Thibaut Bardyn

Universität Bern, Bern, BE, Switzerland

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Publications (14)11.18 Total impact

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    ABSTRACT: This short communication briefly outlines the major components and the integration steps of the Oncosimulator that is being developed within the framework of the European Commission funded ContraCancrum project. The Oncosimulator is a technologically advanced multiscale tumor growth and treatment response system aiming at supporting patient individualized treatment decisions. An indicative example of the adopted mathematical approaches as well as a simple example of numerical code validation are provided. The document concludes with a short discussion on the characteristics of the major modeling approaches that refer to the cellular and higher biocomplexity levels since the latter constitute the basis for the entire Oncosimulator integration.
    4 th Int. Adv. Res. Workshop on In Silico Oncology and Cancer Investigation (4 th IARWISOCI) –The ContraCancrum Workshop; 09/2010
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    ABSTRACT: An implantable transducer for monitoring the flow of Cerebrospinal fluid (CSF) for the treatment of hydrocephalus has been developed which is based on measuring the heat dissipation of a local thermal source. The transducer uses passive telemetry at 13.56 MHz for power supply and read out of the measured flow rate. The in vitro performance of the transducer has been characterized using artificial Cerebrospinal Fluid (CSF) with increased protein concentration and artificial CSF with 10% fresh blood. After fresh blood was added to the artificial CSF a reduction of flow rate has been observed in case that the sensitive surface of the flow sensor is close to the sedimented erythrocytes. An increase of flow rate has been observed in case that the sensitive surface is in contact with the remaining plasma/artificial CSF mix above the sediment which can be explained by an asymmetric flow profile caused by the sedimentation of erythrocytes having increased viscosity compared to artificial CSF. After removal of blood from artificial CSF, no drift could be observed in the transducer measurement which could be associated to a deposition of proteins at the sensitive surface walls of the packaged flow transducer. The flow sensor specification requirement of +-10% for a flow range between 2 ml/h and 40 ml/h. could be confirmed at test conditions of 37 degrees C.
    Biomedical Microdevices 03/2010; 12(4):607-18. · 2.72 Impact Factor
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    ABSTRACT: Despite its importance, implant removal torque can be assessed at present only after implantation. This paper presents a new technique to help clinicians preoperatively evaluate implant stability. Planning software has been combined with an in-house finite element solver. Once the clinician has chosen the implant position on the planner, a finite element analysis automatically calculates the primary stability. The process was designed to be as simple and fast as possible for clinical use. This paper describes application of the method to the prediction of removal torque. A preliminary validation has been performed in both polyurethane foam and sheep bone. The predicted torque is quantitatively equivalent to experimental values with correlation coefficients of >0.7 in both materials. This preliminary study is a first step toward the introduction of finite element models in computer-assisted surgery. The fact that the process is fast and automatic makes it suitable for a clinical use.
    Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontology 02/2010; 109(4):594-603. · 1.50 Impact Factor
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    ABSTRACT: An implantable thermal flow sen treatment of hydrocephalus has been developed.The sensor uses passive telemetry at 13.56 MHz for power supply and read out of the measured flow rate. The in vitro performance of the sensor has been characterized using artificial Cerebrospinal Fluid (CSF) with increased protein concentration and artificial CSF with 10% fresh blood. No drift could be observed in the flow sensor measurement which could be associated to a deposition of proteins at the sensitive surface walls of the packaged flow sensor. Keywordsimplant–flow sensor–hydrocephalus–protein adsorption
    01/2010: pages 265-268;
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    ABSTRACT: The ContraCancrum project aims at developing a composite multilevel platform for simulating malignant tumor development and tumor and normal tissue response to therapeutic modalities and treatment schedules. The project aims at having an impact primarily in (a) the better under-standing of the natural phenomenon of cancer at different levels of biocomplexity and most importantly (b) the disease treatment optimization procedure in the patient’s individualized context by simulating the response to various therapeutic regimens. Fundamental biological mechanisms involved in tumor development and tumor and normal tissue treatment response such as metabolism, cell cycle, tissue mechanics, cell survival following treatment etc. are modeled also addressing stem cells in the context of both tumor and normal tissue behavior. The simulators exploit several discrete and continuous mathematics methods such as cellular automata, the generic Monte Carlo technique, finite elements, differential equations, novel dedicated algorithms etc. The predictions of the simulators rely on the imaging, histopathological, molecular and clinical data of the patient. ContraCancrum deploys two important clinical studies for validating the models, one on lung cancer and one on gliomas. The crucial validation work is based on comparing the multi-level therapy simulation predictions with multi-level patient data, acquired before and after therapy. ContraCancrum aims to pave the way for translating clinically validated multilevel cancer models into clinical practice.
