1. |
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2. |
- 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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4. |
- Barausse, Enrico, et al.
(författare)
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Prospects for fundamental physics with LISA
- 2020
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Ingår i: General Relativity and Gravitation. - : SPRINGER/PLENUM PUBLISHERS. - 0001-7701 .- 1572-9532. ; 52:8
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- In this paper, which is of programmatic rather than quantitative nature, we aim to further delineate and sharpen the future potential of the LISA mission in the area of fundamental physics. Given the very broad range of topics that might be relevant to LISA,we present here a sample of what we view as particularly promising fundamental physics directions. We organize these directions through a "science-first" approach that allows us to classify how LISA data can inform theoretical physics in a variety of areas. For each of these theoretical physics classes, we identify the sources that are currently expected to provide the principal contribution to our knowledge, and the areas that need further development. The classification presented here should not be thought of as cast in stone, but rather as a fluid framework that is amenable to change with the flow of new insights in theoretical physics.
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5. |
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6. |
- Weinstein, John N., et al.
(författare)
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The cancer genome atlas pan-cancer analysis project
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:10, s. 1113-1120
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Forskningsöversikt (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. © 2013 Nature America, Inc. All rights reserved.
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7. |
- Zhang, Y., et al.
(författare)
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Galaxies in X-ray selected clusters and groups in Dark Energy Survey data - II. Hierarchical Bayesian modelling of the red-sequence galaxy luminosity function
- 2019
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Ingår i: Monthly notices of the Royal Astronomical Society. - : OXFORD UNIV PRESS. - 0035-8711 .- 1365-2966. ; 488:1, s. 1-17
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Tidskriftsartikel (refereegranskat)abstract
- Using similar to 100 X-ray selected clusters in the Dark Energy Survey Science Verification data, we constrain the luminosity function ( LF) of cluster red-sequence galaxies as a function of redshift. This is the first homogeneous optical/X-ray sample large enough to constrain the evolution of the LF simultaneously in redshift ( 0.1 < z < 1.05) and cluster mass ( 13.5 <= log(10)( M-200crit) similar to< 15.0). We pay particular attention to completeness issues and the detection limit of the galaxy sample. We then apply a hierarchical Bayesian model to fit the cluster galaxy LFs via a Schechter function, including its characteristic break ( m*) to a faint end power-law slope ( alpha). Our method enables us to avoid known issues in similar analyses based on stacking or binning the clusters. We find weak and statistically insignificant (similar to 1.9 sigma) evolution in the faint end slope alpha versus redshift. We also find no dependence in alpha or m* with the X-ray inferred cluster masses. However, the amplitude of the LF as a function of cluster mass is constrained to similar to 20 per cent precision. As a by-product of our algorithm, we utilize the correlation between the LF and cluster mass to provide an improved estimate of the individual cluster masses as well as the scatter in true mass given the X-ray inferred masses. This technique can be applied to a larger sample of X-ray or optically selected clusters from the Dark Energy Survey, significantly improving the sensitivity of the analysis.
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8. |
- Yan, C., et al.
(författare)
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Size-dependent influence of NOx on the growth rates of organic aerosol particles
- 2020
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 6:22
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Tidskriftsartikel (refereegranskat)abstract
- Atmospheric new-particle formation (NPF) affects climate by contributing to a large fraction of the cloud condensation nuclei (CCN). Highly oxygenated organic molecules (HOMs) drive the early particle growth and therefore substantially influence the survival of newly formed particles to CCN. Nitrogen oxide (NOx) is known to suppress the NPF driven by HOMs, but the underlying mechanism remains largely unclear. Here, we examine the response of particle growth to the changes of HOM formation caused by NOx. We show that NOx suppresses particle growth in general, but the suppression is rather nonuniform and size dependent, which can be quantitatively explained by the shifted HOM volatility after adding NOx. By illustrating how NOx affects the early growth of new particles, a critical step of CCN formation, our results help provide a refined assessment of the potential climatic effects caused by the diverse changes of NOx level in forest regions around the globe.
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9. |
- Zhang, Y., et al.
