Technical University of Dortmund

About: Technical University of Dortmund is a education organization based out in Dortmund, Nordrhein-Westfalen, Germany. It is known for research contribution in the topics: Large Hadron Collider & Neutrino. The organization has 13028 authors who have published 27666 publications receiving 615557 citations. The organization is also known as: Dortmund University & University of Dortmund.

Regular symbolic analysis of dynamic networks of pushdown systems

Abstract: We introduce two abstract models for multithreaded programs based on dynamic networks of pushdown systems. We address the problem of symbolic reachability analysis for these models. More precisely, we consider the problem of computing effective representations of their reachability sets using finite-state automata. We show that, while forward reachability sets are not regular in general, backward reachability sets starting from regular sets of configurations are always regular. We provide algorithms for computing backward reachability sets using word/tree automata, and show how these algorithms can be applied for flow analysis of multithreaded programs.

Recommender systems — beyond matrix completion

Abstract: The future success of these systems depends on more than a Netflix challenge.

Toxicogenomics directory of chemically exposed human hepatocytes.

Abstract: A long-term goal of numerous research projects is to identify biomarkers for in vitro systems predicting toxicity in vivo. Often, transcriptomics data are used to identify candidates for further evaluation. However, a systematic directory summarizing key features of chemically influenced genes in human hepatocytes is not yet available. To bridge this gap, we used the Open TG-GATES database with Affymetrix files of cultivated human hepatocytes incubated with chemicals, further sets of gene array data with hepatocytes from human donors generated in this study, and publicly available genome-wide datasets of human liver tissue from patients with non-alcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular cancer (HCC). After a curation procedure, expression data of 143 chemicals were included into a comprehensive biostatistical analysis. The results are summarized in the publicly available toxicotranscriptomics directory (http://wiki.toxbank.net/toxicogenomics-map/) which provides information for all genes whether they are up- or downregulated by chemicals and, if yes, by which compounds. The directory also informs about the following key features of chemically influenced genes: (1) Stereotypical stress response. When chemicals induce strong expression alterations, this usually includes a complex but highly reproducible pattern named ‘stereotypical response.’ On the other hand, more specific expression responses exist that are induced only by individual compounds or small numbers of compounds. The directory differentiates if the gene is part of the stereotypical stress response or if it represents a more specific reaction. (2) Liver disease-associated genes. Approximately 20 % of the genes influenced by chemicals are up- or downregulated, also in liver disease. Liver disease genes deregulated in cirrhosis, HCC, and NASH that overlap with genes of the aforementioned stereotypical chemical stress response include CYP3A7, normally expressed in fetal liver; the phase II metabolizing enzyme SULT1C2; ALDH8A1, known to generate the ligand of RXR, one of the master regulators of gene expression in the liver; and several genes involved in normal liver functions: CPS1, PCK1, SLC2A2, CYP8B1, CYP4A11, ABCA8, and ADH4. (3) Unstable baseline genes. The process of isolating and the cultivation of hepatocytes was sufficient to induce some stress leading to alterations in the expression of genes, the so-called unstable baseline genes. (4) Biological function. Although more than 2,000 genes are transcriptionally influenced by chemicals, they can be assigned to a relatively small group of biological functions, including energy and lipid metabolism, inflammation and immune response, protein modification, endogenous and xenobiotic metabolism, cytoskeletal organization, stress response, and DNA repair. In conclusion, the introduced toxicotranscriptomics directory offers a basis for a rationale choice of candidate genes for biomarker evaluation studies and represents an easy to use source of background information on chemically influenced genes.

The distribution of points on the sphere and corresponding cubature formulae

Abstract: In applications, for instance in optics and astrophysics, there is a need for high-accuracy integration formulae for functions on the sphere. To construct better formulae than previously used, almost equidistantly spaced nodes on the sphere and weights belonging to these nodes are required. This problem is closely related to an optimal dispersion problem on the sphere and to the theories of spherical designs and multivariate Gauss quadrature formulae. We propose a two-stage algorithm to compute optimal point locations on the unit sphere and an appropriate algorithm to calculate the corresponding weights of the cubature formulae. Points as well as weights are computed to high accuracy. These algorithms can be extended to other integration problems. Numerical examples show that the constructed formulae yield impressively small integration errors of up to 10 -12 .