Finding small somatic structural variants in exome sequencing data: a machine learning approach

Genetic variation forms the basis for diversity but can as well be harmful and cause diseases, such as tumors. Structural variants (SV) are an example of complex genetic variations that comprise of many nucleotides ranging up to several megabases. Based on recent developments in sequencing technology it has become feasable to elucidate the genetic state of a person’s genes (i.e. the exome) or even the complete genome. Here, a machine learning approach is presented to find small disease-related SVs with the help of sequencing data. The method uses differences in characteristics of mapping patterns between tumor and normal samples at a genomic locus. This way, the method aims to be directly applicable for exome sequencing data to improve detection of SVs since specific SV detection methods are currently lacking. The method has been evaluated based on a simulation study as well as with exome data of patients with acute myeloid leukemia. An implementation of the algorithm is available at https://github.com/lenz99-/svmod.     

Localization of André-Quillen-Goodwillie towers, and the periodic homology of infinite loopspaces

Let K(n) be the nth Morava K-theory at a prime p, and let T(n) be the telescope of a v_n-self map of a finite complex of type n. In this paper we study the K(n)_*-homology of Ω^∞X, the 0th space of a spectrum X, and many related matters.We give a sampling of our results.Let PX be the free commutative S-algebra generated by X: it is weakly equivalent to the wedge of all the extended powers of X. We construct a natural map

s_n(X):L_T(n)P(X)→L_T(n)Σ^∞(Ω^∞X)₊     

Exponential Finite Elements for a Phase Field Fracture Model

Sharp interface material models can be related to phase field models by introducing an order parameter, whose value is assigned to the different phases of a material. The elastic material law is coupled to the evolution equation of the order parameter and cracking is addressed as a phase transition problem instead of a moving boundary value problem. A regularization parameter ϵ controls the width of the diffuse cracks represented by the order parameter and the underlying sharp interface model can be recovered from the phase field model by the limit ϵ → 0. However, in numerical simulations using standard finite elements with linear shape functions, the minimum value of ϵ is restricted by the grid size and therefore the discretization of the crack field requires extensive mesh refinement for small values of ϵ. In this work, we construct special 2d shape functions which take into account the exponential character of the crack field and its dependence on the parameter ϵ. Especially in simulations with small values of ϵ and a rather coarse mesh, the elements with exponential shape functions perform significantly better than standard linear elements. (© 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Messung des Reinigungsverlaufs von Milchtanks

Zur Verfolgung des zeitlichen Verlaufs von Reinigungsvorgängen in Milchtanks wurde Milch mit unstabilisiertem kolloidalem ¹⁹⁸Au markiert. Die Messung der “Schmutzmenge” erfolgte an der Innen- oder Auβenwand bzw. im ausflieβenden Schmutzwasser. Das Verfahren wurde wiederholt zur Prüfung bei der Entwicklung von Tankreinigungsgeräten angewendet.     

Pressure dependence of the absorption edge at the E0 gap of mocvd - Grown ZnTe films

Abstract

We have investigated the direct gap absorption of 1μm thick ZnTe-epilayers grown on GaAs substrates by metalorganic chemical vapour deposition (MOCVD). Free ZnTe-layers were obtained by selective etching. The absorption coefficient was measured up to about 50000 cm^?1 in a diamand anvil cell in the temperature range from 115–300 K. The spectra near the direct gap E₀ are dominated by a sharp excitonic structure. Its change with pressure is evaluated by a model which allows to determine the pressure shift of the gap energy dE₀/dP and the change of the Rydberg energies of the excitons dR*/dP.^[1]     

Potential‐Induced Fine‐Tuning of the Enantioaffinity of Chiral Metal Phases

Concepts leading to single enantiomers of chiral molecules are of crucial importance for many applications, including pharmacology and biotechnology. Recently, mesoporous metal phases encoded with chiral information have been developed. Fine‐tuning of the enantioaffinity of such structures by imposing an electric potential is proposed, which can influence the electrostatic interactions between the chiral metal and the target enantiomer. This allows the binding affinity between the chiral metal and the target enantiomer to be increased, and thus, the discrimination between two enantiomers to be improved. The concept is illustrated by generating chiral encoded metals in a microfluidic channel by reduction of a platinum salt in the presence of a liquid crystal and l ‐tryptophan as a chiral model template. After removal of the template molecules, the modified microchannel retains a pronounced chiral character. The chiral recognition efficiency of the microchannel can be fine‐tuned by applying a suitable potential to the metal phase. This enables the separation of both components of a racemate flowing through the channel. The approach constitutes a promising and complementary strategy in the frame of chiral discrimination technologies.     

Spiral growth and step edge barriers

The growth of spiral mounds containing a screw dislocation is compared to the growth of wedding cakes by two-dimensional nucleation. Using phase field simulations and homoepitaxial growth experiments on the Pt(111) surface we show that both structures attain the same large scale shape when a significant step-edge barrier suppresses interlayer transport. The higher vertical growth rate of the spiral mounds on Pt(111) reflects the different incorporation mechanisms for atoms in the top region and can be formally represented by an enhanced apparent step-edge barrier.