Publikationen

@article{Maier2024,

title = {OpenDiHu: An efficient and scalable framework for biophysical simulations of the neuromuscular system},

author = {Benjamin Maier and Dominik G\"{o}ddeke and Felix Huber and Thomas Klotz and Oliver R\"{o}hrle and Miriam Schulte},

editor = {Elsevier},

url = {https://www.sciencedirect.com/science/article/pii/S187775032400084X},

doi = {https://doi.org/10.1016/j.jocs.2024.102291},

isbn = {1877-7503},

year  = {2024},

date = {2024-04-20},

journal = {Journal of Computational Science},

issue = {79},

pages = {102291},

abstract = {The versatile neuromuscular system, consisting of skeletal muscles and the nervous system, enables human to perform crucial everyday tasks. To investigate its functioning and dysfunctioning with computer simulations, highly resolved, multi-scale models are favorable, whose numerical solutions demand for high performance computing. We present OpenDiHu, a versatile, high-performance computing, open source software framework for detailed, systemic simulations of skeletal muscles and their recruitment mechanisms. OpenDiHu allows to solve a variety of multi-scale models, including 3D muscle mechanics, measurable electromyographic signals, action potential propagation in the muscle tissue, subcellular bio-chemo-electrical processes, and the neural drive to the muscle. All these components can be combined with a wide range of numerical solution schemes into comprehensive simulation setups for the entire system. Experiments on up to almost 27 000 cores demonstrate the efficiency and parallel scalability of OpenDiHu. This enables in silico experiments at very high spatial and temporal resolutions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1007/s11548-023-03045-3,

title = {Image-based Hemodynamic Simulations for Intracranial Aneurysms \textendash The Impact of Complex Vasculatures},

author = {Franziska Gaidzik and Jana Korte and Sylvia Saalfeld and Gabor Janiga and Philipp Berg},

url = {https://pubmed.ncbi.nlm.nih.gov/38206468/},

year  = {2024},

date = {2024-04-01},

urldate = {2024-04-01},

journal = {International Journal of Computer Assisted Radiology and Surgery},

volume = {19},

issue = {4},

pages = {687-697},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Homs-Pons2024,

title = {Coupled simulations and parameter inversion for neural system and electrophysiological muscle models},

author = {Carme Homs-Pons and Robin Lautenschlager and Laura Schmid and Jennifer Ernst and Dominik G\"{o}ddeke and Oliver R\"{o}hrle and Miriam Schulte},

editor = {Wiley Online Library},

url = {https://onlinelibrary.wiley.com/doi/10.1002/gamm.202370009},

doi = {https://doi.org/10.1002/gamm.202370009},

year  = {2024},

date = {2024-03-31},

urldate = {2024-03-31},

journal = {GAMM-Mitteilungen},

abstract = {The functioning of the neuromuscular system is an important factor for quality of life. With the aim of restoring neuromuscular function after limb amputation, novel clinical techniques such as the agonist-antagonist myoneural interface (AMI) are being developed. In this technique, the residual muscles of an agonist-antagonist pair are (re-)connected via a tendon in order to restore their mechanical and neural interaction. Due to the complexity of the system, the AMI can substantially profit from in silico analysis, in particular to determine the prestretch of the residual muscles that is applied during the procedure and determines the range of motion of the residual muscle pair. We present our computational approach to facilitate this. We extend a detailed multi-X model for single muscles to the AMI setup, that is, a two-muscle-one-tendon system. The model considers subcellular processes as well as 3D muscle and tendon mechanics and is prepared for neural process simulation. It is solved on high performance computing systems. We present simulation results that show (i) the performance of our numerical coupling between muscles and tendon and (ii) a qualitatively correct dependence of the range of motion of muscles on their prestretch. Simultaneously, we pursue a Bayesian parameter inference approach to invert for parameters of interest. Our approach is independent of the underlying muscle model and represents a first step toward parameter optimization, for instance, finding the prestretch, to be applied during surgery, that maximizes the resulting range of motion. Since our multi-X fine-grained model is computationally expensive, we present inversion results for reduced Hill-type models. Our numerical results for cases with known ground truth show the convergence and robustness of our approach.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gerh\"{a}usser2024,

title = {Simulation of zonation-function relationships in the liver using coupled multiscale models: Application to drug-induced liver injury},

author = {Steffen Gerh\"{a}usser and Lena Lambers and Luis Mandl and Julian Franquinet and Tim Ricken and Matthias K\"{o}nig },

editor = {bioRxiv},

url = {https://doi.org/10.1101/2024.03.26.586870},

doi = {https://doi.org/10.1101/2024.03.26.586870 },

year  = {2024},

date = {2024-03-29},

urldate = {2024-03-29},

journal = {[PrePrint], bioRxiv},

abstract = {Multiscale modeling requires the coupling of models on different scales, often based on different mathematical approaches and developed by different research teams. This poses many challenges, such as defining interfaces for coupling, reproducible exchange of submodels, efficient simulation of the models, or reproducibility of results. Here, we present a multiscale digital twin of the liver that couples a partial differential equation (PDE)-based porous media approach for the hepatic lobule with cellular-scale ordinary differential equation (ODE)-based models. The models based on the theory of porous media describe transport, tissue mechanical properties, and deformations at the lobular scale, while the cellular models describe hepatic metabolism in terms of drug metabolism and damage in terms of necrosis. The resulting multiscale model of the liver was used to simulate perfusion-zonation-function relationships in the liver spanning scales from single cell to the lobulus. The model was applied to study the effects of (i) protein zonation patterns (metabolic zonation) and (ii) drug concentration dependence on spatially heterogeneous liver damage in the form of necrosis. Depending on the zonation pattern, different liver damage patterns could be reproduced, including periportal and pericentral necrosis as seen in drug-induced liver injury (DILI). Increasing the drug concentration led to an increase in the observed damage pattern. A key point for the success was the integration of domain-specific simulators based on standard exchange formats, i.e., libroadrunner for the high-performance simulation of ODE-based systems and FEBio for the simulation of the continuum-biomechanical part. This allows a standardized and reproducible exchange of cellular scale models in the Systems Biology Markup Language (SBML) between research groups.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Are hemodynamics responsible for inflammatory changes in venous vessel walls? A quantitative study of wall-enhancing intracranial arteriovenous malformation draining veins},

author = {Janneck Stahl and Laura Stone McGuire and Mark Rizko and Sylvia Saalfeld and Philipp Berg and and Ali Alaraj},

url = {https://thejns.org/view/journals/j-neurosurg/aop/article-10.3171-2024.1.JNS232625/article-10.3171-2024.1.JNS232625.xml},

