@article{Werneck2023,

title = {A Simple Quantitative Model of Neuromodulation. Part I: Ion Flow Through Neural Ion Channels},

author = {Linda Werneck and Mertcan Han and Erdost Yildiz and Marc-André Keip and Metin Sitti and Michael Ortiz},

editor = {Biological Physics},

url = {https://arxiv.org/abs/2309.01393},

doi = {https://doi.org/10.48550/arXiv.2309.01393},

year  = {2023},

date = {2023-09-04},

journal = {Biological Physics},

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-Nernst-Planck (PNP) model of ion transport through individual mechanosensitive 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-voltage curves for the differentiated human neural cells. All relevant data and code related to the ion flow models are available at DaRUS.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokeym,

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 Barış 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{nokeyn,

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 Voß and Gábor 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 = {617–630},

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 König and Debnath Pal},

editor = {Frontiers 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{Cornelissen2023,

title = {In-Vivo Assessment of Vascular Injury for the Prediction of In-Stent Restenosis},

author = {A. Cornelissen and R. A. Florescu and S. Reese and M. Behr and A. Ranno and K. Manjunatha and N. Schaaps and C. Böhm and E. A. Liehn and L. Zhao and P. Nilcham and A. Milzi and J. Schröder and F. J. Vogt},

editor = {National Library Medicine},

url = {https://pubmed.ncbi.nlm.nih.gov/37423572/},

doi = {10.1016/j.ijcard.2023.131151},

year  = {2023},

date = {2023-07-07},

urldate = {2023-07-07},

journal = {International Journal of Cardiology},

issue = {388},

abstract = {Background: Despite optimizations of coronary stenting technology, a residual risk of in-stent restenosis (ISR) remains. Vessel wall injury has important impact on the development of ISR. While injury can be assessed in histology, there is no injury score available to be used in clinical practice. 

Methods: Seven rats underwent abdominal aorta stent implantation. At 4 weeks after implantation, animals were euthanized, and strut indentation, defined as the impression of the strut into the vessel wall, as well as neointimal growth were assessed. Established histological injury scores were assessed to confirm associations between indentation and vessel wall injury. In addition, stent strut indentation was assessed by optical coherence tomography (OCT) in an exemplary clinical case. Results: Stent strut indentation was associated with vessel wall injury in histology. Furthermore, indentation was positively correlated with neointimal thickness, both in the per-strut analysis (r = 0.5579) and in the per-section analysis (r = 0.8620; both p ≤ 0.001). In a clinical case, indentation quantification in OCT was feasible, enabling assessment of injury in vivo. 

Conclusion: Assessing stent strut indentation enables periprocedural assessment of stent-induced damage in vivo and therefore allows for optimization of stent implantation. The assessment of stent strut indentation might become a valuable tool in clinical practice. 

Keywords: In stent restenosis; Optical coherence tomography; Patient-individualized percutaneous coronary intervention; Prediction; Stent malapposition.},

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 Barış 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—Integrating models along the corticomuscular pathway},

author = {Lysea Haggie and Laura Schmid and Oliver Röhrle and Thor Besier and Angus McMorland and Harnoor Saini},

editor = {Sec. Computational Physiology Frontiers in 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{König2023,

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

author = {Matthias König 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 Björn 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{Rauchfuß2023,

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

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

editor = {Annals 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{nokeyo,

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 = {2243–2252},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyp,

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 = {2013–2022},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Orth2023,

title = {Simulation-based prediction of bone healing and treatment recommendations for lower leg fractures: Effects of motion, weight-bearing and fibular mechanics},

author = {Marcel Orth and Bergita Ganse and Annchristin Andres and Kerstin Wickert and Elke Warmerdam and Max Müller and Stefan Diebels and Michael Roland and Tim Pohlemann},

