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Search Results: 1 - 10 of 243 matches for " Tilo Baumbach "
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Improved ground-state estimate by thermal resummation
Carlos Falquez,Ralf Hofmann,Tilo Baumbach
Physics , 2010,
Abstract: For the deconfining phase of SU(2) Yang-Mills thermodynamics and for high temperatures we point out that a linear dependence on temperature of a one-loop selfconsistently resummed thermal correction to the pressure and the energy density takes place despite a quartic dependence arising from an unsummed two-loop correction. This linearity is hierarchically smaller than the one belonging to the tree-level estimate of the thermal ground-state. We discuss and interprete this result.
Improved success rate and stability for phase retrieval by including randomized overrelaxation in the hybrid input output algorithm
Martin K?hl,A. A. Minkevich,Tilo Baumbach
Physics , 2012, DOI: 10.1364/OE.20.017093
Abstract: In this paper, we study the success rate of the reconstruction of objects of finite extent given the magnitude of its Fourier transform and its geometrical shape. We demonstrate that the commonly used combination of the hybrid input output and error reduction algorithm is significantly outperformed by an extension of this algorithm based on randomized overrelaxation. In most cases, this extension tremendously enhances the success rate of reconstructions for a fixed number of iterations as compared to reconstructions solely based on the traditional algorithm. The good scaling properties in terms of computational time and memory requirements of the original algorithm are not influenced by this extension.
Three-Dimensional Reconstructions Come to Life – Interactive 3D PDF Animations in Functional Morphology
Thomas van de Kamp, Tomy dos Santos Rolo, Patrik Vagovi?, Tilo Baumbach, Alexander Riedel
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0102355
Abstract: Digital surface mesh models based on segmented datasets have become an integral part of studies on animal anatomy and functional morphology; usually, they are published as static images, movies or as interactive PDF files. We demonstrate the use of animated 3D models embedded in PDF documents, which combine the advantages of both movie and interactivity, based on the example of preserved Trigonopterus weevils. The method is particularly suitable to simulate joints with largely deterministic movements due to precise form closure. We illustrate the function of an individual screw-and-nut type hip joint and proceed to the complex movements of the entire insect attaining a defence position. This posture is achieved by a specific cascade of movements: Head and legs interlock mutually and with specific features of thorax and the first abdominal ventrite, presumably to increase the mechanical stability of the beetle and to maintain the defence position with minimal muscle activity. The deterministic interaction of accurately fitting body parts follows a defined sequence, which resembles a piece of engineering.
Correlative Nanoscale 3D Imaging of Structure and Composition in Extended Objects
Feng Xu, Lukas Helfen, Heikki Suhonen, Dan Elgrabli, Sam Bayat, Péter Reischig, Tilo Baumbach, Peter Cloetens
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050124
Abstract: Structure and composition at the nanoscale determine the behavior of biological systems and engineered materials. The drive to understand and control this behavior has placed strong demands on developing methods for high resolution imaging. In general, the improvement of three-dimensional (3D) resolution is accomplished by tightening constraints: reduced manageable specimen sizes, decreasing analyzable volumes, degrading contrasts, and increasing sample preparation efforts. Aiming to overcome these limitations, we present a non-destructive and multiple-contrast imaging technique, using principles of X-ray laminography, thus generalizing tomography towards laterally extended objects. We retain advantages that are usually restricted to 2D microscopic imaging, such as scanning of large areas and subsequent zooming-in towards a region of interest at the highest possible resolution. Our technique permits correlating the 3D structure and the elemental distribution yielding a high sensitivity to variations of the electron density via coherent imaging and to local trace element quantification through X-ray fluorescence. We demonstrate the method by imaging a lithographic nanostructure and an aluminum alloy. Analyzing a biological system, we visualize in lung tissue the subcellular response to toxic stress after exposure to nanotubes. We show that most of the nanotubes are trapped inside alveolar macrophages, while a small portion of the nanotubes has crossed the barrier to the cellular space of the alveolar wall. In general, our method is non-destructive and can be combined with different sample environmental or loading conditions. We therefore anticipate that correlative X-ray nano-laminography will enable a variety of in situ and in operando 3D studies.
CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks
Jan Baumbach
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-429
Abstract: Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB.The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at http://www.CoryneRegNet.DE webcite.Recently several whole-genome sequencing projects have generated huge amounts of data related to various microorganisms including gene and protein sequences and their functional annotation
Es gibt keine objektive Subjektivit t in der Untersuchung sozialer Interaktionen There Is No Objective Subjectivity in the Study of Social Interaction No hay subjetividad objetiva en el estudio de la interacción social
Tilo Weber
Forum : Qualitative Social Research , 2003,
Abstract: Die Variante der ethnomethodologischen Konversationsanalyse, die von Emanuel A. SCHEGLOFF vertreten wird, will Diskurs in einer streng empirizistischen Weise analysieren. Dies bedeutet insbesondere, dass der Einfluss der subjektiven Vorannahmen und spezifischen Interessen des Forschers/der Forscherin im Untersuchungsprozess neutralisiert werden sollen. Der vorliegende Beitrag skizziert die Forschungsstrategie SCHEGLOFFs und charakterisiert sie als eine Form des methodischen – im Gegensatz zu einem naiven – epistemologischen Realismus. Es wird deutlich, dass dieser Ansatz die ihm gelegentlich unterstellte Zirkularit t vermeidet. Sein Anspruch jedoch, soziale Interaktion "in ihrem eigenen Recht" zur Geltung zu bringen (vgl. SCHELGOFF 1997a, S.174), erweist sich als uneinl sbar. Dies wird hier in seinen praktischen Konsequenzen am Beispiel eines der klassischen Themen der Konversationsanalyse, den "konversationellen Reparaturen" (vgl. SCHEGLOFF, JEFFERSON & SACKS 1977), illustriert. Es wird gezeigt, dass das Ergebnis jeder konversationsanalytischen Datenanalyse von Vorannahmen und -entscheidungen beeinflusst ist, die die Auswahl, die Aufbereitung und die (Re-) Pr sentation der Daten betreffen, ohne selbst empirisch gerechtfertigt werden zu k nnen. Hieraus wird geschlossen, dass die Angemessenheit konversationsanalytischer Befunde viel eher von den "praktischen Zwecken" derjenigen Prozesse abh ngt, die diese Befunde zu Tage f rdern, als von ihrer übereinstimmung mit dem Diskurs als einer "in sich selbst begründeten eigenen Wirklichkeit" (vgl. SCHEGLOFF 1997a, S.171). Mit dieser Schlussfolgerung wird die ethnomethodologische Einsicht in die lokale Konstruiertheit sozialen Sinns und sozialer Realit t auf die Sozialwissenschaft selbst angewendet. URN: urn:nbn:de:0114-fqs0302432 The variant of ethnomethodological Conversation Analysis (CA) represented and advocated by Emanuel A. SCHEGLOFF pursues the goal of analyzing discourse in a strictly empiricist manner that excludes the impact of the researcher's subjective "preoccupations" and "presuppositions" from the investigative process. This paper outlines the SCHEGLOFFian research strategy and characterizes it as representing a methodologist—as opposed to na ve—variant of epistemological realism. It is argued that this approach, while avoiding circularity, fails to make feasible an "account of the object itself" (SCHEGLOFF 1997a, p.174). This line of argument is illustrated by its practical consequences apropos one of CA's classical themes, viz. conversational repair (cf. SCHEGLOFF, JEFFERSON & SACKS 1977). It is
Das Sandm nnchen, das aus der K lte kam – DDR-Filmproduktionen im Kulturaustausch mit Schweden
Tilo Herrmann
Nordeuropaforum , 2006,
Abstract: This essay uses the example of GDR film export to Sweden to examine specific objectives, internal planning, and results of GDR cultural policy in Sweden. It also investigates the Swedish receptions and the appraisals and patterns of argumentation to be found. The study is based on articles in Swedish daily press and technical journals and on internal documents of the East-German bureaucracy. The analysis is divided into several case studies which are restricted to the late 1960s and early 1970s, the heyday of GDR cultural activities in Sweden. After a glance at the situation in commercial film business, the focus shifts to a series of special film showings at the Swedish Film Institute's film club (SFI:s filmklubb).
Predictions of chiral random matrix theory and lattice QCD results
Tilo Wettig
Physics , 1999,
Abstract: Chiral random matrix theory makes very detailed predictions for the spectral correlations of the QCD Dirac operator, both in the bulk of the spectrum and near zero virtuality. These predictions have been successfully tested in lattice QCD simulations by several groups. Moreover, the domain of validity of random matrix theory has been predicted theoretically and identified in lattice data. In this talk, the current numerical evidence is reviewed.
Performance of machines for lattice QCD simulations
Tilo Wettig
Physics , 2005,
Abstract: We review the architecture of massively parallel machines used for lattice QCD simulations and present benchmarks for the performance of popular algorithms on these platforms. We cover commercial supercomputers, PC clusters, and custom-designed machines. We also speculate on future developments.
Linking Cytoscape and the corynebacterial reference database CoryneRegNet
Jan Baumbach, Leonard Apeltsin
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-184
Abstract: We introduce two novel plugins for the Cytoscape environment designed to enhance in silico studies of procaryotic transcriptional regulatory networks. Our plugins leverage the information from the cornyebacterial reference database CoryneRegNet with the graph analysis capabilities of Cytoscape. CoryneRegNetLoader queries the CoryneRegNet database to extract a gene regulatory network represented as a directed graph. Additional information is stored as node/edge attributes within the graph. COMA facilitates consistency checks for gene expression studies given a gene regulatory network. COMA tests whether all gene expression levels correlate properly with the given network topology.The plugins facilitate in silico studies of procaryotic transcriptional gene regulation, particularly in Corynebacteria and E. coli, by combining the knowledge from the corynebacterial reference database with the graph analysis capabilities of Cytoscape, which is one of the most-widely used tools for biological network analyses.Recently, the research community has seen an influx of data relating to transcriptional regulatory interactions of microorganisms. Information derived from DNA microarray hybridization experiments, computational predictions, and literature-based text mining has opened the way for the graph-based analysis of gene regulatory networks across entire organisms [1,2]. The large-scale reconstruction of these networks allows for in silico simulation of cell behavior in response to changing environmental conditions [3].Corynebacteria are highly relevant to fields of systems biology, biotechnology, and human medicine [4]. The ontology-based reference database for corynebacterial transcription factors and regulatory networks CoryneRegNet [5-8] provides methods for the storage, analysis, and reconstruction of gene regulatory networks of corynebacteria. Data on the model organism Escherichia coli K12 has been imported from RegulonDB release 5.0 [9,10] and integrated together with
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