doi = {10.3171/2024.1.JNS232625},

year  = {2024},

date = {2024-03-29},

journal = {Journal of Neurosurgery},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{schwarting24aneurysm,

title = {Numerical simulation of individual coil placement -- A proof-of-concept study for the prediction of recurrence after aneurysm coiling},

author = {Julian Schwarting and Fabian Holzberger and Markus Muhr and Martin Renz and Tobias Boeckh-Behrens and Barbara Wohlmuth and Jan Kirschke},

editor = {arXiv},

url = {https://arxiv.org/abs/2403.06889},

doi = {https://doi.org/10.48550/arXiv.2403.06889},

year  = {2024},

date = {2024-03-11},

journal = {[PrePrint], arXiv},

abstract = {Rupture of intracranial aneurysms results in severe subarachnoidal hemorrhage, which is associated with high morbidity and mortality. Neurointerventional occlusion of the aneurysm through coiling has evolved to a therapeutical standard. The choice of the specific coil has an important influence on secondary regrowth requiring retreatment. Aneurysm occlusion was simulated either through virtual implantation of a preshaped 3D coil or with a porous media approach. In this study, we used a recently developed numerical approach to simulate aneurysm shapes in specific challenging aneurysm anatomies and correlated these with aneurysm recurrence 6 months after treatment. The simulation showed a great variety of coil shapes depending on the variability in possible microcatheter positions. Aneurysms with a later recurrence showed a tendency for more successful coiling attempts. Results revealed further trends suggesting lower simulated packing densities in aneurysms with reoccurrence. Simulated packing densities did not correlate with those calculated by conventional software, indicating the potential for our approach to offer additional predictive value. Our study, therefore, pioneers a comprehensive numerical model for simulating aneurysm coiling, providing insights into individualized treatment strategies and outcome prediction. Future directions involve expanding the model's capabilities to simulate intraprocedural outcomes and long-term predictions, aiming to refine occlusion quality criteria and validate prediction parameters in larger patient cohorts. This simulation framework holds promise for enhancing clinical decision-making and optimizing patient outcomes in endovascular aneurysm treatment. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{duswald24matern,

title = {Finite elements for Mat\'{e}rn-type random fields: Uncertainty in computational mechanics and design optimization},

author = {Tobias Duswald and Brendan Keith and Boyan Lazarov and Socratis Petrides and Barbara Wohlmuth},

editor = {arXiv},

url = {https://arxiv.org/abs/2403.03658},

doi = {https://doi.org/10.48550/arXiv.2403.03658},

year  = {2024},

date = {2024-03-06},

urldate = {2024-03-06},

journal = {[PrePrint], arXiv},

abstract = {This work highlights an approach for incorporating realistic uncertainties into scientific computing workflows based on finite elements, focusing on applications in computational mechanics and design optimization. We leverage Mat\'{e}rn-type Gaussian random fields (GRFs) generated using the SPDE method to model aleatoric uncertainties, including environmental influences, variating material properties, and geometric ambiguities. Our focus lies on delivering practical GRF realizations that accurately capture imperfections and variations and understanding how they impact the predictions of computational models and the topology of optimized designs. We describe a numerical algorithm based on solving a generalized SPDE to sample GRFs on arbitrary meshed domains. The algorithm leverages established techniques and integrates seamlessly with the open-source finite element library MFEM and associated scientific computing workflows, like those found in industrial and national laboratory settings. Our solver scales efficiently for large-scale problems and supports various domain types, including surfaces and embedded manifolds. We showcase its versatility through biomechanics and topology optimization applications. The flexibility and efficiency of SPDE-based GRF generation empower us to run large-scale optimization problems on 2D and 3D domains, including finding optimized designs on embedded surfaces, and to generate topologies beyond the reach of conventional techniques. Moreover, these capabilities allow us to model geometric uncertainties of reconstructed submanifolds, such as the surfaces of cerebral aneurysms. In addition to offering benefits in these specific domains, the proposed techniques transcend specific applications and generalize to arbitrary forward and backward problems in uncertainty quantification involving finite elements. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lambers2024,

title = {Quantifying Fat Zonation in Liver Lobules: An Integrated Multiscale In-silico Model Combining Disturbed Microperfusion and Fat Metabolism via a Continuum-Biomechanical Bi-scale, Tri-phasic Approach},

author = {Lena Lambers and Navina Waschinsky and Jana Schleicher and Matthias K\"{o}nig and Hans-Michael Tautenhahn and Mohamed Albadry and Uta Dahmen and Tim Ricken},

editor = {Springer Link},

url = {https://link.springer.com/article/10.1007/s10237-023-01797-0#citeas},

doi = {https://doi.org/10.1007/s10237-023-01797-0},

year  = {2024},

date = {2024-02-25},

urldate = {2024-02-25},

journal = {Biomechanics and Modeling in Mechanobiology},

abstract = {Metabolic zonation refers to the spatial separation of metabolic functions along the sinusoidal axes of the liver. This phenomenon forms the foundation for adjusting hepatic metabolism to physiological requirements in health and disease (e.g., metabolic dysfunction-associated steatotic liver disease/MASLD). Zonated metabolic functions are influenced by zonal morphological abnormalities in the liver, such as periportal fibrosis and pericentral steatosis. We aim to analyze the interplay between microperfusion, oxygen gradient, fat metabolism and resulting zonated fat accumulation in a liver lobule. Therefore we developed a continuum biomechanical, tri-phasic, bi-scale, and multicomponent in silico model, which allows to numerically simulate coupled perfusion-function-growth interactions two-dimensionally in liver lobules. The developed homogenized model has the following specifications: (i) thermodynamically consistent, (ii) tri-phase model (tissue, fat, blood), (iii) penta-substances (glycogen, glucose, lactate, FFA, and oxygen), and (iv) bi-scale approach (lobule, cell). Our presented in silico model accounts for the mutual coupling between spatial and time-dependent liver perfusion, metabolic pathways and fat accumulation. The model thus allows the prediction of fat development in the liver lobule, depending on perfusion, oxygen and plasma concentration of free fatty acids (FFA), oxidative processes, the synthesis and the secretion of triglycerides (TGs). The use of a bi-scale approach allows in addition to focus on scale bridging processes. Thus, we will investigate how changes at the cellular scale affect perfusion at the lobular scale and vice versa. This allows to predict the zonation of fat distribution (periportal or pericentral) depending on initial conditions, as well as external and internal boundary value conditions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Computational Flow Diverter Implantation\textemdashA Comparative Study on Pre-Interventional Simulation and Post-Interventional Device Positioning for a Novel Blood Flow Modulator},