doi = {10.3389/fbioe.2023.1067845},

issn = {2296-4185},

year  = {2023},

date = {2023-02-20},

urldate = {2023-02-20},

journal = {Front. Bioeng. Biotechnol.},

volume = {11},

publisher = {Frontiers Media SA},

abstract = {<jats:p>Despite recent experimental and clinical progress in the treatment of tibial and fibular fractures, in clinical practice rates of delayed bone healing and non-union remain high. The aim of this study was to simulate and compare different mechanical conditions after lower leg fractures to assess the effects of postoperative motion, weight-bearing restrictions and fibular mechanics on the strain distribution and the clinical course. Based on the computed tomography (CT) data set of a real clinical case with a distal diaphyseal tibial fracture, a proximal and a distal fibular fracture, finite element simulations were run. Early postoperative motion data, recorded <jats:italic>via</jats:italic> an inertial measuring unit system and pressure insoles were recorded and processed to study strain. The simulations were used to compute interfragmentary strain and the von Mises stress distribution of the intramedullary nail for different treatments of the fibula, as well as several walking velocities (1.0 km/h; 1.5 km/h; 2.0 km/h) and levels of weight-bearing restriction. The simulation of the real treatment was compared to the clinical course. The results show that a high postoperative walking speed was associated with higher loads in the fracture zone. In addition, a larger number of areas in the fracture gap with forces that exceeded beneficial mechanical properties longer was observed. Moreover, the simulations showed that surgical treatment of the distal fibular fracture had an impact on the healing course, whereas the proximal fibular fracture barely mattered. Weight-bearing restrictions were beneficial in reducing excessive mechanical conditions, while it is known that it is difficult for patients to adhere to partial weight-bearing recommendations. In conclusion, it is likely that motion, weight bearing and fibular mechanics influence the biomechanical milieu in the fracture gap. Simulations may improve decisions on the choice and location of surgical implants, as well as give recommendations for loading in the postoperative course of the individual patient.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyq,

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 Schmeißer and Rüdiger 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{Braun2023,

title = {“Bring Your Own Device”—A New Approach to Wearable Outcome Assessment in Trauma},

author = {Benedikt J. Braun and Tina Histing and Maximilian M. Menger and Julian Platte and Bernd Grimm and Andrew M. Hanflik and Peter H. Richter and Sureshan Sivananthan and Seth R. Yarboro and Boyko Gueorguiev and Dmitry Pokhvashchev and Meir T. Marmor},

doi = {10.3390/medicina59020403},

issn = {1648-9144},

year  = {2023},

date = {2023-02-00},

urldate = {2023-02-00},

journal = {Medicina},

volume = {59},

number = {2},

publisher = {MDPI AG},

abstract = {<jats:p>Background and Objectives: Outcome data from wearable devices are increasingly used in both research and clinics. Traditionally, a dedicated device is chosen for a given study or clinical application to collect outcome data as soon as the patient is included in a study or undergoes a procedure. The current study introduces a new measurement strategy, whereby patients’ own devices are utilized, allowing for both a pre-injury baseline measure and ability to show achievable results. Materials and Methods: Patients with a pre-existing musculoskeletal injury of the upper and lower extremity were included in this exploratory, proof-of-concept study. They were followed up for a minimum of 6 weeks after injury, and their wearable outcome data (from a smartphone and/or a body-worn sensor) were continuously acquired during this period. A descriptive analysis of the screening characteristics and the observed and achievable outcome patterns was performed. Results: A total of 432 patients was continuously screened for the study, and their screening was analyzed. The highest success rate for successful inclusion was in younger patients. Forty-eight patients were included in the analysis. The most prevalent outcome was step count. Three distinctive activity data patterns were observed: patients recovering, patients with slow or no recovery, and patients needing additional measures to determine treatment outcomes. Conclusions: Measuring outcomes in trauma patients with the Bring Your Own Device (BYOD) strategy is feasible. With this approach, patients were able to provide continuous activity data without any dedicated equipment given to them. The measurement technique is especially suited to particular patient groups. Our study’s screening log and inclusion characteristics can help inform future studies wishing to employ the BYOD design.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyr,

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 = {837–844},

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{Manjunatha2023a,

title = {A continuum chemo-mechano-biological model for in-stent restenosis with consideration of hemodynamic effects},

author = {Kiran Manjunatha and Anna Ranno and Jianye Shi and Nicole Schaaps and Pakhwan Nilcham and Anne Cornelissen and Felix Vogt and Marek Behr and Stefanie Reese},

doi = {https://doi.org/10.1002/gamm.202370008},

year  = {2023},

date = {2023-00-00},

urldate = {2023-00-00},

journal = {GAMM-Mitteilungen},

volume = {n/a},

number = {n/a},

pages = {e202370008},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Albadry2022,

