| 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. |
- Fernandez, J. L. Abelleira, et al.
(författare)
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A Large Hadron Electron Collider at CERN
- 2012
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Ingår i: Journal of Physics G. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 39:7
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Tidskriftsartikel (refereegranskat)
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| 4. |
- Adlarson, Patrik, et al.
(författare)
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Investigation of the dd -> (3)Hen pi(0) reaction with the FZ Julich WASA-at-COSY facility
- 2013
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 88:1, s. 014004-
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Tidskriftsartikel (refereegranskat)abstract
- An exclusive measurement of the dd -> (3)Hen pi(0) reaction was carried out at a beam momentum of p(d) = 1.2 GeV/c using the WASA-at-COSY facility. Information on the total cross section as well as differential distributions was obtained. The data are described by a phenomenological approach based on a combination of a quasifree model and a partial wave expansion for the three-body reaction. The total cross section is found to be sigma(tot) = ( 2.89 +/- 0.01(stat) +/- 0.06(sys) +/- 0.29(norm)) mu b. The contribution of the quasifree processes ( with the beam or target neutron being a spectator) accounts for 38% of the total cross section and dominates the differential distributions in specific regions of phase space. The remaining part of the cross section can be described by a partial wave decomposition indicating the significance of p-wave contributions in the final state.
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| 5. |
- Adlarson, Patrik, et al.
(författare)
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Measurement of the pn -> pp pi(0)pi(-) reaction in search for the recently observed resonance structure in d pi(0)pi(0) and d pi(+)pi(-) systems
- 2013
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 88:5, s. 055208-
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Tidskriftsartikel (refereegranskat)abstract
- Exclusive measurements of the quasifree pn -> pp pi(0)pi(-) reaction have been performed by means of pd collisions at T-p = 1.2 GeV using the wide angle shower apparatus (WASA) detector setup at the cooler synchrotron COSY (Institut fur Kernphysik, Julich). Total and differential cross sections have been obtained covering the energy region root s = (2.35-2.46) GeV, which includes the region of the ABC effect and its associated resonance structure. NoABCeffect, i.e., low-mass enhancement is found in the pi(0)pi(-) -invariant mass spectrum, in agreement with the constraint from Bose statistics that the isovector pion pair can not be in relative s wave. At the upper end of the covered energy region t-channel processes for Roper, Delta(1600) and Delta Delta excitations provide a reasonable description of the data, but at low energies the measured cross sections are much larger than predicted by such processes. Adding a resonance amplitude for the resonance at m = 2.37 GeV with Gamma = 70 MeV and I (J(P)) = 0(3(+)) observed recently in pn -> d pi(0)pi(0) and pn -> d pi(+)pi(-) reactions leads to an agreement with the data also at low energies.
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| 6. |
- Polme, S., et al.
(författare)
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FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles
- 2020
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 105:1, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
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| 7. |
- Abbafati, Cristiana, et al.
(författare)
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- 2020
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Tidskriftsartikel (refereegranskat)
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| 8. |
- Adlarson, P., et al.
(författare)
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Isospin decomposition of the basic double-pionic fusion in the region of the ABC effect
- 2013
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 721:4-5, s. 229-236
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Tidskriftsartikel (refereegranskat)abstract
- Exclusive and kinematically complete high-statistics measurements of the basic double-pionic fusion reactions pn -> d pi(0)pi(0), pn -> d pi(+)pi(-) and pp -> d pi(+)pi(0) have been carried out simultaneously over the energy region of the ABC effect using the WASA detector setup at COSY. Whereas the isoscalar reaction part given by the d pi(0)pi(0) channel exhibits the ABC effect, i.e. a low-mass enhancement in the pi pi-invariant mass distribution, as well as the associated resonance structure in the total cross section, the isovector part given by the d pi(+)pi(0) channel shows a smooth behavior consistent with the conventional t-channel Delta Delta process. The d pi(+)pi(-) data are very well reproduced by combining the data for isovector and isoscalar contributions, if the kinematical consequences of the isospin violation due to different masses for charged and neutral pions are taken into account.
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| 9. |
- Adolph, C, et al.
(författare)
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Measurement of the eta -> 3 pi(0) Dalitz plot distribution with the WASA detector at COSY
- 2009
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 677:1-2, s. 24-29
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Tidskriftsartikel (refereegranskat)abstract
- In the first production run of the WASA experiment at COSY, the eta decay into three neutral pions was measured in proton-proton interactions at a proton beam kinetic energy of 1.4 GeV. The Dalitz plot of the three pious was Studied using 1.2 x 10(5) fully reconstructed events. and the quadratic slope parameter alpha was determined to be -0.027 +/- 0.008(stat) +/- 0.005(syst). The result is consistent with previous measurements and further corroborates the importance of pion-pion final state interactions. (C) 2009 Elsevier B.V. All rights reserved.
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| 10. |
- Adlarson, Patrik, et al.
(författare)
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Abashian-Booth-Crowe resonance structure in the double pionic fusion to He-4
- 2012
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Ingår i: Physical Review C. Nuclear Physics. - 0556-2813 .- 1089-490X. ; 86:3, s. 032201-
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Tidskriftsartikel (refereegranskat)abstract
- Exclusive and kinematically complete high-statistics measurements of the double pionic fusion reaction dd -> He-4 pi(0)pi(0) have been performed in the energy range 0.8-1.4 GeV covering thus the region of the Abashian-Booth-Crowe effect, which denotes a pronounced low-mass enhancement in the pi pi invariant mass spectrum. The experiments were carried out with the WASA detector setup at the cooler synchrotron at Forshungszentrum Julich GmbH. Similar to the observation in the basic pn -> d pi(0)pi(0) reaction, the data reveal a correlation between the ABC effect and a resonancelike energy dependence in the total cross section. The maximum occurs at m = 2.37 GeV + 2m(N), i.e., at the same position as in the basic reaction. The observed resonance width Gamma approximate to 160 MeV can be understood from broadening due to Fermi motion of the nucleons in initial and final nuclei together with collision damping. Differential cross sections are described equally well by the hypothesis of a pn resonance formation during the reaction process.
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