| 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. |
- Diakaki, M., et al.
(författare)
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Towards the high-accuracy determination of the 238U fission cross section at the threshold region at CERN -€“ n_TOF
- 2016
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Ingår i: EPJ Web of Conferences. - : EDP Sciences. - 2100-014X.
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Konferensbidrag (refereegranskat)abstract
- The U-238 fission cross section is an international standard beyond 2 MeV where the fission plateau starts. However, due to its importance in fission reactors, this cross-section should be very accurately known also in the threshold region below 2 MeV. The U-238 fission cross section has been measured relative to the U-235 fission cross section at CERN - n_TOF with different detection systems. These datasets have been collected and suitably combined to increase the counting statistics in the threshold region from about 300 keV up to 3 MeV. The results are compared with other experimental data, evaluated libraries, and the IAEA standards.
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| 3. |
- Abbondanno, U, et al.
(författare)
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The data acquisition system of the neutron time-of-flight facility n_TOF at CERN
- 2005
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 538:1-3, s. 692-702
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Tidskriftsartikel (refereegranskat)abstract
- The n_TOF facility at CERN has been designed for the measurement of neutron capture, fission and (n, xn) cross-sections with high accuracy. This requires a flexible and-due to the high instantaneous neutron flux-almost dead time free data acquisition system. A scalable and versatile data solution has been designed based on 8-bit flash-ADCs with sampling rates up to 2 GHz and 8 Mbyte memory buffer. The software is written in C and C++ and is running on PCs equipped with RedHat Linux.
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| 4. |
- Paradela, C., et al.
(författare)
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High-accuracy determination of the 238U/235U fission cross section ratio up to ~1 GeV at n_TOF at CERN
- 2015
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 91, s. 024602-
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Tidskriftsartikel (refereegranskat)abstract
- The U238 to U235 fission cross section ratio has been determined at n_TOF up to ≈1 GeV, with two different detection systems, in different geometrical configurations. A total of four datasets has been collected and compared. They are all consistent to each other within the relative systematic uncertainty of 3–4%. The data collected at n_TOF have been suitably combined to yield a unique fission cross section ratio as a function of neutron energy. The result confirms current evaluations up to 200 MeV. Good agreement is also observed with theoretical calculations based on the INCL++/Gemini++ combination up to the highest measured energy. The n_TOF results may help solve a long-standing discrepancy between the two most important experimental datasets available so far above 20 MeV, while extending the neutron energy range for the first time up to ≈1 GeV.
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| 5. |
- Paradela, C., et al.
(författare)
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High accuracy 235U(n,f) data in the resonance energy region
- 2016
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Ingår i: EPJ Web of Conferences. - : EDP Sciences. - 2100-014X.
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Konferensbidrag (refereegranskat)abstract
- The U-235 neutron-induced cross section is widely used as reference cross section for measuring other fission cross sections, but in the resonance region it is not considered as an IAEA standard because of the scarce experimental data covering the full region. In this work, we deal with a new analysis of the experimental data obtained with a detection setup based on parallel plate ionization chambers (PPACs) at the CERN n_TOF facility in the range from 1 eV to 10 keV. The relative cross section has been normalised to the IAEA value in the region between 7.8 and 11 eV, which is claimed as well-known. Comparison with the ENDF/B-VII evaluation and the IAEA reference file from 100 eV to 10 keV are provided.
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| 6. |
- Rheinbay, E, et al.
(författare)
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 102-
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Tidskriftsartikel (refereegranskat)abstract
- The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53, in the 3′ untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
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| 7. |
- Carlevaro-Fita, J, et al.
(författare)
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Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis
- 2020
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1, s. 56-
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Tidskriftsartikel (refereegranskat)abstract
- Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.
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| 8. |
- Isaev, E. I., et al.