    IFMBE proceedings 01/2010; 25(4):2124-2127.
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    ABSTRACT: We propose a new and clinically oriented approach to perform atlas-based segmentation of brain tumor images. A mesh-free method is used to model tumor-induced soft tissue deformations in a healthy brain atlas image with subsequent registration of the modified atlas to a pathologic patient image. The atlas is seeded with a tumor position prior and tumor growth simulating the tumor mass effect is performed with the aim of improving the registration accuracy in case of patients with space-occupying lesions. We perform tests on 2D axial slices of five different patient data sets and show that the approach gives good results for the segmentation of white matter, grey matter, cerebrospinal fluid and the tumor.
    Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 01/2010; 2010:4080-3.
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    ABSTRACT: The interest in automatic volume meshing for finite element analysis (FEA) has grown more since the appearance of microfocus CT (μCT), due to its high resolution, which allows for the assessment of mechanical behaviour at a high precision. Nevertheless, the basic meshing approach of generating one hexahedron per voxel produces jagged edges. To prevent this effect, smoothing algorithms have been introduced to enhance the topology of the mesh. However, whether smoothing also improves the accuracy of voxel-based meshes in clinical applications is still under question. There is a trade-off between smoothing and quality of elements in the mesh. Distorted elements may be produced by excessive smoothing and reduce accuracy of the mesh. In the present work, influence of smoothing on the accuracy of voxel-based meshes in micro-FE was assessed. An accurate 3D model of a trabecular structure with known apparent mechanical properties was used as a reference model. Virtual CT scans of this reference model (with resolutions of 16, 32 and 64μm) were then created and used to build voxel-based meshes of the microarchitecture. Effects of smoothing on the apparent mechanical properties of the voxel-based meshes as compared to the reference model were evaluated. Apparent Young’s moduli of the smooth voxel-based mesh were significantly closer to those of the reference model for the 16 and 32μm resolutions. Improvements were not significant for the 64μm, due to loss of trabecular connectivity in the model. This study shows that smoothing offers a real benefit to voxel-based meshes used in micro-FE. It might also broaden voxel-based meshing to other biomechanical domains where it was not used previously due to lack of accuracy. As an example, this work will be used in the framework of the European project ContraCancrum, which aims at providing a patient-specific simulation of tumour development in brain and lungs for oncologists. For this type of clinical application, such a fast, automatic, and accurate generation of the mesh is of great benefit. KeywordsFinite element-Meshing-Smoothing-Validation-Microfocus CT
    12/2009: pages 85-93;
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    ABSTRACT: Resonance frequency analysis (RFA) offers the opportunity to monitor the osseointegration of an implant in a simple, noninvasive way. A better comprehension of the relationship between RFA and parameters related to bone quality would therefore help clinicians improve diagnoses. In this study, a bone analog made from polyurethane foam was used to isolate the influences of bone density and cortical thickness in RFA. Straumann standard implants were inserted in polyurethane foam blocks, and primary implant stability was measured with RFA. The blocks were composed of two superimposed layers with different densities. The top layer was dense to mimic cortical bone, whereas the bottom layer had a lower density to represent trabecular bone. Different densities for both layers and different thicknesses for the simulated cortical layer were tested, resulting in eight different block combinations. RFA was compared with two other mechanical evaluations of primary stability: removal torque and axial loading response. The primary stability measured with RFA did not correlate with the two other methods, but there was a significant correlation between removal torque and the axial loading response (P < .005). Statistical analysis revealed that each method was sensitive to different aspects of bone quality. RFA was the only method able to detect changes in both bone density and cortical thickness. However, changes in trabecular bone density were easier to distinguish with removal torque and axial loading than with RFA. This study shows that RFA, removal torque, and axial loading are sensitive to different aspects of the bone-implant interface. This explains the absence of correlation among the methods and proves that no standard procedure exists for the evaluation of primary stability.