author = {Maximilian Thormann and Janneck Stahl and Laurel Marsh and Sylvia Saalfeld and Nele Sillis and Andreas Ding and Anastasios Mpotsaris and Philipp Berg and Daniel Behme},

url = {https://www.mdpi.com/2311-5521/9/3/55},

year  = {2024},

date = {2024-02-23},

journal = {Fluids },

volume = {9},

number = {55},

issue = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{horvat24lbm,

title = {A lattice Boltzmann method for non-Newtonian blood flow in coiled intracranial aneurysms},

author = {Medeea Horvat and Stephan B. Lunowa and Dmytro Sytnyk and Barbara Wohlmuth},

editor = {arXiv},

url = {https://arxiv.org/abs/2402.10809},

doi = {https://doi.org/10.48550/arXiv.2402.10809},

year  = {2024},

date = {2024-02-16},

journal = {[PrePrint], arXiv},

abstract = {Intracranial aneurysms are the leading cause of stroke. One of the established treatment approaches is the embolization induced by coil insertion. However, the prediction of treatment and subsequent changed flow characteristics in the aneurysm, is still an open problem. In this work, we present an approach based on patient specific geometry and parameters including a coil representation as inhomogeneous porous medium. The model consists of the volume-averaged Navier-Stokes equations including the non-Newtonian blood rheology. We solve these equations using a problem-adapted lattice Boltzmann method and present a comparison between fully-resolved and volume-averaged simulations. The results indicate the validity of the model. Overall, this workflow allows for patient specific assessment of the flow due to potential treatment. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{holzberger24coiling,

title = {A Comprehensive Numerical Approach to Coil Placement in Cerebral Aneurysms: Mathematical Modeling and In Silico Occlusion Classification},

author = {Fabian Holzberger and Markus Muhr and Barbara Wohlmuth},

editor = {arXiv},

url = {https://arxiv.org/abs/2402.02798},

doi = {https://doi.org/10.48550/arXiv.2402.02798},

year  = {2024},

date = {2024-02-05},

journal = {[PrePrint], arXiv},

abstract = {Endovascular coil embolization is one of the primary treatment techniques for cerebral aneurysms. Although it is a well established and minimally invasive method, it bears the risk of sub-optimal coil placement which can lead to incomplete occlusion of the aneurysm possibly causing recurrence. One of the key features of coils is that they have an imprinted natural shape supporting the fixation within the aneurysm. For the spatial discretization our mathematical coil model is based on the Discrete Elastic Rod model which results in a dimension-reduced 1D system of differential equations. We include bending and twisting responses to account for the coils natural curvature. Collisions between coil segments and the aneurysm-wall are handled by an efficient contact algorithm that relies on an octree based collision detection. The numerical solution of the model is obtained by a symplectic semi-implicit Euler time stepping method. Our model can be easily incorporated into blood flow simulations of embolized aneurysms. In order to differentiate optimal from sub-optimal placements, we employ a suitable in silico Raymond-Roy type occlusion classification and measure the local packing density in the aneurysm at its neck, wall-region and core. We investigate the impact of uncertainties in the coil parameters and embolization procedure. To this end, we vary the position and the angle of insertion of the microcatheter, and approximate the local packing density distributions by evaluating sample statistics. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{frank24gamm,

title = {Numerical simulation of endovascular treatment options for cerebral aneurysms},

author = {Martin Frank and Fabian Holzberger and Medeea Horvat and Jan Kirschke and Matthias Mayr and Markus Muhr and Natalia Nebulishvili and Alexander Popp and Julian Schwarting and Barbara Wohlmuth},

editor = {arXiv},

url = {https://arxiv.org/abs/2402.00550},

doi = {https://doi.org/10.48550/arXiv.2402.00550},

year  = {2024},

date = {2024-02-01},

journal = {[PrePrint], arXiv},

abstract = {Predicting the long-term success of endovascular interventions in the clinical management of cerebral aneurysms requires detailed insight into the patient-specific physiological conditions. In this work, we not only propose numerical representations of endovascular medical devices such as coils, flow diverters or Woven EndoBridge but also outline numerical models for the prediction of blood flow patterns in the aneurysm cavity right after a surgical intervention. Detailed knowledge about the post-surgical state then lays the basis to assess the chances of a stable occlusion of the aneurysm required for a long-term treatment success. To this end, we propose mathematical and mechanical models of endovascular medical devices made out of thin metal wires. These can then be used for fully resolved flow simulations of the post-surgical blood flow, which in this work will be performed by means of a Lattice Boltzmann method applied to the incompressible Navier-Stokes equations and patient-specific geometries. To probe the suitability of homogenized models, we also investigate poro-elastic models to represent such medical devices. In particular, we examine the validity of this modeling approach for flow diverter placement across the opening of the aneurysm cavity. For both approaches, physiologically meaningful boundary conditions are provided from reduced-order models of the vascular system. The present study demonstrates our capabilities to predict the post-surgical state and lays a solid foundation to tackle the prediction of thrombus formation and, thus, the aneurysm occlusion in a next step. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tautenhahn2024,

title = {SimLivA\textendashModeling ischemia-reperfusion injury in the liver: A first step towards a clinical decision support tool},

author = {Hans-Michael Tautenhahn and Tim Ricken and Uta Dahmen and Luis Mandl and Laura B\"{u}tow and Steffen Gerh\"{a}usser and Lena Lambers and Xinpei Chen and Elina Lehmann and Olaf Dirsch and Matthias K\"{o}nig},

editor = {Wiley Online Library},

url = {https://onlinelibrary.wiley.com/doi/10.1002/gamm.202370003},

doi = {https://doi.org/10.1002/gamm.202370003},

year  = {2024},

date = {2024-01-23},

journal = {GAMM-Mitteilungen e202370003},

abstract = {The SIMulation supported LIVer Assessment for donor organs (SimLivA) project aims to develop a mathematical model to accurately simulate the influence of mechanical alterations in marginal liver grafts (specifically steatotic ones) and cold ischemia on early ischemia-reperfusion injury (IRI) during liver transplantation. Our project tackles significant research challenges, including the co-development of computational methodologies, experimental studies, clinical processes, and technical workflows. We aim to refine a continuum-biomechanical model for enhanced IRI prediction, collect pivotal experimental and clinical data, and assess the clinical applicability of our model. Our efforts involve augmenting and tailoring a coupled continuum-biomechanical, multiphase, and multi-scale partial differential equation-ordinary differential equation (PDE-ODE) model of the liver lobule, allowing us to numerically simulate IRI depending on the degree of steatosis and the duration of ischemia. The envisaged model will intertwine the structure, perfusion, and function of the liver, serving as a crucial aid in clinical decision-making processes. We view this as the initial step towards an in-silico clinical decision support tool aimed at enhancing the outcomes of liver transplantation. In this paper, we provide an overview of the SimLivA project and our preliminary findings, which include: a cellular model that delineates critical processes in the context of IRI during transplantation; and the integration of this model into a multi-scale PDE-ODE model using a homogenized, multi-scale, multi-component approach within the Theory of Porous Media (TPM) framework. The model has successfully simulated the interconnected relationship between structure, perfusion, and function\textemdashall of which are integral to IRI. Initial results show simulations at the cellular scale that describe critical processes related to IRI during transplantation. After integrating this model into a multiscale PDE-ODE model, first simulations were performed on the spatial distribution of key functions during warm and cold ischaemia. In addition, we were able to study the effect of tissue perfusion and temperature, two critical parameters in the context of liver transplantation and IRI.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Inter-model and inter-modality analysis of left ventricular hemodynamics: comparative study of two CFD approaches based on TTE and MRI},

