| 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. |
- 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.
|
|
| 5. |
- 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.
|
|
| 6. |
- 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.
|
|
| 7. |
- Kozina, M., et al.
(författare)
-
Terahertz-driven phonon upconversion in SrTiO3
- 2019
-
Ingår i: Nature Physics. - : Springer Science and Business Media LLC. - 1745-2473 .- 1745-2481. ; 15:4, s. 387-
-
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.
|
|
| 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. |
- 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.
|
|
| 10. |
- 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.
|
|
