| 1. |
- Campbell, PJ, et al.
(författare)
-
Pan-cancer analysis of whole genomes
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
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.
|
|
| 2. |
- Yakneen, S, et al.
(författare)
-
Butler enables rapid cloud-based analysis of thousands of human genomes
- 2020
-
Ingår i: Nature biotechnology. - : Springer Science and Business Media LLC. - 1546-1696 .- 1087-0156. ; 38:3, s. 288-
-
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.
|
|
| 3. |
|
|
| 4. |
- Rettig, L., et al.
(författare)
-
Disentangling transient charge order from structural dynamics contributions during coherent atomic motion studied by ultrafast resonant x-ray diffraction
- 2019
-
Ingår i: Physical Review B. - 2469-9950. ; 99:13
-
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.
|
|
| 5. |
- Tamai, Anna, et al.
(författare)
-
High-Resolution Photoemission on Sr2RuO4 Reveals Correlation-Enhanced Effective Spin-Orbit Coupling and Dominantly Local Self-Energies
- 2019
-
Ingår i: Physical Review X. - New York : American Physical Society. - 2160-3308. ; 9:2
-
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.
|
|
| 6. |
- Hakola, A., et al.
(författare)
-
Plasma-wall interaction studies in the full-W ASDEX upgrade during helium plasma discharges
- 2017
-
Ingår i: Nuclear Fusion. - : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 57:6
-
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.
|
|
| 7. |
|
|
| 8. |
- Güttler, M., et al.
(författare)
-
Divalent EuRh 2 Si 2 as a reference for the Luttinger theorem and antiferromagnetism in trivalent heavy-fermion YbRh 2 Si 2
- 2019
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
-
Tidskriftsartikel (refereegranskat)abstract
- Application of the Luttinger theorem to the Kondo lattice YbRh 2 Si 2 suggests that its large 4f-derived Fermi surface (FS) in the paramagnetic (PM) regime should be similar in shape and volume to that of the divalent local-moment antiferromagnet (AFM) EuRh 2 Si 2 in its PM regime. Here we show by angle-resolved photoemission spectroscopy that paramagnetic EuRh 2 Si 2 has a large FS essentially similar to the one seen in YbRh 2 Si 2 down to 1 K. In EuRh 2 Si 2 the onset of AFM order below 24.5 K induces an extensive fragmentation of the FS due to Brillouin zone folding, intersection and resulting hybridization of the Fermi-surface sheets. Our results on EuRh 2 Si 2 indicate that the formation of the AFM state in YbRh 2 Si 2 is very likely also connected with similar changes in the FS, which have to be taken into account in the controversial analysis and discussion of anomalies observed at the quantum critical point in this system.
|
|
| 9. |
|
|
| 10. |
- Plummer, G., et al.
(författare)
-
On the origin of kinking in layered crystalline solids
- 2021
-
Ingår i: Materials Today. - : Elsevier Science Ltd. - 1369-7021 .- 1873-4103. ; 43, s. 45-52
-
Tidskriftsartikel (refereegranskat)abstract
- Kinking is a deformation mechanism ubiquitous to layered systems, ranging from the nanometer scale in layered crystalline solids, to the kilometer scale in geological formations. Herein, we demonstrate its origins in the former through multiscale experiments and atomistic simulations. When compressively loaded parallel to their basal planes, layered crystalline solids first buckle elastically, then nucleate atomic-scale, highly stressed ripplocation boundaries - a process driven by redistributing strain from energetically expensive in-plane bonds to cheaper out-of-plane bonds. The consequences are far reaching as the unique mechanical properties of layered crystalline solids are highly dependent upon their ability to deform by kinking. Moreover, the compressive strength of numerous natural and engineered layered systems depends upon the ease of kinking or lack there of.
|
|
| 11. |
- Baljozovic, Milos, et al.
(författare)
-
Self-Assembly and Magnetic Order of Bi-Molecular 2D Spin Lattices of M(II,III) Phthalocyanines on Au(111)
- 2021
-
Ingår i: MAGNETOCHEMISTRY. - : MDPI. - 2312-7481. ; 7:8
-
Tidskriftsartikel (refereegranskat)abstract
- Single layer low-dimensional materials are presently of emerging interest, including in the context of magnetism. In the present report, on-surface supramolecular architecturing was further developed and employed to create surface supported two-dimensional binary spin arrays on atomically clean non-magnetic Au(111). By chemical programming of the modules, different checkerboards were produced combining phthalocyanines containing metals of different oxidation and spin states, diamagnetic zinc, and a metal-free 'spacer'. In an in-depth, spectro-microscopy and theoretical account, we correlate the structure and the magnetic properties of these tunable systems and discuss the emergence of 2D Kondo magnetism from the spin-bearing components and via the physico-chemical bonding to the underlying substrate. The contributions of the individual elements, as well as the role of the electronic surface state in the bottom substrate, are discussed, also looking towards further in-depth investigations.
|
|
| 12. |
- Goossens, Nick, et al.
