Photon-assisted electron transmission resonance through a quantum well with spin-orbit coupling

Using the effective-mass approximation and Floquet theory, we study the electron transmission over a quantum well in semiconductor heterostructures with Dresselhaus spin-orbit coupling and an applied oscillation field. It is demonstrated by the numerical evaluations that Dresselhaus spin-orbit coupling eliminates the spin degeneracy and leads to the splitting of asymmetric Fano-type resonance peaks in the conductivity. In turn, the splitting of Fano-type resonance induces the spin- polarization-dependent electron-current. The location and line shape of Fano-type resonance can be controlled by adjusting the oscillation frequency and the amplitude of external field as well. These interesting features may be a very useful basis for devising tunable spin filters.Comment: 10pages,4figure

Effects of sea-buckthorn leaves on performance and serum metabolic profiles in Altay lambs

In this study, the effects of sea-buckthorn (Hippophae rhamnoides L.) leaves (SL) on the biochemical parameters and metabolomic profiling in Altay lamb (Ovis aries) were observed. Sixty six-month-old male Altay lambs (body weight 28.0 ± 3.5 kg) were randomly assigned to four groups (n=15). The experimental groups were named as CON, 2.5%, 5.0% and 7.5%. The group CON, contained animals fed with a basal diet. Animals of the other groups were fed a treatment diet consisting of 2.5% (Group 2.5%), 5.0% (Group 5.0%) and 7.5% (Group 7.5%) SL. The experimental period lasted 56 days. The results showed that the average daily gain (ADG) and average daily feed intake (ADFI) increased with the increase in the levels of dietary SL. Dietary SL showed a direct relationship with total protein (TP), albumin, globulin and total cholesterol (TC) content of the experimental animals. However, an indirect relationship was observed between dietary SL and the concentration of urea nitrogen (UN). The concentrations of glucose, high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) showed quadratic change. Additional changes occurred in the endogenous metabolites involving multiple pathways. The pathways were tricarboxylic acid (TCA) cycle, the metabolism of protein and amino acid and the metabolism of fatty acid and steroid. The changes in metabolites primarily revealed an increase in amino acids and carbohydrates and a decrease in lipid metabolites. These findings provide a comprehensive insight into the effects of the metabolic aspects of sea-buckthorn leaves on Altay lambs. In addition, the present research results provide a better understanding to the development and utilization of sea-buckthorn as a healthy additive for small ruminant production.Keywords: Hippophae rhamnoides L., lamb, metabolomics, growth performance, serum parameter

In Situ Observations during Chemical Vapor Deposition of Hexagonal Boron Nitride on Polycrystalline Copper.

Using a combination of complementary in situ X-ray photoelectron spectroscopy and X-ray diffraction, we study the fundamental mechanisms underlying the chemical vapor deposition (CVD) of hexagonal boron nitride (h-BN) on polycrystalline Cu. The nucleation and growth of h-BN layers is found to occur isothermally, i.e., at constant elevated temperature, on the Cu surface during exposure to borazine. A Cu lattice expansion during borazine exposure and B precipitation from Cu upon cooling highlight that B is incorporated into the Cu bulk, i.e., that growth is not just surface-mediated. On this basis we suggest that B is taken up in the Cu catalyst while N is not (by relative amounts), indicating element-specific feeding mechanisms including the bulk of the catalyst. We further show that oxygen intercalation readily occurs under as-grown h-BN during ambient air exposure, as is common in further processing, and that this negatively affects the stability of h-BN on the catalyst. For extended air exposure Cu oxidation is observed, and upon re-heating in vacuum an oxygen-mediated disintegration of the h-BN film via volatile boron oxides occurs. Importantly, this disintegration is catalyst mediated, i.e., occurs at the catalyst/h-BN interface and depends on the level of oxygen fed to this interface. In turn, however, deliberate feeding of oxygen during h-BN deposition can positively affect control over film morphology. We discuss the implications of these observations in the context of corrosion protection and relate them to challenges in process integration and heterostructure CVD.P.R.K. acknowledges funding from the Cambridge Commonwealth Trust and the Lindemann Trust Fellowship. R.S.W. acknowledges a research fellowship from St. John’s College, Cambridge. S.H. acknowledges funding from ERC grant InsituNANO (no. 279342), EPSRC under grant GRAPHTED (project reference EP/K016636/1), Grant EP/H047565/1 and EU FP7 Work Programme under grant GRAFOL (project reference 285275). The European Synchrotron Radiation Facility (ESRF) is acknowledged for provision of synchrotron radiation and assistance in using beamline BM20/ROBL. We acknowledge Helmholtz-Zentrum-Berlin Electron storage ring BESSY II for synchrotron radiation at the ISISS beamline and continuous support of our experiments.This is the final version. It was first published by ACS at http://pubs.acs.org/doi/abs/10.1021/cm502603

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

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe