| 1. |
- 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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Tidskriftsartikel (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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| 2. |
- Arridge, Christopher S., et al.
(författare)
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Uranus Pathfinder : exploring the origins and evolution of Ice Giant planets
- 2012
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Ingår i: Experimental astronomy. - : Springer Science and Business Media LLC. - 0922-6435 .- 1572-9508. ; 33:2-3, s. 753-791
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Tidskriftsartikel (refereegranskat)abstract
- The "Ice Giants" Uranus and Neptune are a different class of planet compared to Jupiter and Saturn. Studying these objects is important for furthering our understanding of the formation and evolution of the planets, and unravelling the fundamental physical and chemical processes in the Solar System. The importance of filling these gaps in our knowledge of the Solar System is particularly acute when trying to apply our understanding to the numerous planetary systems that have been discovered around other stars. The Uranus Pathfinder (UP) mission thus represents the quintessential aspects of the objectives of the European planetary community as expressed in ESA's Cosmic Vision 2015-2025. UP was proposed to the European Space Agency's M3 call for medium-class missions in 2010 and proposed to be the first orbiter of an Ice Giant planet. As the most accessible Ice Giant within the M-class mission envelope Uranus was identified as the mission target. Although not selected for this call the UP mission concept provides a baseline framework for the exploration of Uranus with existing low-cost platforms and underlines the need to develop power sources suitable for the outer Solar System. The UP science case is based around exploring the origins, evolution, and processes at work in Ice Giant planetary systems. Three broad themes were identified: (1) Uranus as an Ice Giant, (2) An Ice Giant planetary system, and (3) An asymmetric magnetosphere. Due to the long interplanetary transfer from Earth to Uranus a significant cruise-phase science theme was also developed. The UP mission concept calls for the use of a Mars Express/Rosetta-type platform to launch on a Soyuz-Fregat in 2021 and entering into an eccentric polar orbit around Uranus in the 2036-2037 timeframe. The science payload has a strong heritage in Europe and beyond and requires no significant technology developments.
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| 3. |
- 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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| 4. |
- Hudson, Thomas J., et al.
(författare)
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International network of cancer genome projects
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 464:7291, s. 993-998
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Tidskriftsartikel (refereegranskat)abstract
- The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.
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| 5. |
- Aad, G., et al.
(författare)
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- 2011
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swepub:Mat__t (refereegranskat)
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| 6. |
- Harrison, Craig D., et al.
(författare)
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THE XMM CLUSTER SURVEY : THE STELLAR MASS ASSEMBLY OF FOSSIL GALAXIES
- 2012
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 752:1, s. 12-
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents both the result of a search for fossil systems (FSs) within the XMM Cluster Survey and the Sloan Digital Sky Survey and the results of a study of the stellar mass assembly and stellar populations of their fossil galaxies. In total, 17 groups and clusters are identified at z < 0.25 with large magnitude gaps between the first and fourth brightest galaxies. All the information necessary to classify these systems as fossils is provided. For both groups and clusters, the total and fractional luminosity of the brightest galaxy is positively correlated with the magnitude gap. The brightest galaxies in FSs (called fossil galaxies) have stellar populations and star formation histories which are similar to normal brightest cluster galaxies (BCGs). However, at fixed group/cluster mass, the stellar masses of the fossil galaxies are larger compared to normal BCGs, a fact that holds true over a wide range of group/cluster masses. Moreover, the fossil galaxies are found to contain a significant fraction of the total optical luminosity of the group/cluster within 0.5 R-200, as much as 85%, compared to the non-fossils, which can have as little as 10%. Our results suggest that FSs formed early and in the highest density regions of the universe and that fossil galaxies represent the end products of galaxy mergers in groups and clusters.
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| 7. |
- Hilton, Matt, et al.
(författare)
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THE XMM CLUSTER SURVEY : ACTIVE GALACTIC NUCLEI AND STARBURST GALAXIES IN XMMXCS J2215.9-1738 AT z=1.46
- 2010
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Ingår i: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 718:1, s. 133-147
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Tidskriftsartikel (refereegranskat)abstract
- We use Chandra X-ray and Spitzer infrared (IR) observations to explore the active galactic nucleus (AGN) and starburst populations of XMMXCS J2215.9-1738 at z = 1.46, one of the most distant spectroscopically confirmed galaxy clusters known. The high-resolution X-ray imaging reveals that the cluster emission is contaminated by point sources that were not resolved in XMM-Newton observations of the system, and have the effect of hardening the spectrum, leading to the previously reported temperature for this system being overestimated. From a joint spectroscopic analysis of the Chandra and XMM-Newton data, the cluster is found to have temperature T = 4.1(-0.9)(+0.6) keV and luminosity LX = (2.92(-0.35)(+0.24)) x 1044 erg s(-1), extrapolated to a radius of 2 Mpc. As a result of this revised analysis, the cluster is found to lie on the sigma(v)-T relation, but the cluster remains less luminous than would be expected from self-similar evolution of the local L-X-T relation. Two of the newly discovered X-ray AGNs are cluster members, while a third object, which is also a prominent 24 mu m source, is found to have properties consistent with it being a high-redshift, highly obscured object in the background. We find a total of eight > 5 sigma 24 mu m sources associated with cluster members (four spectroscopically confirmed and four selected using photometric redshifts) and one additional 24 mu m source with two possible optical/near-IR counterparts that may be associated with the cluster. Examining the Infrared Array Camera colors of these sources, we find that one object is likely to be an AGN. Assuming that the other 24 mu m sources are powered by star formation, their IR luminosities imply star formation rates similar to 100 M-circle dot yr(-1). We find that three of these sources are located at projected distances of <250 kpc from the cluster center, suggesting that a large amount of star formation may be taking place in the cluster core, in contrast to clusters at low redshift.
