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

A plasmonic spanner for metal particle manipulation

Typically, metal particles are difficult to manipulate with conventional optical vortex (OV) tweezers, because of their strong absorption and scattering. However, it has been shown that the vortex field of surface plasmonic polaritons, called plasmonic vortex (PV), is capable of stable trapping and dynamic rotation of metal particles, especially those of mesoscopic and Mie size. To uncover the different physical mechanisms of OV and PV tweezers, we investigated the force distribution and trapping potential of metal particles. In OV tweezers the stronger scattering force causes a positive potential barrier that repels particles, whereas in PV tweezers the dominant gradient force contributes to a negative potential well, resulting in stably trapped particles. Compared with OV, the orbital angular momentum of PV produces an azimuthal scattering force that rotates the trapped particles with more precise radius and position. Our results demonstrate that PV tweezers are superior in manipulation of metal particles.ImPhys/Imaging PhysicsApplied Science

Delamination toughening in a low carbon microalloyed steel plate rolled in the dual-phase region

It is still a big challenge to obtain excellent low-temperature toughness for bulk steel materials. Delamination is an effective method to improve low-temperature toughness. In the present study, delamination toughening in a low carbon microalloyed steel plate with elongated and ultrafine-grained microstructure rolled in the dual-phase region has been investigated in detail. When toughness was measured along normal direction, the steel plate had a high upper shelf energy and no delamination occurred in the upper shelf region. A large delaminated crack parallel to rolling plane started to appear and changed the propagation path of main crack when testing temperature was lower than −60 °C. We find this kind of delamination induces a second upper shelf in the Charpy transition–temperature curve. The second upper shelf, reaching up to 300 J in the temperature range of −60 °C to −140 °C, results in excellent low-temperature toughness for the steel plate, and the ductile-brittle transition temperature is lowered to −157 °C. The developed steel plate also has high low-temperature toughness measured along transverse direction due to delamination. The effect factors on upper shelf energy, delamination mechanism and delamination toughening are discussed.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.RST/Fundamental Aspects of Materials and EnergyNovel Aerospace Material

The on-orbit calibration of DArk Matter Particle Explorer

The DArk Matter Particle Explorer (DAMPE), a satellite-based cosmic ray and gamma-ray detector, was launched on December 17, 2015, and began its on-orbit operation on December 24, 2015. In this work we document the on-orbit calibration procedures used by DAMPE and report the calibration results of the Plastic Scintillator strip Detector (PSD), the Silicon-Tungsten tracKer-converter (STK), the BGO imaging calorimeter (BGO), and the Neutron Detector (NUD). The results are obtained using Galactic cosmic rays, bright known GeV gamma-ray sources, and charge injection into the front-end electronics of each sub-detector. The determination of the boundary of the South Atlantic Anomaly (SAA), the measurement of the live time, and the alignments of the detectors are also introduced. The calibration results demonstrate the stability of the detectors in almost two years of the on-orbit operation

The on-orbit calibration of DArk Matter Particle Explorer

The DArk Matter Particle Explorer (DAMPE), a satellite-based cosmic ray and gamma-ray detector, was launched on December 17, 2015, and began its on-orbit operation on December 24, 2015. In this work we document the on-orbit calibration procedures used by DAMPE and report the calibration results of the Plastic Scintillator strip Detector (PSD), the Silicon-Tungsten tracKer-converter (STK), the BGO imaging calorimeter (BGO), and the Neutron Detector (NUD). The results are obtained using Galactic cosmic rays, bright known GeV gamma-ray sources, and charge injection into the front-end electronics of each sub-detector. The determination of the boundary of the South Atlantic Anomaly (SAA), the measurement of the live time, and the alignments of the detectors are also introduced. The calibration results demonstrate the stability of the detectors in almost two years of the on-orbit operation

The on-orbit calibration of DArk Matter Particle Explorer

The DArk Matter Particle Explorer (DAMPE), a satellite-based cosmic ray and gamma-ray detector, was launched on December 17, 2015, and began its on-orbit operation on December 24, 2015. In this work we document the on-orbit calibration procedures used by DAMPE and report the calibration results of the Plastic Scintillator strip Detector (PSD), the Silicon-Tungsten tracKer-converter (STK), the BGO imaging calorimeter (BGO), and the Neutron Detector (NUD). The results are obtained using Galactic cosmic rays, bright known GeV gamma-ray sources, and charge injection into the front-end electronics of each sub-detector. The determination of the boundary of the South Atlantic Anomaly (SAA), the measurement of the live time, and the alignments of the detectors are also introduced. The calibration results demonstrate the stability of the detectors in almost two years of the on-orbit operation