(författare)
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Dark Energy Surveyed Year 1 results : calibration of cluster mis-centring in the redMaPPer catalogues
- 2019
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Ingår i: Monthly notices of the Royal Astronomical Society. - : OXFORD UNIV PRESS. - 0035-8711 .- 1365-2966. ; 487:2, s. 2578-2593
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Tidskriftsartikel (refereegranskat)abstract
- The centre determination of a galaxy cluster from an optical cluster finding algorithm can be offset from theoretical prescriptions or N-body definitions of its host halo centre. These offsets impact the recovered cluster statistics, affecting both richness measurements and the weak lensing shear profile around the clusters. This paper models the centring performance of the redMaPPer cluster finding algorithm using archival X-ray observations of redMaPPer-selected clusters. Assuming the X-ray emission peaks as the fiducial halo centres, and through analysing their offsets to the redMaPPer centres, we find that similar to 75 +/- 8 per cent of the redMaPPer clusters are well centred and the mis-centred offset follows a Gamma distribution in normalized, projected distance. These mis-centring offsets cause a systematic underestimation of cluster richness relative to the well-centred clusters, for which we propose a descriptive model. Our results enable the DES Y1 cluster cosmology analysis by characterizing the necessary corrections to both the weak lensing and richness abundance functions of the DES Y1 redMaPPer cluster catalogue.
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10. |
- Mehrtens, N., et al.
(författare)
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The XMM Cluster Survey : the halo occupation number of BOSS galaxies in X-ray clusters
- 2016
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 463:2, s. 1929-1943
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Tidskriftsartikel (refereegranskat)abstract
- We present a direct measurement of the mean halo occupation distribution (HOD) of galaxies taken from the eleventh data release (DR11) of the Sloan Digital Sky Survey-III Baryon Oscillation Spectroscopic Survey (BOSS). The HOD of BOSS low-redshift (LOWZ: 0.2 < z < 0.4) and Constant-Mass (CMASS: 0.43 < z < 0.7) galaxies is inferred via their association with the dark matter haloes of 174 X-ray-selected galaxy clusters drawn from the XMM Cluster Survey (XCS). Halo masses are determined for each galaxy cluster based on X-ray temperature measurements, and range between log10(M180/M⊙) = 13 and 15. Our directly measured HODs are consistent with the HOD-model fits inferred via the galaxy-clustering analyses of Parejko et al. for the BOSS LOWZ sample and White et al. for the BOSS CMASS sample. Under the simplifying assumption that the other parameters that describe the HOD hold the values measured by these authors, we have determined a best-fitting alpha-index of 0.91 ± 0.08 and 1.27−0.04+0.03" role="presentation">1.27+0.03−0.04 for the CMASS and LOWZ HOD, respectively. These alpha-index values are consistent with those measured by White et al. and Parejko et al. In summary, our study provides independent support for the HOD models assumed during the development of the BOSS mock-galaxy catalogues that have subsequently been used to derive BOSS cosmological constraints.
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11. |
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12. |
- Mehrtens, Nicola, et al.
(författare)
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The XMM Cluster Survey : optical analysis methodology and the first data release
- 2012
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 423:2, s. 1024-1052
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Tidskriftsartikel (refereegranskat)abstract
- The XMM Cluster Survey (XCS) is a serendipitous search for galaxy clusters using all publicly available data in the XMMNewton Science Archive. Its main aims are to measure cosmological parameters and trace the evolution of X-ray scaling relations. In this paper we present the first data release from the XMM Cluster Survey (XCS-DR1). This consists of 503 optically confirmed, serendipitously detected, X-ray clusters. Of these clusters, 256 are new to the literature and 357 are new X-ray discoveries. We present 463 clusters with a redshift estimate (0.06 < z < 1.46), including 261 clusters with spectroscopic redshifts. The remainder have photometric redshifts. In addition, we have measured X-ray temperatures (TX) for 401 clusters (0.4 < TX < 14.7 keV). We highlight seven interesting subsamples of XCS-DR1 clusters: (i) 10 clusters at high redshift (z > 1.0, including a new spectroscopically confirmed cluster at z= 1.01); (ii) 66 clusters with high TX (>5 keV); (iii) 130 clusters/groups with low TX (<2 keV); (iv) 27 clusters with measured TX values in the Sloan Digital Sky Survey (SDSS) Stripe 82 co-add region; (v) 77 clusters with measured TX values in the Dark Energy Survey region; (vi) 40 clusters detected with sufficient counts to permit mass measurements (under the assumption of hydrostatic equilibrium); (vii) 104 clusters that can be used for applications such as the derivation of cosmological parameters and the measurement of cluster scaling relations. The X-ray analysis methodology used to construct and analyse the XCS-DR1 cluster sample has been presented in a companion paper, Lloyd-Davies et al.
