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Berlin, Germany

Natale M.,Polytechnic University of Turin | Natale M.,BioDigitalValley Srl | Caiazzo A.,WIAS Berlin | Bucci E.M.,BioDigitalValley Srl | And 2 more authors.
Genomics, Proteomics and Bioinformatics | Year: 2012

Analysis of images obtained from two-dimensional gel electrophoresis (2D-GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software available currently has proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this work, we present an effective technique for the detection and the reconstruction of over-saturated protein spots. Firstly, the algorithm reveals overexposed areas, where spots may be truncated, and plateau regions caused by smeared and overlapping spots. Next, it reconstructs the correct distribution of pixel values in these overexposed areas and plateau regions, using a two-dimensional least-squares fitting based on a generalized Gaussian distribution. Pixel correction in saturated and smeared spots allows more accurate quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2D-GE images, comparing reconstructed spots with the corresponding non-saturated image, demonstrating that the algorithm enables correct spot quantification. © 2012 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Source

Guibert R.,French Institute for Research in Computer Science and Automation | Guibert R.,University Pierre and Marie Curie | McLeod K.,Simula Research Laboratory | Caiazzo A.,WIAS Berlin | And 10 more authors.
Medical Image Analysis | Year: 2014

3D computational fluid dynamics (CFD) in patient-specific geometries provides complementary insights to clinical imaging, to better understand how heart disease, and the side effects of treating heart disease, affect and are affected by hemodynamics. This information can be useful in treatment planning for designing artificial devices that are subject to stress and pressure from blood flow. Yet, these simulations remain relatively costly within a clinical context. The aim of this work is to reduce the complexity of patient-specific simulations by combining image analysis, computational fluid dynamics and model order reduction techniques. The proposed method makes use of a reference geometry estimated as an average of the population, within an efficient statistical framework based on the currents representation of shapes. Snapshots of blood flow simulations performed in the reference geometry are used to build a POD (Proper Orthogonal Decomposition) basis, which can then be mapped on new patients to perform reduced order blood flow simulations with patient specific boundary conditions. This approach is applied to a data-set of 17 tetralogy of Fallot patients to simulate blood flow through the pulmonary artery under normal (healthy or synthetic valves with almost no backflow) and pathological (leaky or absent valve with backflow) conditions to better understand the impact of regurgitated blood on pressure and velocity at the outflow tracts. The model reduction approach is further tested by performing patient simulations under exercise and varying degrees of pathophysiological conditions based on reduction of reference solutions (rest and medium backflow conditions respectively). © 2013 Elsevier B.V. Source

Caiazzo A.,WIAS Berlin | Evans D.,University of Sheffield | Falcone J.-L.,University of Geneva | Hegewald J.,TU Braunschweig | And 12 more authors.
Journal of Computational Science | Year: 2011

In-stent restenosis, the maladaptive response of a blood vessel to injury caused by the deployment of a stent, is a multiscale system involving a large number of biological and physical processes. We describe a Complex Automata model for in-stent restenosis, coupling bulk flow, drug diffusion, and smooth muscle cell models, all operating on different time scales. Details of the single scale models and of the coupling interfaces are described, together with first simulation results, obtained with a dedicated software environment for Complex Automata simulations. Preliminary results show that the model can reproduce growth trends observed in experimental studies and facilitate testing of hypotheses concerning the interaction of key factors. © 2011 Elsevier B.V. Source

Kramer J.,University of Munster | Deppe M.,University of Munster | Gobel K.,University of Munster | Tabelow K.,WIAS Berlin | And 2 more authors.
Journal of the Neurological Sciences | Year: 2015

Abstract Introduction The underlying pathophysiology of neurological complications in patients with hemolytic-uremic syndrome (HUS) remains unclear. It was recently attributed to a direct cytotoxic effect of Shiga toxin 2 (Stx2) in the thalamus. Conventional MRI of patients with Stx2-caused HUS revealed - despite severe neurological symptoms - only mild alterations if any, mostly in the thalamus. Against this background, we questioned: Does diffusion tensor imaging (DTI) capture the thalamic damage better than conventional MRI? Are neurological symptoms and disease course better reflected by thalamic alterations as detected by DTI? Are other brain regions also affected? Methods Three women with serious neurological deficits due to Stx2-associated HUS were admitted to MRI/DTI at disease onset. Two of them were longitudinally examined. Fractional anisotropy (FA) and mean diffusivity were computed to assess Stx2-caused microstructural damage. Results Compared to 90 healthy women, all three patients had significantly reduced thalamic FA. Thalamic mean diffusivity was only reduced in two patients. DTI of the longitudinally examined women demonstrated slow normalization of thalamic FA, which was paralleled by clinical improvement. Conclusion Whereas conventional MRI only shows slight alterations based on subjective evaluation, DTI permits quantitative, objective, and longitudinal assessment of cytotoxic cerebral damage in individual patients. © 2015 Elsevier B.V. Source

It is investigated in what sense thermoplasticity can be written as a generalized gradient system with respect to the total entropy and the entropy-production potential. The difficulty is that the quasistatic equilibrium equation for the elastic forces is obtained by minimizing the total energy and that this condition must be eliminated suitably. The subtle interplay between energy and entropy is treated via the formalism of GENERIC. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

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