| 1. |
- Niemi, MEK, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 2. |
- 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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| 3. |
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| 4. |
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| 5. |
- Aalbers, Jelle, et al.
(författare)
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Solar neutrino detection sensitivity in DARWIN via electron scattering
- 2020
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Ingår i: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 80:12
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Tidskriftsartikel (refereegranskat)abstract
- We detail the sensitivity of the proposed liquid xenon DARWIN observatory to solar neutrinos via elastic electron scattering. We find that DARWIN will have the potential to measure the fluxes of five solar neutrino components: pp, 7Be, 13N, 15O and pep. The precision of the 13N, 15O and pep components is hindered by the double-beta decay of 136Xe and, thus, would benefit from a depleted target. A high-statistics observation of pp neutrinos would allow us to infer the values of the electroweak mixing angle, sin2 theta w, and the electron-type neutrino survival probability, Pee, in the electron recoil energy region from a few keV up to 200 keV for the first time, with relative precision of 5% and 4%, respectively, with 10 live years of data and a 30 tonne fiducial volume. An observation of pp and 7Be neutrinos would constrain the neutrino-inferred solar luminosity down to 0.2%. A combination of all flux measurements would distinguish between the high- (GS98) and low-metallicity (AGS09) solar models with 2.1-2.5 sigma significance, independent of external measurements from other experiments or a measurement of 8B neutrinos through coherent elastic neutrino-nucleus scattering in DARWIN. Finally, we demonstrate that with a depleted target DARWIN may be sensitive to the neutrino capture process of 131Xe.
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| 6. |
- Elhai, M, et al.
(författare)
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Outcomes of patients with systemic sclerosis treated with rituximab in contemporary practice: a prospective cohort study
- 2019
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Ingår i: Annals of the rheumatic diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 78:7, s. 979-987
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Tidskriftsartikel (refereegranskat)abstract
- To assess the safety and efficacy of rituximab in systemic sclerosis (SSc) in clinical practice.MethodsWe performed a prospective study including patients with SSc from the European Scleroderma Trials and Research (EUSTAR) network treated with rituximab and matched with untreated patients with SSc. The main outcomes measures were adverse events, skin fibrosis improvement, lung fibrosis worsening and steroids use among propensity score-matched patients treated or not with rituximab.Results254 patients were treated with rituximab, in 58% for lung and in 32% for skin involvement. After a median follow-up of 2 years, about 70% of the patients had no side effect. Comparison of treated patients with 9575 propensity-score matched patients showed that patients treated with rituximab were more likely to have skin fibrosis improvement (22.7 vs 14.03 events per 100 person-years; OR: 2.79 [1.47–5.32]; p=0.002). Treated patients did not have significantly different rates of decrease in forced vital capacity (FVC)>10% (OR: 1.03 [0.55–1.94]; p=0.93) nor in carbon monoxide diffusing capacity (DLCO) decrease. Patients having received rituximab were more prone to stop or decrease steroids (OR: 2.34 [1.56–3.53], p<0.0001). Patients treated concomitantly with mycophenolate mofetil had a trend for better outcomes as compared with patients receiving rituximab alone (delta FVC: 5.22 [0.83–9.62]; p=0.019 as compared with controls vs 3 [0.66–5.35]; p=0.012).ConclusionRituximab use was associated with a good safety profile in this large SSc-cohort. Significant change was observed on skin fibrosis, but not on lung. However, the limitation is the observational design. The potential stabilisation of lung fibrosis by rituximab has to be addressed by a randomised trial.
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| 7. |
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| 8. |
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| 9. |
- Aalbers, J., et al.
