Chiral Steering of Molecular Organization in the Limit of Weak Adsorbate-Substrate Interactions: Enantiopure and Racemic Tartaric Acid Domains on Ag(111)

Article on the chiral steering of molecular organization in the limit of weak adsorbate-substrate interactions

Radiation Engineering of Optical Antennas for Maximum Field Enhancement

Optical antennas have generated much interest in recent years due to their ability to focus optical energy beyond the diffraction limit, benefiting a broad range of applications such as sensitive photodetection, magnetic storage, and surfaceenhanced Raman spectroscopy. To achieve the maximum field enhancement for an optical antenna, parameters such as the antenna dimensions, loading conditions, and coupling efficiency have been previously studied. Here, we present a framework, based on coupled-mode theory, to achieve maximum field enhancement in optical antennas through optimization of optical antennas’ radiation characteristics. We demonstrate that the optimum condition is achieved when the radiation quality factor (Q_(rad)) of optical antennas is matched to their absorption quality factor (Q_(abs)). We achieve this condition experimentally by fabricating the optical antennas on a dielectric (SiO2) coated ground plane (metal substrate) and controlling the antenna radiation through optimizing the dielectric thickness. The dielectric thickness at which the matching condition occurs is approximately half of the quarter-wavelength thickness, typically used to achieve constructive interference, and leads to ∼20% higher field enhancement relative to a quarter-wavelength thick dielectric layer

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

Variations in particulate matter over Indo-Gangetic Plains and Indo-Himalayan Range during four field campaigns in winter monsoon and summer monsoon: Role of pollution pathways

Both in-situ and space-borne observations reveal an extremely high loading of particulates over the Indo-Gangetic Plains (IGP), all year around. With a burgeoning population and combustion sources (fossil fuels (FFs) and biofuels (BFs)) in close proximity to each other, the IGP is widely regarded as a hotspot for anthropogenic aerosol emission in South Asia. The deteriorating air quality over this region, particularly during winters, is a cause of major concern, since the pollutants undergo long range transport from their source regions to the Indo-Himalayan Range (IHR), Bay of Bengal (BoB) and other remote areas, polluting their pristine atmospheric conditions. Seasonal reversal in winds over the Indian mainland leads to an outflow of continental pollutants into the BoB during winters and a net advection of desert dust aerosols into the IGP from southwest Asia (SW-Asia), northwest India (NW-India) and northern Africa (N-Africa) during summers. Through the course of this study, four observational campaigns were conducted for sampling the ambient PM2.5 and PM10 during winter and summer seasons of 2014-2015, at multiple locations (18 sites) in the IGP, IHR, and semi-arid/arid sites towards their south and west, in order to accurately determine the inter-seasonal and inter-annual changes in the aerosol loading at the sites. We have also utilized data from Moderate Resolution Imaging Spectroradiometer (MODIS) on-board Earth Observing System (EOS) Terra satellite for estimating the columnar Aerosol Optical Depth at 550 nm (AOD(550)) and data from EOS Terra and Aqua satellites for discovering openly burning fires in the vicinity of sampling sites. Determination of the major source regions and key transport pathways during both seasons have also been attempted, using back-trajectory cluster analyses, as well as receptor models such as PSCF and CWT

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