author = {Lukas Obermeier and Jana Korte and Katharina Vellguth and Fabian Barbieri and Florian Hellmeier and Philipp Berg and Leonid Goubergrits},

url = {https://onlinelibrary.wiley.com/doi/full/10.1002/gamm.202370004},

doi = {10.1002/gamm.202370004},

year  = {2024},

date = {2024-01-23},

journal = {GAMM-Mitteilungen},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schmid2024,

title = {Postinhibitory excitation in motoneurons},

author = {Laura Schmid and Thomas Klotz and Oliver R\"{o}hrle and Randall K. Powers and Francesco Negro and Utku \c{S}. Yavuz},

editor = {PLOS Computational Biology},

url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011487#abstract1},

doi = {https://doi.org/10.1371/journal.pcbi.1011487},

year  = {2024},

date = {2024-01-19},

urldate = {2024-01-19},

journal = {PLOS Computational Biology},

volume = {20},

issue = {1},

abstract = {Human movement is determined by the activity of specialized nerve cells, the motoneurons. Each motoneuron activates a specific set of muscle fibers. The functional unit consisting of a neuron and muscle fibers is called a motor unit. The activity of motoneurons can be observed noninvasively in living humans by recording the electrical activity of the motor units using the electromyogram. We studied the behavior of human motor units in an inhibitory reflex pathway and found an unexpected response pattern: a rebound-like excitation following the inhibition. This has occasionally been reported for human motor units, but its origin has never been systematically studied. In non-human cells of the neural system, earlier studies reported that a specific membrane protein, the so-called h-channel, can cause postinhibitory excitation. Our study uses a computational motoneuron model to investigate whether h-channels can cause postinhibitory excitation, as observed in the experimental recordings. Using the model, we developed a method to detect features of h-channel activity in human recordings. Because we found these features in half of the recorded motor units, we conclude that h-channels can facilitate postinhibitory excitation in human motoneurons.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Fusiform versus Saccular Intracranial Aneurysms\textemdashHemodynamic Evaluation of the Pre-Aneurysmal, Pathological, and Post-Interventional State},

author = {Jana Korte and Laurel M. M. Marsh and Sylvia Saalfeld and Daniel Behme and Alberto Aliseda and Philipp Berg},

url = {https://www.mdpi.com/2077-0383/13/2/551},

year  = {2024},

date = {2024-01-18},

journal = {Journal of Clinical Medicine},

volume = {13},

number = {551},

issue = {2},

pages = {1-14},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gerach2024,

title = {Differential effects of mechano-electric feedback mechanisms on whole-heart activation, repolarization, and tension},

author = {Tobias Gerach and Axel Loewe},

editor = {John Wiley \& Sons Ltd on behalf of The Physiological Society},

url = {https://physoc.onlinelibrary.wiley.com/doi/10.1113/JP285022},

doi = { https://doi.org/10.1113/JP285022},

year  = {2024},

date = {2024-01-07},

urldate = {2024-01-07},

journal = {The Journal of Physiology},

abstract = {The human heart is subject to highly variable amounts of strain during day-to-day activities and needs to adapt to a wide range of physiological demands. This adaptation is driven by an autoregulatory loop that includes both electrical and the mechanical components. In particular, mechanical forces are known to feed back into the cardiac electrophysiology system, which can result in pro- and anti-arrhythmic effects. Despite the widespread use of computational modelling and simulation for cardiac electrophysiology research, the majority of in silico experiments ignore this mechano-electric feedback entirely due to the high computational cost associated with solving cardiac mechanics. In this study, we therefore use an electromechanically coupled whole-heart model to investigate the differential and combined effects of electromechanical feedback mechanisms with a focus on their physiological relevance during sinus rhythm. In particular, we consider troponin-bound calcium, the effect of deformation on the tissue diffusion tensor, and stretch-activated channels. We found that activation of the myocardium was only significantly affected when including deformation into the diffusion term of the monodomain equation. Repolarization, on the other hand, was influenced by both troponin-bound calcium and stretch-activated channels and resulted in steeper repolarization gradients in the atria. The latter also caused afterdepolarizations in the atria. Due to its central role for tension development, calcium bound to troponin affected stroke volume and pressure. In conclusion, we found that mechano-electric feedback changes activation and repolarization patterns throughout the heart during sinus rhythm and lead to a markedly more heterogeneous electrophysiological substrate. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Multi-Dimensional Modeling of Cerebral Hemodynamics: A Systematic Review},

author = {Jana Korte and Ehlar Sophie Klopp and Philipp Berg},

url = {https://www.mdpi.com/2306-5354/11/1/72},

year  = {2024},

date = {2024-01-06},

urldate = {2024-01-06},

journal = {Bioengineering },

volume = {11},

issue = {1},

pages = {1-24},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fr\"{o}hlich2024,

title = {Numerical evaluation of elasto-mechanical and visco-elastic electro-mechanical models of the human heart},

author = {Jonathan Fr\"{o}hlich and Tobias Gerach and Jonathan Krau\ss and Axel Loewe and Laura Stengel and Christian Wieners},

editor = {Gesellschaft f\"{u}r Angewandte Mathematik und Mechanik},

url = {https://onlinelibrary.wiley.com/doi/10.1002/gamm.202370010},

doi = { https://doi.org/10.1002/gamm.202370010},

issn = {1522-2608},

year  = {2024},

date = {2024-01-02},

urldate = {2024-01-02},

journal = {GAMM Mitteilungen },

volume = {46},

issue = {2},

abstract = {We investigate the properties of static mechanical and dynamic electro-mechanical models for the deformation of the human heart. Numerically this is realized by a staggered scheme for the coupled partial/ordinary differential equation (PDE-ODE) system. First, we consider a static and purely mechanical benchmark configuration on a realistic geometry of the human ventricles. Using a penalty term for quasi-incompressibility, we test different parameters and mesh sizes and observe that this approach is not sufficient for lowest order conforming finite elements. Then, we compare the approaches of active stress and active strain for cardiac muscle contraction. Finally, we compare in a coupled anatomically realistic electro-mechanical model numerical Newmark damping with a visco-elastic model using Rayleigh damping. Nonphysiological oscillations can be better mitigated using viscosity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {A simple quantitative model of neuromodulation, Part I: Ion flow through neural ion channels},

