| 1. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)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. |
- Barucca, G., et al.
(author)
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The potential of Λ and Ξ- studies with PANDA at FAIR
- 2021
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In: European Physical Journal A. - : Springer Nature. - 1434-6001 .- 1434-601X. ; 57:4
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Journal article (peer-reviewed)abstract
- The antiproton experiment PANDA at FAIR is designed to bring hadron physics to a new level in terms of scope, precision and accuracy. In this work, its unique capability for studies of hyperons is outlined. We discuss ground-state hyperons as diagnostic tools to study non-perturbative aspects of the strong interaction, and fundamental symmetries. New simulation studies have been carried out for two benchmark hyperon-antihyperon production channels: p¯ p→ Λ¯ Λ and p¯ p→ Ξ¯ +Ξ-. The results, presented in detail in this paper, show that hyperon-antihyperon pairs from these reactions can be exclusively reconstructed with high efficiency and very low background contamination. In addition, the polarisation and spin correlations have been studied, exploiting the weak, self-analysing decay of hyperons and antihyperons. Two independent approaches to the finite efficiency have been applied and evaluated: one standard multidimensional efficiency correction approach, and one efficiency independent approach. The applicability of the latter was thoroughly evaluated for all channels, beam momenta and observables. The standard method yields good results in all cases, and shows that spin observables can be studied with high precision and accuracy already in the first phase of data taking with PANDA.
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| 3. |
- Barucca, G., et al.
(author)
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Study of excited Ξ baryons with the P¯ ANDA detector
- 2021
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In: European Physical Journal A. - : Springer Nature. - 1434-6001 .- 1434-601X. ; 57:4
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Journal article (peer-reviewed)abstract
- The study of baryon excitation spectra provides insight into the inner structure of baryons. So far, most of the world-wide efforts have been directed towards N∗ and Δ spectroscopy. Nevertheless, the study of the double and triple strange baryon spectrum provides independent information to the N∗ and Δ spectra. The future antiproton experiment P¯ANDA will provide direct access to final states containing a Ξ¯ Ξ pair, for which production cross sections up to μb are expected in p¯p reactions. With a luminosity of L= 10 31 cm- 2 s- 1 in the first phase of the experiment, the expected cross sections correspond to a production rate of ∼106events/day. With a nearly 4 π detector acceptance, P¯ANDA will thus be a hyperon factory. In this study, reactions of the type p¯p → Ξ¯ +Ξ∗ - as well as p¯p → Ξ¯ ∗ +Ξ- with various decay modes are investigated. For the exclusive reconstruction of the signal events a full decay tree fit is used, resulting in reconstruction efficiencies between 3 and 5%. This allows high statistics data to be collected within a few weeks of data taking.
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| 4. |
- Stroth, U., et al.
(author)
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Progress from ASDEX Upgrade experiments in preparing the physics basis of ITER operation and DEMO scenario development
- 2022
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In: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 62:4
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Journal article (peer-reviewed)abstract
- An overview of recent results obtained at the tokamak ASDEX Upgrade (AUG) is given. A work flow for predictive profile modelling of AUG discharges was established which is able to reproduce experimental H-mode plasma profiles based on engineering parameters only. In the plasma center, theoretical predictions on plasma current redistribution by a dynamo effect were confirmed experimentally. For core transport, the stabilizing effect of fast ion distributions on turbulent transport is shown to be important to explain the core isotope effect and improves the description of hollow low-Z impurity profiles. The L-H power threshold of hydrogen plasmas is not affected by small helium admixtures and it increases continuously from the deuterium to the hydrogen level when the hydrogen concentration is raised from 0 to 100%. One focus of recent campaigns was the search for a fusion relevant integrated plasma scenario without large edge localised modes (ELMs). Results from six different ELM-free confinement regimes are compared with respect to reactor relevance: ELM suppression by magnetic perturbation coils could be attributed to toroidally asymmetric turbulent fluctuations in the vicinity of the separatrix. Stable improved confinement mode plasma phases with a detached inner divertor were obtained using a feedback control of the plasma β. The enhanced D α H-mode regime was extended to higher heating power by feedback controlled radiative cooling with argon. The quasi-coherent exhaust regime was developed into an integrated scenario at high heating power and energy confinement, with a detached divertor and without large ELMs. Small ELMs close to the separatrix lead to peeling-ballooning stability and quasi continuous power exhaust. Helium beam density fluctuation measurements confirm that transport close to the separatrix is important to achieve the different ELM-free regimes. Based on separatrix plasma parameters and interchange-drift-Alfvén turbulence, an analytic model was derived that reproduces the experimentally found important operational boundaries of the density limit and between L- and H-mode confinement. Feedback control for the X-point radiator (XPR) position was established as an important element for divertor detachment control. Stable and detached ELM-free phases with H-mode confinement quality were obtained when the XPR was moved 10 cm above the X-point. Investigations of the plasma in the future flexible snow-flake divertor of AUG by means of first SOLPS-ITER simulations with drifts activated predict beneficial detachment properties and the activation of an additional strike point by the drifts.
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| 5. |
- Saito, T. R., et al.
