Center for Biomedical Computing (SFF)

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Publications at Center for Biomedical Computing (SFF)
Book Chapter
Multi-penalty regularization for detecting relevant variables
In Recent Applications of Harmonic Analysis to Function Spaces, Differential Equations, and Data Science, 889-916. Novel Methods in Harmonic Analysis, ed. Vol. 2. Springer International Publishing, 2017.Status: Published
Multi-penalty regularization for detecting relevant variables
In this paper we propose a new method for detecting relevant variables
from a priori given high-dimensional data under the assumption that input-
output dependence is described by a nonlinear function depending on a few
variables. The method is based on the inspection of the behavior of discrepan-
cies of a multi-penalty regularization with a component-wise penalization for
small and large values of regularization parameters. We provide the justifica-
tion of the proposed method under a certain condition on sampling operators.
The effectiveness of the method is demonstrated in the example with synthetic
data and in the reconstruction of gene regulatory networks. In the latter ex-
ample, the obtained results provide a clear evidence of the competitiveness of
the proposed method.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Book Chapter |
Year of Publication | 2017 |
Book Title | Recent Applications of Harmonic Analysis to Function Spaces, Differential Equations, and Data Science |
Volume | 2 |
Edition | Novel Methods in Harmonic Analysis, |
Pagination | 889-916 |
Publisher | Springer International Publishing |
Keywords | causality networks, gene regulatory networks., multi-penalty regularization, variables detection |
URL | http://www.springer.com/de/book/9783319555553 |
Journal Article
Species-Dependent Mechanisms of Cardiac Arrhythmia: A Cellular Focus
Clinical Medicine Insights: Cardiology 11 (2017).Status: Published
Species-Dependent Mechanisms of Cardiac Arrhythmia: A Cellular Focus
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Clinical Medicine Insights: Cardiology |
Volume | 11 |
Publisher | SAGE Publications |
ISSN | 1179-5468 |
DOI | 10.1177/1179546816686061 |
Cerebral aneurysm blood flow simulations: There’s solver settings and then there’s solver settings
Journal of Biomechanics 61 (2017): 280.Status: Published
Cerebral aneurysm blood flow simulations: There’s solver settings and then there’s solver settings
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Journal of Biomechanics |
Volume | 61 |
Pagination | 280-280 |
Publisher | Journal of Biomechanics |
DOI | 10.1016/j.jbiomech.2017.04.039 |
Rupture prediction of intracranial aneurysms: a nationwide matched case-control study of hemodynamics at the time of diagnosis
Journal of Neurosurgery (2017).Status: Published
Rupture prediction of intracranial aneurysms: a nationwide matched case-control study of hemodynamics at the time of diagnosis
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Journal of Neurosurgery |
Date Published | Online 11/2017 |
Publisher | AANS |
DOI | 10.3171/2017.5.JNS17195 |
Robustness of common hemodynamic indicators with respect to numerical resolution in 38 middle cerebral artery aneurysms.
PLoS ONE 12, no. 6 (2017): e0177566.Status: Published
Robustness of common hemodynamic indicators with respect to numerical resolution in 38 middle cerebral artery aneurysms.
BACKGROUND:
Using computational fluid dynamics (CFD) to compute the hemodynamics in cerebral aneurysms has received much attention in the last decade. The usability of these methods depends on the quality of the computations, highlighted in recent discussions. The purpose of this study is to investigate the convergence of common hemodynamic indicators with respect to numerical resolution.
METHODS:
38 middle cerebral artery bifurcation aneurysms were studied at two different resolutions (one comparable to most studies, and one finer). Relevant hemodynamic indicators were collected from two of the most cited studies, and were compared at the two refinements. In addition, correlation to rupture was investigated.
RESULTS:
Most of the hemodynamic indicators were very well resolved at the coarser resolutions, correlating with the finest resolution with a correlation coefficient >0.95. The oscillatory shear index (OSI) had the lowest correlation coefficient of 0.83. A logarithmic Bland-Altman plot revealed noticeable variations in the proportion of the aneurysm under low shear, as well as in spatial and temporal gradients not captured by the correlation alone.