author = {Linda Werneck and Mertacan Han and Erdost Yildiz and Marc-Andr\'{e} Keip and Metin Sitti and Michael Ortiz},

editor = {Elsevier},

doi = {https://doi.org/10.1016/j.jmps.2023.105457},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Journal of the Mechanics and Physics of Solids },

volume = {Vol. 182},

abstract = {We develop a simple model of ionic current through neuronal membranes as a function of membrane potential and extracellular ion concentration. The model combines a simplified Poisson\textendashNernst\textendashPlanck (PNP) model of ion transport through individual ion channels with channel activation functions calibrated from ad hoc in-house experimental data. The simplified PNP model is validated against bacterial gramicidin A ion channel data. The calibrated model accounts for the transport of calcium, sodium, potassium, and chloride and exhibits remarkable agreement with the experimentally measured current\textendashvoltage curves for the differentiated human neural cells. All relevant data and code related to the ion flow models are available at Werneck et al. (2023).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gjerde23perivascular,

title = {Directional flow in perivascular networks: Mixed finite elements for reduced-dimensional models on graphs},

author = {Ingeborg G. Gjerde and Miroslav Kuchta and Marie E. Rognes and Barbara Wohlmuth},

editor = {arXiv},

url = {https://arxiv.org/abs/2401.00484},

doi = {https://doi.org/10.48550/arXiv.2401.00484},

year  = {2023},

date = {2023-12-31},

journal = {[PrePrint], arXiv},

abstract = {The flow of cerebrospinal fluid through the perivascular spaces of the brain is believed to play a crucial role in eliminating toxic waste proteins. While the driving forces of this flow have been enigmatic, experiments have shown that arterial wall motion is central. In this work, we present a network model for simulating pulsatile fluid flow in perivascular networks. We establish the well-posedness of this model in the primal and dual mixed variational settings, and show how it can be discretized using mixed finite elements. Further, we utilize this model to investigate fundamental questions concerning the physical mechanisms governing perivascular fluid flow. Notably, our findings reveal that arterial pulsations can induce directional flow in branching perivascular networks. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Albadry2023,

title = {Cross-Species Variability in Lobular Geometry and Cytochrome P450 Hepatic Zonation: Insights into CYP1A2, CYP2E1, CYP2D6 and CYP3A4},

author = {Mohamed Albadry and Jonas Kuettner and Jan Grzegorzewski and Olaf Dirsch and Eva Kindler and Robert Klopfleisch and Vaclav Liska and Vladimira Moulisova and Sandra Nickel and Richard Palek and Jachym Rosendorf and Sylvia Saalfeld and Utz Settmacher and Hans-Michael Tautenhahn and Matthias K\"{o}nig and Uta Dahmen},

editor = {bioRxiv},

url = {https://www.biorxiv.org/content/10.1101/2023.12.28.573567v1},

doi = {https://doi.org/10.1101/2023.12.28.573567},

year  = {2023},

date = {2023-12-28},

journal = {[PrePrint], bioRxiv},

abstract = {This study explores the critical interplay between lobular geometry and the zonated distribution of cytochrome P450 (CYP) enzymes across species. We present an innovative approach to assess lobular geometry and zonation patterns using whole slide imaging (WSI). This method allows a detailed, systematic comparison of lobular structures and spatial distribution of key CYP450 enzymes and glutamine synthetase in four different species (mouse, rat, pig, and human). Our results shed light on species differences in lobular geometry and enzymatic zonation, providing critical insights for drug metabolism research. Based on our approach we could determine the minimum number of lobules required for a statistically representative analysis, an important piece of information when evaluating liver biopsies and deriving information from WSI.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Azhdari2023,

title = {Non-local three phase lag bio thermal modeling of skin tissue and experimental evaluation},

author = {Mohammad Azhdari and Seyed Morteza Seyedpour and Lena Lambers and Hans-Michael Tautenhahn and Franziska Tautenhahn and Tim Ricken and Ghader Rezazadeh},

editor = {Elsevier},

url = {https://www.sciencedirect.com/science/article/pii/S0735193323005353?via%3Dihub},

doi = {https://doi.org/10.1016/j.icheatmasstransfer.2023.107146},

year  = {2023},

date = {2023-11-10},

journal = {Heat and Mass Transfer (149)},

abstract = {In this paper, the thermal behavior of living tissue has been modeled using a non-local three-phase lag approach. The simulation results of this model- ing have been compared with experimental results of alternating radiation with different periods on human skin, yielding satisfactory alignments. Ad- ditionally, it has been investigated that the TPL model, which is an equation with an integral term, can simulate energy accumulation within the dermal tissue. Moreover, the non-local nature of the modeling has been explored to alter the influence of phase lag terms. Furthermore, apart from numer- ically solving the equation, an analytical solution has been derived for the frequency equation, demonstrating the effects of simulation parameters on the frequency equation and simulation results. The obtained results indi cate that these parameters not only independently affect the outcomes but also interact with other parameters, leading to variations beyond their direct impacts.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {In vitro and in silico assessment of flow modulation after deploying the Contour Neurovascular System in intracranial aneurysm models},

author = {Jana Korte and Franziska Gaidzik and Naomi Larsen and Erik Sch\"{u}tz and Timo Damm and Fritz Wodarg and Jan-Bernd H\"{o}vener and Olav Jansen and G\'{a}bor Janiga and Philipp Berg and Mariya S Pravdivtseva},

url = {https://jnis.bmj.com/content/early/2023/10/24/jnis-2023-020403},

year  = {2023},

date = {2023-10-18},

journal = {Journal of NeuroInterventional Surgery},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mandl2023,

title = {Affine transformations accelerate the training of physics-informed neural networks of a one-dimensional consolidation problem},

author = {Luis Mandl and Andr\'{e} Mielke and Seyed Morteza Seyedpour and Tim Ricken},

