| 1. |
- 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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| 2. |
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- 2019
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Journal article (peer-reviewed)
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| 3. |
- Ueda, K, et al.
(author)
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Anisotropic ultrafast dissociation probed by the Doppler effect in resonant photoemission from CF4
- 2003
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In: Physical Review Letters. - 1079-7114. ; 90:23: 233006
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Journal article (peer-reviewed)abstract
- The resonant Auger spectrum from the decay of F 1s-excited CF4 is measured. Several lines exhibit a nondispersive kinetic energy as the exciting photon energy is tuned through the resonance region. The F 1s(-1) atomiclike Auger line is split into two components due to the emission of Auger electrons by a fragment in motion, when electron emission is observed along the polarization vector of the light. This Doppler splitting is direct evidence that the core excitation leads to T-d-->C-3v symmetry lowering, by elongation of a specific C-F bond preferentially aligned along the polarization vector of the incident photon.
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| 4. |
- Ueda, K, et al.
(author)
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Nuclear motion and symmetry breaking of the B 1s-excited BF3 molecule
- 2003
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In: Chemical Physics. - 0301-0104. ; 289:1, s. 135-147
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Journal article (peer-reviewed)abstract
- Out-of-plane nuclear motion stimulated in the core-excited state and symmetry breaking due to this nuclear motion have been investigated for B Is excitation in the BF3 molecule by a combination of three different experimental methods: angle-resolved ion-yield spectroscopy, vibrationally resolved resonant Auger electron spectroscopy and quadruple-ion coincidence momentum-imaging technique. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 5. |
- Feifel, R, et al.
(author)
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Probing doubly excited ionic states of N-2(+) via a triple excitation above the N 1s threshold in the N-2 molecule
- 2003
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In: Physical Review A (Atomic, Molecular and Optical Physics). - 1050-2947. ; 67:3: 032504
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Journal article (peer-reviewed)abstract
- Angle-resolved resonant Auger-electron spectroscopy has been carried out on the nitrogen molecule at selected photon energies around 419 eV, where a 1s core electron and two valence electrons are promoted into the lowest unoccupied molecular orbital 1pi(g). Significant enhancement of a specific band, which cannot be disentangled in direct photoionization, is observed at a binding energy of 37.6 eV, with a value of the anisotropy parameter beta much smaller than 2. We assign this new band to the transition to a doubly excited cationic state of N-2, in which two of the excited valence electrons remain in the 1pi(g) orbital, proposing a "double spectator" type decay mechanism. This observation shows how to preferentially probe multiply excited configurations of cations using multiple resonant excitation.
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| 6. |
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| 7. |
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| 8. |
- Kitajima, M., et al.
(author)
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Doppler effect in resonant photoemission from SF6 : Correlation between doppler profile and auger emission anisotropy
- 2003
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 91:21
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Journal article (peer-reviewed)abstract
- Fragmentation of the SF6 molecule upon F 1s excitation has been studied by resonant photoemission. The F atomiclike Auger line exhibits the characteristic Doppler profile that depends on the direction of the photoelectron momentum relative to the polarization vector of the radiation as well as on the photon energy. The measured Doppler profiles are analyzed by the model simulation that takes account of the anisotropy of the Auger emission in the molecular frame. The Auger anisotropy extracted from the data decreases with an increase in the F-SF5 internuclear distance.
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| 9. |
- R. Feifel, K. Ueda, A. De Fanis, K. Okada, S. Tanimoto, T. Furuta, H. Shindo, M. Kitajima, H. Tanaka, O. Björneholm, L. Karlsson, S. Svensson and S. L. Sorensen
(author)
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Probing doubly excited ionic states of N2+ via a triple excitation above the N1s threshold in the N2 moecule
- 2003
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In: Phys. Rev.. ; A:67, s. 32504-
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Journal article (peer-reviewed)
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| 10. |
- Sato, T., et al.
(author)
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Overview of particle and heavy ion transport code system PHITS
- 2015
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In: Annals of Nuclear Energy. - : Elsevier BV. - 0306-4549 .- 1873-2100. ; 82, s. 110-115
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Journal article (peer-reviewed)abstract
- A general purpose Monte Carlo Particle and Heavy Ion Transport code System, PHITS, is being developed through the collaboration of several institutes in Japan and Europe. The Japan Atomic Energy Agency is responsible for managing the entire project. PHITS can deal with the transport of nearly all particles, including neutrons, protons, heavy ions, photons, and electrons, over wide energy ranges using various nuclear reaction models and data libraries. It is written in Fortran language and can be executed on almost all computers. All components of PHITS such as its source, executable and data-library files are assembled in one package and then distributed to many countries via the Research Organization for Information Science and Technology, the Data Bank of the Organization for Economic Co-operation and Development's Nuclear Energy Agency, and the Radiation Safety Information Computational Center. More than 1500 researchers have been registered as PHITS users, and they apply the code to various research and development fields such as nuclear technology, accelerator design, medical physics, and cosmic-ray research. This paper briefly summarizes the physics models implemented in PHITS, and introduces some important functions useful for specific applications, such as an event generator mode and beam transport functions. (C) 2014 Elsevier Ltd. All rights reserved.
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