CONCLUSION:
Statistically, hemodynamic indicators agree well across the different resolutions studied here. However, there are clear outliers visible in several of the hemodynamic indicators, which suggests that special care should be taken when considering individual assessment.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | PLoS ONE |
Volume | 12 |
Issue | 6 |
Pagination | e0177566 |
Publisher | Public Library of Science |
Interstitial Solute Transport in 3D Reconstructed Neuropil Occurs by Diffusion Rather than Bulk Flow
Proceedings of the National Academy of Sciences 114, no. 37 (2017): 9894-9899.Status: Published
Interstitial Solute Transport in 3D Reconstructed Neuropil Occurs by Diffusion Rather than Bulk Flow
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF), Waterscape: The Numerical Waterscape of the Brain |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Proceedings of the National Academy of Sciences |
Volume | 114 |
Issue | 37 |
Pagination | 9894-9899 |
Publisher | National Academy og Sciences |
DOI | 10.1073/pnas.1706942114 |
Nanoindentation and finite element modelling of chitosan–alginate multilayer coated hydrogels
Soft Matter 12 (2017): 7338-7349.Status: Published
Nanoindentation and finite element modelling of chitosan–alginate multilayer coated hydrogels
Composite soft materials are used as compounds for determining the effects of mechanical cues on cell behavior and cell encapsulation and for controlling drug release. The appropriate composite soft materials are conventionally prepared by selective deposition of polymers at the surface of an ionic hydrogel. In the present study we address the impact of a mechanically stratified two-layer structure of these materials on their overall mechanical characterization by applying a combination of nanoindentation, confocal microscopy and finite element modelling. We prepare covalent cross-linked hydrogels based on acrylamide (AAM) and including an anionic group, and impregnate them using a multilayer deposition strategy of alternating exposure to cationic chitosan and anionic alginate. The thickness of the chitosan–alginate layer on the hydrogels was determined to be 0.4 ± 0.05 μm for 4 bilayers, and 0.7 ± 0.1 μm for the 8 bilayer deposition procedure employing a fluorescently labelled chitosan and confocal microscopy. The force–indentation data for the AAM gels were highly reproducible, whereas 77% and 50% of the force–indentation data were reproducible following the 4 and 8 bilayer deposition. The main trends in the reproducible force–distance data were found to yield an apparent increased Young's modulus after the deposition. Finite element modelling showed that adaption of a homogeneous Young's modulus for the specimens with deposited layers yields approximately three times too low stiffness compared to the estimate of the mechanical properties of the outer part in the two-layered mechanical model. The thickness of the multilayer region determined by confocal microscopy was used in the model. This study shows that the mechanical layered property needs to be included in the interpretation of the nanoindentation data when there is a significant mechanical contrast.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Soft Matter |
Volume | 12 |
Number | 35 |
Pagination | 7338-7349 |
Publisher | Royal Society of Chemestry |
Contributions of prestrains, hyperelasticity, and muscle fiber activation on mitral valve systolic performance
International Journal for Numerical Methods in Biomedical Engineering 33 (2017).Status: Published
Contributions of prestrains, hyperelasticity, and muscle fiber activation on mitral valve systolic performance
The present study addresses the contributions of prestrains and muscle fiber activation to the global response of the mitral valve during systole. A finite element model of a porcine mitral valve is created using anatomical measurements and 3D echocardiographic recordings. The passive behavior of the leaflets is modeled using a transversely isotropic hyperelastic constitutive model, and we assume orthotropic muscle activations in the anterior leaflet. A simple approach to incorporate prestrains in the mitral valve apparatus is used by expanding the mitral annulus before applying the ventricular pressure to the mitral leaflets. Several finite element analyses are run with or without muscle activation and with or without prestrains. The analysis results are compared at peak systole with the echocardiograpic recordings. The case where prestrains and activation are accounted for simultaneously is the most efficient to approach the physiological flat shape of the closed valve observed in the echocardiograpic measurements. These results suggest that the active components present in the mitral leaflets and the presence of prestrains contribute to the physiological deformations of the mitral valve at peak systole and that material models based on in vitro mechanical testing are not sufficient for numerical studies of the mitral apparatus.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | International Journal for Numerical Methods in Biomedical Engineering |
Volume | 33 |
Number | 4 |
Publisher | John Wiley & Sons |
Modeling the differentiation of A- and C-type baroreceptor firing patterns
Journal of Computational Neuroscience 41 (2017): 11-30.Status: Published
Modeling the differentiation of A- and C-type baroreceptor firing patterns
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Journal of Computational Neuroscience |
Volume | 41 |
Number | 1 |
Pagination | 11-30 |
Publisher | Springer |
Effects of arterial wall models and measurement uncertainties on cardiovascular model predictions
Journal of Biomechanics 50 (2017): 188-194.Status: Published
Effects of arterial wall models and measurement uncertainties on cardiovascular model predictions
We developed a methodology to assess and compare the prediction quality of cardiovascular models for patient-specific simulations calibrated with uncertainty-hampered measurements. The methodology was applied in a one-dimensional blood flow model to estimate the impact of measurement uncertainty in wall model parameters on the predictions of pressure and flow in an arterial network. We assessed the prediction quality of three wall models that have been widely used in one-dimensional blood flow simulations. A 37-artery network, previously used in one experimental and several simulation studies, was adapted to patient-specific conditions with a set of three clinically measurable inputs: carotid–femoral wave speed, mean arterial pressure and area in the brachial artery. We quantified the uncertainty of the predicted pressure and flow waves in eight locations in the network and assessed the sensitivity of the model prediction with respect to the measurements of wave speed, pressure and cross-sectional area. Furthermore, we developed novel time-averaged sensitivity indices to assess the contribution of model parameters to the uncertainty of time-varying quantities (e.g., pressure and flow). The results from our patient-specific network model demonstrated that our novel indices allowed for a more accurate sensitivity analysis of time-varying quantities compared to conventional Sobol sensitivity indices.
Afilliation | Scientific Computing |
Project(s) | Center for Biomedical Computing (SFF) |
Publication Type | Journal Article |
Year of Publication | 2017 |
Journal | Journal of Biomechanics |
Volume | 50 |
Pagination | 188--194 |
Publisher | Elsevier |
DOI | 10.1016/j.jbiomech.2016.11.042 |