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

Spin Hall-induced auto-oscillations in ultrathin YIG grown on Pt.

We experimentally study nanowire-shaped spin-Hall nano-oscillators based on nanometer-thick epitaxial films of Yttrium Iron Garnet grown on top of a layer of Pt. We show that, although these films are characterized by significantly larger magnetic damping in comparison with the films grown directly on Gadolinium Gallium Garnet, they allow one to achieve spin current-driven auto-oscillations at comparable current densities, which can be an indication of the better transparency of the interface to the spin current. These observations suggest a route for improvement of the flexibility of insulator-based spintronic devices and their compatibility with semiconductor technology

Spin Hall-induced auto-oscillations in ultrathin YIG grown on Pt

We experimentally study nanowire-shaped spin-Hall nano-oscillators based on nanometer-thick epitaxial films of Yttrium Iron Garnet grown on top of a layer of Pt. We show that, although these films are characterized by significantly larger magnetic damping in comparison with the films grown directly on Gadolinium Gallium Garnet, they allow one to achieve spin current-driven auto-oscillations at comparable current densities, which can be an indication of the better transparency of the interface to the spin current. These observations suggest a route for improvement of the flexibility of insulator-based spintronic devices and their compatibility with semiconductor technology

Spin Hall-induced auto-oscillations in ultrathin YIG grown on Pt.

We experimentally study nanowire-shaped spin-Hall nano-oscillators based on nanometer-thick epitaxial films of Yttrium Iron Garnet grown on top of a layer of Pt. We show that, although these films are characterized by significantly larger magnetic damping in comparison with the films grown directly on Gadolinium Gallium Garnet, they allow one to achieve spin current-driven auto-oscillations at comparable current densities, which can be an indication of the better transparency of the interface to the spin current. These observations suggest a route for improvement of the flexibility of insulator-based spintronic devices and their compatibility with semiconductor technology

Diagnostic accuracy of transvaginal ultrasound examination for assigning a specific diagnosis to adnexal masses

Objectives To determine the sensitivity and specificity of subjective evaluation of gray-scale and Doppler ultrasound findings (here called pattern recognition) when used by experienced ultrasound examiners with regard to making a specific diagnosis of adnexal masses. Methods Within the framework of a European multi-center study, the International Ovarian Tumor Analysis study, comprising nine ultrasound centers, women with at least one adnexal mass were examined with gray-scale and color Doppler ultrasonography by experienced ultrasound examiners. A standardized examination technique, and standardized terms and definitions were used. Using pattern recognition the examiners classified each mass as benign or malignant and suggested a specific diagnosis (e.g. dermoid cyst or endometrioma). The reference standard was the histology of the surgically removed adnexal tumors. Results A total of 1066 women were included, of whom 800 bad a benign mass and 266 a malignant mass. A specific diagnosis based on ultrasound findings was suggested in 899 (84%) tumors. The specificity was high for all diagnoses (range, 94-100%). The sensitivity was highest for benign teratoma/dermoid cysts (86%, 100/116), hydrosalpinges (86%, 18/21), peritoneal pseudocysts (80%, 4/5) and endometriomas (77%, 1531199), and lowest for functional cysts (17%, 4124), paraovarian/parasalpingeal cysts (14%, 3121), benign rare tumors (11%, 119), adenofibromas (8%, 3/39), simple cysts (6%, 1/18) and struma ovarii (0%, 0/5). The positive and negative likelihood ratios of pattern recognition with regard to dermoid cysts, hydrosalpinges and endometriomas were 68.2 and 0.14, 38.9 and 0.15, and 33.3 and 0.24, respectively. Dermoid cysts, hydrosalpinges, functional cysts, paraovarian cysts, peritoneal pseudocysts, fibromas/fibrothecomas and simple cysts were never misdiagnosed as malignancies by the ultrasound examiner, whereas more than 10% of inflammatory processes, adenofibromas and rare benign tumors including struma ovarii were misdiagnosed as malignancies. Conclusions Using subjective evaluation of gray-scale and Doppler ultrasound findings it is possible to make an almost conclusive diagnosis of a dermoid cyst, endometrioma and hydrosalpinx. Many other adnexal pathologies can be recognized but not confidently confirmed or excluded. Copyright (C) 2009 ISUOG. Published by John Wiley & Sons, Ltd

Spin-wave-beam driven synchronization of nanocontact spin-torque oscillators

The synchronization of multiple nanocontact spin-torque oscillators (NC-STOs) is mediated by propagating spin waves (SWs). Although it has been shown that the Oersted field generated in the vicinity of the NC can dramatically alter the emission pattern of SWs, its role in the synchronization behaviour of multiple NCs has not been considered so far. Here we investigate the synchronization behaviour in multiple NC-STOs oriented either vertically or horizontally, with respect to the in-plane component of the external field. Synchronization is promoted (impeded) by the Oersted field landscape when the NCs are oriented vertically (horizontally) due to the highly anisotropic SW propagation. Not only is robust synchronization between two oscillators observed for separations larger than 1,000 nm, but synchronization of up to five oscillators, a new record, has been observed in the vertical array geometry. Furthermore, the synchronization can no longer be considered mutual in nature