(författare)
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DARWIN : towards the ultimate dark matter detector
- 2016
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Ingår i: Journal of Cosmology and Astroparticle Physics. - : IOP Publishing. - 1475-7516. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- DARk matter WImp search with liquid xenoN (DARWIN(2)) will be an experiment for the direct detection of dark matter using a multi-ton liquid xenon time projection chamber at its core. Its primary goal will be to explore the experimentally accessible parameter space for Weakly Interacting Massive Particles (WIMPs) in a wide mass-range, until neutrino interactions with the target become an irreducible background. The prompt scintillation light and the charge signals induced by particle interactions in the xenon will be observed by VUV sensitive, ultra-low background photosensors. Besides its excellent sensitivity to WIMPs above a mass of 5 GeV/c(2), such a detector with its large mass, low-energy threshold and ultra-low background level will also be sensitive to other rare interactions. It will search for solar axions,galactic axion-like particles and the neutrinoless double-beta decay of Xe-136, as well as measure the low-energy solar neutrino flux with <1% precision, observe coherent neutrino-nucleus interactions, and detect galactic supernovae. We present the concept of the DARWIN detector and discuss its physics reach, the main sources of backgrounds and the ongoing detector design and R&D efforts.
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| 10. |
- Amendola, L., et al.
(författare)
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Cosmology and fundamental physics with the Euclid satellite
- 2018
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Ingår i: Living Reviews in Relativity. - : Springer. - 1433-8351 .- 2367-3613. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- Euclid is a European Space Agency medium-class mission selected for launch in 2020 within the cosmic vision 2015–2025 program. The main goal of Euclid is to understand the origin of the accelerated expansion of the universe. Euclid will explore the expansion history of the universe and the evolution of cosmic structures by measuring shapes and red-shifts of galaxies as well as the distribution of clusters of galaxies over a large fraction of the sky. Although the main driver for Euclid is the nature of dark energy, Euclid science covers a vast range of topics, from cosmology to galaxy evolution to planetary research. In this review we focus on cosmology and fundamental physics, with a strong emphasis on science beyond the current standard models. We discuss five broad topics: dark energy and modified gravity, dark matter, initial conditions, basic assumptions and questions of methodology in the data analysis. This review has been planned and carried out within Euclid’s Theory Working Group and is meant to provide a guide to the scientific themes that will underlie the activity of the group during the preparation of the Euclid mission.
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| 11. |
- Althueser, L., et al.
(författare)
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GPU-based optical simulation of the DARWIN detector
- 2022
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 17:7
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Tidskriftsartikel (refereegranskat)abstract
- Understanding propagation of scintillation light is critical for maximizing the discovery potential of next-generation liquid xenon detectors that use dual-phase time projection chamber technology. This work describes a detailed optical simulation of the DARWIN detector implemented using Chroma, a GPU-based photon tracking framework. To evaluate the framework and to explore ways of maximizing efficiency and minimizing the time of light collection, we simulate several variations of the conventional detector design. Results of these selected studies are presented. More generally, we conclude that the approach used in this work allows one to investigate alternative designs faster and in more detail than using conventional Geant4 optical simulations, making it an attractive tool to guide the development of the ultimate liquid xenon observatory.
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| 12. |
- Gadea, A., et al.
(författare)
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Observation of Ni-54 : Cross-conjugate symmetry in f(7/2) mirror energy differences
- 2006
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 97:15, s. 152501-
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Tidskriftsartikel (refereegranskat)abstract
- Gamma decays from excited states up to J(pi)=6(+) in the N=Z-2 nucleus Ni-54 have been identified for the first time. Level energies are compared with those of the isobars Co-54 and Fe-54 and of the cross-conjugate nuclei of mass A=42. The good but puzzling f(7/2) cross-conjugate symmetry in mirror and triplet energy differences is analyzed. Shell model calculations reproduce the new data but the necessary nuclear charge-dependent phenomenology is not fully explained by modern nucleon-nucleon potentials.
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| 13. |
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| 14. |
- Baiser, Benjamin, et al.
