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

Unified deep learning architecture for the detection of all catenary support components

With the rapid development of deep learning technologies, researchers have begun to utilize convolutional neural network (CNN)-based object detection methods to detect multiple catenary support components (CSCs). The literature has focused on the detection of specified large-scale CSCs. Additionally, CNN architectures have faced difficulties in identifying overlapping CSCs, especially small-scale components. In this paper, a unified CNN architecture is proposed for detecting all components at various scales of CSCs. First, a detection network for CSCs with large scales is proposed by optimizing and improving Faster R-CNN. Next, a cascade network for the detection of CSCs with small scales is proposed and is integrated into the detection network for CSCs with large scales to construct the unified network architecture. The experimental results demonstrate that the detection accuracy of the proposed CNN architecture can reach 92.8%; hence, it outperforms the popular CNN architectures.Railway Engineerin

Effect of natural carbonation on chloride binding behaviours in OPC paste investigated by a thermodynamic model

The combined effects of carbonation and chloride attack can accelerate the degradation of reinforced concrete (RC) structures. In this study, the effect of natural carbonation on the chloride binding behaviours in Ordinary Portland cement (OPC) paste was investigated. The phase-equilibrium model for the dissolution/precipitation reactions and the surface complexation model for the ionic adsorption of C–S–H were adopted. An experiment from the literature was used as the benchmark. The results indicate that Kuzel's salt is produced when OPC paste is exposed to a mild chloride attack. During the natural carbonation process, Kuzel's salt is converted into Friedel's salt. As the carbonation continues, the Friedel's salt disappears. Complete natural carbonation results in a total loss of chemical binding capacity, and only a partial loss of the physical binding capacity in cement-based materials. This completely differs from the accelerated carbonation commonly used in the laboratory, which can cause complete loss of both chemical and physical binding capacity. Therefore, the durability design of RC structures vulnerable to the combined attack of chloride and carbonation based on the results of the accelerated carbonation is conservative.Materials and Environmen

Interaction between microcapsules and cementitious matrix after cracking in a self-healing system

A new type of self-healing cementitious composites by using organic microcapsules is designed in Guangdong Key Laboratory of Durability for Coastal Civil Engineering, Shenzhen University. For the organic microcapsules, the shell material is urea formoldehyde (UF), and the core healing agent is Epoxy. The effect of organic microcapsules on mechanical behaviors of the composite specimens and the interaction between an organic microcapsule and an approaching crack is investigated in this study. The mechanical behaviors of bending and compression strengths for mortar specimens are tested. The results show that the strength may increase with a small amount of microcapsules and then decrease with increasing of microcapsules. The FEM numerical simulation is carried out to study the interaction between a crack and a microcapsule in the concrete matrix. It is known that there exist two possibilities when a crack approaches a microcapsule, the microcapsule is ruptured or debonded from the matrix. The self-healing function is based on the rupture of microcapsules. Thus determination of judgment criterion (The physical trigger mechanism-cracking) that under what condition a microcapsule ruptures is necessary. For simplicity, a two-dimensional plane square area is considered, in which the side length is 1 cm. A microcapsule of radius 0.1mm is located at the center of the area. Left hand side is a line crack. The interface between the microcapsule and the mortar matrix, as well as the bonding behavior of the microcapsule shell wall is modeled using the cohesive traction-separation constitutive relationship. The actual parameters of the materials may lead to rupture or debonding of a microcapsule. Through numerical simulation, the criterion of the possible failure pattern for a microcapsule is obtained in terms of the intensity of microcapsule wall, the intensity of the interface, thickness of the microcapsule wall, location of the crack, and the microcapsule radius.Structural EngineeringCivil Engineering and Geoscience

Nanomechanical Characteristics of Interfacial Transition Zone in Nano-Engineered Concrete

This study investigates the effects of nanofillers on the interfacial transition zone (ITZ) between aggregate and cement paste by using nanoindentation and statistical nanoindentation techniques. Moreover, the underlying mechanisms are revealed through micromechanical modeling. The nanoindentation results indicate that incorporating nanofillers increases the degree of hydration in the ITZ, reduces the content of micropores and low-density calcium silicate hydrate (LD C–S–H), and increases the content of high-density C–S–H (HD C–S–H) and ultrahigh-density C–S–H (UHD C–S–H). In particular, a new phase, namely nano-core-induced low-density C–S–H (NCILD C–S–H), with a superior hardness of 2.50 GPa and an indentation modulus similar to those of HD C–S–H or UHD C–S–H was identified in this study. The modeling results revealed that the presence of nanofillers increased the packing density of LD C–S–H and significantly enhanced the interaction (adhesion and friction) among the basic building blocks of C–S–H gels owing to the formation of nano-core–shell elements, thereby facilitating the formation of NCILD C–S–H and further improving the performance of the ITZ. This study provides insight into the effects of nanofillers on the ITZ in concrete at the nanoscale.Materials and Environmen

Experimental Study on Cementitious Composites Embedded with Organic Microcapsules

