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Search Results: 1 - 10 of 32321 matches for " Peter Ahnert "
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Association of ITGAV supports a role of angiogenesis in rheumatoid arthritis
Peter Ahnert, Holger Kirsten
Arthritis Research & Therapy , 2007, DOI: 10.1186/ar2313
Abstract: Jacq and colleagues [1] have presented a candidate gene association study in French and European Caucasian populations, showing evidence that the rs3738919-C variant (major allele) of the gene ITGAV may be associated with rheumatoid arthritis (RA), with an overall odds ratio (OR) for C-containing genotypes of 1.94 and a 95% confidence interval (CI) of 1.3 to 2.9 (P = 0.002). In the light of difficulties surrounding studies on candidate gene associations, how did the authors arrive at this result, what needs to be done further, and how does the discovery fit in the quest for solving RA genetics?ITGAV was selected as a candidate gene for RA for two reasons. First, it is localized 194 centimorgans from the p-telomere of chromosome 2, within a region stretching from 193 to 202 centimorgans that has been implicated by an RA genome scan [2]. Second, there is a strong functional hypothesis: ITGAV encodes the protein αv (CD51 antigen) of the integrin family, which combines with β3 to form the vitronectin receptor [3] and has a central role in angiogenesis [4]. Angiogenesis, in turn, is involved in hyperplasia of the synovial membrane in the RA pannus [5]. Modulation of angiogenesis by ITGAV variants is supported by the association of ITGAV with priapism [6].The genomic region of ITGAV does not show any apparent functional implication of rs3738919. However, some SNPs are predicted to be located inside functional elements of ITGAV and part of the region seems to show variation in copy number. It is possible that rs3738919 reports on these polymorphisms as a result of linkage disequilibrium. Without haplotype analyses and functional studies it remains unknown whether rs3738919 is itself a disease-modifying variant or whether it is a signpost for a causative variant that has yet to be discovered. Identification of the causative variant, or of a comprehensive haplotype carrying it, would greatly facilitate replication studies needed to verify this new association.In their candid
Differential allelic expression of IL13 and CSF2 genes associated with asthma
Burkhardt, Jana;Kirsten, Holger;Wolfram, Grit;Quente, Elfi;Ahnert, Peter;
Genetics and Molecular Biology , 2012, DOI: 10.1590/S1415-47572012005000055
Abstract: an important area of genetic research is the identification of functional mechanisms in polymorphisms associated with diseases. a highly relevant functional mechanism is the influence of polymorphisms on gene expression levels (differential allelic expression, dae). the coding single nucleotide polymorphisms (snps) csf2rs25882 and il13rs20541 have been associated with asthma. in this work, we investigated whether the mrna expression levels of csf2 or il13 were correlated with these snps. samples were analyzed by mass spectrometry-based quantification of gene expression. both snps influenced gene expression levels (csf2rs25882: poverall = 0.008 and pdae samples = 0.00006; il13rs20541: poverall = 0.059 and pdae samples = 0.036). for csf2, the expression level was increased by 27.4% (95% ci: 18.5%-35.4%) in samples with significant dae in the presence of one copy of risk variant csf2rs25882-t. the average expression level of il13 was increased by 29.8% (95% ci: 3.1%-63.4%) in samples with significant dae in the presence of one copy of risk variant il13rs20541-a. enhanced expression of csf2 could stimulate macrophages and neutrophils during inflammation and may be related to the etiology of asthma. for il-13, higher expression could enhance the functional activity of the asthma-associated isoform. overall, the analysis of dae provides an efficient approach for identifying possible functional mechanisms that link disease-associated variants with altered gene expression levels.