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

author = {Mohamed Albadry and Sebastian Höpfl and Nadia Ehteshamzad and Matthias König and Michael Böttcher 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 König 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{Manjunatha2022b,

title = {A Multiphysics Modeling Approach for In-Stent Restenosis: Theoretical Aspects and Finite Element Implementation},

author = {K. Manjunatha and M. Behr and F. Vogt and S. Reese},

editor = {Elsevier},

url = {https://www.sciencedirect.com/science/article/pii/S0010482522008745},

doi = {10.1016/j.compbiomed.2022.106166},

year  = {2022},

date = {2022-11-15},

urldate = {2022-11-15},

journal = {Computers in Biology and Medicine},

volume = {150},

abstract = {Development of in silico models that capture progression of diseases in soft biological tissues are intrinsic in the validation of the hypothesized cellular and molecular mechanisms involved in the respective pathologies. In addition, they also aid in patient-specific adaptation of interventional procedures. In this regard, a fully-coupled high-fidelity Lagrangian finite element framework is proposed within this work which replicates the pathology of in-stent restenosis observed post stent implantation in a coronary artery. Advection–reaction–diffusion equations are set up to track the concentrations of the platelet-derived growth factor, the transforming growth factor-, the extracellular matrix, and the density of the smooth muscle cells. A continuum mechanical description of volumetric growth involved in the restenotic process, coupled to the evolution of the previously defined vessel wall constituents, is presented. Further, the finite element implementation of the model is discussed, and the behavior of the computational model is investigated via suitable numerical examples. Qualitative validation of the computational model is presented by emulating a stented artery. Patient-specific data are intended to be integrated into the model to predict the risk of in-stent restenosis, and thereby assist in the tuning of stent implantation parameters to mitigate the risk.},

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}

}

@article{Keles2022,

title = {Botulinum Toxin Intervention in Cerebral Palsy-Induced Spasticity Management: Projected and Contradictory Effects on Skeletal Muscles},

author = {Cemre Su Kaya Keles and Filiz Ates},

editor = {Toxins},

url = {https://www.mdpi.com/2072-6651/14/11/772},

doi = {https://doi.org/10.3390/toxins14110772},

year  = {2022},

date = {2022-11-08},

urldate = {2022-11-08},

journal = {Toxins},

volume = {14},

issue = {11},

pages = {772},

abstract = {Spasticity, following the neurological disorder of cerebral palsy (CP), describes a pathological condition, the central feature of which is involuntary and prolonged muscle contraction. The persistent resistance of spastic muscles to stretching is often followed by structural and mechanical changes in musculature. This leads to functional limitations at the respective joint. Focal injection of botulinum toxin type-A (BTX-A) is effectively used to manage spasticity and improve the quality of life of the patients. By blocking acetylcholine release at the neuromuscular junction and causing temporary muscle paralysis, BTX-A aims to reduce spasticity and hereby improve joint function. However, recent studies have indicated some contradictory effects such as increased muscle stiffness or a narrower range of active force production. The potential of these toxin- and atrophy-related alterations in worsening the condition of spastic muscles that are already subjected to changes should be further investigated and quantified. By focusing on the effects of BTX-A on muscle biomechanics and overall function in children with CP, this review deals with which of these goals have been achieved and to what extent, and what can await us in the future.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Grzegorzewski2022,

title = {Physiologically based pharmacokinetic (PBPK) modeling of the role of CYP2D6 polymorphism for metabolic phenotyping with dextromethorphan},

author = {Jan Grzegorzewski and Janosch Brandhorst and Matthias König},

editor = {Sec. Pharmacogenetics Frontiers in Pharmacology and Pharmacogenomics},

url = {https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2022.1029073/full},

doi = {https://doi.org/10.3389/fphar.2022.1029073},

year  = {2022},

date = {2022-10-24},

journal = {Frontiers in Pharmacology},

abstract = {The cytochrome P450 2D6 (CYP2D6) is a key xenobiotic-metabolizing enzyme involved in the clearance of many drugs. Genetic polymorphisms in CYP2D6 contribute to the large inter-individual variability in drug metabolism and could affect metabolic phenotyping of CYP2D6 probe substances such as dextromethorphan (DXM). To study this question, we (i) established an extensive pharmacokinetics dataset for DXM; and (ii) developed and validated a physiologically based pharmacokinetic (PBPK) model of DXM and its metabolites dextrorphan (DXO) and dextrorphan O-glucuronide (DXO-Glu) based on the data. Drug-gene interactions (DGI) were introduced by accounting for changes in CYP2D6 enzyme kinetics depending on activity score (AS), which in combination with AS for individual polymorphisms allowed us to model CYP2D6 gene variants. Variability in CYP3A4 and CYP2D6 activity was modeled based on in vitro data from human liver microsomes. Model predictions are in very good agreement with pharmacokinetics data for CYP2D6 polymorphisms, CYP2D6 activity as described by the AS system, and CYP2D6 metabolic phenotypes (UM, EM, IM, PM). The model was applied to investigate the genotype-phenotype association and the role of CYP2D6 polymorphisms for metabolic phenotyping using the urinary cumulative metabolic ratio (UCMR), DXM/(DXO + DXO-Glu). The effect of parameters on UCMR was studied via sensitivity analysis. Model predictions indicate very good robustness against the intervention protocol (i.e. application form, dosing amount, dissolution rate, and sampling time) and good robustness against physiological variation. The model is capable of estimating the UCMR dispersion within and across populations depending on activity scores. Moreover, the distribution of UCMR and the risk of genotype-phenotype mismatch could be estimated for populations with known CYP2D6 genotype frequencies. The model can be applied for individual prediction of UCMR and metabolic phenotype based on CYP2D6 genotype. Both, model and database are freely available for reuse.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Chourdakis2022,

