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

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

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

Flood adaptive cities: Towards climate change adaption and urban development in the Mekong Delta

For three hundred years, Mekong delta has become a water society where inhabitants in this region developed adaptive strategies, often called “shaking hand with floods”. Historically, people first settled on the lightly higher terraces and later on the levees along the river. With the digging of canals, people started to settle along the canal banks; such settlement has formed a typical pattern of ribbon-like settlement. At the confluences of network system, intensified urban expansion is occurring. Over twenty years after the introduction of “DOI MOI” policy (innovation), Mekong delta in Vietnam has experienced significant expansion of cities and rapid growth of population. The water cities are transforming into the road cities in which the role of water in the city structure is going to be neglected. Thus, the cities are losing its unique characteristic and inhabitants are facing more vulnerable to flooding. Furthermore, the consequences of human interventions into natural process have caused an essential change in the natural landscape. The transformation from a natural dynamic water system in which people adapted to the forces of nature into an infrastructure system in which the forces of nature are attempted to be controlled, turns out to be more problematic. Finally, climate change will have a serve impact on the natural system of the delta and in the lives of those living in these areas, namely: flood events, storm surge, water scarcity, subsidence and salinization. The projects aimed at answering a research question: How a new form of urban development for the Mekong delta can provide a water safety condition, improve the environmental quality, spatial quality and meanwhile provide economic value for its inhabitants? As the first step, the project researched in the complex system of Mekong delta cities. Research question was step by step answered through triple three layer approach and different layer analysis through different scales. These researches provided a clear understanding in: how nature layer, infrastructure layer and urban layer proceeded and integrated throughout 300 year history of Mekong Delta; what current image of development in Mekong Delta is and why water should be maintained for future development. Equipped with this knowledge, the project proposed to apply the theory of Transit Oriented Development in combination of water management. The result is compact urban areas in regional scale or compact neighborhood in city scale that are protected on high levees, connected by public transports, surrounded by natural delta landscape and provided with diverse economic values.Delta Interventions StudioUrbanismArchitectur

The reliability of coastal structures in Vietnam in relation to the reliability of wave and water level data

In designing marine and coastal structures there always exists a considerable uncertainty, especially regarding the reliability of the data to be used. This is primarily due to the stochastic nature of sea waves - one of the most complex, volatile, pertinacious and uncomprehensible of nature's forces. Indeed, even if using all the available sourees and methods presently available, the confidence level in the determination of the design load still falls far short of what is expected in other branches of civil engineering. In comparison with countries like Holland, U.S.A, Japan, etc. the problem with the uncertainty in designing and constructing marine structures is far more serious in Vietnam, and perhaps in many other countries of developing world. This is a consequence of usually uncertain hydraulic design conditions, the lack of knowledge and experience in design and construction, the pressure in time, constraints in money, and so on. The purpose of this study is to provide solutions to the problems discussed above. This entails working out an appropriate design philosophy and altematives to cope with uncertainties in designing and constructing coastal structures (in Vietnam), and thereby enhance their reliability. Chapter-l gives a brief description of coastal engineering in Vietnam: the typical hydrometeorlogical features of the South China Sea, necessity and potential for constructing coastal engineering works, present design practice and shortcomings. Chapter-2 and chapter-3 deal with hydraulic environmental conditions and hydraulic design parameters (HDP). In chapter-2, emphasis is given to methods of determination of the main HDP and to identification of sourees of uncertainty related to them. In chapter-3, some possibilities and measures for improving the reliability of the main HDP are investigated. Chapter-4 is devoted to the determination of general principles/ philosophies to aid in design of coastal structures in Vietnam, at present and in the coming years. In chapter-5 and chapter-6, sensitivity analysis for sea dikes and breakwaters is performed, aiming at obtaining relevant types of structures and armour units for the situation of coastal engineering in Vietnam. Chapter-7 deals with possibilities to control the hydraulic loading and structure's strength, while in chapter-8, probabilistic design approach and possibility of applying it in Vietnam is considered.KWP-collectio

Linear versus nonlinear approaches for the stability analysis of aluminium production cells

The modelling of magnetohydrodynamics (MHD) phenomena in aluminium electrolysis cells is a challenging problem. The basic equations are the MHD equations in parabolic form, for two immiscible fluids. Among the various nonlinearities in the model, one is due to the moving interface between the two fluids. The basic question that numerical simulations contribute to solve is the study of the stability of the cell. In previous works, we have developed and implemented a fully nonlinear approach to solve the two-fluid MHD system. On the other hand, many approaches rely on a simplified version of the equations, and linear stability analysis. The present study compares and discusses the results obtained in the two approaches

Linear-Quadratic Model Predictive Control for Urban Traffic Networks

Advancements in the efficiency, quality and manufacturability of sensing and communication systems are driving the field of intelligent transport systems (ITS) into the twenty first century. One key aspect of ITS is the need for efficient and robust integrated network management of urban traffic networks. This paper presents a general model predictive control framework for both centralized traffic signal and route guidance systems aiming to minimize network congestion. Our novel model explicitly captures both non-zero travel time and spill-back constraints while remaining linear and thus generally tractable with quadratic costs. The end result is a central control scheme that may be realized for large urban networks containing thousands of sensors and actuators. We demonstrate the essences of our model and controller through a detailed mathematical description coupled with simulation results of specific scenarios. We show that using a central scheme such as ours may reduce the congestion inside the network by up to half while still achieving better throughput compared to that of other conventional control schemes.Transport & PlanningCivil Engineering and Geoscience

Predicting protein retention in ion-exchange chromatography using an open source QSPR workflow

