all but one of the models estimated larger trends, on average, for the second period. Decreasing trends were also observed at most sites for WNHx, although larger trends, on average, were observed for the first period. This pattern was not reproduced by the models, which estimated smaller decreasing trends, on average, than those observed or even small increasing trends. The largest observed trends were for WSOx, with decreasing trends at more than 80 % of the sites. On average, the observed trends were larger for the first period. All models were able to reproduce this pattern, although some models underestimated the trends (by up to a factor of 4) and others overestimated them (by up to 40 %), on average. These biases in modelled trends were directly related to the tendency of the models to under- or overestimate annual wet deposition and were smaller for the relative trends (expressed as % yr−1 relative to the deposition at the start of the period). The fact that model biases were fairly constant throughout the time series makes it possible to improve the predictions of wet deposition for future scenarios by adjusting the model estimates using a bias correction calculated from past observations. An analysis of the contributions of various factors to the modelled trends suggests that the predominantly decreasing trends in wet deposition are mostly due to reductions in emissions of the precursors NOx, NH3 and SOx. However, changes in meteorology (e.g. precipitation) and other (non-linear) interactions partially offset the decreasing trends due to emission reductions during the first period but not the second. This suggests that the emission reduction measures had a relatively larger effect on wet deposition during the second period, at least for the sites with observations.
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| 10. |
- Colette, Augustin, et al.
(författare)
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EURODELTA-Trends, a multi-model experiment of air quality hindcast in Europe over 1990–2010
- 2017
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Ingår i: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 10:9, s. 3255-3276
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Tidskriftsartikel (refereegranskat)abstract
- The EURODELTA-Trends multi-model chemistry-transport experiment has been designed to facilitate a better understanding of the evolution of air pollution and its drivers for the period 1990–2010 in Europe. The main objective of the experiment is to assess the efficiency of air pollutant emissions mitigation measures in improving regional-scale air quality. The present paper formulates the main scientific questions and policy issues being addressed by the EURODELTA-Trends modelling experiment with an emphasis on how the design and technical features of the modelling experiment answer these questions. The experiment is designed in three tiers, with increasing degrees of computational demand in order to facilitate the participation of as many modelling teams as possible. The basic experiment consists of simulations for the years 1990, 2000, and 2010. Sensitivity analysis for the same three years using various combinations of (i) anthropogenic emissions, (ii) chemical boundary conditions, and (iii) meteorology complements it. The most demanding tier consists of two complete time series from 1990 to 2010, simulated using either time-varying emissions for corresponding years or constant emissions. Eight chemistry-transport models have contributed with calculation results to at least one experiment tier, and five models have – to date – completed the full set of simulations (and 21-year trend calculations have been performed by four models). The modelling results are publicly available for further use by the scientific community. The main expected outcomes are (i) an evaluation of the models' performances for the three reference years, (ii) an evaluation of the skill of the models in capturing observed air pollution trends for the 1990–2010 time period, (iii) attribution analyses of the respective role of driving factors (e.g. emissions, boundary conditions, meteorology), (iv) a dataset based on a multi-model approach, to provide more robust model results for use in impact studies related to human health, ecosystem, and radiative forcing.
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