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13. |
- Viana, P. T. P., et al.
(författare)
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The XMM Cluster Survey : Present status and latest results
- 2013
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Ingår i: Astronomical Notes - Astronomische Nachrichten. - : Wiley. - 0004-6337 .- 1521-3994. ; 334:4-5, s. 462-465
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Tidskriftsartikel (refereegranskat)abstract
- The XMM Cluster Survey (XCS) is a serendipitous search for galaxy clusters using all publicly available data in the XMM-Newton Science Archive. Our recent first data release (XCS-DR1) contains 503 optically confirmed groups and clusters, among which 256 new to the literature and 357 whose X-ray emission was detected for the first time. We discuss their properties and provide an update on the work being done. As examples of the applications of XCS-DR1, we mention the 17 fossil groups/clusters identified with the help of the Sloan Digital Sky Survey. Their brightest galaxies have stellar populations and star-formation histories which are similar to normal brightest cluster galaxies, but their stellar masses are significantly larger and correspond to a much bigger fraction of the total group/cluster optical luminosity. We also highlight the 15 clusters expected to be also detected by the Planck satellite, and characterize the expected overlap between the final XCS and Planck cluster catalogues.
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14. |
- Hilton, Matt, et al.
(författare)
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The XMM Cluster Survey : evidence for energy injection at high redshift from evolution of the X-ray luminosity-temperature relation
- 2012
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 424:3, s. 2086-2096
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Tidskriftsartikel (refereegranskat)abstract
- We measure the evolution of the X-ray luminositytemperature (LX - T) relation since z similar to 1.5 using a sample of 211 serendipitously detected galaxy clusters with spectroscopic redshifts drawn from the XMM Cluster Survey first data release (XCS-DR1). This is the first study spanning this redshift range using a single, large, homogeneous cluster sample. Using an orthogonal regression technique, we find no evidence for evolution in the slope or intrinsic scatter of the relation since z similar to 1.5, finding both to be consistent with previous measurements at z similar to 0.1. However, the normalization is seen to evolve negatively with respect to the self-similar expectation: we find E-1(z)?LX = 1044.67 +/- 0.09(T/5)3.04 +/- 0.16(1 + z)-1.5 +/- 0.5, which is within 2 sigma of the zero evolution case. We see milder, but still negative, evolution with respect to self-similar when using a bisector regression technique. We compare our results to numerical simulations, where we fit simulated cluster samples using the same methods used on the XCS data. Our data favour models in which the majority of the excess entropy required to explain the slope of the LX - T relation is injected at high redshift. Simulations in which active galactic nucleus feedback is implemented using prescriptions from current semi-analytic galaxy formation models predict the positive evolution of the normalization, and differ from our data at more than 5 sigma. This suggests that more efficient feedback at high redshift may be needed in these models.
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15. |
- Stott, John P., et al.
(författare)
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The XMM Cluster Survey : the interplay between the brightest cluster galaxy and the intracluster medium via AGN feedback
- 2012
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 422:3, s. 2213-2229
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Forskningsöversikt (refereegranskat)abstract
- Using a sample of 123 X-ray clusters and groups drawn from the XMM Cluster Survey first data release, we investigate the interplay between the brightest cluster galaxy (BCG), its black hole and the intracluster/group medium (ICM). It appears that for groups and clusters with a BCG likely to host significant active galactic nuclei (AGN) feedback, gas cooling dominates in those with TX > 2 keV while AGN feedback dominates below. This may be understood through the subunity exponent found in the scaling relation we derive between the BCG mass and cluster mass over the halo mass range 1013 < M500 < 1015 M? and the lack of correlation between radio luminosity and cluster mass, such that BCG AGN in groups can have relatively more energetic influence on the ICM. The LXTX relation for systems with the most massive BCGs, or those with BCGs co-located with the peak of the ICM emission, is steeper than that for those with the least massive and most offset, which instead follows self-similarity. This is evidence that a combination of central gas cooling and powerful, well fuelled AGN causes the departure of the ICM from pure gravitational heating, with the steepened relation crossing self-similarity at TX= 2 keV. Importantly, regardless of their black hole mass, BCGs are more likely to host radio-loud AGN if they are in a massive cluster (TX? 2 keV) and again co-located with an effective fuel supply of dense, cooling gas. This demonstrates that the most massive black holes appear to know more about their host cluster than they do about their host galaxy. The results lead us to propose a physically motivated, empirical definition of cluster and group, delineated at 2 keV.