editor = {Scientific Reports},

url = {https://www.nature.com/articles/s41598-023-42141-x},

doi = {https://doi.org/10.1038/s41598-023-42141-x},

year  = {2023},

date = {2023-09-20},

urldate = {2023-09-20},

journal = {Nature Scientific Reports},

abstract = {Physics-informed neural networks (PINNs) leverage data and knowledge about a problem. They provide a nonnumerical pathway to solving partial differential equations by expressing the field solution as an artificial neural network. This approach has been applied successfully to various types of differential equations. A major area of research on PINNs is the application to coupled partial differential equations in particular, and a general breakthrough is still lacking. In coupled equations, the optimization operates in a critical conflict between boundary conditions and the underlying equations, which often requires either many iterations or complex schemes to avoid trivial solutions and to achieve convergence. We provide empirical evidence for the mitigation of bad initial conditioning in PINNs for solving one-dimensional consolidation problems of porous media through the introduction of affine transformations after the classical output layer of artificial neural network architectures, effectively accelerating the training process. These affine physics-informed neural networks (AfPINNs) then produce nontrivial and accurate field solutions even in parameter spaces with diverging orders of magnitude. On average, AfPINNs show the ability to improve the L_2 relative error by 64.84% after 25,000 epochs for a one-dimensional consolidation problem based on Biot’s theory, and an average improvement by 58.80% with a transfer approach to the theory of porous media.



},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Fabrication of flexible intracranial aneurysm models using stereolithography 3D printing},

author = {Janneck Stahl and Leheng Kassem and Daniel Behme and Stefan Klebingat and Sylvia Saalfeld and Philipp Berg},

url = {https://www.degruyter.com/document/doi/10.1515/cdbme-2023-1099/html},

year  = {2023},

date = {2023-09-20},

journal = {Current Directions in Biomedical Engineering},

volume = {9},

issue = {1},

pages = {395-389},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Resolution-based comparative analysis of 4D-phase-contrast magnetic resonance images and hemodynamic simulations of the aortic arch},

author = {Jana Korte and Paula Groschopp and Philipp Berg},

url = {https://www.degruyter.com/document/doi/10.1515/cdbme-2023-1163/html},

year  = {2023},

date = {2023-09-20},

journal = {Current Directions in Biomedical Engineering},

volume = {9},

issue = {1},

pages = {650-653},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Accuracy of Devereaux and Teichholz formulas for left ventricular mass calculation in different geometric patterns: comparison with cardiac magnetic resonance imaging},

author = {Krunoslav Michael Sveric and Barı\c{s} Cansız and Anna Winkler and Stefan Ulbrich and Georg Ende and Felix Heidrich and Michael Kaliske and Axel Linke and Stefanie Jellinghaus},

editor = {Nature},

url = {https://rdcu.be/doEBI},

doi = {https://doi.org/10.1038/s41598-023-41020-9},

year  = {2023},

date = {2023-08-28},

urldate = {2023-08-28},

journal = {Scientific reports},

volume = {13},

abstract = {Left ventricular (LV) myocardial mass is important in the evaluation of cardiac remodeling and requires accurate assessment when performed on linear measurements in two-dimensional echocardiography (Echo). We aimed to compare the accuracy of the Devereux formula (DEV) and the Teichholz formula (TEICH) in calculating LV myocardial mass in Echo using cardiac magnetic resonance (CMR) as the reference method. Based on preceding mathematical calculations, we identified primarily LV size rather than wall thickness as the main source of bias between DEV and TEICH in a retrospective derivation cohort (n = 1276). Although LV mass from DEV and TEICH were correlated with CMR, TEICH did not show a proportional bias as did DEV (− 2 g/m2 vs. + 22 g/m2). This could be validated in an independent prospective cohort (n = 226) with symptomatic non-ischemic heart failure. DEV systematically overestimated LV mass in all tiers of LV remodeling as compared to TEICH. In conclusion, the TEICH method accounts for the changes in LV geometry with increasing LV mass and thus better reflects the different pattern of LV remodeling than the DEV method. This has important clinical implications, as TEICH may be more appropriate for use in clinical practice, rather than DEV, currently recommended.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Is accurate lumen segmentation more important than outlet boundary condition in image-based blood flow simulations for intracranial aneurysms?},

author = {Jana Korte and Samuel Vo\ss and G\'{a}bor Janiga and Oliver Beuing and Daniel Behme and Sylvia Saalfeld and Philipp Berg },

url = {https://link.springer.com/article/10.1007/s13239-023-00675-1},

year  = {2023},

date = {2023-08-15},

urldate = {2023-08-15},

journal = {Cardiovascular Engineering and Technology },

volume = {14},

issue = {5},

pages = {617\textendash630},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Maheshvare2023,

title = {A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell},

author = {M. Deepa Maheshvare and Soumyendu Raha and Matthias K\"{o}nig and Debnath Pal},

editor = {Frontiers in Endocrinology},

url = {https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1185656/full},

doi = {https://doi.org/10.3389/fendo.2023.1185656 },

year  = {2023},

date = {2023-08-02},

journal = {Frontiers in Endocrinology},

abstract = {The pancreas plays a critical role in maintaining glucose homeostasis through the secretion of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by the pancreatic β-cell is the main mechanism for reducing elevated plasma glucose. Here we present a systematic modeling workflow for the development of kinetic pathway models using the Systems Biology Markup Language (SBML). Steps include retrieval of information from databases, curation of experimental and clinical data for model calibration and validation, integration of heterogeneous data including absolute and relative measurements, unit normalization, data normalization, and model annotation. An important factor was the reproducibility and exchangeability of the model, which allowed the use of various existing tools. The workflow was applied to construct a novel data-driven kinetic model of GSIS in the pancreatic β-cell based on experimental and clinical data from 39 studies spanning 50 years of pancreatic, islet, and β-cell research in humans, rats, mice, and cell lines. The model consists of detailed glycolysis and phenomenological equations for insulin secretion coupled to cellular energy state, ATP dynamics and (ATP/ADP ratio). Key findings of our work are that in GSIS there is a glucose-dependent increase in almost all intermediates of glycolysis. This increase in glycolytic metabolites is accompanied by an increase in energy metabolites, especially ATP and NADH. One of the few decreasing metabolites is ADP, which, in combination with the increase in ATP, results in a large increase in ATP/ADP ratios in the β-cell with increasing glucose. Insulin secretion is dependent on ATP/ADP, resulting in glucose-stimulated insulin secretion. The observed glucose-dependent increase in glycolytic intermediates and the resulting change in ATP/ADP ratios and insulin secretion is a robust phenomenon observed across data sets, experimental systems and species. Model predictions of the glucose-dependent response of glycolytic intermediates and biphasic insulin secretion are in good agreement with experimental measurements. Our model predicts that factors affecting ATP consumption, ATP formation, hexokinase, phosphofructokinase, and ATP/ADP-dependent insulin secretion have a major effect on GSIS. In conclusion, we have developed and applied a systematic modeling workflow for pathway models that allowed us to gain insight into key mechanisms in GSIS in the pancreatic β-cell.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lee2023,