(författare)
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Phonon related properties of transition metals, their carbides, and nitrides : A first-principles study
- 2007
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Ingår i: Journal of Applied Physics. - : AIP Publishing. - 0021-8979 .- 1089-7550. ; 101:12
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Forskningsöversikt (refereegranskat)abstract
- Lattice dynamics of body-centered cubic (bcc) V-b-VIb group transition metals (TM), and B1-type monocarbides and mononitrides of IIIb-VIb transition metals are studied by means of first-principles density functional perturbation theory, ultra soft pseudopotentials, and generalized gradient approximation to the exchange-correlation functional. Ground state parameters of transition metals and their compounds are correctly reproduced with the generated ultrasoft pseudopotentials. The calculated phonon spectra of the bcc metals are in excellent agreement with results of inelastic neutron scattering experiments. We show that the superconductivity of transition metal carbides (TMC) and transition metal nitrides (TMN) is related to peculiarities of the phonon spectra, and the anomalies of the spectra are connected to the number of valence electrons in crystals. The calculated electron-phonon interaction constants for TM, TMC, and TMN are in excellent agreement with experimentally determined values. Phonon spectra for a number of monocarbides and mononitrides of transition metals within the cubic NaCl- and hexagonal WC-type structures are predicted. Ideal stoichiometric B1 crystals of ScC, YC, and VC are predicted to be dynamically stable and superconducting materials. We also conclude that YN is a semiconductor.
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| 9. |
- Korzhavyi, Pavel A., 1966-, et al.
(författare)
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Defect-induced magnetic structure in (Ga1-xMnx)As
- 2002
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 88:18, s. 187202-
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Tidskriftsartikel (refereegranskat)abstract
- We show that magnetic structures involving partial disorder of local magnetic moments on the Mn atoms in (Ga1-xMnx)As lower the total energy, compared to the case of perfect ferromagnetic ordering, when As defects on the Ga sublattice are present. Such magnetic structures are found to be stable for a range of concentrations of As antisites, and this result accounts for the observed magnetic moments and critical temperatures in (Ga1-xMnx)As . We propose an explanation for the stabilization of the partially disordered magnetic structures and conclude that the magnetization and critical temperatures should increase substantially by reducing the number of As antisite defects.
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| 10. |
- Baykov, Vitaly, et al.
(författare)
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Ab Initio Studies of the Energy Characteristics and Magnetic Properties of Point Defects in GaAs
- 2005
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Ingår i: Physics of the solid state. - : Pleiades Publishing Ltd. - 1063-7834 .- 1090-6460. ; 47:10, s. 1831-1836
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Tidskriftsartikel (refereegranskat)abstract
- The formation energies of intrinsic point defects and solution energies of transition metal impurities in gallium arsenide are determined on the basis of ab initio calculations using the method of a locally self-consistent Green's function, which is a generalization of the coherent potential approximation. Based on the calculated energies, the conclusion is made that the As-Ga antisite defect is the most common intrinsic defect in GaAs. Calculations showed that transition metal impurities, except for Ni, preferentially occupy gallium sites substitutionally. The magnetic moments of impurity atoms are calculated as a function of the chemical environment. It is shown that, in compensated GaAs, Mn atoms tend to form clusters.
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| 11. |
- Dubrovinskaia, N., et al.
(författare)
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Compressibility of boron-doped diamond
- 2006
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Ingår i: High Pressure Research. - : Informa UK Limited. - 0895-7959 .- 1477-2299. ; 26, No. 2, s. 79-85
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Tidskriftsartikel (refereegranskat)
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| 12. |
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| 13. |
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| 14. |
- Isaeva, L E, et al.
(författare)
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Dynamic stability of palladium hydride: An ab initio study
- 2011
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Ingår i: INTERNATIONAL JOURNAL OF HYDROGEN ENERGY. - : Elsevier Science B.V., Amsterdam.. - 0360-3199. ; 36:1, s. 1254-1258
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Tidskriftsartikel (refereegranskat)abstract
- We present results of our ab initio studies of electronic and dynamic properties of ideal palladium hydride PdH and its vacancy ordered defect phase Pd(3)VacH(4) ("Vac" - vacancy on palladium site) with L1(2) crystal structure found experimentally and studied theoretically. Quantum and thermodynamic properties of these hydrides, such as phonon dispersion relations and the vacancy formation enthalpies have been studied. Dynamic stability of the defect phase Pd(3)VacH(4) with respect to different site occupation of hydrogen atoms at the equilibrium state and under pressure was analyzed. It was shown that positions of hydrogen atoms in the defect phase strongly affect its stability and may be a reason for further phase transitions in the defect phase.