Protein-based biopharmaceuticals require high purity before final formulation to ensure product safety, making process development time consuming. Implementation of computational approaches at the initial stages of process development offers a significant reduction in development efforts. By preselecting process conditions, experimental screening can be limited to only a subset. One such computational selection approach is the application of Quantitative Structure Property Relationship (QSPR) models that describe the properties exploited during purification. This work presents a novel open-source Python tool capable of extracting a range of features from protein 3D models on a local computer allowing total transparency of the calculations. As open-source tool, it also impacts initial investments in constructing a QSPR workflow for protein property prediction for third parties, making it widely applicable within the field of bioprocess development. The focus of current calculated molecular features is projection onto the protein surface by constructing surface grid representations. Linear regression models were trained with the calculated features to predict chromatographic retention times/volumes. Model validation shows a high accuracy for anion and cation exchange chromatography data (cross-validated R2 of 0.87 and 0.95). Hence, these models demonstrate the potential of the use of QSPR to accelerate process design.BT/Bioprocess EngineeringBT/Design and Engineering Educatio

Comparative Study on the Early Stage of Skid Resistance Development between Polyurethane-Bound Porous Mixture and Asphalt Mixture

Polyurethane-bound porous mixture (PPM) is a new type of pavement material that has shown some potential for overcoming common asphalt mixtures mechanical failures. However, little research has been done on its skid resistance performance. This work presents a comparative study of the skid resistance development between PPM and asphalt mixtures at their early stage. In this study, the three mixtures were bonded by three type binders. The three type binders were polyurethane, 70# virgin bitumen, and styrene-butadiene-styrene (SBS) modified asphalt. In order to distinguished the three type mixtures, we named them PPM, BAM, and SAM respectively. A Taber abraser was used to test the polishing property of binders. A third-scale model mobile loading simulator (MMLS3) was used to simulate the traffic loadings on mixtures, and a British pendulum tester was used to measure the skid resistance of the three types of mixtures in the loading process. The binder polishing test results show a good linear relationship between the binder's mass loss and the polishing cycle. The slope of the fitting line of the two parameters was defined as binder coefficient (BC) to characterize the polishing property of the binder. The mixture test results show that the skid resistance development trend of three mixtures is similar, as it first increases, then decreases, then finally flattens. However, the British pendulum number peak value and stable value of PPM are lower than that of SAM. The order of the number of loading times of peak (NLTP) of the three mixtures is SAM>PPM>BAM. Another good linear relationship is found between BC and NLTP, and the R2 of the fitting model is 0.85, which indicates that the polishing property of binder is effective for predicting the moment of occurrence of the mixture skid resistance peak.Accepted Author ManuscriptUrban Studie

The Durban Dig-Out Port, Project Durban

The Port of Durban is South Africa's premier port and hub of the region, especially for the Johannesburg (Gauteng Province) area. The current port will eventually not be sufficient to handle the capacity demand. The focus is on the development of a new port in the direct surroundings of Durban. A suitable new location is found at the old international airport. The Durban Dig-out Port is designed to cover a yearly container throughput of 10,000,000 TEU, a yearly liquid bulk throughput of 5,000,000 kL and 300,000 vehicles throughput per year. The governing vessel for the design is a 22,000 TEU container vessel with a length of 430 m, a width of 43.4 m and a draft of 16.3 m. The choice for the 22,000 TEU design vessel is reviewed. Based on global developments in ship manufacturing and a brief look at the developments in South Africa's container trade it is concluded that the 22,000 TEU vessel is recommended for the design of the port. In the proposed port layout the entrance channel is aligned such that it gives possibilities to bring the Isipingo estuary and its protected mangroves back to life. New land becomes available for an extension of the mangrove area and a new natural equilibrium between fresh and salt water inflow can be developed. The direction of the entrance channel also results in the central location of the turning circle and therefore the basins are relatively short. This makes manoeuvring for the vessels in the port convenient. A slight bend in the entrance channel is proposed to mitigate the wave action in the port. A straight entrance channel would lead to large downtime and has a direct impact on the port efficiency. The southern swell waves cannot enter the port due to the breakwaters and the eastern wind waves are either absorbed at the inside of the southern breakwater or at the safety beach at the end of the turning circle. The proposed sand bypass system makes sure that the coastal evolution is sustainable. In the proposed layout two configurations for the breakwaters are distinguished in terms of orientation and length. The proposed breakwaters are based on either a relatively high (10 kn) or low (6 kn) maximum vessel entrance speed. From research with a simplified wave model it is concluded that the shorter breakwaters cause downtime for the liquid bulk terminal during storm conditions from the south. During normal conditions it is however found that the liquid bulk terminal can be operational for more than 99% of the time. Next to that, it is found from the design of the breakwaters' cross sections that the breakwater dimensions become significantly larger at greater depths. However both breakwaters are found stable with numerical stability analysis and in combination with the result of the wave model it is concluded that the shorter configuration is preferred. This leads to significantly lower construction costs and the downtime of the liquid bulk terminal is limited.Civil Engineering and Geoscience

Entanglement and decoherence of N atoms and a mesoscopic field in a cavity

We investigate the behavior of N atoms resonantly coupled to a single electromagnetic field mode sustained by a high quality cavity, containing a mesoscopic coherent field. We show with a simple effective Hamiltonian model that the strong coupling between the cavity and the atoms produces an atom-field entangled state, involving N+1 nearly coherent components slowly rotating at different paces in the phase plane. The periodic overlap of these components results in a complex collapse and revival pattern for the Rabi oscillation. We study the influence of decoherence due to the finite cavity quality factor. We propose a simple analytical model, based on the Monte Carlo approach to relaxation. We compare its predictions with exact calculations and show that these interesting effects could realistically be observed on a two or three atoms sample in a 15 photon field with circular Rydberg atoms and superconducting cavities.Kavli Institute of NanoscienceApplied Science