title = {preCICE v2: A sustainable and user-friendly coupling library},

author = {Gerasimos Chourdakis and Kyle Davis and Benjamin Rodenberg and Miriam Schulte and Frédéric Simonis and Benjamin Uekermann and Georg Abrams and Hans-Joachim Bungartz and Lucia Cheung Yau and Ishaan Desai and Konrad Eder and Richard Hertrich and Florian Lindner and Alexander Rusch and Dmytro Sashko and David Schneider and Amin Totounferoush and Dominik Volland and Peter Vollmer and Oguz Ziya Koseomur},

editor = {Open Research Europe},

url = {https://open-research-europe.ec.europa.eu/articles/2-51/v2},

doi = {10.12688/openreseurope.14445.2},

year  = {2022},

date = {2022-09-30},

urldate = {2022-09-30},

journal = {Open Research Europe},

abstract = {preCICE is a free/open-source coupling library. It enables creating partitioned multi-physics simulations by gluing together separate software packages. 

This paper summarizes the development efforts in preCICE of the past five years. During this time span, we have turned the software from a working prototype – sophisticated numerical coupling methods and scalability on ten thousands of compute cores – to a sustainable and user-friendly software project with a steadily-growing community. Today, we know through forum discussions, conferences, workshops, and publications of more than 100 research groups using preCICE. We cover the fundamentals of the software alongside a performance and accuracy analysis of different data mapping methods. Afterwards, we describe ready-to-use integration with widely-used external simulation software packages, tests, and continuous integration from unit to system level, and community building measures, drawing an overview of the current preCICE ecosystem.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bertrand2022,

title = {On robust discretization methods for poroelastic problems: Numerical examples and counter-examples},

author = {Fleurianne Bertrand and Maximilian Brodbeck and Tim Ricken},

editor = {Elsevier},

url = {https://www.sciencedirect.com/science/article/pii/S2666657X22000209?via%3Dihub},

doi = {https://doi.org/10.1016/j.exco.2022.100087},

year  = {2022},

date = {2022-09-24},

journal = {Examples and Counterexamples (2)},

abstract = {Finite element approximations of poroelastic materials are nowadays used within multiple applications. Due to wide variation of possible material parameters, robustness of the considered discretization is important. Within this contribution robust of discretization schemes, initially developed for Biot’s theory, will be applied within the Theory of Porous Media. Selected numerical test-cases, special attention will be paid to incompressible and impermeable regimes, are conducted.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vellguth2022,

title = {Effect of transcatheter edge-to-edge repair device position on diastolic hemodynamic parameters: An echocardiography-based simulation study},

author = {Katharina Vellguth and Fabian Barbieri and Markus Reinthaler and Mario Kasner and Ulf Landmesser and Titus Kuehne and Anja Hennemuth and Lars Walczak and Leonid Goubergrits},

