Johannes Kepler University of Linz

About: Johannes Kepler University of Linz is a education organization based out in Linz, Oberösterreich, Austria. It is known for research contribution in the topics: Thin film & Quantum dot. The organization has 6605 authors who have published 19243 publications receiving 385667 citations.

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

Abstract: Quantitative analyses of next-generation sequencing (NGS) data, such as the detection of copy number variations (CNVs), remain challenging. Current methods detect CNVs as changes in the depth of coverage along chromosomes. Technological or genomic variations in the depth of coverage thus lead to a high false discovery rate (FDR), even upon correction for GC content. In the context of association studies between CNVs and disease, a high FDR means many false CNVs, thereby decreasing the discovery power of the study after correction for multiple testing. We propose ‘Copy Number estimation by a Mixture Of PoissonS’ (cn.MOPS), a data processing pipeline for CNV detection in NGS data. In contrast to previous approaches, cn.MOPS incorporates modeling of depths of coverage across samples at each genomic position. Therefore, cn.MOPS is not affected by read count variations along chromosomes. Using a Bayesian approach, cn.MOPS decomposes variations in the depth of coverage across samples into integer copy numbers and noise by means of its mixture components and Poisson distributions, respectively. The noise estimate allows for reducing the FDR by filtering out detections having high noise that are likely to be false detections. We compared cn.MOPS with the five most popular methods for CNV detection in NGS data using four benchmark datasets: (i) simulated data, (ii) NGS data from a male HapMap individual with implanted CNVs from the X chromosome, (iii) data from HapMap individuals with known CNVs, (iv) high coverage data from the 1000 Genomes Project. cn.MOPS outperformed its five competitors in terms of precision (1–FDR) and recall for both gains and losses in all benchmark data sets. The software cn.MOPS is publicly available as an R package at http://www.bioinf.jku.at/ software/cnmops/ and at Bioconductor.

The Shadow Economy: An International Survey

Abstract: List of figures List of tables Foreword Vito Tanzi 1. The shadow economy: a challenge for economic and social policy 2. Defining the shadow economy 3. Methods to estimate the size of the shadow economy 4. Size of shadow economies around the world 5. The size of the shadow economy labour force 6. An integrated approach to explain deviant behaviour 7. Analysing the causes and measures of economic policy 8. Effects of the increasing shadow economy 9. The 'two-pillar strategy' 10. Conclusion and outlook List of references Index.

Context-awareness on mobile devices - the hydrogen approach

Abstract: Information about the user's environment offers new opportunities and exposes new challenges in terms of time-aware, location-aware, device-aware and personalized applications. Such applications constantly need to monitor the environment - called context - to allow the application to react accordingly to this context. Context-awareness is especially interesting in mobile scenarios where the context of the application is highly dynamic and allows the application to deal with the constraints of mobile devices in terms of presentation and interaction abilities and communication restrictions. Current context-aware applications often realize sensing of context information in an ad hoc manner. The application programmer needs to deal with the supply of the context information including the sensing of the environment, its interpretation and its disposal for further processing in addition to the primary purpose of the application. The close interweavement of device specific context handling with the application obstructs its reuse with other hardware configurations. Recently, architectures providing support for context-aware applications have been developed. Up to now such architectures are not trimmed to the special requirements of mobile devices regarding particularly the limitations of network connections, limited computing power and the characteristics of mobile users. This paper proposes an architecture and a software framework - the hydrogen context framework -which support context-awareness for considering these constraints. It is extensible to consider all kind of context information and comprises a layered architecture. To prove the feasibility the framework has been implemented to run on mobile devices. A context-aware postbox is realized to demonstrate the capabilities of the framework.

Deblurring and Denoising of Images by Nonlocal Functionals

Abstract: This paper investigates the use of regularization functionals with nonlocal correlation terms for the problem of image denoising and image deblurring. These functionals are expressed as integrals o...

Self-Organized Growth of Three- Dimensional Quantum-Dot Crystals with fcc-Like Stacking and a Tunable Lattice Constant

Abstract: The self-organization of pyramidal PbSe islands that spontaneously form during strained-layer epitaxial growth of PbSe/Pb1−xEuxTe (x = 0.05 to 0.1) superlattices results in the formation of three-dimensional quantum-dot crystals. In these crystals, the dots are arranged in a trigonal lattice with a face-centered cubic (fcc)–like A-B-C-A-B-C vertical stacking sequence. The lattice constant of the dot crystal can be tuned continuously by changing the superlattice period. As shown by theoretical calculations, the elastic anisotropy in these artificial dot crystals acts in a manner similar to that of the directed chemical bonds of crystalline solids. The narrow size distribution and excellent control of the dot arrangement may be advantageous for optoelectronic device applications.