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16. |
- Stott, J. P., et al.
(författare)
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THE XMM CLUSTER SURVEY : THE BUILD-UP OF STELLAR MASS IN BRIGHTEST CLUSTER GALAXIES AT HIGH REDSHIFT
- 2010
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 718:1, s. 23-30
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Tidskriftsartikel (refereegranskat)abstract
- We present deep J-and K-s-band photometry of 20 high redshift galaxy clusters between z = 0.8 and 1.5, 19 of which are observed with the MOIRCS instrument on the Subaru telescope. By using near-infrared light as a proxy for stellar mass we find the surprising result that the average stellar mass of Brightest Cluster Galaxies (BCGs) has remained constant at similar to 9 x 10(11) M-circle dot since z similar to 1.5. We investigate the effect on this result of differing star formation histories generated by three well-known and independent stellar population codes and find it to be robust for reasonable, physically motivated choices of age and metallicity. By performing Monte Carlo simulations we find that the result is unaffected by any correlation between BCG mass and cluster mass in either the observed or model clusters. The large stellar masses imply that the assemblage of these galaxies took place at the same time as the initial burst of star formation. This result leads us to conclude that dry merging has had little effect on the average stellar mass of BCGs over the last 9-10 Gyr in stark contrast to the predictions of semi-analytic models, based on the hierarchical merging of dark matter halos, which predict a more protracted mass build-up over a Hubble time. However, we discuss that there is potential for reconciliation between observation and theory if there is a significant growth of material in the intracluster light over the same period.
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17. |
- Wexler, J. B., et al.
(författare)
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The effect of ocean acidification on otolith morphology in larvae of a tropical, epipelagic fish species, yellowfin tuna (Thunnus albacares)
- 2023
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Ingår i: Journal of Experimental Marine Biology and Ecology. - 0022-0981. ; 569
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Tidskriftsartikel (refereegranskat)abstract
- Increasing ocean acidification is a concern due to its potential effects on the growth, development, and survival of early life stages of tuna in oceanic habitats and on the spatial extent of their suitable nursery habitat. To investigate the potential effects of increasing CO2 on otolith calcification of 9-day old pre-flexion stage yellowfin tuna (Thunnus albacares), an experiment was conducted at the Inter-American Tropical Tuna Commission's Achotines Laboratory in Panama during 2011. Fertilized eggs and larvae were exposed to mean pCO2 levels that ranged from present day (355 mu atm) to two levels predicted to occur in some areas of the Pacific in the near future (2013 and 3321 mu atm), and to an extreme value equivalent to long-term projections for 300 years in the future (9624 mu atm). The results indicated significantly larger otoliths (in area and perimeter) with significant, and increasing, fluctuating asymmetry at acidification levels similar to those projected for the near future and long-term. Otoliths increased significantly in size despite a significant decrease in somatic length with increasing pCO2. A consistent correlation between otolith and somatic growth of yellowfin tuna larvae among treatments was evident (i.e., larger otoliths were still associated with larger larvae within a treatment). The observed changes in otolith morphology with increasing ocean acidification have the potential to indirectly affect larval survival through dysfunction of the mechanosensory organs, but this remains to be verified in yellowfin tuna larvae.
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18. |
- Bromhead, D., et al.
(författare)
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The potential impact of ocean acidification on eggs and larvae of the Yellowfin Tuna.