    The International journal of oral & maxillofacial implants 01/2009; 24(6):1006-14. · 1.91 Impact Factor
  • 8th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering, Porto, Portugal; 02/2008
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    ABSTRACT: Concerns have been raised that the use of calcium phosphate (CaP) cements for the augmentation of fractured, osteoporotic bones may aggravate cardiovascular deterioration in the event of pulmonary cement embolism by stimulating coagulation. The aim of the present study was therefore to investigate the cardiovascular changes after pulmonary embolism of CaP cement using an animal model. In 14 sheep, 2.0 mL CaP or polymethylmethacrylate cement were injected intravenously. Cardiovascular parameters and antithrombin levels were monitored until 60 min postinjection. Postmortem, lungs were subjected to CT scanning, and 3D reconstruction of the cement was performed. Intravenous injection of CaP cement resulted in a more severe increase in pulmonary arterial pressure and decrease in arterial blood pressure. Disintegration of the CaP cement seemed to be the reason for the more severe reaction. There was no evidence of thromboembolism. Disintegration of CaP cement in circulating blood does not only compromise the mechanical properties, but also represents a risk of cardiovascular complications. Reliable cohesion of CaP cements in an aqueous environment is essential for clinical applications such as osteoporotic bone augmentation.
    Journal of Biomedical Materials Research Part B Applied Biomaterials 09/2007; 82(2):526-32. · 2.31 Impact Factor
  • Automatisierungstechnische Verfahren für die Medizin, Fortschrittsberichte VDI, Reihe 17, Nr. 267, p. 63-64; 01/2007
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    ABSTRACT: Concerns have been raised that the use of calcium phosphate (CaP) cements for the augmentation of fractured, osteoporotic bones may aggravate cardiovascular deterioration in the event of pulmonary cement embolism by stimulating coagulation. The aim of the present study was therefore to investigate the cardiovascular changes after pulmonary embolism of CaP cement using an animal model. In 14 sheep, 2.0 mL CaP or polymethylmethacrylate cement were injected intravenously. Cardiovascular parameters and antithrombin levels were monitored until 60 min postinjection. Postmortem, lungs were subjected to CT scanning, and 3D reconstruction of the cement was performed. Intravenous injection of CaP cement resulted in a more severe increase in pulmonary arterial pressure and decrease in arterial blood pressure. Disintegration of the CaP cement seemed to be the reason for the more severe reaction. There was no evidence of thromboembolism. Disintegration of CaP cement in circulating blood does not only compromise the mechanical properties, but also represents a risk of cardiovascular complications. Reliable cohesion of CaP cements in an aqueous environment is essential for clinical applications such as osteoporotic bone augmentation. © 2007 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2007
    01/2007;
  • Plastic and reconstructive surgery 07/2006; 117(7):2431-7. · 2.74 Impact Factor
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    ABSTRACT: In the framework of the ContraCancrum project, automatic generation of an accurate finite element mesh is necessary for minimum user-interaction. The interest on automatic volume meshing for finite element (FE) has grown more popular since the apparition of microfocus CT (μCT) due to its high resolution, allowing assessment of mechanical behavior at a high precision. However, the basic meshing approach of generating one hexahedron per voxel produces jagged edges. The Laplacian operator can be used to smooth the generated mesh, but this method produces mesh shrinkage and volume changes. In this paper an automatic meshing and smoothing algorithm for FE meshes from 3D image data is presented. The method includes a regularization step to assure good element’s shape based on a quality measure. The algorithm introduces a novel technique to combine hexahedron and prism elements in order to increase the degree of mesh smoothness while maintaining good quality of elements. The smoothing method is based on low-pass signal filtering using transfer functions approximated by Chebyshev polynomials, resulting in a fast and computationally efficient method being extended here for FE meshes. The smoothing process was evaluated on various data based on the quality of the elements after smoothing, and stress distribution.