Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). 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 promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Autonomous crack healing in Cr₂AlC and Ti₂AlC MAX phase

The excellent mechanical properties in combination with the capability to autonomously repair microcracks when exposed to air of high temperatures make certain MAX phase metallo ceramics promising candidate materials for components in a turbine engine, in particular for those components exposed to high temperatures and having the risk of being exposed to erosion due to loose airborne particles being sucked into the engine. Cr2AlC is a member of the family of self healing MAX phases but relatively little is known about its healing behaviour under controlled laboratory conditions or simulated turbine engine conditions as a function of its synthesis, composition and microstructure. The aim of the work as described in this thesis was to study the healing behaviour of(micro-) cracks formed by erosive damage.(OLD) MSE-

Dipolar spin waves in uniaxial easy-axis antiferromagnets: A natural topological nodal-line semimetal

The existence of magnetostatic surface spin waves in ferromagnets, known as the Damon-Eshbach mode, was recently demonstrated to originate from the topology of the dipole-dipole interaction. In this work, we study the topological characteristics of magnons in easy-axis antiferromagnets with uniaxial anisotropy. The dipolar spin waves are found to be, driven by the dipole-dipole interaction, in a topological nodal-line semimetal phase, which hosts Damon-Eshbach-type surface modes due to the bulk-edge correspondence. The long-wavelength character of dipolar spin waves makes our proposal valid for any natural uniaxial easy-axis antiferromagnet and, thus, enriches the candidates of topological magnonic materials. In contrast to the nonreciprocal property in the ferromagnetic case, surface modes with opposite momentum coexist at each surface, but with different chiralities. Such chirality-momentum or spin-momentum locking, similar to that of electronic surface states in topological insulators, offers the opportunity to design novel chirality-based magnonic devices in antiferromagnets.Publisher Copyright: © 2020 authors. Published by the American Physical Society. Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.QN/Akhmerov Grou

Spin-orbit coupling and linear crossings of dipolar magnons in van der Waals antiferromagnets

A magnon spin-orbit coupling, induced by the dipole-dipole interaction, is derived in monoclinic-stacked bilayer honeycomb spin lattice with perpendicular magnetic anisotropy and antiferromagnetic interlayer coupling. Linear crossings are predicted in the magnon spectrum around the band minimum in Γ valley, as well as in the high-frequency range around the zone boundary. The linear crossings in K and K′ valleys, which connect the acoustic and optical bands, can be gapped when the intralayer dipole-dipole or Kitaev interactions exceed the interlayer dipole-dipole interaction, resulting in a phase transition from semimetal to insulator. Our results are useful for analyzing the magnon spin dynamics and transport properties in van der Waals antiferromagnets.QN/Akhmerov Grou

When Game Becomes Life: The Creators and Spectators of Online Game Replays and Live Streaming

Online gaming franchises such as World of Tanks, Defense of the Ancients, and StarCraft have attracted hundreds of millions of users who, apart from playing the game, also socialize with each other through gaming and viewing gamecasts. As a form of User Generated Content (UGC), gamecasts play an important role in user entertainment and gamer education. They deserve the attention of both industrial partners and the academic communities, corresponding to the large amount of revenue involved and the interesting research problems associated with UGC sites and social networks. Although previous work has put much effort into analyzing general UGC sites such as YouTube, relatively little is known about the gamecast sharing sites. In this work, we provide the first comprehensive study of gamecast sharing sites, including commercial streaming-based sites such as Amazon's Twitch.tv and community-maintained replay-based sites such as WoTreplays. We collect and share a novel dataset on WoTreplays that includes more than 380,000 game replays, shared by more than 60,000 creators with more than 1.9 million gamers. Together with an earlier published dataset on Twitch.tv, we investigate basic characteristics of gamecast sharing sites, and we analyze the activities of their creators and spectators. Among our results, we find that (i) WoTreplays and Twitch.tv are both fast-consumed repositories, with millions of gamecasts being uploaded, viewed, and soon forgotten; (ii) both the gamecasts and the creators exhibit highly skewed popularity, with a significant heavy tail phenomenon; and (iii) the upload and download preferences of creators and spectators are different: while the creators emphasize their individual skills, the spectators appreciate team-wise tactics. Our findings provide important knowledge for infrastructure and service improvement, for example, in the design of proper resource allocation mechanisms that consider future gamecasting and in the tuning of incentive policies that further help player retention.Accepted Author ManuscriptDistributed System

A 23.8–30.4-GHz Vector-Modulated Phase Shifter With Two-Stage Current-Reused Variable-Gain Amplifiers Achieving 0.23° Minimum RMS Phase Error

This letter presents a millimeter-wave (mm-wave) vector-modulated phase shifter (VMPS) for phased-array applications. To improve the phase-shift accuracy without drastically increasing design complexity, the proposed VMPS structure employs variable-gain amplifiers (VGAs) that offer 2× better resolution at their low-gain states compared to their high-gain states. A two-stage current-reused structure is also proposed to implement the desired VGAs with minimal layout complexity, negligible gain penalty, and no extra power. Moreover, the proposed VMPS can maintain its phase-shift accuracy even at lower voltage gains. Fabricated in 40-nm CMOS, the prototype core consumes 11 mW from a 1.1-V supply and occupies a core area of 0.19 mm2. At 28 GHz, with a phase resolution of 0.61°, the measured RMS phase error is 0.23° at the maximum gain and remains <0.5∘ at 9-dB gain back-off. With a fixed set of VGA’s codewords, the RMS phase error and gain variation error are, respectively, lower than 1° and 0.24-dB over a bandwidth of 23.8–30.4 GHz.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Electronic

Comparison of vehicle-track interaction models to simulate vertical wheel/rail impact contact

This study compares various assumptions in different models to assess their capabilities to model vehicle-track interactions up to 2 kHz at a single rail-top defect. Field measurement data are used to evaluate discrepancies. The characteristics of contact force and axle-box acceleration (ABA) are first identified and qualitatively correlated with track, wheelset and contact models. Subsequently, the results from different models are quantitatively compared in terms of their capabilities to reproduce those characteristics. It is found that the differences in sleeper and wheel-rail contact models lead to the most significant discrepancies. The causes and physical implications of the quantified discrepancies are also discussed.Railway Engineerin

Oxidation induced crack healing of Cr2(Al,Si)C max phase ceramic

The oxidation crack healing of Cr2AlC and Cr2(Al,Si)C was studied and compared with known healing of Ti2AlC. The oxidation induced crack healing of Ti2AlC is relatively fast and leads to full strength recovery, but the oxidation product contains besides ?-Al2O3 also undesired TiO2. However, when oxidizing Cr2AlC only ?-Al2O3 is formed, but full crack healing is relatively slow. The efficiency of the oxidation induced crack healing of Cr2AlC is enhanced if Al is partially replaced by Si atoms.Materials Science and EngineeringMechanical, Maritime and Materials Engineerin

Analyzing Implicit Social Networks in Multiplayer Online Games

Distributed SystemsSoftware EngineeringNetwork Architectures and Service