- 2015
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Ingår i: Deep-sea research. Part II, Topical studies in oceanography. - : Elsevier BV. - 0967-0645. ; 113, s. 268-279
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Tidskriftsartikel (refereegranskat)abstract
- Anthropogenic carbon dioxide (CO2) emissions are resulting in increasing absorption of CO2 by the earth's oceans, which has led to a decline in ocean pH, a process known as ocean acidification (OA). Evidence suggests that OA may have the potential to affect the distribution and population dynamics of many marine organisms. Early life history processes (e.g. fertilization) and stages (eggs, larvae, juveniles) may be relatively more vulnerable to potential OA impacts, with implications for recruitment in marine populations. The potential impact of OA upon tuna populations has not been investigated, although tuna are key components of pelagic ecosystems and, in the Pacific Ocean, form the basis of one of the largest and most valuable fisheries in the world. This paper reviews current knowledge of potential OA impacts on fish and presents results from a pilot study investigating how OA may affect eggs and larvae of yellowfin tuna, Thunnus albacares. Two separate trials were conducted to test the impact of pCO2 on yellowfin egg stage duration, larval growth and survival. The pCO2 levels tested ranged from present day ($400 μatm) to levels predicted to occur in some areas of the spawning habitat within the next 100 years (o2500 μatm) to 300 years ($ o5000 μatm) to much more extreme levels ($10,000 μatm). In trial 1, there was evidence for significantly reduced larval survival (at mean pCO2 levelsZ4730 μatm) and growth (at mean pCO2 levels Z 2108 μatm), while egg hatch time was increased at extreme pCO2 levelsZ10,000 μatm (nintermediate levels were not tested). In trial 2, egg hatch times were increased at mean pCO2 levelsZ1573 μatm, but growth was only impacted at higher pCO2 (Z8800 μatm) and there was no relationship with survival. Unstable ambient conditions during trial 2 are likely to have contributed to the difference in results between trials. Despite the technical challenges with these experiments, there is a need for future empirical work which can in turn support modeling-based approaches to assess how OA will affect the ecologically and economically important tropical tuna resources.
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19. |
- Lloyd-Davies, E. J., et al.
(författare)
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The XMM Cluster Survey : X-ray analysis methodology
- 2011
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 418:1, s. 14-53
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Tidskriftsartikel (refereegranskat)abstract
- The XMM Cluster Survey (XCS) is a serendipitous search for galaxy clusters using all publicly available data in the XMMNewton Science Archive. Its main aims are to measure cosmological parameters and trace the evolution of X-ray scaling relations. In this paper we describe the data processing methodology applied to the 5776 XMM observations used to construct the current XCS source catalogue. A total of 3675 > 4s cluster candidates with > 50 background-subtracted X-ray counts are extracted from a total non-overlapping area suitable for cluster searching of 410 deg2. Of these, 993 candidates are detected with > 300 background-subtracted X-ray photon counts, and we demonstrate that robust temperature measurements can be obtained down to this count limit. We describe in detail the automated pipelines used to perform the spectral and surface brightness fitting for these candidates, as well as to estimate redshifts from the X-ray data alone. A total of 587 (122) X-ray temperatures to a typical accuracy of < 40 (< 10) per cent have been measured to date. We also present the methodology adopted for determining the selection function of the survey, and show that the extended source detection algorithm is robust to a range of cluster morphologies by inserting mock clusters derived from hydrodynamical simulations into real XMMimages. These tests show that the simple isothermal beta-profiles is sufficient to capture the essential details of the cluster population detected in the archival XMM observations. The redshift follow-up of the XCS cluster sample is presented in a companion paper, together with a first data release of 503 optically confirmed clusters.
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20. |
- von Hobe, M, et al.
(författare)
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Reconciliation of essential process parameters for an enhanced predictability of Arctic stratospheric ozone loss and its climate interactions (RECONCILE): activities and results
- 2013
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Ingår i: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 13:18, s. 9233-9268
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Tidskriftsartikel (refereegranskat)abstract
- The international research project RECONCILE has addressed central questions regarding polar ozone depletion, with the objective to quantify some of the most relevant yet still uncertain physical and chemical processes and thereby improve prognostic modelling capabilities to realistically predict the response of the ozone layer to climate change. This overview paper outlines the scope and the general approach of RECONCILE, and it provides a summary of observations and modelling in 2010 and 2011 that have generated an in many respects unprecedented dataset to study processes in the Arctic winter stratosphere. Principally, it summarises important outcomes of RECONCILE including (i) better constraints and enhanced consistency on the set of parameters governing catalytic ozone destruction cycles, (ii) a better understanding of the role of cold binary aerosols in heterogeneous chlorine activation, (iii) an improved scheme of polar stratospheric cloud (PSC) processes that includes heterogeneous nucleation of nitric acid trihydrate (NAT) and ice on non-volatile background aerosol leading to better model parameterisations with respect to denitrification, and (iv) long transient simulations with a chemistryclimate model (CCM) updated based on the results of RECONCILE that better reproduce past ozone trends in Antarctica and are deemed to produce more reliable predictions of future ozone trends. The process studies and the global simulations conducted in RECONCILE show that in the Arctic, ozone depletion uncertainties in the chemical and microphysical processes are now clearly smaller than the sensitivity to dynamic variability.
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21. |
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