doi = {10.3389/fcvm.2022.915074},

issn = {2297-055X},

year  = {2022},

date = {2022-08-24},

urldate = {2022-08-24},

journal = {Front. Cardiovasc. Med.},

volume = {9},

publisher = {Frontiers Media SA},

abstract = {<jats:sec><jats:title>Background</jats:title><jats:p>Transcatheter edge-to-edge repair (TEER) has developed from innovative technology to an established treatment strategy of mitral regurgitation (MR). The risk of iatrogenic mitral stenosis after TEER is, however, a critical factor in the conflict of interest between maximal reduction of MR and minimal impairment of left ventricular filling. We aim to investigate systematically the impact of device position on the post treatment hemodynamic outcome by involving the patient-specific segmentation of the diseased mitral valve.</jats:p></jats:sec><jats:sec><jats:title>Materials and methods</jats:title><jats:p>Transesophageal echocardiographic image data of ten patients with severe MR (age: 57 ± 8 years, 20% female) were segmented and virtually treated with TEER at three positions by using a position based dynamics approach. Pre- and post-interventional patient geometries were preprocessed for computational fluid dynamics (CFD) and simulated at peak-diastole with patient-specific blood flow boundary conditions. Simulations were performed with boundary conditions mimicking rest and stress. The simulation results were compared with clinical data acquired for a cohort of 21 symptomatic MR patients (age: 79 ± 6 years, 43% female) treated with TEER.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Virtual TEER reduces the mitral valve area (MVA) from 7.5 ± 1.6 to 2.6 ± 0.6 cm<jats:sup>2</jats:sup>. Central device positioning resulted in a 14% smaller MVA than eccentric device positions. Furthermore, residual MVA is better predictable for central than for eccentric device positions (<jats:italic>R</jats:italic><jats:sup>2</jats:sup> = 0.81 vs. <jats:italic>R</jats:italic><jats:sup>2</jats:sup> = 0.49). The MVA reduction led to significantly higher maximal diastolic velocities (pre: 0.9 ± 0.2 m/s, post: 2.0 ± 0.5 m/s) and pressure gradients (pre: 1.5 ± 0.6 mmHg, post: 16.3 ± 9 mmHg) in spite of a mean flow rate reduction by 23% due to reduced MR after the treatment. On average, velocities were 12% and pressure gradients were 25% higher with devices in central compared to lateral or medial positions.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>Virtual TEER treatment combined with CFD is a promising tool for predicting individual morphometric and hemodynamic outcomes. Such a tool can potentially be used to support clinical decision making, procedure planning, and risk estimation to prevent post-procedural iatrogenic mitral stenosis.</jats:p></jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Braun2022,

title = {Bewegungsanalyse und muskuloskeletale Simulation in der Pseudarthrosentherapie – Erfahrungen und erste klinische Ergebnisse},

author = {Benedikt J. Braun and Tina Histing and Steven C. Herath and Mika F. R. Rollmann and Marie Reumann and Maximilian M. Menger and Fabian Springer and Annchristin Andres and Stefan Diebels and Michael Roland},

doi = {10.1007/s00113-022-01208-6},

issn = {2731-703X},

year  = {2022},

date = {2022-08-00},

urldate = {2022-08-00},

journal = {Unfallchirurgie},

volume = {125},

number = {8},

pages = {619--627},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1515/cdbme-2022-0004,

title = {Centerline and blockstructure for faststructured mesh generation},

author = {Annika Niemann and Gabor Janiga and Bernhard Preim and Daniel Behme and Sylvia Saalfeld},

editor = {De Gruyter},

url = {https://www.degruyter.com/document/doi/10.1515/cdbme-2022-0004/html},

doi = {https://doi.org/10.1515/cdbme-2022-0004},

year  = {2022},

date = {2022-07-30},

urldate = {2022-07-30},

journal = {Current Directions in Biomedical Engineering},

abstract = {In contrast to unstructured meshes, structured meshes yield faster simulation results for bio-medical simulations, but are very time-consuming to create. A preprocessing step in the generation of structured meshes is the manual construction of a block structure approximating the vessel. Here, we present an automatic centreline calculation and blockstructure generation to reduce the user effort and time of structured mesh generation. The center line is detected as points in between opposite faces. Based on the centerline, cross sections are determined and a blockstructure which approximates the vessel is automatically generated. The centreline detection does not require time-consuming user input and meshes with more than 195,000 vertices are processed in less than 160 seconds. The results of the presented automatic centreline detection are compared to a centreline with manual input generated by the widely used vmtk tool. The centerlines are similar, small differences occur at bifurcation and at the aneurysm.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1515/cdbme-2022-0032,

title = {Impact of patient-specific inflow boundary conditions on intracranial aneurysm hemodynamics},

author = {Janneck Stahl and Anna Bernovskis and Daniel Behme and Sylvia Saalfeld and Philipp Berg},

