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

Modelling of temperature, moisture and stresses in young concrete

The present study consists of three areas, namely modelling of- (1) temperature, (2) moisture state, and (3) stresses in young concrete. The derivation of models, examination of material data, and development of computer programs have progressed differently in these areas. The first area, modelling of temperatures, is the most comprehensive and complete, since it has been researched more extensively than the other areas. On the other hand, the way of modelling stresses in this study is purely theoretical and has not been tested against empirical data, but gives some guidelines for future applications. Finally, the modelling of moisture state is somewhere in between the other two areas. The results can be applied to different fields of concreting, such as estimation of form stripping times, estimation of necessary measures to be taken in winter concreting, study of drying shrinkage cracking, and study of stresses due to varying temperatures in early age concretes. The aim of this report is not to discuss applications, but to give the background and material data used in the models for calculating the temperature, moisture state, and stresses in young concrete. It is shown that temperature can be modelled to within an accuracy of 1 to 2°C which is acceptable for most applications. However, it is essential to have good knowledge of both material data and environmental conditions. For the study of moisture states, a consistent model for the description of desorption and absorption isotherms has been developed. The treatment of both desorption and absorption isotherms in the same theoretical framework makes it possible to introduce scanning curves between these limit curves for subsequent drying and wetting. The effects of alkali have been modelled as an alkali equilibrium isotherm estimated from the known amounts of sodium and potassium oxides in the cement. The alkali influenced curve can be combined with any description of the isotherms with respect to the physically bound water. The need for considering the effects of alkali for higher humidities has been shown in moisture calculations.Godkänd; 1994; 20070426 (ysko

Materialdata för betong SKANSKA-K6516P

Denna utredning, som omfattar mätning av materialegenskaper för hårdnande betong och utvärdering av resultaten anpassade för att användas i datorsystemet ConTeSt, är ett uppdrag från SKANSKA till LTU (Luleå tekniska universitet).Godkänd; 2005; 20080522 (ysko

Shrinkage measurements of mortars with energetically modified fly ash

The shrinkage tests performed show a significant lower final shrinkage for higher fly ash content. The shrinkage level is in the order of size that is typical for mortars, and the level of shrinkage would be much lower, say about half as large, for concrete mixtures with the same type of binders. It would be interesting to study the shrinkage, both drying shrinkage and autogenous shrinkage, for the same type of binders used in concrete mixes.Godkänd; 2005; 20080522 (ysko

Mätning och modellering av hållfasthets- och värmeutveckling för betonger med Svenska Cement

Godkänd; 2011; 20111220 (ysko

Linear logarithmic model for concrete creep : I. Formulation and evaluation

Control of thermal cracking in young concrete is of great importance to ensure a desired service lifetime and function of a structure. Young concrete is here defined as the period up to approximately 100 days after casting. Making reliable predictions about thermal stresses, and thereby cracking risks, the creep behaviour forms an important part of the material modelling. Up until now few studies have been made to investigate how different creep modelling influences calculated thermal stresses. Existing creep models for young concrete are often pure mathematical expressions with no direct relation to the material behaviour and thereby complicated to understand and use in a more practical context. In this paper a new basic creep model primarily aimed for early age purposes is outlined. The formulation with its model parameters, which have an easy to understand meaning in the material behaviour, is based on piece-wise linear curves in logarithm of time and therefore denoted the Linear Logarithmic Model (LLM). Comparison with experimental creep data and other more commonly used creep formulations for young concrete is made to achieve an opinion about the accuracy of the new model. The new model is a flexible and robust formulation that can model the behaviour of both young and mature concrete. The robustness enables it to make reliable creep modelling with very few test data. Another advantage with the LLM formulation is that the appearance of negative relaxation in linear viscoelastic modelling is very small and negligible with respect to thermal stresses. This means that the original formulation may be used directly in a thermal stress analysis for young concrete without any adjustment for negative relaxation. The LLM formulation shows very good agreement directly with experimental creep data and indirectly with measured thermal stresses, whereby the formulation has been used to model the viscoelastic behaviour of the concrete. The formulation also has the best correlation with experimental data compared to other commonly used creep models that have been analysed in this paper.Validerad; 2003; 20080523 (ysko)</p

Linear logarithmic model for concrete creep : II. Prediction formulas for description of creep behaviour

