Photochemical solution processing of films of metastable phases for flexible devices: the beta-Bi2O3 polymorph

The potential of UV-light for the photochemical synthesis and stabilization of non-equilibrium crystalline phases in thin films is demonstrated for the beta-Bi2O3 polymorph. The pure beta-Bi2O3 phase is thermodynamically stable at high temperature (450-667 degrees C), which limits its applications in devices. Here, a tailored UV-absorbing bismuth(III)-N-methyldiethanolamine complex is selected as an ideal precursor for this phase, in order to induce under UV-light the formation of a -Bi-O-Bi- continuous network in the deposited layers and the further conversion into the beta-Bi2O3 polymorph at a temperature as low as 250 degrees C. The stabilization of the beta-Bi2O3 films is confirmed by their conductivity behavior and a thorough characterization of their crystal structure. This is also supported by their remarkable photocatalytic activity. Besides, this processing method has allowed us for the first time the preparation of beta-Bi2O3 films on flexible plastic substrates, which opens new opportunities for using these materials in potential applications not available until now (e.g., flexible photocatalytic reactors, self-cleaning surfaces or wearable antimicrobial fabrics). Therefore, photochemical solution deposition (PCSD) demonstrates to be not only an efficient approach for the low temperature processing of oxide films, but also an excellent alternative for the stabilization of metastable phases

Recent Acceleration of Plastid Sequence and Structural Evolution Coincides with Extreme Mitochondrial Divergence in the Angiosperm Genus Silene

The angiosperm genus Silene exhibits some of the most extreme and rapid divergence ever identified in mitochondrial genome architecture and nucleotide substitution rates. These patterns have been considered mitochondrial specific based on the absence of correlated changes in the small number of available nuclear and plastid gene sequences. To better assess the relationship between mitochondrial and plastid evolution, we sequenced the plastid genomes from four Silene species with fully sequenced mitochondrial genomes. We found that two species with fast-evolving mitochondrial genomes, S. noctiflora and S. conica, also exhibit accelerated rates of sequence and structural evolution in their plastid genomes. The nature of these changes, however, is markedly different from those in the mitochondrial genome. For example, in contrast to the mitochondrial pattern, which appears to be genome wide and mutationally driven, the plastid substitution rate accelerations are restricted to a subset of genes and preferentially affect nonsynonymous sites, indicating that altered selection pressures are acting on specific plastid-encoded functions in these species. Indeed, some plastid genes in S. noctiflora and S. conica show strong evidence of positive selection. In contrast, two species with more slowly evolving mitochondrial genomes, S. latifolia and S. vulgaris, have correspondingly low rates of nucleotide substitution in plastid genes as well as a plastid genome structure that has remained essentially unchanged since the origin of angiosperms. These results raise the possibility that common evolutionary forces could be shaping the extreme but distinct patterns of divergence in both organelle genomes within this genus

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

Study of annealing-induced interdiffusion in In2_2O3_3/Ag/In2_2O3_3 structures by a combined X-ray reflectivity and grazing incidence X-ray fluorescence analysis

International audienceThe combination of X-ray reflectivity and grazing incidence X-ray fluorescence has been applied to the characterization of an In$_2$ O$_3$/Ag/In$_2$O$_3$ stack for advanced photovoltaic applications. X-ray reflectivity is a well-known method for the characterization of multilayered structures by providing information on the thickness and the in-depth electronic density. Grazing incidence X-ray fluorescence provides information about the elemental depth distribution. As these techniques are based on similar measurement procedures and data evaluation approaches, their combination reduces the uncertainties of the individual techniques and provides an accurate depth-resolving analysis of multi-layers. It has been shown that the combination of the techniques give insight into the material composition and the layers structure (thickness, density) as well as modifications induced by a thermal annealing. As X-ray fluorescence signals have been acquired at different excitation energies, the influence of this parameter on the sensitivity of the measurements to the structural properties has been shown

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

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

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

Hierarchical structural design for fracture resistance in the shell of the pteropod Clio pyramidata

The thecosomes are a group of planktonic pteropods with thin, 1 mm-sized aragonitic shells, which are known to possess a unique helical microstructure consisting of interlocking nanofibres. Here we investigate the detailed hierarchical structural and mechanical design of the pteropod Clio pyramidata. We quantify and elucidate the macroscopic distribution of the helical structure over the entire shell (~1 mm), the structural characteristics of the helical assembly (~10–100 μm), the anisotropic cross-sectional geometry of the fibrous building blocks (~0.5–10 μm) and the heterogeneous distribution of intracrystalline organic inclusions within individual fibres (<0.5 μm). A global fibre-like crystallographic texture is observed with local in-plane rotations. Microindentation and electron microscopy studies reveal that the helical organization of the fibrous building blocks effectively constrains mechanical damages through tortuous crack propagation. Uniaxial micropillar compression and cross-sectional transmission electron microscopy directly reveal that the interlocking fibrous building blocks further retard crack propagation at the nanometre scale.National Science Foundation (U.S.) ((Massachusetts Institute of Technology. Center for Materials Science and Engineering (DMR-0819762))United States. Army Research Office (Massachusetts Institute of Technology. Institute for Soldier Nanotechnologies (Contract W911NF-07-D-0004))United States. Department of Defense. National Security Science and Engineering Faculty Fellow