Berlin, Germany
Berlin, Germany

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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.


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.


PubMed | Polytechnic University of Turin, WIAS Berlin and Unicredit SpA
Type: | Journal: Methods in molecular biology (Clifton, N.J.) | Year: 2015

Analysis of images obtained from two-dimensional gel electrophoresis (2-D GE) is a topic of utmost importance in bioinformatics research, since commercial and academic software currently available have proven to be neither completely effective nor fully automatic, often requiring manual revision and refinement of computer generated matches. In this chapter, 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 proteins quantification, providing more reliable image analysis results. The method is validated for processing highly exposed 2-D GE images, comparing reconstructed spots with the corresponding non-saturated image. The results demonstrate that the algorithm enables correct spot quantification.


Tabelow K.,WIAS Berlin | Mohammadi S.,University College London | Weiskopf N.,University College London | Polzehl J.,WIAS Berlin
Neuroinformatics | Year: 2014

We present an implementation of a recently developed noise reduction algorithm for dMRI data, called multi-shell position orientation adaptive smoothing (msPOAS), as a toolbox for SPM. The method intrinsically adapts to the structures of different size and shape in dMRI and hence avoids blurring typically observed in non-adaptive smoothing. We give examples for the usage of the toolbox and explain the determination of experiment-dependent parameters for an optimal performance of msPOAS. © 2014, The Author(s).


Natale M.,Polytechnic University of Turin | Natale M.,BioDigitalValley S.r.l. | Caiazzo A.,WIAS Berlin | Bucci E.M.,BioDigitalValley S.r.l. | 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.


Arnold T.,WIAS Berlin | Rathsfeld A.,WIAS Berlin
International Conference on Mathematical Methods in Electromagnetic Theory, MMET | Year: 2012

In many modern industrial processes, diffractive optical elements employ light with small wavelengths. The current technological progress is based on the steady decrease in wavelengths (e.g. EUV light). For such wavelengths, the effect of random surface roughness of gratings has an increasingly high impact on the behaviour of the scattered wave. Consequently, the roughness should be included into the modelling of the scattering and, maybe, into the numerical solution process of inverse problems. Since the solution for the full Maxwell system for rough surfaces is extremely difficult, many authors employ simplified models. One way to do so is proposed by Stearns [1] and is based on the Born approximation of the Maxwell equations. We will discuss mathematically strict assumptions which allow the use of the manipulations in Stearns' approach. Under these assumptions, we give a rigorous definition of an approximate solution and derive the corresponding formulas for the reflected far field. © 2012 IEEE.


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.


Glitzky A.,WIAS Berlin | Mielke A.,WIAS Berlin
Zeitschrift fur Angewandte Mathematik und Physik | Year: 2013

We derive gradient-flow formulations for systems describing drift-diffusion processes of a finite number of species which undergo mass-action type reversible reactions. Our investigations cover heterostructures, where material parameter may depend in a nonsmooth way on the space variable. The main results concern a gradient-flow formulation for electro-reaction-diffusion systems with active interfaces permitting drift-diffusion processes and reactions of species living on the interface and transfer mechanisms allowing bulk species to jump into an interface or to pass through interfaces. The gradient flows are formulated in terms of two functionals: the free energy and the dissipation potential. Both functionals consist of a bulk and an interface integral. The interface integrals determine the interface dynamics as well as the self-consistent coupling to the model in the bulk. The advantage of the gradient structure is that it automatically generates thermodynamically consistent models. © 2012 Springer Basel AG.


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.


PubMed | WIAS Berlin
Type: Journal Article | Journal: Neuroinformatics | Year: 2015

We present an implementation of a recently developed noise reduction algorithm for dMRI data, called multi-shell position orientation adaptive smoothing (msPOAS), as a toolbox for SPM. The method intrinsically adapts to the structures of different size and shape in dMRI and hence avoids blurring typically observed in non-adaptive smoothing. We give examples for the usage of the toolbox and explain the determination of experiment-dependent parameters for an optimal performance of msPOAS.

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