title = {A multiphysical computational model of myocardial growth adopted to human pathological ventricular remodelling},

author = {Yongjae Lee and Barı\c{s} Cansız and Michael Kaliske},

editor = { Comput Mech (2023)},

url = {https://rdcu.be/doEvG},

doi = {https://doi.org/10.1007/s00466-023-02346-3},

year  = {2023},

date = {2023-06-13},

urldate = {2023-06-13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.3389/fphys.2023.1095260,

title = {Linking cortex and contraction\textemdashIntegrating models along the corticomuscular pathway},

author = {Lysea Haggie and Laura Schmid and Oliver R\"{o}hrle and Thor Besier and Angus McMorland and Harnoor Saini},

editor = {Frontiers in Physiology, Sec. Computational Physiology and Medicine },

url = {https://www.frontiersin.org/articles/10.3389/fphys.2023.1095260/full},

doi = {https://doi.org/10.3389/fphys.2023.1095260},

year  = {2023},

date = {2023-05-10},

urldate = {2023-05-10},

journal = {Frontiers in Physiology, Sec. Computational Physiology and Medicine },

issue = {Vol 14-2023},

abstract = {Computational models of the neuromusculoskeletal system provide a deterministic approach to investigate input-output relationships in the human motor system. Neuromusculoskeletal models are typically used to estimate muscle activations and forces that are consistent with observed motion under healthy and pathological conditions. However, many movement pathologies originate in the brain, including stroke, cerebral palsy, and Parkinson’s disease, while most neuromusculoskeletal models deal exclusively with the peripheral nervous system and do not incorporate models of the motor cortex, cerebellum, or spinal cord. An integrated understanding of motor control is necessary to reveal underlying neural-input and motor-output relationships. To facilitate the development of integrated corticomuscular motor pathway models, we provide an overview of the neuromusculoskeletal modelling landscape with a focus on integrating computational models of the motor cortex, spinal cord circuitry, α-motoneurons  and skeletal muscle in regard to their role in generating voluntary muscle contraction. Further, we highlight the challenges and opportunities associated with an integrated corticomuscular pathway model, such as challenges in defining neuron connectivities, modelling standardisation, and opportunities in applying models to study emergent behaviour. Integrated corticomuscular pathway models have applications in brain-machine-interaction, education, and our understanding of neurological disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Stahl2023,

title = {Assessment of the Flow-Diverter Efficacy for Intracranial Aneurysm Treatment Considering Pre- and Post-Interventional Hemodynamics},

author = {Janneck Stahl and Laurel Morgan Miller Marsh and Maximilian Thormann and Andreas Ding and Sylvia Saalfeld and Daniel Behme and Philipp Berg},

url = {https://www.sciencedirect.com/science/article/abs/pii/S0010482523001853},

year  = {2023},

date = {2023-04-06},

journal = {Computers in Biology and Medicine},

volume = {156},

issue = {106720},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{K\"{o}nig2023,

title = {Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022},

author = {Matthias K\"{o}nig and Padraig Gleeson and Martin Golebiewski and Thomas E. Gorochowski and Michael Hucka and Sarah M. Keating and Chris J. Myers and David P. Nickerson and Bj\"{o}rn Sommer and Dagmar Waltemath and Falk Schreiber},

editor = {De Gruyter},

url = {https://www.degruyter.com/document/doi/10.1515/jib-2023-0004/html},

doi = {https://doi.org/10.1515/jib-2023-0004},

year  = {2023},

date = {2023-03-29},

journal = {Journal of Integrative Bioinformatics},

abstract = {This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COM-BINE standards in systems and synthetic biology. The 2022 special issue presents three updates to the standards:CellML 2.0.1, SBML Level 3 Package: Spatial Processes, Version 1, Release 1, and Synthetic Biology Open Lan-guage (SBOL) Version 3.1.0. This document can also be used to identify the latest specifications for all COMBINEstandards. In addition, this editorial provides a brief overview of the COMBINE 2022 meeting in Berlin.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rauchfu\ss2023,

title = {Critical Evaluation of Discarded Donor Livers in the Eurotransplant Region: Potential Implications for Machine Perfusion},

author = {Falk Rauchfu\ss and Hans-Michael Tautenhahn and Felix Dondorf and Aladdin Ali-Deeb and Utz Settmacher },

editor = {Annals of Transplantation},

url = {https://annalsoftransplantation.com/abstract/full/idArt/938132},

doi = {10.12659/AOT.938132},

year  = {2023},

date = {2023-03-17},

journal = {Annals of Transplantation},

abstract = { BACKGROUND: There are still many offered donor livers that are declined during the allocation process. Machine perfusion offers the option to evaluate (especially marginal) donor organs and to better decide whether a graft has the potential of being transplanted or not. There is a lack of clear detailed data on why organs are declined and how many donor livers would have the potential of being evaluated in the machine.



MATERIAL AND METHODS: We retrospectively reviewed 1356 donor livers between 2016 and 2018, which were offered by Eurotransplant and were declined during the allocation process; 284 grafts were from donor after cardiac death (DCD) and 1072 donations were from after brain death (DBD). The analysis was performed independently and blinded by senior transplant surgeons.



RESULTS: There were 904 (66.6%) donor livers with potential to be evaluated as suitable grafts in machine perfusion, whereas 417 (30.8%) organs were definitely not-transplantable, mainly due to liver cirrhosis, (untreated) donor malignancy, cardiac diseases of the donor leading to a hepatic congestion, and/or systemic infections in the donor. Donors in blood group “AB” were disproportionally often rejected. Due to missing data, 35 (2.6%) organs could not be sufficiently evaluated.