(författare)
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Ecogeographical rules and the macroecology of food webs
- 2019
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Ingår i: Global Ecology and Biogeography. - : Wiley-Blackwell Publishing Inc.. - 1466-822X .- 1466-8238. ; 28:9, s. 1204-1218
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Tidskriftsartikel (refereegranskat)abstract
- AimHow do factors such as space, time, climate and other ecological drivers influence food web structure and dynamics? Collections of well‐studied food webs and replicate food webs from the same system that span biogeographical and ecological gradients now enable detailed, quantitative investigation of such questions and help integrate food web ecology and macroecology. Here, we integrate macroecology and food web ecology by focusing on how ecogeographical rules [the latitudinal diversity gradient (LDG), Bergmann's rule, the island rule and Rapoport's rule] are associated with the architecture of food webs.LocationGlobal.Time periodCurrent.Major taxa studiedAll taxa.MethodsWe discuss the implications of each ecogeographical rule for food webs, present predictions for how food web structure will vary with each rule, assess empirical support where available, and discuss how food webs may influence ecogeographical rules. Finally, we recommend systems and approaches for further advancing this research agenda.ResultsWe derived testable predictions for some ecogeographical rules (e.g. LDG, Rapoport's rule), while for others (e.g., Bergmann's and island rules) it is less clear how we would expect food webs to change over macroecological scales. Based on the LDG, we found weak support for both positive and negative relationships between food chain length and latitude and for increased generality and linkage density at higher latitudes. Based on Rapoport's rule, we found support for the prediction that species turnover in food webs is inversely related to latitude.Main conclusionsThe macroecology of food webs goes beyond traditional approaches to biodiversity at macroecological scales by focusing on trophic interactions among species. The collection of food web data for different types of ecosystems across biogeographical gradients is key to advance this research agenda. Further, considering food web interactions as a selection pressure that drives or disrupts ecogeographical rules has the potential to address both mechanisms of and deviations from these macroecological relationships. For these reasons, further integration of macroecology and food webs will help ecologists better understand the assembly, maintenance and change of ecosystems across space and time.
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| 15. |
- Basset, F. Basso, et al.
(författare)
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Entanglement Swapping with Photons Generated on Demand by a Quantum Dot
- 2019
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Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 123:16
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Tidskriftsartikel (refereegranskat)abstract
- Photonic entanglement swapping, the procedure of entangling photons without any direct interaction, is a fundamental test of quantum mechanics and an essential resource to the realization of quantum networks. Probabilistic sources of nonclassical light were used for seminal demonstration of entanglement swapping, but applications in quantum technologies demand push-button operation requiring single quantum emitters. This, however, turned out to be an extraordinary challenge due to the stringent prerequisites on the efficiency and purity of the generation of entangled states. Here we show a proof-of-concept demonstration of all-photonic entanglement swapping with pairs of polarization-entangled photons generated on demand by a GaAs quantum dot without spectral and temporal filtering. Moreover, we develop a theoretical model that quantitatively reproduces the experimental data and provides insights on the critical figures of merit for the performance of the swapping operation. Our theoretical analysis also indicates how to improve stateof-the-art entangled-photon sources to meet the requirements needed for implementation of quantum dots in long-distance quantum communication protocols.
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| 16. |
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| 17. |
- Hanschke, Lukas, et al.
(författare)
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Origin of Antibunching in Resonance Fluorescence
- 2020
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 125:17
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Tidskriftsartikel (refereegranskat)abstract
- Resonance fluorescence has played a major role in quantum optics with predictions and later experimental confirmation of nonclassical features of its emitted light such as antibunching or squeezing. In the Rayleigh regime where most of the light originates from the scattering of photons with subnatural linewidth, antibunching would appear to coexist with sharp spectral lines. Here, we demonstrate that this simultaneous observation of subnatural linewidth and antibunching is not possible with simple resonant excitation. Using an epitaxial quantum dot for the two-level system, we independently confirm the single-photon character and subnatural linewidth by demonstrating antibunching in a Hanbury Brown and Twiss type setup and using high-resolution spectroscopy, respectively. However, when filtering the coherently scattered photons with filter bandwidths on the order of the homogeneous linewidth of the excited state of the two-level system, the antibunching dip vanishes in the correlation measurement. Our observation is explained by antibunching originating from photon-interferences between the coherent scattering and a weak incoherent signal in a skewed squeezed state. This prefigures schemes to achieve simultaneous subnatural linewidth and antibunched emission.
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| 18. |
- Jebaraj, I. C., et al.
