Chromosomal rearrangements and karyotype evolution in carnivores revealed by chromosome painting

Chromosomal evolution in carnivores has been revisited extensively using cross-species chromosome painting. Painting probes derived from flow-sorted chromosomes of the domestic dog, which has one of the most rearranged karyotypes in mammals and the highest dipoid number (2n=78) in carnivores, are a powerful tool in detecting both evolutionary intra- and inter-chromosomal rearrangements. However, only a few comparative maps have been established between dog and other non-Canidae species. Here, we extended cross-species painting with dog probes to seven more species representing six carnivore families: Eurasian lynx (Lynx lynx), the stone marten (Martes foina), the small Indian civet (Viverricula indica), the Asian palm civet (Paradoxurus hermaphrodites), Javan mongoose (Hepestes javanicas), the raccoon (Procyon lotor) and the giant panda (Ailuropoda melanoleuca). The numbers and positions of intra-chromosomal rearrangements were found to differ among these carnivore species. A comparative map between human and stone marten, and a map among the Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis), stone marten and human were also established to facilitate outgroup comparison and to integrate comparative maps between stone marten and other carnivores with such maps between human and other species. These comparative maps give further insight into genome evolution and karyotype phylogenetic relationships among carnivores, and will facilitate the transfer of gene mapping data from human, domestic dog and cat to other species

Spatial variability of soil salinity in Bohai Sea coastal wetlands, China: Partition into four management zones

Soil salinization constitutes an environmental hazard worldwide. The Bohai Sea coastal wetland area is experiencing dramatic soil salinization, which is affecting its economic development. This study focused on the spatial variation and distribution characteristics of soil salinity in this area using geostatistical analysis combined with the kriging interpolation method, based on a large-scale field investigation and layered soil sampling (0-30, 30-60 and 60-100cm). The results revealed that soil salinity in these layers demonstrated strong variability, obvious spatial structure characteristics and strong spatial autocorrelation. Soil salinity displayed a significant zonal distribution, gradually decreasing with increasing distance from the coastline. Apart from the northern part of the study area, which appeared to be not affected by soil salinization, there were varying degrees of soil salinization in nearly 70% of the total area. With increasing soil depth, the areas of non-salinized and mild salinized soil gradually decreased, while those of moderate salinized and strong salinized soils increased. The area of saline soil first decreased and then increased. The study area could be divided into four management zones according to soil salinities in the top 1-m soil body, and utilization measures, adapted to local conditions, were proposed for each zone. The results of our study present an important theoretical basis for the improvement of saline soils, for wetland re-vegetation and for the sustainable utilization of soil resources in the Bohai Sea coastal wetland.Soil salinization constitutes an environmental hazard worldwide. The Bohai Sea coastal wetland area is experiencing dramatic soil salinization, which is affecting its economic development. This study focused on the spatial variation and distribution characteristics of soil salinity in this area using geostatistical analysis combined with the kriging interpolation method, based on a large-scale field investigation and layered soil sampling (0-30, 30-60 and 60-100cm). The results revealed that soil salinity in these layers demonstrated strong variability, obvious spatial structure characteristics and strong spatial autocorrelation. Soil salinity displayed a significant zonal distribution, gradually decreasing with increasing distance from the coastline. Apart from the northern part of the study area, which appeared to be not affected by soil salinization, there were varying degrees of soil salinization in nearly 70% of the total area. With increasing soil depth, the areas of non-salinized and mild salinized soil gradually decreased, while those of moderate salinized and strong salinized soils increased. The area of saline soil first decreased and then increased. The study area could be divided into four management zones according to soil salinities in the top 1-m soil body, and utilization measures, adapted to local conditions, were proposed for each zone. The results of our study present an important theoretical basis for the improvement of saline soils, for wetland re-vegetation and for the sustainable utilization of soil resources in the Bohai Sea coastal wetland

Train model acceleration and deceleration

In order to accelerate a heavy train model with great dimensions to a speed higher than 300 km h(-1) in a moving train model testing system, compressed air is utilized to drive the train model indirectly. The gas from an air gun pushes the piston in an accelerating tube forward. The piston is connected to the trailer through a rope, and the trailer pulls the train model to the desired speed. After the testing section, the train model enters the deceleration section. The speed of the train model gradually decreases because of the braking force of the magnetic braking device on the bottom of the train model and the steel plates fixed on the floor of this device. The dissipation of kinetic energy of the trailer is also based on a similar principle. The feasibility of these methods has been examined in a 180 m-long moving train model testing system. The speed of the trailer alone reaches up to 490 km h(-1). Consequently, a 34.8 kg model accelerates up to 350 km h(-1); the smooth and safe stopping of the model is also possible

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

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Design as Exploration: Multi-Objective and Multi- Disciplinary Optimization (MOMDO) of Indoor Sports Halls