editor = {De Gruyter},

url = {https://www.degruyter.com/document/doi/10.1515/cdbme-2022-0032/html},

doi = {https://doi.org/10.1515/cdbme-2022-0032},

year  = {2022},

date = {2022-07-30},

urldate = {2022-07-30},

journal = {Current Directions in Biomedical Engineering},

volume = {8},

issue = {1},

pages = {125-128},

abstract = {For hemodynamic simulations of intracranial aneurysms boundary conditions (BC) are required. In most cases, these are not patient-specific and thus do not reflect the real flow conditions in the patient. This study investigates the influence of patient-specific inflow BC on intra-aneurysmal hemodynamics. The focus lies on gender and age variations of the patients. To asses the impact, four different inflow curves representing the velocity profile of the inflow over one cardiac cycle is modeled. These four inflow BC are varied in the simulations of each aneurysm from selected subgroups. From the results of the simulations, the hemodynamic parameters are determined for each inflow BC and the percent differences between inflow BC are determined. The results show that the hemodynamic parameters are not obust to varying inflow BC. It can be seen that age has more influence on the hemodynamic parameters than gender. This study demonstrates the dependence of valid hemodynamic parameters on realistic inflow BC. Thus, if available, patient-specific inflow curves are recommended.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1515/cdbme-2022-0033,

title = {Segmentation of Circle of Willis from 7T TOF-MRI data and immersive exploration using VR},

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

editor = {De Gruyter},

url = {https://www.degruyter.com/document/doi/10.1515/cdbme-2022-0033/html},

doi = {https://doi.org/10.1515/cdbme-2022-0033},

year  = {2022},

date = {2022-07-30},

urldate = {2022-07-30},

journal = {Current Directions in Biomedical Engineering},

volume = {8},

issue = {1},

pages = {129-132},

abstract = {7T TOF MRI scans provide high resolution images of intracranial vasculature. When segmented, the Circle of Willis is detailed and thus opens up new possibilities, in research but also in education. We propose a segmentation pipeline for the Circle ofWillis, and introduce a prototype that enables exploration of not just the entire Circle of Willis, but also of its centerline, in an immersive VR enviroment. In our prototype, the model can be freely rotated, placed and scaled. A qualitative evaluation was performed with two experienced neuroradiologists, who rated the prototype and its potential positively.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.3389/fcvm.2022.901902,

title = {CT-Based Analysis of Left Ventricular Hemodynamics Using Statistical Shape Modeling and Computational Fluid Dynamics},

author = {Leonid Goubergrits and Katharina Vellguth and Lukas Obermeier and Adriano Schlief and Lennart Tautz and Jan Bruening and Hans Lamecker and Angelika Szengel and Olena Nemchyna and Christoph Knosalla and Titus Kuehne and Natalia Solowjowa},

editor = {Frontiers Cardiovascular Medicine},

url = {https://www.frontiersin.org/articles/10.3389/fcvm.2022.901902/full},

doi = {10.3389/fcvm.2022.901902“},

year  = {2022},

date = {2022-07-05},

urldate = {2022-07-05},

journal = {Front. Cardiovasc. Med., 05 July 2022},

volume = {Sec. Cardiovascular Imaging},

issue = {Volume 9 - 2022},

pages = {901902},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ganse2022,

title = {Concepts and clinical aspects of active implants for the treatment of bone fractures},

author = {Bergita Ganse and Marcel Orth and Michael Roland and Stefan Diebels and Paul Motzki and Stefan Seelecke and Susanne-Marie Kirsch and Felix Welsch and Annchristin Andres and Kerstin Wickert and Benedikt J Braun and Tim Pohlemann},

doi = {10.1016/j.actbio.2022.05.001},

issn = {1742-7061},

year  = {2022},

date = {2022-07-00},

urldate = {2022-07-00},

journal = {Acta Biomaterialia},

volume = {146},

pages = {1--9},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyx,

title = {A comparative study of fully implicit staggered and monolithic solution methods. Part II: Coupled excitation-contraction equations of cardiac electromechanics},

author = {Barış Cansız and Michael Kaliske},

editor = {Journal Computational and Applied Mathematics},

doi = {https://doi.org/10.1016/j.cam.2021.114021},

year  = {2022},

date = {2022-06-30},

urldate = {2022-06-30},

journal = {Journal of Computational and Applied Mathematics},

volume = {Vol. 407},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nogatz2022,

title = {3D optical flow for large CT data of materials microstructures},

author = {Tessa Nogatz and Claudia Redenbach and Katja Schladitz},

doi = {10.1111/str.12412},

issn = {1475-1305},

year  = {2022},

date = {2022-06-00},

urldate = {2022-06-00},

journal = {Strain},

volume = {58},

number = {3},

publisher = {Wiley},

abstract = {<jats:title>Abstract</jats:title><jats:p>We compute three‐dimensional displacement vector fields to estimate the deformation of microstructural data sets in mechanical tests. For this, we extend the well‐known optical flow by Brox et al. to three dimensions, with special focus on the discretization of nonlinear terms. We evaluate our method first by synthetically deforming foams and comparing against this ground truth and second with data sets of samples that underwent real mechanical tests. Our results are compared to those from state‐of‐the‐art algorithms in materials science and medical image registration. By a thorough evaluation, we show that our proposed method is able to resolve the displacement best among all chosen comparison methods.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fritz20221d,