Programming CUDA and OpenCL: A Case Study Using Modern C++ Libraries
Denis Demidov,Karsten Ahnert,Karl Rupp,Peter Gottschling
Physics , 2012,
Abstract: We present a comparison of several modern C++ libraries providing high-level interfaces for programming multi- and many-core architectures on top of CUDA or OpenCL. The comparison focuses on the solution of ordinary differential equations and is based on odeint, a framework for the solution of systems of ordinary differential equations. Odeint is designed in a very flexible way and may be easily adapted for effective use of libraries such as Thrust, MTL4, VexCL, or ViennaCL, using CUDA or OpenCL technologies. We found that CUDA and OpenCL work equally well for problems of large sizes, while OpenCL has higher overhead for smaller problems. Furthermore, we show that modern high-level libraries allow to effectively use the computational resources of many-core GPUs or multi-core CPUs without much knowledge of the underlying technologies.
5HT2A polymorphism His452Tyr in a German Caucasian systemic sclerosis population
Holger Kirsten, Jana Burkhardt, Helene Hantmann, Nico Hunzelmann, Peter Vaith, Peter Ahnert, Inga Melchers
Arthritis Research & Therapy , 2009, DOI: 10.1186/ar2606
Abstract: We performed a population-based replication study in an independent and larger German Caucasian SSc cohort, approved by local ethics committees. DNA was purified from blood samples after obtaining written informed consent. Patients were included according to the German Network for Systemic Scleroderma guidelines [3]. The patient cohort was characterised as follows [4]: all fulfilled minimal requirements of LeRoy and colleagues [5] and 81% fulfilled ACR criteria [6]; 80% were females, 50% presented with the limited cutaneous form (lSSc [3]), 33% with the diffuse cutaneous form (dSSc [3]), 89% carried antinuclear antibodies (ANA-positive), 43% anticentromere antibodies (ACA-positive), 39% antitopoisomerase I antibodies (ATA-positive), and they had a mean age of disease onset of 49.5 ± 13.8 years. Mass spectrometry-based genotyping was applied as described, with minor modifications [4]. Power was >96% to replicate the allelic association and >99% to replicate a decreased minor allele frequency within cases [7], as reported for the Italian population.HapMap data reveal considerable variation of Tyr452 frequency among populations. It is especially high within Africans, emphasizing the importance of appropriate case-control matching. The frequency in our controls was very similar to that in the Caucasian HapMap cohort (0.065 versus 0.063, respectively). It was higher in the Italian population (0.124).We did not find a protective association of His452Tyr with SSc. In contrast, the frequency of Tyr452 was not decreased, but even increased in all SSc patients (Table 1). Also, no association was found when SSc subgroups stratified for the fulfilment of ACR-criteria, clinical classification (lSSc, dSSc), autoantibody status (ANA-, ACA-, ATA-positive) or sex were compared to healthy donors. However, Tyr452-positive SSc patients were less frequently dSSc positive than His452 homozygous SSc patients (P = 0.048, 9% versus 20%, respectively). This might indicate that the 5HT2A poly
Network analysis and data mining in food science: the emergence of computational gastronomy
Sebastian E Ahnert
Flavour , 2013, DOI: 10.1186/2044-7248-2-4
Abstract: The past two decades have seen the advent of high-throughput technologies in biology, making it possible to sequence genomes cheaply and quickly, to measure gene expression for thousands of genes in parallel, and to test large numbers of potential regulatory interactions between genes in a single experiment. The large amounts of data created by these technologies have given rise to entire new research areas in biology, such as computational biology and systems biology. The latter, which attempts to understand biological processes at a ‘systems’ level, is particularly indicative of the potential advantage that large datasets and their analysis can offer to biology, and to other fields of research. This advantage is a ‘birds-eye’ perspective, which, with the right kind of analysis, can complement the more established research methods that take place ‘on the ground’ and investigate the system in much more detail. An example would be the analysis of high-throughput gene expression data of tumour tissues in order to highlight a set of potential candidate genes that may play a role in causing a particular cancer. These candidates would then be investigated one by one, for instance by creating mutant organisms in which one of these genes is deactivated.Similar large-scale data analysis methods have more recently arrived in the social sciences as a result of rapidly growing mobile communications networks and online social networking sites. Here too data analysis offers a birds-eye perspective of large social networks and the opportunity to study social dynamics and human mobility on an unprecedented scale. The most recent research areas to be transformed by information technology are the Arts and Humanities, which have witnessed the emergence of ‘digital humanities’. As more and more literary and historical documents are digitized, it becomes possible to uncover fundamental relationships that underlie large corpora of literary texts, or long-term historical and political de