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| 15. |
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| 16. |
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| 17. |
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| 18. |
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| 19. |
- Utyushev, A. D., et al.
(författare)
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Engineering novel tunable optical high-Q nanoparticle array filters for a wide range of wavelengths
- 2020
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Ingår i: Optics Express. - : Optical Society of America. - 1094-4087. ; 28:2, s. 1426-1438
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Tidskriftsartikel (refereegranskat)abstract
- The interaction of non-monochromatic radiation with arrays comprising plasmonic and dielectric nanoparticles has been studied using the finite-difference time-domain electrodynamics method. It is shown that LiNbO3, TiO2, GaAs, Si, and Ge all-dielectric nanoparticle arrays can provide a complete selective reflection of an incident plane wave within a narrow spectral line of collective lattice resonance with a Q-factor of 103 or larger at various spectral ranges, while plasmonic refractory TiN and chemically stable Au nanoparticle arrays provide high-Q resonances with moderate reflectivity. Arrays with fixed dimensional parameters make it possible to fine-tune the position of a selected resonant spectral line by tilting the array relative to the direction of the incident radiation. These effects provide grounds for engineering novel selective tunable optical high-Q filters in a wide range of wavelengths, from visible to middle-IR.
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| 20. |
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| 21. |
- Zarechnaya, E. Y., et al.
(författare)
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Theoretical study of linear monoatomic nanowires, dimer and bulk of Cu, Ag, Au, Ni, Pd and Pt
- 2008
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Ingår i: Computational materials science. - : Elsevier BV. - 0927-0256 .- 1879-0801. ; 43:3, s. 522-530
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Tidskriftsartikel (refereegranskat)abstract
- The binding and electronic properties of monoatomic nanowires, dimers and bulk structures of Cu, Ag, Au and Ni, Pd, Pt have been studied by the projector augmented-wave method (PAW) within the density functional theory (DFT) using the local density approximation (LDA) as well as generalized gradient approximation (GGA) in both Perdew-Wang (PW91) and Perdew-Burke-Ernzerhof (PBE) parameterizations. Our results show that the formation of atomic chains is not equally plausible for all the studied elements. In agreement with experimental observations Pt and An stand out as most likely elements to form monoatomic wires. Changes in the electronic structure and magnetic properties of metal chains at stretching are analyzed.
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| 22. |
- Belonoshko, Anatoly B., et al.
(författare)
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Stability of the body-centered-tetragonal phase of Fe at high pressure : Ground-state energies, phonon spectra, and molecular dynamics simulations
- 2006
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 74:21
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Tidskriftsartikel (refereegranskat)abstract
- It is well established that at a pressure of several megabars and low temperature Fe is stable in the hexagonal-close-packed (hcp) phase. However, there are indications that on heating a high-pressure hcp phase of Fe transforms to a less dense (open structure) phase. Two phases have been suggested as candidates for these high-temperature stable phases: namely, body-centered-cubic and body-centered-tetragonal (bct) phases. We performed first-principles molecular dynamics and phonon analysis of the bct Fe phase and demonstrated its dynamical instability. This allows us to dismiss the existence of the bct Fe phase under the high-pressure high-temperature conditions of the Earth's inner core.
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| 23. |
- Bleskov, I. D., et al.
(författare)
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Ab initio calculations of elastic properties of Ru1-xNixAl superalloys
- 2009
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 94:16
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Tidskriftsartikel (refereegranskat)abstract
- Ab initio total energy calculations based on the exact muffin-tin orbitals method, combined with the coherent potential approximation, have been used to study the thermodynamical and elastic properties of substitutional refractory Ru1-xNixAl alloys. We have found that the elastic constants C' and C11 exhibit pronounced peculiarities near the concentration of about 40 at. % Ni, which we ascribe to electronic topological transitions. Our suggestion is supported by the Fermi surface calculations in the whole concentration range. Results of our calculations show that one can design Ru-Ni-Al alloys substituting Ru by Ni (up to 40 at. %) with almost invariable elastic constants and reduced density.