title = {A 1D–0D–3D coupled model for simulating blood flow and transport processes in breast tissue},

author = {Marvin Fritz and Tobias Köppl and John Tinsley Oden and Andreas Wagner and Barbara Wohlmuth and Chengyue Wu},

editor = {Wiley Online Library},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cnm.3612},

doi = {https://doi.org/10.1002/cnm.3612},

year  = {2022},

date = {2022-05-06},

urldate = {2022-05-06},

journal = {International Journal for Numerical Methods in Biomedical Engineering},

volume = {38},

issue = {7},

pages = {e3612},

abstract = {In this work, we present mixed dimensional models for simulating blood flow and transport processes in breast tissue and the vascular tree supplying it. These processes are considered, to start from the aortic inlet to the capillaries and tissue of the breast. Large variations in biophysical properties and flow conditions exist in this system necessitating the use of different flow models for different geometries and flow regimes. In total, we consider four different model types. First, a system of 1D nonlinear hyperbolic partial differential equations (PDEs) is considered to simulate blood flow in larger arteries with highly elastic vessel walls. Second, we assign 1D linearized hyperbolic PDEs to model the smaller arteries with stiffer vessel walls. The third model type consists of ODE systems (0D models). It is used to model the arterioles and peripheral circulation. Finally, homogenized 3D porous media models are considered to simulate flow and transport in capillaries and tissue within the breast volume. Sink terms are used to account for the influence of the venous and lymphatic systems. Combining the four model types, we obtain two different 1D–0D–3D coupled models for simulating blood flow and transport processes: The first model results in a fully coupled 1D–0D–3D model covering the complete path from the aorta to the breast combining a generic arterial network with a patient specific breast network and geometry. The second model is a reduced one based on the separation of the generic and patient specific parts. The information from a calibrated fully coupled model is used as inflow condition for the patient specific sub-model allowing a significant computational cost reduction. Several numerical experiments are conducted to calibrate the generic model parameters and to demonstrate realistic flow simulations compared to existing data on blood flow in the human breast and vascular system. Moreover, we use two different breast vasculature and tissue data sets to illustrate the robustness of our reduced sub-model approach.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{klotz2021investigating,

title = {Investigating the spatial resolution of EMG and MMG based on a systemic multi-scale model},

author = {Thomas Klotz and Leonardo Gizzi and Oliver Röhrle},

editor = {Springer},

url = {https://link.springer.com/article/10.1007/s10237-022-01572-7 

https://rdcu.be/dpxtQ},

doi = {https://doi.org/10.48550/arXiv.2108.05046},

year  = {2022},

date = {2022-04-20},

urldate = {2022-01-01},

journal = {Biomechanics and Modeling in Mechanobiology},

volume = {21},

pages = {983-997},

abstract = {While electromyography (EMG) and magnetomyography (MMG) are both methods to measure the electrical activity of skeletal muscles, no systematic comparison between both signals exists. Within this work, we propose a systemic in silico model for EMG and MMG and test the hypothesis that MMG surpasses EMG in terms of spatial selectivity. The results show that MMG provides a slightly better spatial selectivity than EMG when recorded directly on the muscle surface. However, there is a remarkable difference in spatial selectivity for non-invasive surface measurements. The spatial selectivity of the MMG 

components aligned with the muscle fibres and normal to the body surface outperforms the spatial selectivity of surface EMG. Particularly, for the MMG's normal-to-the-surface component the influence of subcutaneous fat is minimal. Further, for the first time, we analyse the contribution of different structural components, i.e., muscle fibres from different motor units and the extracellular space, to the measurable biomagnetic field. Notably, the simulations show that the normal-to-the-surface MMG component, the contribution from volume currents in the extracellular space and in surrounding inactive 

tissues is negligible. Further, our model predicts a surprisingly high contribution of the passive muscle fibres to the observable magnetic field.},

note = {cite arxiv:2108.05046Comment: Preprint, Submitted to Biomechanics and Modeling in Mechanobiology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Obermeier2022,

title = {CT-Based Simulation of Left Ventricular Hemodynamics: A Pilot Study in Mitral Regurgitation and Left Ventricle Aneurysm Patients},