The recovery behavior for strength and impermeability of cementitious composites embedded with organic microcapsules was investigated in this study. Mortar specimens were formed by mixing the organic microcapsules and a catalyst with cement and sand. The mechanical behaviors of flexural and compression strength were tested. The results showed that strength could increase by up to nine percent with the addition of a small amount of microcapsules and then decrease with an increasing amount of microcapsules. An orthogonal test for investigating the strength recovery rate was designed and implemented for bending and compression using the factors of water/cement ratio, amount of microcapsules, and preloading rate. It is shown that the amount of microcapsules plays a key role in the strength recovery rate. Chloride ion permeability tests were also carried out to investigate the recovery rate and healing effect. The initial damage was obtained by subjecting the specimens to compression. Both the recovery rate and the healing effect were nearly proportional to the amount of microcapsules. The obtained cementitious composites can be seen as self-healing owing to their recovery behavior for both strength and permeability.Structural EngineeringCivil Engineering and Geoscience

Highly dispersed Cd cluster supported on TiO2 as an efficient catalyst for CO2 hydrogenation to methanol

The conversion of CO2 with high activity and high selectivity to methanol remains challenging because of both the kinetics and thermodynamics difficulties associated with the chemical reactivity of CO2. Herein, we report a new catalyst of Cd/TiO2 enabling 81% methanol selectivity at 15.8% CO2 conversion with the CH4 selectivity below 0.7%. The combination of experimental and computational studies show that the unique electronic properties of Cd cluster supported on TiO2 are responsible for the high selectivity for CO2 hydrogenation to methanol via a HCOO* pathway realized at the interface catalytic sites.ChemE/Inorganic Systems Engineerin

Asymmetric Excitation of Surface Plasmon Polaritons via Paired Slot Antennas for Angstrom Displacement Sensing

Optical antennas enable efficient coupling between propagating light and bonding electromagnetic waves like surface plasmon polaritons (SPPs). Under the illumination of inhomogeneous optical fields, propagating SPPs mediated by multimode antennas could be spatially asymmetric and the asymmetry strongly depends on the position of the antennas relative to the illumination field. Here we develop such asymmetric excitation of SPPs through illuminating a pair of slot antennas with the (1,0) mode Hermite-Gaussian beam. The physical scenario of the interaction between the illumination optical field and the paired slot antennas are elaborated by full-wave electromagnetic simulations. We also carry out experiments to monitor the asymmetric SPPs propagation with a back-focal plane imaging technique. By retrieving the asymmetric intensity ratio of the SPP pattern in the back-focal plane image, lateral displacement of the antennas down to angstrom level is demonstrated. ImPhys/Optic

Rheological behaviors and viscosity prediction model of cementitious composites with various carbon nanotubes

This study aims to understand the effects and mechanisms of length, diameter, and functional group of carbon nanotubes (CNTs) on rheological behaviors of cementitious composites. The experimental results show that the addition of CNTs decreases the flow index and increases the critical shear rate of cementitious composites. CNTs with a sub-micrometer length and small diameter endow cementitious composites with high yield stresses and minimum viscosities. Influenced by the high water absorption of hydroxylic groups, the minimum viscosity of cementitious composites with hydroxyl functionalized CNTs is larger than that of composites with pristine carbon nanotubes (p-CNTs). By contrast, the yield stress and minimum viscosity of cementitious composites with carboxyl functionalized CNTs are smaller than that of cementitious composites with p-CNTs at most contents due to the high dispersion induced by carboxyl groups. The effect mechanisms of CNTs on rheological behaviors can be attributed to adsorption effect and entanglement effect, which are closely related to length, diameter and functionalization groups of CNTs. The established minimum viscosity prediction model considering the influence of CNT physicochemical features can provide guidance for regulating the workability and hardened performance of CNTs modified cementitious composites.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.Materials and Environmen

Nickel hexacyanoferrate electrodes for high mono/divalent ion-selectivity in capacitive deionization

Selective ion removal has been a point of focus in capacitive deionization because of its industrial applications such as water purification, water softening, heavy metal separation and resource recovery. Conventionally, carbon is used as electrode material for selectivity. However, recent developments focus on intercalation materials such as Prussian Blue Analogues, due to their size-based preference towards cations. Selectivity of nickel hexacyanoferrate electrodes from a mixture of Na+, Mg2+, and Ca2+ ions was studied in this work. Here, a CDI cell with two identical NiHCF electrodes was operated in two desalination modes: (a) cyclic, in which ions are removed from and released into the same water reservoir and thus, the ion concentration remains the same after one cycle, and (b) continuous, in which ions are removed from one water reservoir and released back in a different reservoir. An average separation factor of ≈15 and 25, reflecting the selectivity of the electrodes, was obtained for Na+ over Ca2+ and Mg2+ from an equimolar solution of Na+, Ca2+ and Mg2+ in both, cyclic and continuous desalination. It was concluded that NiHCF, used in a symmetric CDI cell, is a promising material for highly selective removal of Na+ from a multivalent ion mixture.OLD ChemE/Organic Materials and Interface