| 1. |
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| 2. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)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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| 3. |
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| 4. |
- Barausse, Enrico, et al.
(author)
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Prospects for fundamental physics with LISA
- 2020
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In: General Relativity and Gravitation. - : SPRINGER/PLENUM PUBLISHERS. - 0001-7701 .- 1572-9532. ; 52:8
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Journal article (other academic/artistic)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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| 6. |
- Weinstein, John N., et al.
(author)
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The cancer genome atlas pan-cancer analysis project
- 2013
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:10, s. 1113-1120
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Research review (peer-reviewed)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.
(author)
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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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In: Monthly notices of the Royal Astronomical Society. - : OXFORD UNIV PRESS. - 0035-8711 .- 1365-2966. ; 488:1, s. 1-17
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Journal article (peer-reviewed)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. |
- Hoyle, C. R., et al.
(author)
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Ice nucleation properties of volcanic ash from Eyjafjallajokull
- 2011
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In: Atmospheric Chemistry And Physics. - : Copernicus GmbH. - 1680-7316 .- 1680-7324. ; 11:18, s. 9911-9926
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Journal article (peer-reviewed)abstract
- The ice nucleation ability of volcanic ash particles collected close to the Icelandic volcano Eyjafjallajokull during its eruptions in April and May 2010 is investigated experimentally, in the immersion and deposition modes, and applied to atmospheric conditions by comparison with airborne measurements and microphysical model calculations. The number of ash particles which are active as ice nuclei (IN) is strongly temperature dependent, with a very small minority being active in the immersion mode at temperatures of 250-263 K. Average ash particles show only a moderate effect on ice nucleation, by inducing freezing at temperatures between 236K and 240K (i.e. approximately 3-4K higher than temperatures required for homogeneous ice nucleation, measured with the same instrument). By scaling the results to aircraft and lidar measurements of the conditions in the ash plume days down wind of the eruption, and by applying a simple microphysical model, it was found that the IN active in the immersion mode in the range 250-263K generally occurred in atmospheric number densities at the lower end of those required to have an impact on ice cloud formation. However, 3-4K above the homogeneous freezing point, immersion mode IN number densities a few days down wind of the eruption were sufficiently high to have a moderate influence on ice cloud formation. The efficiency of IN in the deposition mode was found to be poor except at very cold conditions (<238 K), when they reach an efficiency similar to that of mineral dust with the onset of freezing at 10% supersaturation with respect to ice, and with the frozen fraction nearing its maximum value at a supersaturation 20%. In summary, these investigations suggest volcanic ash particles to have only moderate effects on atmospheric ice formation.
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| 9. |
- Zhang, Y., et al.
(author)
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Dark Energy Surveyed Year 1 results : calibration of cluster mis-centring in the redMaPPer catalogues
- 2019
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In: Monthly notices of the Royal Astronomical Society. - : OXFORD UNIV PRESS. - 0035-8711 .- 1365-2966. ; 487:2, s. 2578-2593
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Journal article (peer-reviewed)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. |
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| 11. |
- Manolopoulou, M., et al.
(author)
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Environmental dependence of X-ray and optical properties of galaxy clusters
- 2021
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In: Monthly notices of the Royal Astronomical Society. - : Oxford University Press. - 0035-8711 .- 1365-2966. ; 500:2, s. 1953-1963
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Journal article (peer-reviewed)abstract
- Galaxy clusters are widely used to constrain cosmological parameters through their properties, such as masses, luminosity, and temperature distributions. One should take into account all kind of biases that could affect these analyses in order to obtain reliable constraints. In this work, we study the difference in the properties of clusters residing in different large-scale environments, defined by their position within or outside of voids, and the density of their surrounding space. We use both observational and simulation cluster and void catalogues, i.e. XMM Cluster Survey (XCS) and redMaPPer clusters, Baryon Oscillation Spectroscopic Survey (BOSS) voids, and Magneticum simulations. We devise two different environmental proxies for the clusters and study their redshift, richness, mass, X-ray luminosity, and temperature distributions, as well as some properties of their galaxy populations. We use the Kolmogorov-Smirnov two-sample test to discover that richer and more massive clusters are more prevalent in overdense regions and outside of voids. We also find that clusters of matched richness and mass in overdense regions and outside voids tend to have higher X-ray luminosities and temperatures. These differences could have important implications for precision cosmology with clusters of galaxies, since cluster mass calibrations can vary with environment.
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| 12. |
- Mehrtens, N., et al.
(author)
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The XMM Cluster Survey : the halo occupation number of BOSS galaxies in X-ray clusters
- 2016
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In: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 463:2, s. 1929-1943
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Journal article (peer-reviewed)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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| 13. |
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| 14. |
- Nicholson, Anna M., et al.
(author)
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Fixation and Spread of Somatic Mutations in Adult Human Colonic Epithelium
- 2018
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In: Cell Stem Cell. - : CELL PRESS. - 1934-5909 .- 1875-9777. ; 22:6, s. 909-918.e8
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Journal article (peer-reviewed)abstract
- We investigated the means and timing by which mutations become fixed in the human colonic epithelium by visualizing somatic clones and mathematical inference. Fixation requires two sequential steps. First, one of approximately seven active stem cells residing within each colonic crypt has to be mutated. Second, the mutated stem cell has to replace neighbors to populate the entire crypt in a process that takes several years. Subsequent clonal expansion due to crypt fission is infrequent for neutral mutations (around 0.7% of all crypts undergo fission in a single year). Pro-oncogenic mutations subvert both stem cell replacement to accelerate fixation and clonal expansion by crypt fission to achieve high mutant allele frequencies with age. The benchmarking of these behaviors allows the advantage associated with different gene-specific mutations to be compared irrespective of the cellular mechanisms by which they are conferred.
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| 15. |
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| 16. |
- Stott, J. P., et al.
(author)
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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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In: Astrophysical Journal. - 0004-637X .- 1538-4357. ; 718:1, s. 23-30
-
Journal article (peer-reviewed)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. |
- Viana, P. T. P., et al.
(author)
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The XMM Cluster Survey : Present status and latest results
- 2013
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In: Astronomical Notes - Astronomische Nachrichten. - : Wiley. - 0004-6337 .- 1521-3994. ; 334:4-5, s. 462-465
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Journal article (peer-reviewed)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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| 18. |
- Wexler, J. B., et al.
(author)
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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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In: Journal of Experimental Marine Biology and Ecology. - 0022-0981. ; 569
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Journal article (peer-reviewed)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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