(författare)
-
Upscaled Synthesis Protocol for Phase-Pure, Colloidally Stable MXenes with Long Shelf Lives
- 2023
-
Ingår i: Small Methods. - : WILEY-V C H VERLAG GMBH. - 2366-9608.
-
Tidskriftsartikel (refereegranskat)abstract
- MXenes are electrically conductive 2D transition metal carbides/nitrides obtained by the etching of nanolaminated MAX phase compounds, followed by exfoliation to single- or few-layered nanosheets. The mainstream chemical etching processes have evolved from pure hydrofluoric acid (HF) etching into the innovative "minimally intensive layer delamination" (MILD) route. Despite their current popularity and remarkable application potential, the scalability of MILD-produced MXenes remains unproven, excluding MXenes from industrial applications. This work proposes a "next-generation MILD" (NGMILD) synthesis protocol for phase-pure, colloidally stable MXenes that withstand long periods of dry storage. NGMILD incorporates the synergistic effects of a secondary salt, a richer lithium (Li) environment, and iterative alcohol-based washing to achieve high-purity MXenes, while improving etching efficiency, intercalation, and shelf life. Moreover, NGMILD comprises a sulfuric acid (H2SO4) post-treatment for the selective removal of the Li3AlF6 impurity that commonly persists in MILD-produced MXenes. This work demonstrates the upscaled NGMILD synthesis of (50 g) phase-pure Ti(3)C(2)Tz MXene clays with high extraction yields (>22%) of supernatant dispersions. Finally, NGMILD-produced MXene clays dry-stored for six months under ambient conditions experience minimal degradation, while retaining excellent redispersibility. Overall, the NGMILD protocol is a leap forward toward the industrial production of MXenes and their subsequent market deployment.
|
|
| 13. |
- Kokkoris, M., et al.
(författare)
-
Benchmarking the evaluated proton differential cross sections suitable for the EBS analysis of natSi and 16O
- 2017
-
Ingår i: Nuclear Instruments and Methods in Physics Research Section B. - : Elsevier BV. - 0168-583X .- 1872-9584. ; 405, s. 50-60
-
Tidskriftsartikel (refereegranskat)abstract
- The evaluated proton differential cross sections suitable for the Elastic Backscattering Spectroscopy (EBS) analysis of Si-nat and O-16, as obtained from SigmaCalc 2.0, have been benchmarked over a wide energy and angular range at two different accelerator laboratories, namely at N.C.S.R. 'Demokritos', Athens, Greece and at Ruder Boskovic Institute (RBI), Zagreb, Croatia, using a variety of high-purity thick targets of known stoichiometry. The results are presented in graphical and tabular forms, while the observed discrepancies, as well as, the limits in accuracy of the benchmarking procedure, along with target related effects, are thoroughly discussed and analysed. In the case of oxygen the agreement between simulated and experimental spectra was generally good, while for silicon serious discrepancies were observed above E-p,E-lab = 2.5 MeV, suggesting that a further tuning of the appropriate nuclear model parameters in the evaluated differential cross-section datasets is required.
|
|
| 14. |
- Kozina, M., et al.
(författare)
-
Local terahertz field enhancement for time-resolved x-ray diffraction
- 2017
-
Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 110:8
-
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.
|
|
| 15. |
- Matt, C. E., et al.
(författare)
-
Electron scattering, charge order, and pseudogap physics in La1.6-xNd0.4SrxCuO4 : An angle-resolved photoemission spectroscopy study
- 2015
-
Ingår i: Physical Review B. Condensed Matter and Materials Physics. - : American Physical Society. - 1098-0121 .- 1550-235X. ; 92:13
-
Tidskriftsartikel (refereegranskat)abstract
- We report an angle-resolved photoemission study of the charge stripe ordered La1.6-xNd0.4SrxCuO4 (Nd-LSCO) system. A comparative and quantitative line-shape analysis is presented as the system evolves from the overdoped regime into the charge ordered phase. On the overdoped side (x = 0.20), a normal-state antinodal spectral gap opens upon cooling below 80 K. In this process, spectral weight is preserved but redistributed to larger energies. A correlation between this spectral gap and electron scattering is found. A different line shape is observed in the antinodal region of charge ordered Nd-LSCO x = 1/8. Significant low-energy spectral weight appears to be lost. These observations are discussed in terms of spectral-weight redistribution and gapping originating from charge stripe ordering.
|
|
| 16. |
- Patterson, Nick, et al.