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| 8. |
- Hudson, Lawrence N., et al.
(författare)
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The PREDICTS database : a global database of how local terrestrial biodiversity responds to human impacts
- 2014
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:24, s. 4701-4735
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Tidskriftsartikel (refereegranskat)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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| 9. |
- Jones, Felicity C., et al.
(författare)
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The genomic basis of adaptive evolution in threespine sticklebacks
- 2012
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 484:7392, s. 55-61
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Tidskriftsartikel (refereegranskat)abstract
- Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.
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| 10. |
- 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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| 11. |
- 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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| 12. |
- Middleton, Matthew J., et al.
(författare)
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Bright radio emission from an ultraluminous stellar-mass microquasar in M 31
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 493:7431, s. 187-190
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Tidskriftsartikel (refereegranskat)abstract
- A subset of ultraluminous X-ray sources (those with luminosities of less than 10(40) erg s(-1); ref. 1) are thought to be powered by the accretion of gas onto black holes with masses of similar to 5-20M(circle dot), probably by means of an accretion disk(2,3). The X-ray and radio emission are coupled in such Galactic sources; the radio emission originates in a relativistic jet thought to be launched from the innermost regions near the black hole(4,5), with the most powerful emission occurring when the rate of infalling matter approaches a theoretical maximum (the Eddington limit). Only four such maximal sources are known in the Milky Way(6), and the absorption of soft X-rays in the interstellar medium hinders the determination of the causal sequence of events that leads to the ejection of the jet. Here we report radio and X-ray observations of a bright new X-ray source in the nearby galaxy M 31, whose peak luminosity exceeded 10(39) erg s(-1). The radio luminosity is extremely high and shows variability on a timescale of tens of minutes, arguing that the source is highly compact and powered by accretion close to the Eddington limit onto a black hole of stellar mass. Continued radio and X-ray monitoring of such sources should reveal the causal relationship between the accretion flow and the powerful jet emission.
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| 13. |
- Mozelius, Peter, et al.
(författare)
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Let the students contruct their own fun and knowledge - learning to program by building computer games
- 2013
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Ingår i: Proceedings of the 7th European Conference on Games Based Learning, Vol. 1 and 2. - : Academic Conferences and Publishing International. - 9781909507654 ; , s. 418-426
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Konferensbidrag (refereegranskat)abstract
- Computer programming is a core subject in most Computer science programmes at university level but many students have difficulties with both the understanding of theoretical concepts and with the learning of practical programming skills. Several studies have pointed out that there exist pedagogical and motivational problems resulting in high drop-out rates and low learning outcomes. On the other hand today’s students have grown up in a digital and internet connected world where playing computer games is a common and appreciated spare time activity. It has been discussed during many years amongst teachers and researchers which important features a programming language should have to support learning and which the appropriate programming paradigms are for introductory programming courses. Less has been discussed and written about modifying the actual course content and use the recognised attraction and catalytic effect of computer games. The aim of this case study is to describe, analyze and discuss the concept of learning to program by game construction. In this case study two course analyses have been combined with a literature review on pedagogy for Game Based Learning (GBL Findings from the literature review show that the idea of students constructing knowledge in their interactions with their environment is not a new one and that games have been used in educational contexts long before the introduction of computers. The idea of Game based learning has support in the constructivist learning theory concept that was introduced theoretically at university level in the 1970s by Jean Piaget and Lev Vygotsky. Results from the study also indicate that the practical application of the game construction concept has been successful in the two investigated programming courses both when it comes to student motivation and learning outcomes. Furthermore, this game based pedagogy can motivate students not only to develop themselves as future programmers but also to become more innovative and entrepreneurial by improving the quality and performance of the games in order to deploy, promote and sell them.
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| 14. |
- Pinto, Dalila, et al.
(författare)
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Functional impact of global rare copy number variation in autism spectrum disorders.
- 2010
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 466:7304, s. 368-372
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Tidskriftsartikel (refereegranskat)abstract
- The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
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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. |
- Viana, Pedro T. P., et al.
(författare)
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The XMM Cluster Survey : predicted overlap with the Planck Cluster Catalogue
- 2012
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 422:2, s. 1007-1013
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Tidskriftsartikel (refereegranskat)abstract
- We present a list of 15 clusters of galaxies, serendipitously detected by the XMM Cluster Survey (XCS), that have a high probability of detection by the Planck satellite. Three of them already appear in the Planck Early Sunyaev-Zel'dovich (ESZ) catalogue. The estimation of the Planck detection probability assumes the flat Lambda cold dark matter (Lambda CDM) cosmology most compatible with 7-year Wilkinson Microwave Anisotropy Probe (WMAP7) data. It takes into account the XCS selection function and Planck sensitivity, as well as the covariance of the cluster X-ray luminosity, temperature and integrated Comptonization parameter, as a function of cluster mass and redshift, determined by the Millennium gas simulations. We also characterize the properties of the galaxy clusters in the final data release of the XCS that we expect Planck will have detected by the end of its extended mission. Finally, we briefly discuss possible joint applications of the XCS and Planck data.
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