Numerical differentiation: local versus global methods
Karsten Ahnert,Markus Abel
Physics , 2005,
Abstract: In the context of the analysis of measured data, one is often faced with the task to differentiate data numerically. Typically, this occurs when measured data are concerned or data are evaluated numerically during the evolution of partial or ordinary differential equations. Usually, one does not take care for accuracy of the resulting estimates of derivatives because modern computers are assumed to be accurate to many digits. But measurements yield intrinsic errors, which are often much less accurate than the limit of the machine used, and there exists the effect of ``loss of significance'', well known in numerical mathematics and computational physics. The problem occurs primarily in numerical subtraction, and clearly, the estimation of derivatives involves the approximation of differences. In this article, we discuss several techniques for the estimation of derivatives. As a novel aspect, we divide into local and global methods, and explain the respective shortcomings. We have developed a general scheme for global methods, and illustrate our ideas by spline smoothing and spectral smoothing. The results from these less known techniques are confronted with the ones from local methods. As typical for the latter, we chose Savitzky-Golay filtering and finite differences. Two basic quantities are used for characterization of results: The variance of the difference of the true derivative and its estimate, and as important new characteristic, the smoothness of the estimate. We apply the different techniques to numerically produced data and demonstrate the application to data from an aeroacoustic experiment. As a result, we find that global methods are generally preferable if a smooth process is considered. For rough estimates local methods work acceptably well.
Compactons and Chaos in Strongly Nonlinear Lattices
Karsten Ahnert,Arkady Pikovsky
Physics , 2008, DOI: 10.1103/PhysRevE.79.026209
Abstract: We study localized traveling waves and chaotic states in strongly nonlinear one-dimensional Hamiltonian lattices. We show that the solitary waves are super-exponentially localized, and present an accurate numerical method allowing to find them for an arbitrary nonlinearity index. Compactons evolve from rather general initially localized perturbations and collide nearly elastically, nevertheless on a long time scale for finite lattices an extensive chaotic state is generally observed. Because of the system's scaling, these dynamical properties are valid for any energy.
Traveling waves and Compactons in Phase Oscillator Lattices
Karsten Ahnert,Arkardy Pikovsky
Physics , 2008, DOI: 10.1063/1.2955758
Abstract: We study waves in a chain of dispersively coupled phase oscillators. Two approaches -- a quasi-continuous approximation and an iterative numerical solution of the lattice equation -- allow us to characterize different types of traveling waves: compactons, kovatons, solitary waves with exponential tails as well as a novel type of semi-compact waves that are compact from one side. Stability of these waves is studied using numerical simulations of the initial value problem.
Odeint - Solving ordinary differential equations in C++
Karsten Ahnert,Mario Mulansky
Physics , 2011, DOI: 10.1063/1.3637934
Abstract: Many physical, biological or chemical systems are modeled by ordinary differential equations (ODEs) and finding their solution is an every-day-task for many scientists. Here, we introduce a new C++ library dedicated to find numerical solutions of initial value problems of ODEs: odeint (www.odeint.com). odeint is implemented in a highly generic way and provides extensive interoperability at top performance. For example, due to it's modular design it can be easily parallized with OpenMP and even runs on CUDA GPUs. Despite that, it provides a convenient interface that allows for a simple and easy usage.
Metaprogramming Applied to Numerical Problems
Mario Mulansky,Karsten Ahnert
Physics , 2011, DOI: 10.1063/1.3637933
Abstract: From the discovery that the template system of C++ forms a Turing complete language in 1994, a programming technique called Template Metaprogramming has emerged that allows for the creation of faster, more generic and better code. Here, we apply Template Metaprogramming to implement a generic Runge-Kutta scheme that can be used to numerically solve ordinary differential equations. We show that using Template Metaprogramming results in a significantly improved performance compared to a classical implementation.
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