(författare)
-
Large-scale migration into Britain during the Middle to Late Bronze Age
- 2022
-
Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; , s. 588-594
-
Tidskriftsartikel (refereegranskat)abstract
- Present-day people from England and Wales harbour more ancestry derived from Early European Farmers (EEF) than people of the Early Bronze Age1. To understand this, we generated genome-wide data from 793 individuals, increasing data from the Middle to Late Bronze and Iron Age in Britain by 12-fold, and Western and Central Europe by 3.5-fold. Between 1000 and 875 BC, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of Iron Age people of England and Wales, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2-6. There was comparatively less gene flow from continental Europe during the Iron Age, and Britain's independent genetic trajectory is also reflected in the rise of the allele conferring lactase persistence to ~50% by this time compared to ~7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period.
|
|
| 17. |
- Razzoli, E., et al.
(författare)
-
Rotation symmetry breaking in La2-xSrxCuO4 revealed by angle-resolved photoemission spectroscopy
- 2017
-
Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 95:22
-
Tidskriftsartikel (refereegranskat)abstract
- Using angle-resolved photoemission spectroscopy it is revealed that in the vicinity of optimal doping the electronic structure of La2-x SrxCuO4 cuprate undergoes an electronic reconstruction associated with a wave vector q(a) = (pi, 0). The reconstructed Fermi surface and folded band are distinct to the shadow bands observed in BSCCO cuprates and in underdoped La2-xSrxCuO4 with x <= 0.12, which shift the primary band along the zone diagonal direction. Furthermore, the folded bands appear only with q(a) = (pi, 0) vector, but not with q(b) = (0, pi). We demonstrate that the absence of q(b) reconstruction is not due to thematrix-element effects in the photoemission process, which indicates the fourfold symmetry is broken in the system.
|
|
| 18. |
- Razzoli, E., et al.
(författare)
-
The Fermi surface and band folding in La2-xSrxCuO4, probed by angle-resolved photoemission
- 2010
-
Ingår i: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 12, s. 125003-
-
Tidskriftsartikel (refereegranskat)abstract
- A systematic angle-resolved photoemission study of the electronic structure of La2-xSrxCuO4 in a wide doping range is presented in this paper. In addition to the main energy band, we observed a weaker additional band, the (pi, pi) folded band, which shows unusual doping dependence. The appearance of the folded band suggests that a Fermi surface reconstruction is doping dependent and could already occur at zero magnetic field.
|
|
| 19. |
- Spencer, C B, et al.
(författare)
-
Phase Evaluation in Al(2)O(3) Fiber-Reinforced Ti(2)AlC During Sintering in the 1300 degrees C-1500 degrees C Temperature Range
- 2011
-
Ingår i: Journal of The American Ceramic Society. - : Wiley-Blackwell. - 0002-7820 .- 1551-2916. ; 94:10, s. 3327-3334
-
Tidskriftsartikel (refereegranskat)abstract
- In this article, the reactivity of Ti(2)AlC powders, with 3 and 10 mu m alumina, Al(2)O(3), fibers during pressure-assisted sintering is explored. Samples were fabricated by hot-isostatic-pressing (HIPed) or hot-pressing (HPed), and characterized by X-ray diffraction, differential thermal analysis, and electron microscopy-both scanning and transmission-equipped with energy dispersive X-ray spectroscopes. Samples prepared at 1300 degrees C were fully dense, with no apparent reaction between fiber and matrix. In samples HPed to 1500 degrees C, even pure Ti(2)AlC powders dissociated to Ti(3)AlC(2) according to: 2 Ti(2)AlC = Ti(3)AlC(2) + TiAl(x) (l) + (1-x) Al (l/v), with x andlt; 1. More severe Al loss results in the formation of TiC(y). The presence of the Al(2)O(3) fibers delayed densification enough to allow most of the Al and some of the Ti to escape into the vacuum of the hot press or react with the encapsulating glass during HIPing a resulting in a more intensive dissociation of the Ti(2)AlC. Although, in principle Ti(2)AlC can be reinforced with Al(2)O(3) fibers, the processing/use temperature will have to be kept below 1500 degrees C, as, at that temperature the fibers, used here, sinter together.
|
|