(författare)
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Relativistic electron beams accelerated by an interplanetary shock
- 2023
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 680
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Tidskriftsartikel (refereegranskat)abstract
- Context: Collisionless shock waves have long been considered to be among the most prolific particle accelerators in the universe. Shocks alter the plasma they propagate through, and often exhibit complex evolution across multiple scales. Interplanetary (IP) traveling shocks have been recorded in situ for over half a century and act as a natural laboratory for experimentally verifying various aspects of large-scale collisionless shocks. A fundamentally interesting problem in both heliophysics and astrophysics is the acceleration of electrons to relativistic energies (> 300 keV) by traveling shocks.Aims: The reason for an incomplete understanding of electron acceleration at IP shocks is due to scale-related challenges and a lack of instrumental capabilities. This Letter presents the first observations of field-aligned beams of relativistic electrons upstream of an IP shock, observed thanks to the instrumental capabilities of Solar Orbiter. This study presents the characteristics of the electron beams close to the source and contributes to the understanding of their acceleration mechanism.Methods: On 25 July 2022, Solar Orbiter encountered an IP shock at 0.98 AU. The shock was associated with an energetic storm particle event, which also featured upstream field-aligned relativistic electron beams observed 14 min prior to the actual shock crossing. The distance of the beam's origin was investigated using a velocity dispersion analysis (VDA). Peak-intensity energy spectra were anaylzed and compared with those obtained from a semi-analytical fast-Fermi acceleration model.Results: By leveraging Solar Orbiter's high temporal resolution Energetic Particle Detector (EPD), we successfully showcase an IP shock's ability to accelerate relativistic electron beams. Our proposed acceleration mechanism offers an explanation for the observed electron beam and its characteristics, while we also explore the potential contributions of more complex mechanisms.
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| 19. |
- Kajdic, P., et al.
(författare)
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ULF Wave Transmission Across Collisionless Shocks : 2.5D Local Hybrid Simulations
- 2021
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Ingår i: Journal of Geophysical Research - Space Physics. - : American Geophysical Union (AGU). - 2169-9380 .- 2169-9402. ; 126:11
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Tidskriftsartikel (refereegranskat)abstract
- We study the interaction of upstream ultralow frequency (ULF) waves with collisionless shocks by analyzing the outputs of 11 2D local hybrid simulation runs. Our simulated shocks have Alfvenic Mach numbers between 4.29 and 7.42 and their theta BN angles are 15 degrees, 30 degrees, 45 degrees, and 50 degrees. The ULF wave foreshocks develop upstream of all of them. The wavelength and the amplitude of the upstream waves exhibit a complex dependence on the shock's MA and theta BN. The wavelength positively correlates with both parameters, with the dependence on theta BN being much stronger. The amplitude of the ULF waves is proportional to the product of the reflected beam velocity and density, which also depend on MA and theta BN. The interaction of the ULF waves with the shock causes large-scale (several tens of upstream ion inertial lengths) shock rippling. The properties of the shock ripples are related to the ULF wave properties, namely their wavelength and amplitude. In turn, the ripples have a large impact on the ULF wave transmission across the shock because they change local shock properties (theta BN, strength), so that different sections of the same ULF wavefront encounter shock with different characteristics. Downstream fluctuations do not resemble the upstream waves in terms the wavefront extension, orientation or their wavelength. However, some features are conserved in the Fourier spectra of downstream compressive waves that present a bump or flattening at wavelengths approximately corresponding to those of the upstream ULF waves. In the transverse downstream spectra, these features are weaker.
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| 20. |
- Schöll, Eva, et al.
(författare)
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Crux of Using the Cascaded Emission of a Three-Level Quantum Ladder System to Generate Indistinguishable Photons
- 2020
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 125:23
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the degree of indistinguishability of cascaded photons emitted from a three-level quantum ladder system; in our case the biexciton-exciton cascade of semiconductor quantum dots. For the three-level quantum ladder system we theoretically demonstrate that the indistinguishability is inherently limited for both emitted photons and determined by the ratio of the lifetimes of the excited and intermediate states. We experimentally confirm this finding by comparing the quantum interference visibility of noncascaded emission and cascaded emission from the same semiconductor quantum dot. Quantum optical simulations produce very good agreement with the measurements and allow us to explore a large parameter space. Based on our model, we propose photonic structures to optimize the lifetime ratio and overcome the limited indistinguishability of cascaded photon emission from a three-level quantum ladder system.