There are an increasing number of optimal-design paradigms used in architectural design nowadays. In these paradigms, a design task is formulated, or partially formulated, as an optimization problem. Multi-Disciplinary Optimization and Multi-Objective Optimization, as two important optimal-design paradigms, have shown their great potential in improving the performances of complex buildings in recent decades. Nevertheless, current paradigms for ill‑defined conceptual architectural design still lack ways to ensure the achievement of a reliable optimization problem, which hinders reliable design solutions despite the use of advanced optimization algorithms.To address this problem, it is necessary to shift the focus from Optimization Problem Solving to Optimization Problem Formulation. This research particularly focuses on knowledge‑supported, dynamic and interactive Optimization Problem Re-Formulation in order to construct a new Multi‑Objective and Multi-Disciplinary Optimization (MOMDO) method suitable for use in ill‑defined conceptual architectural design. The proposed method consists of two subtype methods: Non‑dynamic, Interactive Re-formulation method (Subtype-I) and Dynamic, Interactive Re‑formulation method (Subtype-II), which can be used to explore design space in a convergent and divergent manner respectively. To support the re-formulation, various kinds of information and knowledge need to be extracted by utilizing different computational techniques, such as advanced sampling algorithms, Self-Organizing Map, Hierarchical Clustering, Smoothing Spline Analysis of Variance, Two-Level Variable Structure and modular programming. Moreover, a software workflow that can provide these computational techniques is developed; it integrates McNeel’s Grasshopper, ESTECO's modeFRONTIER and simulation software tools Daysim, EnergyPlus and Karamba3D. With the support of this software workflow, the proposed method is demonstrated via two case studies concerning the conceptual design of indoor sports halls.Design Informatic

Cure-Dependent Viscoelastic Behaviour of Electronic Packaging Polymers: Modelling, Characterization, Implementation and Applications

Polymers are widely used in electronic packaging as encapsulants, underfills, adhesives, insulators, and dielectrics, etc. Generally these materials are thermosetting polymers that have to be cured during the fabrication process at elevated temperatures. The curing process will introduce residual stress and warpage in the microelectronic devices, due to the polymerization shrinkage and subsequent cooling down from the curing temperature. During cure these polymers gradually transform from the more or less liquid state into a viscoelastic solid with a relatively high glassy modulus, accompanied with chemical shrinkage. Due to the cross-linking reaction and thermal shrinkage under continuing stiffness increase, stresses will arise in areas where shrinkage is partly prevented by geometrical constraints. Furthermore, if the cross-linked product is cooled down to ambient temperature, the difference in thermal expansion between matrix and adjacent materials will cause additional stresses and deformation. In order to be able to conduct reliable prediction of the process-induced stress and warpage in electronic packaging, cure-dependent viscoelastic constitutive relations for thermosetting polymers are required. Furthermore, material characterization and numerical implementation of the constitutive models into commercial FEM programs are important for providing a base for large scale thermo-mechanical FEM modelling of electronic packaging. And then a simulation-based optimization on the design for package structure, material parameters, and process conditions can be carried out…Electrical Engineering, Mathematics and Computer Scienc

A computational design exploration platform supporting the formulation of design concepts

The comparison of various competing design concepts during conceptual architectural design is commonly needed for achieving a good final concept. For this, computational design exploration is a key approach. Unfortunately, mostof existing research tends to skip this crucial process, and purely focuses on the late-stage design optimization based on a single concept that, they assume, has been good enough or accepted already. This paper focuses on information or knowledge extracted from a multi-objective design exploration for the formulation of a good geometrical building design concept. To better support the exploration process, a new integration plug-in is developed to integrate parametric modelling software and process integration and optimization software. Through a case study that investigates the daylight and energy performances of a large indoor space, this paper 1) tackles the importance of design exploration on the formulation of a good design concept; 2) presents and shows the usability of the new integration plug-in for supporting the exploration process.Design Informatic

Denoising controlled-source electromagnetic data using least-squares inversion

Strong noise is one of the toughest problems in the controlled-source electromagnetic (CSEM) method, which highly affects the quality of recorded data. The three main types of noise existing in CSEM data are periodic noise, Gaussian white noise, and nonperiodic noise, among which the nonperiodic noise is thought to be the most difficult to remove. We have developed a novel and effective method for removing such nonperiodic noise by formulating an inverse problem that is based on inverse discrete Fourier transform and several time windows in which only Gaussian white noise exists. These critical locations, which we call reconstruction locations, can be found by taking advantage of the continuous wavelet transform (CWT) and the temporal derivative of the scalogram generated by CWT. The coefficients of the nonperiodic noise are first estimated using the new least-squares method, and then they are subtracted from the coefficients of the raw data to produce denoised data. Together with the nonperiodic noise, we also remove Gaussian noise using the proposed method. We validate the methodology using real-world CSEM data.ImPhys/Acoustical Wavefield Imagin

Supporting Exploration of Design Alternatives using Multivariate Analysis Algorithms

Parametric modelling allows quick generation of a large number of design alternatives. Ultimately, it can be combined with optimization algorithms for obtaining optimal performance-driven design. However, setup of design space for optimization is a very complex task requiring designer’s a priori knowledge and experience. Therefore, this paper focuses on the process that happens before the optimization. It proposes to use multivariate analysis algorithms for exploring and understanding the relations between various design parameters, after sampling the design space. Additionally, portrayal of geometry isintroduced as an extension of conventional visualization methods, which accounts for evaluation of ill-defined design criteria by using designer’s expertise. The proposed method is computationally efficient and integrated into an environment familiar to architects. It relies on multivariate analysis algorithms together with database querying capabilities and an interactive dashboard developed for geometry portrayal.Design Informatic