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21 papers found.
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Fast test suite-driven model-based fault localisation with application to pinpointing defects in student programs

Poppleton 1 Bernd Fischer 2 Communicated by Prof. Alfonso Pierantonio , Jasmin Blanchette, Francis Bordeleau, Nikolai Kosmatov, Gabi Taentzer, and Manuel Wimmer 3 Stellenbosch University , Matieland 7602

DEHP deregulates adipokine levels and impairs fatty acid storage in human SGBS-adipocytes

Steinstrasse 52, D-06097, Halle (Saale), GermanyKristina Schaedlich, Scarlett Gebauer, Luise Hunger, Laura-Sophie Beier, Bernd Fischer & Jana ErnstInstitute for Prevention and Occupational Medicine of the German ... • PubMed • Google Scholar Search for Holger M. Koch in:Nature Research journals • PubMed • Google Scholar Search for Martin Wabitsch in:Nature Research journals • PubMed • Google Scholar Search for Bernd

Session One: Bridging Across Cultures

Commons. It has been accepted for inclusion in Pepperdine Dispute Resolution Law Journal by an authorized editor of Pepperdine Digital Commons. For more information , please contact 1 Bernd Fischer , Rene

Comparative Analysis of AGE and RAGE Levels in Human Somatic and Embryonic Stem Cells under H2O2-Induced Noncytotoxic Oxidative Stress Conditions

The accumulation of advanced glycation end products (AGEs) occurs in ageing and in many degenerative diseases as a final outcome of persistent oxidative stress on cells and organs. Environmental alterations taking place during early embryonic development can also lead to oxidative damage, reactive oxygen species (ROS) production, and AGE accumulation. Whether similar mechanisms...

SomaticSignatures: inferring mutational signatures from single-nucleotide variants

Summary: Mutational signatures are patterns in the occurrence of somatic single-nucleotide variants that can reflect underlying mutational processes. The SomaticSignatures package provides flexible, interoperable and easy-to-use tools that identify such signatures in cancer sequencing data. It facilitates large-scale, cross-dataset estimation of mutational signatures, implements...

h5vc: scalable nucleotide tallies with HDF5

Summary: As applications of genome sequencing, including exomes and whole genomes, are expanding, there is a need for analysis tools that are scalable to large sets of samples and/or ultra-deep coverage. Many current tool chains are based on the widely used file formats BAM and VCF or VCF-derivatives. However, for some desirable analyses, data management with these formats...

A map of directional genetic interactions in a metazoan cell

Gene–gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene–gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale...

Maternal Diabetes Leads to Adaptation in Embryonic Amino Acid Metabolism during Early Pregnancy

During pregnancy an adequate amino acid supply is essential for embryo development and fetal growth. We have studied amino acid composition and branched chain amino acid (BCAA) metabolism at day 6 p.c. in diabetic rabbits and blastocysts. In the plasma of diabetic rabbits the concentrations of 12 amino acids were altered in comparison to the controls. Notably, the concentrations...

Di-(2-Ethylhexyl)-Phthalate (DEHP) Causes Impaired Adipocyte Function and Alters Serum Metabolites

Di-(2-ethylhexyl)-phthalate (DEHP), an ubiquitous environmental contaminant, has been shown to cause adverse effects on glucose homeostasis and insulin sensitivity in epidemiological studies, but the underlying mechanisms are still unknown. We therefore tested the hypothesis that chronic DEHP exposure causes impaired insulin sensitivity, affects body weight, adipose tissue (AT...

The AhR is constitutively activated and affects granulosa cell features in the human cell line KGN

Katja Horling 0 Anne Navarrete Santos 0 Bernd Fischer 0 0 Department of Anatomy and Cell Biology, Martin Luther University Faculty of Medicine , Grosse Steinstrasse 52, 06097 Halle (Saale) , Germany

CellH5: a format for data exchange in high-content screening

Summary: High-throughput microscopy data require a diversity of analytical approaches. However, the construction of workflows that use algorithms from different software packages is difficult owing to a lack of interoperability. To overcome this limitation, we present CellH5, an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional...

Improved functional prediction of proteins by learning kernel combinations in multilabel settings

Background We develop a probabilistic model for combining kernel matrices to predict the function of proteins. It extends previous approaches in that it can handle multiple labels which naturally appear in the context of protein function. Results Explicit modeling of multilabels significantly improves the capability of learning protein function from multiple kernels. The...

Time-series alignment by non-negative multiple generalized canonical correlation analysis

Background Quantitative analysis of differential protein expressions requires to align temporal elution measurements from liquid chromatography coupled to mass spectrometry (LC/MS). We propose multiple Canonical Correlation Analysis (mCCA) as a method to align the non-linearly distorted time scales of repeated LC/MS experiments in a robust way. Results Multiple canonical...

Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi

Bernd Fischer 0 2 0 EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD , UK 1 German Cancer Research Center (DKFZ), Div. Signaling and Functional Genomics

Effects of Polychlorinated Biphenyls in CD-1 Mice: Reproductive Toxicity and Intergenerational Transmission

Several studies indicate that in utero and perinatal exposure to polychlorinated biphenyls (PCBs) induces adverse reproductive effects, but it remains unclear whether such effects may be transmitted to subsequent generations. We therefore investigated the association between maternal exposure to PCBs and reproductive health in male and female offspring over three generations...

Theo Honnef: Heinrich von Kleist in der Literatur der DDR

­ turgeschichtsschreibung der DDR. Bernd Fischer Ohio State University Heym, Stefan. 5 Tage im Juni. Roman. Berlin: Buchverlag Der Morgen, 1989. 404 pp. Fifteen years after its publication in the West and about thirtyfive

Semi-supervised LC/MS alignment for differential proteomics

Motivation: Mass spectrometry (MS) combined with high-performance liquid chromatography (LC) has received considerable attention for high-throughput analysis of proteomes. Isotopic labeling techniques such as ICAT [5,6] have been successfully applied to derive differential quantitative information for two protein samples, however at the price of significantly increased complexity...

PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra

Motivation: Tandem mass spectrometry allows for high-throughput identification of complex protein samples. Searching tandem mass spectra against sequence databases is the main analysis method nowadays. Since many peptide variations are possible, including them in the search space seems only logical. However, the search space usually grows exponentially with the number of...

Molecular Remodeling of Members of the Relaxin Family During Primate Evolution

Employing comparative analysis of the cDNA-coding sequences of the unique preprorelaxin of the Afro-lorisiform Galago crassicaudatus and the Malagasy lemur Varecia variegata and the relaxin-like factor (RLF) of G. crassicaudatus, we demonstrated distinct differences in the dynamics of molecular remodeling of both hormones during primate evolution. The lorisiform and lemuriform...

Expression of relaxin-like factor is down-regulated in human testicular Leydig cell neoplasia

In addition to their role in steroidogenesis in the male, testicular Leydig cells constitutively express large amounts of the peptide relaxin-like factor (RLF), also known as Ley-IL. The Leydig cell-derived RLF belongs to the insulin-like superfamily, which also includes relaxin, insulin and the insulin-like growth factors, and within the testis is a specific marker of Leydig...