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| 24. |
- Isaev, E. I., et al.
(författare)
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Dynamical stability of Fe-H in the Earth's mantle and core regions
- 2007
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 104:22, s. 9168-9171
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Tidskriftsartikel (refereegranskat)abstract
- The core extends from the depth of 2,900 km to the center of the Earth and is composed mainly of an iron-rich alloy with nickel, with 10% of the mass comprised of lighter elements like hydrogen, but the exact composition is uncertain. We present a quantum mechanical first-principles study of the dynamical stability of FeH phases and their phonon densities of states at high pressure. Our free-energy calculations reveal a phonon-driven stabilization of dhcp FeH at low pressures, thus resolving the present contradiction between experimental observations and theoretical predictions. Calculations reveal a complex phase diagram for FeH under pressure with a dhcp -> hcp -> fcc sequence of structural transitions.
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| 25. |
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| 26. |
- Ponomareva, A., et al.
(författare)
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Ab initio investigations of surface magnetism in V-Mo
- 2004
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Ingår i: Journal of Magnetism and Magnetic Materials. - : Elsevier BV. - 0304-8853 .- 1873-4766. ; 272-276, s. 1198-1200
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Tidskriftsartikel (refereegranskat)abstract
- Magnetic properties of the (0 0 1) surface of pure vanadium and disordered binary Mo-V alloys have been investigated from the first-principles by means of the LMTO-GF-CPA technique, the fixed spin moment method, and the direct exchange Monte-Carlo statistical mechanics simulations. The binary alloys, as well as pure constituent metals, are nonmagnetic in the bulk. However, we have shown that the (1 0 0) surface of uniformly random and segregated Mo-V alloys is magnetic. The magnetism of the V monolayer on the Mo(0 0 1) surface has also been studied. In particular, the surface relaxation effect has resulted in a reduction of the magnetic moments for V atoms, but the surface magnetism is still present in the system. Including of semi-core states as valence ones does not alter this conclusion.
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| 27. |
- Ponomareva, A. V., et al.
(författare)
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Surface segregation energy in bcc Fe-rich Fe-Cr alloys
- 2007
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 75:24, s. 5406-
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Tidskriftsartikel (refereegranskat)abstract
- The exact muffin-tin orbitals (EMTO) technique in conjunction with the coherent-potential approximation (CPA) as well as the projector-augmented-wave (PAW) method have been used to calculate the surface segregation energy of Cr at the (100) surface of Fe-rich bcc Fe-Cr alloys. We find that PAW results strongly depend on the supercell size used in the calculations. In particular, for large supercells, the surface segregation energy of Cr is positive, which means that Cr should not segregate toward the surface of diluted alloys. This is in agreement with our EMTO-CPA results as well as previous surface Green's-function calculations. However, the surface segregation energy of Cr is negative if small unit cells are used for simulations. This is in agreement with previous full-potential supercell calculations. We explain such a size dependence by a peculiar concentration dependence of interatomic interactions in ferromagnetic Fe-Cr alloys.
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| 28. |
- Vekilov, Y. K., et al.
(författare)
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Diamagnetism in quasicrystals
- 2005
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Ingår i: Solid State Communications. - : Elsevier BV. - 0038-1098 .- 1879-2766. ; 133, s. 473-
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Tidskriftsartikel (refereegranskat)
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| 29. |
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| 30. |
- Vekilov, Y. K., et al.
(författare)
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Ferromagnetism in quasicrystals : Symmetry aspects
- 2005
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Ingår i: Journal of Experimental and Theoretical Physics. - : Pleiades Publishing Ltd. - 1063-7761 .- 1090-6509. ; 100, s. 1127-
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Tidskriftsartikel (refereegranskat)
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