| 1. |
- 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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| 2. |
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| 3. |
- Yakneen, S, et al.
(författare)
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Butler enables rapid cloud-based analysis of thousands of human genomes
- 2020
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Ingår i: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 38:3, s. 288-
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Tidskriftsartikel (refereegranskat)abstract
- We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data processing and analysis by 43% compared with current approaches. Butler enabled processing of a 725-terabyte cancer genome dataset from the Pan-Cancer Analysis of Whole Genomes (PCAWG) project in a time-efficient and uniform manner.
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| 4. |
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| 5. |
- Hakola, A., et al.
(författare)
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Plasma-wall interaction studies in the full-W ASDEX upgrade during helium plasma discharges
- 2017
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Ingår i: Nuclear Fusion. - : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 57:6
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Tidskriftsartikel (refereegranskat)abstract
- Plasma-wall interactions have been studied in the full-W ASDEX Upgrade during its dedicated helium campaign. Relatively clean plasmas with a He content of > 80% could be obtained by applying ion cyclotron wall conditioning (ICWC) discharges upon changeover from D to He. However, co-deposited layers with significant amounts of He and D were measured on W samples exposed to ICWC plasmas at the low-field side (outer) midplane. This is a sign of local migration and accumulation of materials and residual fuel in regions shadowed from direct plasma exposure albeit globally D was removed from the vessel. When exposing W samples to ELMy H-mode helium plasmas in the outer strike-point region, no net erosion was observed but the surfaces had been covered with co-deposited layers mainly consisting of W, B, C, and D and being the thickest on rough and modified surfaces. This is different from the typical erosion-deposition patterns in D plasmas, where usually sharp net-erosion peaks surrounded by prominent net-deposition maxima for W are observed close to the strike point. Moreover, no clear signs of W nanostructure growth or destruction could be seen. The growth of deposited layers may impact the operation of future fusion reactors and is attributed to strong sources in the main chamber that under suitable conditions may switch the balance from net erosion into net deposition, even close to the strike points. In addition, the absence of noticeable chemical erosion in helium plasmas may have affected the thickness of the deposited layers. Retention of He, for its part, remained small and uniform throughout the strike-point region although our results indicate that samples with smooth surfaces can contain an order of magnitude less He than their rough counterparts.
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| 6. |
- Kozina, M., et al.
(författare)
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Local terahertz field enhancement for time-resolved x-ray diffraction
- 2017
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 110:8
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Tidskriftsartikel (refereegranskat)abstract
- We report local field strength enhancement of single-cycle terahertz (THz) pulses in an ultrafast time-resolved x-ray diffraction experiment. We show that patterning the sample with gold microstructures increases the THz field without changing the THz pulse shape or drastically affecting the quality of the x-ray diffraction pattern. We find a five-fold increase in THz-induced x-ray diffraction intensity change in the presence of microstructures on a SrTiO3 thin-film sample.
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| 7. |
- Kozina, M., et al.
(författare)
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Terahertz-driven phonon upconversion in SrTiO3
- 2019
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Ingår i: Nature Physics. - : Springer Science and Business Media LLC. - 1745-2473 .- 1745-2481. ; 15:4, s. 387-
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Tidskriftsartikel (refereegranskat)abstract
- Direct manipulation of the atomic lattice using intense long-wavelength laser pulses has become a viable approach to create new states of matter in complex materials. Conventionally, a high-frequency vibrational mode is driven resonantly by a mid-infrared laser pulse and the lattice structure is modified through indirect coupling of this infrared-active phonon to other, lower-frequency lattice modulations. Here, we drive the lowest-frequency optical phonon in the prototypical transition metal oxide SrTiO3 well into the anharmonic regime with an intense terahertz field. We show that it is possible to transfer energy to higher-frequency phonon modes through nonlinear coupling. Our observations are carried out by directly mapping the lattice response to the coherent drive field with femtosecond X-ray pulses, enabling direct visualization of the atomic displacements.
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| 8. |
- Rettig, L., et al.
(författare)
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Disentangling transient charge order from structural dynamics contributions during coherent atomic motion studied by ultrafast resonant x-ray diffraction
- 2019
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Ingår i: Physical Review B. - 2469-9950. ; 99:13
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Tidskriftsartikel (refereegranskat)abstract
- We report on the ultrafast dynamics of charge order and structural response during the photoinduced suppression of charge and orbital order in a mixed-valence manganite. Employing femtosecond time-resolved resonant x-ray diffraction below and at the Mn K absorption edge, we present a method to disentangle the transient charge order and structural dynamics in thin films of Pr0.5Ca0.5MnO3. Based on the static resonant scattering spectra, we extract the dispersion correction of charge-ordered Mn3+ and Mn4+ ions, allowing us to separate the transient contributions of purely charge order from structural contributions to the scattering amplitude after optical excitation. Our finding of a coherent structural mode at around 2.3THz, which primarily modulates the lattice but does not strongly affect the charge order, supports the picture of the charge order being the driving force of the combined charge, orbital, and structural transition.
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| 9. |
- Tamai, Anna, et al.
(författare)
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High-Resolution Photoemission on Sr2RuO4 Reveals Correlation-Enhanced Effective Spin-Orbit Coupling and Dominantly Local Self-Energies
- 2019
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Ingår i: Physical Review X. - New York : American Physical Society. - 2160-3308. ; 9:2
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Tidskriftsartikel (refereegranskat)abstract
- We explore the interplay of electron-electron correlations and spin-orbit coupling in the model Fermi liquid Sr2RuO4 using laser-based angle-resolved photoemission spectroscopy. Our precise measurement of the Fermi surface confirms the importance of spin-orbit coupling in this material and reveals that its effective value is enhanced by a factor of about 2, due to electronic correlations. The self-energies for the β and γ sheets are found to display significant angular dependence. By taking into account the multi-orbital composition of quasiparticle states, we determine self-energies associated with each orbital component directly from the experimental data. This analysis demonstrates that the perceived angular dependence does not imply momentum-dependent many-body effects but arises from a substantial orbital mixing induced by spin-orbit coupling. A comparison to single-site dynamical mean-field theory further supports the notion of dominantly local orbital self-energies and provides strong evidence for an electronic origin of the observed nonlinear frequency dependence of the self-energies, leading to “kinks” in the quasiparticle dispersion of Sr2RuO4.
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