(author)
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The WASA-FRS project at GSI and its perspective
- 2023
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In: Nuclear Instruments and Methods in Physics Research Section B. - : Elsevier. - 0168-583X .- 1872-9584. ; 542, s. 22-25
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Journal article (peer-reviewed)abstract
- A novel technique to study bound states of exotic hadrons in subatomic nuclei, such as hypernuclei and mesic nuclei, has been developed by employing the Fragment Separator FRS and the WASA central detector at GSI. Two experiments, S447 for studying light hypernuclei, especially hypertriton and a Ann bound state, and S490 for searching for ri' mesic-nuclei, were recently performed. Data analyses are currently in progress, and light charged particles such as protons and x & PLUSMN; are clearly observed and identified in the both experiments. For S447, light nuclear fragments that can also be residual nuclei from decays of hypernuclei of interests have been analysed by the FRS, and a momentum resolution, Ap/p, of 5 x 10-4 has been achieved. Further data analyses are to be completed. The WASA-FRS project will be continued and extended with the FRS at FAIR Phase 0, and upgrading of the WASA magnet and detectors is currently in progress. Furthermore, construction of a larger detector system with the Super-FRS at FAIR Phase 1 is also under consideration.
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| 6. |
- Tanaka, Y. K., et al.
(author)
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WASA-FRS EXPERIMENTS IN FAIR PHASE-0 AT GSI
- 2023
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In: ACTA PHYSICA POLONICA B PROCEEDINGS SUPPLEMENT. - : Jagiellonian University.
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Conference paper (peer-reviewed)abstract
- We have developed a new and unique experimental setup integrating the central part of the Wide Angle Shower Apparatus (WASA) into the Fragment Separator (FRS) at GSI. This combination opens up possibilities of new experiments with high-resolution spectroscopy at forward 0 and measurements of light decay particles with nearly full solid-angle acceptance in coincidence. The first series of the WASA-FRS experiments have been successfully carried out in 2022. The developed experimental setup and two physics experiments performed in 2022 including the status of the preliminary data analysis are introduced.
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| 7. |
- Saito, T. R., et al.
(author)
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Studies of three-and four-body hypernuclei with heavy-ion beams, nuclear emulsions and machine learning
- 2023
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In: Journal of Physics, Conference Series. - : Institute of Physics (IOP). - 1742-6588 .- 1742-6596. ; 2586
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Journal article (peer-reviewed)abstract
- Interests on few-body hypernuclei have been increased by recent results of experiments employing relativistic heavy ion beams. Some of the experiments have revealed that the lifetime of the lightest hypernucleus, hypertriton, is significantly shorter than 263 ps which is expected by considering the hypertriton to be a weakly-bound system. The STAR collaboration has also measured the hypertriton binding energy, and the deduced value is contradicting to its formerly known small binding energy. These measurements have indicated that the fundamental physics quantities of the hypertriton such as its lifetime and binding energy have not been understood, therefore, they have to be measured very precisely. Furthermore, an unprecedented Lambda nn bound state observed by the HypHI collaboration has to be studied in order to draw a conclusion whether or not such a bound state exists. These three-body hypernuclear states are studied by the heavy-ion beam data in the WASA-FRS experiment and by analysing J-PARC E07 nuclear emulsion data with machine learning.
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| 8. |
- Sekiya, R., et al.
(author)
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Search for η'-mesic nuclei in 12C(p, dp) reaction with the WASA detector at GSI-FRS
- 2024
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In: Nuovo cimento della societa italiana de fisica. C, Geophysics and space physics. - : Società Italiana di Fisica. - 1124-1896 .- 1826-9885. ; 47:4
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Journal article (peer-reviewed)abstract
- We conducted an experimental search for η′-mesic nuclei, bound systems of an η′ meson and a nucleus, in 12C(p, dp) reactions. We measured the missing mass in the (p, d) reaction to obtain the mass spectrum of the reaction product near the η′ emission threshold. Forward-emitted deuterons were momentum-analyzed in the FRS of GSI. We installed a nearly 4π detector WASA near the 12C target to effectively select formation and decay of the η′-mesic nuclei. We are presently finalizing the analysis.
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| 9. |
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| 10. |
- Morabito, L., et al.
(author)
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Sub-arcsecond imaging with the International LOFAR Telescope: I. Foundational calibration strategy and pipeline
- 2022
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 658
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Journal article (peer-reviewed)abstract
- The International LOFAR Telescope is an interferometer with stations spread across Europe. With baselines of up to ∼2000 km, LOFAR has the unique capability of achieving sub-arcsecond resolution at frequencies below 200 MHz. However, it is technically and logistically challenging to process LOFAR data at this resolution. To date only a handful of publications have exploited this capability. Here we present a calibration strategy that builds on previous high-resolution work with LOFAR. It is implemented in a pipeline using mostly dedicated LOFAR software tools and the same processing framework as the LOFAR Two-metre Sky Survey (LoTSS). We give an overview of the calibration strategy and discuss the special challenges inherent to enacting high-resolution imaging with LOFAR, and describe the pipeline, which is publicly available, in detail. We demonstrate the calibration strategy by using the pipeline on P205+55, a typical LoTSS pointing with an 8 h observation and 13 international stations. We perform in-field delay calibration, solution referencing to other calibrators in the field, self-calibration of these calibrators, and imaging of example directions of interest in the field. We find that for this specific field and these ionospheric conditions, dispersive delay solutions can be transferred between calibrators up to ∼1.5° away, while phase solution transferral works well over ∼1°. We also demonstrate a check of the astrometry and flux density scale with the in-field delay calibrator source. Imaging in 17 directions, we find the restoring beam is typically ∼0.3″ ×0.2″ although this varies slightly over the entire 5 deg2 field of view. We find we can achieve ∼80-300 μJy bm-1 image rms noise, which is dependent on the distance from the phase centre; typical values are ∼90 μJy bm-1 for the 8 h observation with 48 MHz of bandwidth. Seventy percent of processed sources are detected, and from this we estimate that we should be able to image roughly 900 sources per LoTSS pointing. This equates to ∼ 3 million sources in the northern sky, which LoTSS will entirely cover in the next several years. Future optimisation of the calibration strategy for efficient post-processing of LoTSS at high resolution makes this estimate a lower limit.
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