A reliable modelling of the young concrete creep behaviour is of great importance for consistent thermal crack risk estimations that shall contribute to assure a desired service lifetime and function of a structure. All-embracing creep tests aimed for thermal stress analyses are often very time consuming and thereby also costly to perform. Therefore thermal stress calculations in everyday engineering practice are often performed with standard sets of creep data involving no or very limited laboratory testing, which increases the error of the crack risk predictions and consequently also affect the design safety margins. The need for formulations that based on limited test data can make reliable predictions about the creep behaviour of hardening concrete is thus quite evident. This paper is a direct continuation of a previous study by Larson and Jonasson (2003) where a new concrete creep formulation called the Linear Logarithmic Model (LLM) was formulated. Here creep prediction formulas based on the LLM formulation are established and evaluated. It is shown that general model parameters can be established whereby the long-term creep behaviour is clearly dependent on the modulus of elasticity with larger creep deformations for lower E-modulus. An average error related to creep of 15 percent is what can be expected from most thermal stress analyses that are performed with standard sets of creep data today. By use of the prediction formulas based on the proposed LLM formulation for creep compliance it is possible to reduce the error by almost two thirds (2/3) only by adding the results from a test of the modulus of elasticity at the age of 28 days. For more advanced applications, where even better accuracy is required, it is recommended that at least a creep compliance test is performed at two loading ages, of which one at the age of 28 days.Validerad; 2003; 20080523 (ysko)</p

Liten risk för tidiga sprickor i självkompakterande betong

Självkompakterande betong verkar inte - trots hög andel finmaterial och snabb värmeutveckling - vara mer sprickbenägen i ung ålder än traditionell vibrerad betong. Ytan bör dock täckas eller vattnas för att undvika plastiska krympsprickor.Godkänd; 2008; 20080603 (ysko

Casting of concrete walls on slabs : Studies of the risk of cracking due to temperature changes during the hardening process

Tests casting the construction "wall on slab" have in the project been realized for three different situations. Measurements have been performed with respect to temperatures, deformations, strains and mapping of crack patterns. In addition, properties for the young concrete have been investigated to get basic data in order to estimate temperatures and risks of cracking. The construction wall on slab represents a typical case, which can be found in many real structures like walls, retaining walls, tray structures, tunnels and bridges.The project has two main questions: 1) What are the differences in restraint conditions between the three tested constructions? Is it correct to model a wall, that both has a horizontal casting joints against the slab, and a vertical casting joint against an adjacent wall, with a free wall of double length?, and 2) Does a slip in the horizontal casting joint exist, and does is reduce the restraint in the wall?The answers are that the supposed models describe the real behaviour very well. This was confirmed by the fact that both the temperatures as well as the crack risks agreed very well between the test results and the calculation results. For the walls that cracked a slip in the casting joints could be indicated, but these test results could not be quantified. In summary, the project has been successful and clearly answered questions that previously only were based on assumptions.Försök med gjutning av konstruktionen "vägg på platta" har i projektet genomförts för tre olika situationer. Mätningar har utförts vad gäller temperaturer, deformationer, töjningar och sprickkarteringar. Dessutom har den unga betongens egenskaper kartlagts för att få underlag att kunna göra temperatur- och sprickriskberäkningar. Konstruktionen vägg på platta representerar en typkonstruktion, som återfinns i många verkliga konstruktioner såsom väggar, stödmur, tråg, tunnlar och broar.Projektet har två huvudfrågor: 1) Hur skiljer sig tvånget mellan de tre provade konstruktionerna? Är det rätt att modellera en vägg, som båda har en horisontell gjutfog mot plattan och en vertikal gjutfog mot befintlig vägg, med en fristående dubbelt så lång vägg? och 2) Finns det en glidning i den horisontella gjutfogen, vilket reducerar tvånget i väggen?Svaren blev att antagna modeller väl beskriver det verkliga beteendet. Detta bygger på att både temperaturen och spänningsriskerna överensstämmer mycket väl mellan försök och beräkningar. Vid de väggjutningar som ledde till sprickbildning kunde en gjutfogsglidning indikeras, men dessa försöksresultat kunde inte kvantifieras. Sammantaget kan sägas att projektet varit lyckat och entydigt besvarat frågeställningar som tidigare endast varit antaganden.Godkänd; 2009; 20090803 (jej

Modelling of temperature and shrinkage induced cracking risks in young concrete

Control of thermal and shrinkage cracking in hardening concrete is of great importance to ensure desired service life and function of concrete constructions. Making reliable stress estimations, and thereby conclusions about cracking risks caused by temperature movements and shrinkage involves advanced modelling of material properties and structural restraint. Cracking of concrete during the hardening phase must be avoided in order to minimize the risk of durability problems in the future, such as corrosion risk of the reinforcement, water tightness and damages according to frost. Estimation of the risk of early age cracking requires knowledge of the combined effects from temperature development and mechanical behaviour during the hydration. Applications of the present model using the computer program ConTeSt Pro demonstrates that it can be used to decide what measures to be taken to minimize the risk of cracking during the hardening phase for concrete structures. One example of estimated temperatures and cracking risks is shown in Figure 1.Figure 1 Estimated temperatures and cracking risks for the walls of the concrete arch of the Svinesund bridge between Sweden and Norway. The arch was built by the technique of climbing form workGodkänd; 2009; 20091215 (jej