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

The smart releasing behavior of a microcapsule based on chemical self-healing system caused by chemical trigger activation

A novel chemical self-healing system based on microcapsule technology for cementitious composites is established in Guangdong Key Laboratory of Durability for Coastal Civil Engineering, Shenzhen University. The key issue of this system is how to release the healing material and how to activate the healing mechanism. In this paper, the study is focused on the releasing behavior. The smart releasing behavior of healing material in the microcapsule is characterized by EDTA (Ethylene Diamine Tetraacetic Acid) titration method. The experimental results show that releasing procedure of the corrosion inhibitor covered with PS is a function of the time, and is controlled by the wall thickness of the microcapsule. Moreover, the pH value affects the release rate of corrosion inhibitor. With the increasing of pH value, the releasing rate will increase greatly

A study on the steel corrosion protection of a microcapsule based self-healing cementitious system by means of electrochemical impedance spectroscopy

Based on microcapsule technology, a new type of self-healing system for cementitious composites is established. The performance of the system was characterized by means of electrochemical impedance spectroscopy of steel bars immersed in a simulated concrete environment. The results demonstrate strong inhibition of chloride-induced corrosion when microcapsules are added to the solution. A novel equivalent circuit model, which takes into account the inductive effect arising from the generation of corrosion products on the steel bar surface, is proposed to explain the protection performance of the microcapsules against steel bar corrosion in a concrete environment

Design of microcapsule system used for self-healing cementitious material

For a microcapsule based self-healing system in the cementitious material, a fundamental issue is to find and facilitate a suitable microcapsule system, concerning either the material selection or design and manufacture process. In this study, urea formaldehyde resin is used for the shell of microcapsule, and bisphenol – an epoxy resin E-51 diluted by n-butyl glycidy ether (BGE) is adopted as the heal-agent inside the microcapsule. The production process mainly includes pre-polymerization preparation, emulsification, acidification and curing stage. The fundamental reaction mechanisms with respect to the synthesis process and the properties of the obtained microcapsule are discussed in this paper. Meanwhile, the healing mechanism by means of catalyst MC120D is further explored. Results show that the microcapsule obtained with the adopted production process can be used for the self-healing system in the cementitious materials.Structural EngineeringCivil Engineering and Geoscience

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

Design of microcapsule system used for self-healing cementitious material

For a microcapsule based self-healing system in the cementitious material, a fundamental issue is to find and facilitate a suitable microcapsule system, concerning either the material selection or design and manufacture process. In this study, urea formaldehyde resin is used for the shell of microcapsule, and bisphenol \u96 an epoxy resin E-51 diluted by n-butyl glycidy ether (BGE) is adopted as the heal-agent inside the microcapsule. The production process mainly includes pre-polymerization preparation, emulsification, acidification and curing stage. The fundamental reaction mechanisms with respect to the synthesis process and the properties of the obtained microcapsule are discussed in this paper. Meanwhile, the healing mechanism by means of catalyst MC120D is further explored. Results show that the microcapsule obtained with the adopted production process can be used for the self-healing system in the cementitious materials

Evaluation of a microcapsule based self-healing system for cementitious materials

An international cooperation research project has been financially supported by China Nature Science Foundation, which consists of three relatively independent, but strategically integrated research sub-programs, aiming at the formation of a selfhealing system based on the microcapsule principle for the cementitious composites. In this paper, a self-healing system triggered by physical process (cracking) is introduced. The healing material mainly consists of epoxy like materials. The discussion concerning microcapsule techniques are presented in another paper in this conference. This study mainly focuses on the two healing mechanisms: i.e. the mechanical recovery and the permeability related recovery. The primary test results concerning these healing mechanisms are presented and the healing effects on the relevant properties are further discussed.Structural EngineeringCivil Engineering and Geoscience

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

Experimental and numerical study on cement paste degradation under external sulfate attack

External sulfate attack is one of the situations that may cause gradual but severe damage in cementitious materials, which may lead to cracking, increased permeability and strength loss. In this paper, thin-walled hollow cement paste cylinders with a wall thickness of 2.5mm were made considering the slow penetration process of sulfate ions under continuous immersion condition. Three types of longitudinal restraints were applied on the hollow cement paste cylinders by means of a spring and steel bars through the specimens in order to facilitate non-, low- and high-restraint conditions. Strain gauges were glued on the steel bars so as to increase the accuracy of the measurements. During the immersion tests, specimen expansion and generated stress were monitored. Additionally, sulfur element mapping was generated by EDS (energy dispersive X-ray spectrometry). Expansion behaviours of the hollow cement paste cylinders were simulated under the aforementioned restraint conditions which were carried out based on the Delft lattice fracture model. The expansion was assumed to be realized upon formation of ettringite inside the nanopores of the cement hydration products. Local expansion stresses were computed by employing the crystallization pressure theory. A comparison between the simulation and the experimental results showed reasonable correlation and tendency for further exploration of our approach.Materials and Environmen

Ontology-based semantic conceptualisation of historical built heritage to generate parametric structured models from point clouds

Nowadays, cultural and historical built heritage can be more effectively preserved, val-orised and documented using advanced geospatial technologies. In such a context, there is a major issue concerning the automation of the process and the extraction of useful information from a huge amount of spatial information acquired by means of advanced survey techniques (i.e., highly detailed LiDAR point clouds). In particular, in the case of historical built heritage (HBH) there are very few effective efforts. Therefore, in this paper, the focus is on establishing the connections between semantic and geometrical information in order to generate a parametric, structured model from point clouds using ontology as an effective approach for the formal conceptualisation of application domains. Hence, in this paper, an ontological schema is proposed to structure HBH representations, starting with international standards, vocabularies, and ontologies (CityGML-Geography Markup Language, International Committee for Documentation conceptual reference model (CIDOC-CRM), Industry Foundation Classes (IFC), Getty Art and Architecture Thesaurus (AAT), as well as reasoning about morphology of historical centres by analysis of real case studies) to represent the built and architecture domain. The validation of such schema is carried out by means of its use to guide the segmentation of a LiDAR point cloud from a castle, which is later used to generate parametric geometries to be used in a historical building information model (HBIM).Urban Data Scienc