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| 21. |
- Schöll, Eva, et al.
(författare)
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Resonance Fluorescence of GaAs Quantum Dots with Near-Unity Photon Indistinguishability
- 2019
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Ingår i: Nano letters (Print). - : AMER CHEMICAL SOC. - 1530-6984 .- 1530-6992. ; 19:4, s. 2404-2410
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Tidskriftsartikel (refereegranskat)abstract
- Photonic quantum technologies call for scalable quantum light sources that can be integrated, while providing the end user with single and entangled photons on demand. One promising candidate is strain free GaAs/A1GaAs quantum dots obtained by aluminum droplet etching. Such quantum dots exhibit ultra low multi-photon probability and an unprecedented degree of photon pair entanglement. However, different to commonly studied InGaAs/GaAs quantum dots obtained by the Stranski-Krastanow mode, photons with a near-unity indistinguishability from these quantum emitters have proven to be elusive so far. Here, we show on-demand generation of near-unity indistinguishable photons from these quantum emitters by exploring pulsed resonance fluorescence. Given the short intrinsic lifetime of excitons and trions confined in the GaAs quantum dots, we show single photon indistinguishability with a raw visibility of V-raw = (95.0(-6.1)(+5.0))%, without the need for Purcell enhancement. Our results represent a milestone in the advance of GaAs quantum dots by demonstrating the final missing property standing in the way of using these emitters as a key component in quantum communication applications, e.g., as quantum light sources for quantum repeater architectures.
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| 22. |
- Trotta, D., et al.
(författare)
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Three-dimensional modelling of the shock-turbulence interaction
- 2023
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press. - 0035-8711 .- 1365-2966. ; 525:2, s. 1856-1866
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Tidskriftsartikel (refereegranskat)abstract
- The complex interaction between shocks and plasma turbulence is extremely important to address crucial features of energy conversion in a broad range of astrophysical systems. We study the interaction between a supercritical, perpendicular shock and pre-existing, fully developed plasma turbulence, employing a novel combination of magnetohydrodynamic and small-scale, hybrid-kinetic simulations where a shock is propagating through a turbulent medium. The variability of the shock front in the unperturbed case and for two levels of upstream fluctuations is addressed. We find that the behaviour of shock ripples, i.e. shock surface fluctuations with short (a few ion skin depths, di) wavelengths, is modified by the presence of pre-existing turbulence, which also induces strong corrugations of the shock front at larger scales. We link this complex behaviour of the shock front and the shock downstream structuring with the proton temperature anisotropies produced in the shock-turbulence system. Finally, we put our modelling effort in the context of spacecraft observations, elucidating the role of novel cross-scale, multispacecraft measurements in resolving shock front irregularities at different scales. These results are relevant for a broad range of astrophysical systems characterized by the presence of shock waves interacting with plasma turbulence.
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| 23. |
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| 24. |
- Allanach, Benjamin C., et al.
(författare)
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Simple and statistically sound strategies for analysing physical theories
- 2022
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Ingår i: Reports on progress in physics (Print). - : Institute of Physics Publishing (IOPP). - 0034-4885 .- 1361-6633. ; 85:5
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Forskningsöversikt (refereegranskat)abstract
- Physical theories that depend on many parameters or are tested against data from many different experiments pose unique challenges to statistical inference. Many models in particle physics, astrophysics and cosmology fall into one or both of these categories. These issues are often sidestepped with statistically unsound ad hoc methods, involving intersection of parameter intervals estimated by multiple experiments, and random or grid sampling of model parameters. Whilst these methods are easy to apply, they exhibit pathologies even in low-dimensional parameter spaces, and quickly become problematic to use and interpret in higher dimensions. In this article we give clear guidance for going beyond these procedures, suggesting where possible simple methods for performing statistically sound inference, and recommendations of readily-available software tools and standards that can assist in doing so. Our aim is to provide any physicists lacking comprehensive statistical training with recommendations for reaching correct scientific conclusions, with only a modest increase in analysis burden. Our examples can be reproduced with the code publicly available at Zenodo.
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| 25. |
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