CONCLUSIONS: Our data suggest that many declined donor livers have potential of being evaluated by machine perfusion. Comprehensive use of machine perfusion is necessary and useful to improve the current organ shortage. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Multimodal exploration of the intracranial aneurysm wall},

author = {Annika Niemann and Riikka Tulamo and Eliisa Netti and Bernhard Preim and Philipp Berg and Juan Cebral and Anne Robertson and Sylvia Saalfeld},

url = {https://link.springer.com/article/10.1007/s11548-023-02850-0},

year  = {2023},

date = {2023-03-06},

urldate = {2023-03-06},

journal = {International Journal of Computer Assisted Radiology and Surgery },

volume = {18},

issue = {12},

pages = { 2243\textendash2252},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Design of a virtual data shelf to effectively explore a large database of 3D medical surface models in VR},

author = {Mareen Allgaier and Lena Spitz and Daniel Behme and Anastarios Mpotsaris and Philipp Berg and Bernhard Preim and Sylvia Saalfeld },

url = {https://link.springer.com/article/10.1007/s11548-023-02851-z},

year  = {2023},

date = {2023-03-03},

journal = {International Journal of Computer Assisted Radiology and Surgery },

volume = {18},

issue = {11},

pages = {2013\textendash2022},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Hemodynamic assessment of the pathological left ventricle function under rest and exercise conditions},

author = {Jana Korte and Thomas Rauwolf and Jan-Niklas Thiel and Andreas Mitrasch and Paulina Groschopp and Michael Neidlin and Alexander Schmei\sser and R\"{u}diger Braun-Dullaeus and Philipp Berg},

url = {https://www.mdpi.com/2311-5521/8/2/71},

year  = {2023},

date = {2023-02-16},

urldate = {2023-02-16},

journal = {Fluids },

volume = {8},

number = {71},

issue = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {A hybrid hierarchical strategy for registration of 7T TOF-MRI to 7T PC-MRI intracranial vessel data},

author = {Lena Spitz and Franziska Gaidzik and Daniel Stucht and Hendrik Mattern and Bernhard Preim and Sylvia Saalfeld },

url = {https://link.springer.com/article/10.1007/s11548-023-02836-y},

year  = {2023},

date = {2023-01-20},

journal = {International Journal of Computer Assisted Radiology and Surgery },

volume = {18},

pages = {837\textendash844},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Niemann2023_Semantic,

title = {Deep learning-based semantic vessel graph extraction for intracranial aneurysm rupture risk management},

author = {Annika Niemann and Daniel Behme and Naomi Larsen and Bernhard Preim and Sylvia Saalfeld},

url = {https://link.springer.com/article/10.1007/s11548-022-02818-6},

year  = {2023},

date = {2023-01-10},

urldate = {2003-01-10},

journal = {International Journal of Computer Assisted Radiology and Surgery},

volume = {18},

issue = {3},

pages = {515-525},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Albadry2022,

title = {Periportal steatosis in mice affects distinct parameters of pericentral drug metabolism},

author = {Mohamed Albadry and Sebastian H\"{o}pfl and Nadia Ehteshamzad and Matthias K\"{o}nig and Michael B\"{o}ttcher and Jasna Neumann and Amelie Lupp and Olaf Dirsch and Nicole Radde and Bruno Christ and Madlen Christ and Lars Ole Schwen and Hendrik Laue and Robert Klopfleisch and Uta Dahmen},

editor = {Scientific Reports},

url = {https://www.nature.com/articles/s41598-022-26483-6#citeas},

doi = {https://doi.org/10.1038/s41598-022-26483-6},

year  = {2022},

date = {2022-12-17},

journal = {Nature Scientific Reports},

abstract = {Little is known about the impact of morphological disorders in distinct zones on metabolic zonation. It was described recently that periportal fibrosis did affect the expression of CYP proteins, a set of pericentrally located drug-metabolizing enzymes. Here, we investigated whether periportal steatosis might have a similar effect. Periportal steatosis was induced in C57BL6/J mice by feeding a high-fat diet with low methionine/choline content for either two or four weeks. Steatosis severity was quantified using image analysis. Triglycerides and CYP activity were quantified in photometric or fluorometric assay. The distribution of CYP3A4, CYP1A2, CYP2D6, and CYP2E1 was visualized by immunohistochemistry. Pharmacokinetic parameters of test drugs were determined after injecting a drug cocktail (caffeine, codeine, and midazolam). The dietary model resulted in moderate to severe mixed steatosis confined to periportal and midzonal areas. Periportal steatosis did not affect the zonal distribution of CYP expression but the activity of selected CYPs was associated with steatosis severity. Caffeine elimination was accelerated by microvesicular steatosis, whereas midazolam elimination was delayed in macrovesicular steatosis. In summary, periportal steatosis affected parameters of pericentrally located drug metabolism. This observation calls for further investigations of the highly complex interrelationship between steatosis and drug metabolism and underlying signaling mechanisms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Welsh2022,

title = {libRoadRunner 2.0: a high performance SBML simulation and analysis library},

author = {Ciaran Welsh and Jin Xu and Lucian Smith and Matthias K\"{o}nig and Kiri Choi and Herbert M Sauro},

editor = {Oxford Academic},

url = {https://academic.oup.com/bioinformatics/article/39/1/btac770/6883908},

doi = {https://doi.org/10.1093/bioinformatics/btac770},

year  = {2022},

date = {2022-12-08},

journal = {Bioinformatics},

volume = {39},

issue = {1},

abstract = {Motivation



This article presents libRoadRunner 2.0, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using the systems biology markup language (SBML).

Results



libRoadRunner is a self-contained library, able to run either as a component inside other tools via its C++, C and Python APIs, or interactively through its Python or Julia interface. libRoadRunner uses a custom just-in-time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a large variety of processors, making it fast enough to simulate extremely large models or repeated runs in reasonable timeframes. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) as well as several SBML extensions such as hierarchical composition and probability distributions. It offers multiple deterministic and stochastic integrators, as well as tools for steady-state, sensitivity, stability and structural analyses.

Availability and implementation



libRoadRunner binary distributions for Windows, Mac OS and Linux, Julia and Python bindings, source code and documentation are all available at https://github.com/sys-bio/roadrunner, and Python bindings are also available via pip. The source code can be compiled for the supported systems as well as in principle any system supported by LLVM-13, such as ARM-based computers like the Raspberry Pi. The library is licensed under the Apache License Version 2.0.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.1136/bmjopen-2022-063051,

title = {Geometric uncertainty in intracranial aneurysm rupture status discrimination: a two-site retrospective study },

author = {Florian Hellmeier and Jan Bruening and Philipp Berg and Sylvia Saalfeld and Andreas Spuler and Erol I. Sandalcioglu and Oliver Beuing and Naomi Larsen and Jens Schaller and Leonid Goubergrits},

editor = {BMJ Open},

url = {https://pubmed.ncbi.nlm.nih.gov/36351732/},

doi = {10.1136/bmjopen-2022-063051 },

year  = {2022},

date = {2022-11-08},

urldate = {2022-11-08},

journal = {BMJ Open},

volume = {12},

issue = {11},

abstract = {Assessing the risk associated with unruptured intracranial aneurysms (IAs) is essential in clinical decision making. Several geometric risk parameters have been proposed for this purpose. However, performance of these parameters has been inconsistent. This study evaluates the performance and robustness of geometric risk parameters on two datasets and compare it to the uncertainty inherent in assessing these parameters and quantifies interparameter correlations. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}