author = {Lukas Obermeier and Katharina Vellguth and Adriano Schlief and Lennart Tautz and Jan Bruening and Christoph Knosalla and Titus Kuehne and Natalia Solowjowa and Leonid Goubergrits},

doi = {10.3389/fcvm.2022.828556},

issn = {2297-055X},

year  = {2022},

date = {2022-03-22},

urldate = {2022-03-22},

journal = {Frontiers in Cardiovascular Medicine},

issue = {9/2022},

abstract = {Background: Cardiac CT (CCT) is well suited for a detailed analysis of heart structures due to its high spatial resolution, but in contrast to MRI and echocardiography, CCT does not allow an assessment of intracardiac flow. Computational fluid dynamics (CFD) can complement this shortcoming. It enables the computation of hemodynamics at a high spatio-temporal resolution based on medical images. The aim of this proposed study is to establish a CCT-based CFD methodology for the analysis of left ventricle (LV) hemodynamics and to assess the usability of the computational framework for clinical practice. 

Materials and methods: The methodology is demonstrated by means of four cases selected from a cohort of 125 multiphase CCT examinations of heart failure patients. These cases represent subcohorts of patients with and without LV aneurysm and with severe and no mitral regurgitation (MR). All selected LVs are dilated and characterized by a reduced ejection fraction (EF). End-diastolic and end-systolic image data was used to reconstruct LV geometries with 2D valves as well as the ventricular movement. The intraventricular hemodynamics were computed with a prescribed-motion CFD approach and evaluated in terms of large-scale flow patterns, energetic behavior, and intraventricular washout. 

Results: In the MR patients, a disrupted E-wave jet, a fragmentary diastolic vortex formation and an increased specific energy dissipation in systole are observed. In all cases, regions with an impaired washout are visible. The results furthermore indicate that considering several cycles might provide a more detailed view of the washout process. The pre-processing times and computational expenses are in reach of clinical feasibility. 

Conclusion: The proposed CCT-based CFD method allows to compute patient-specific intraventricular hemodynamics and thus complements the informative value of CCT. The method can be applied to any CCT data of common quality and represents a fair balance between model accuracy and overall expenses. With further model enhancements, the computational framework has the potential to be embedded in clinical routine workflows, to support clinical decision making and treatment planning. 

Keywords: cardiac computed tomography; computational fluid dynamics; fluid-structure interaction; image-based modeling; intraventricular hemodynamics; left ventricle aneurysm; mitral regurgitation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ricken2022,

title = {Theoretical formulation and computational aspects of a two-scale homogenization scheme combining the TPM and FE² method for poro-elastic fuid-saturated porous media},

author = {Tim Ricken and Jörg Schröder and Joachim Bluhm and Florian Bartel},

editor = {Elsevier},

url = {https://www.sciencedirect.com/science/article/pii/S0020768321004674?via%3Dihub},

doi = {https://doi.org/10.1016/j.ijsolstr.2021.111412},

year  = {2022},

date = {2022-02-28},

journal = {International Journal of Solids and Structures, 2022},

abstract = {The focus of this investigation lies on the development of a two-scale homogenization scheme for poro-elastic fluid-saturated porous media. For this purpose, the general concepts of the Theory of Porous Media (TPM) are combined with the FE method. After an introduction of the basics of TPM, the weak forms for the macroscopic and the microscopic scale will be formulated and the averaged macroscopic tangent moduli considering the microscale will be derived. Additionally, the formulation of lower level boundary conditions, which refer to the quantities that will be transmitted from the macro- to the microscale, in strict compliance with the Hill–Mandel homogeneity condition, is derived. Finally, a numerical example will be presented, pointing out the gained features of the methodology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schmid2022,

title = {Spindle Model Responsive to Mixed Fusimotor Inputs: an updated version of the Maltenfort and Burke (2003) model},

author = {Laura Schmid and Thomas Klotz and Utku Yavuz and Mitchell Maltenfort and Oliver Roehrle},

doi = {10.36903/physiome.19070171.v2},

year  = {2022},

date = {2022-01-27},

urldate = {2022-01-27},

journal = {Physiome},

abstract = {The muscle spindle model presented in Maltenfort and Burke (2003) calculates muscle spindle primary afferent feedback depending on the muscle fibre stretch and fusimotor drive. The aim of this paper is to provide an updated version of the model, which is now capable of replicating the originally published data. This is achieved by modifying the equations describing the modulation of the muscle spindle output in response to dynamic fusimotor drive. EDITOR'S NOTE V2: Showing manuscript and model files.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}