@article{Eckel2025,

title = {Application of rapid evaporative ionization mass spectrometry in preclinical and clinical analyses of steatotic liver tissues and cells},

author = {Julian Connor Eckel and Lena Seidemann and Mohamed Albadry and Gerda Schicht and Marija Skvoznikova and Sandra Nickel and René Hänsel and Daniel Seehofer and Grit Gesine Ruth Hiller and Hans-Michael Tautenhahn and Uta Dahmen and Georg Damm},

doi = {10.1038/s41598-025-93305-w},

issn = {2045-2322},

year  = {2025},

date = {2025-12-00},

urldate = {2025-12-00},

journal = {Sci Rep},

volume = {15},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

          <jats:p>Rapid evaporative ionization mass spectrometry (REIMS) shows promise as a preparation-free tissue analysis tool with the prospect for real-time diagnostics. Given that hepatic steatosis is characterized by shifts in lipid species and abundance, we selected it as basis for method development, as REIMS specifically measures lipidomic profiles. However, further validation and protocol refinement are necessary to establish its clinical utility. In this study, we applied REIMS to steatotic human liver tissues, focusing on its ability to differentiate varying degrees of steatosis. We established standardized protocols for tissue handling and lipid analysis, which were essential for reliable data interpretation. Notably, our findings revealed that tissue size impacts REIMS sensitivity, with smaller samples yielding lower total ion counts and altered lipid profiles. Through principal component analysis, we identified key lipid classes, namely triacylglycerides, fatty acids, and glycerophospholipids. Despite a missing link between triacylglyceride abundance and degree of steatosis, we successfully identified condition-specific lipid patterns, with ceramides emerging as markers of advanced steatosis. Our study provides a protocol for the measurements of lipid standards showing the detailed degradation of specific lipids using iKnife-coupled REIMS. It highlights the pitfalls and limitations and provides critical recommendations for REIMS use. It also emphasizes the need for standardized biobanking and tissue preparation to ensure accurate lipid profiling, laying the groundwork for future protocol adjustments required for clinical application.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wrigge2025,

title = {Hyperspectral imaging in living and deceased donor kidney transplantation},

author = {Rasmus Wrigge and Robert Sucher and Fabian Haak and Hans-Jonas Meyer and Julia Unruh and Hans-Michael Hau and Matthias Mehdorn and Hans-Michael Tautenhahn and Daniel Seehofer and Uwe Scheuermann},

doi = {10.1186/s12880-025-01576-6},

issn = {1471-2342},

year  = {2025},

date = {2025-12-00},

urldate = {2025-12-00},

journal = {BMC Med Imaging},

volume = {25},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

          <jats:sec>

            <jats:title>Objective and background</jats:title>

            <jats:p>Hyperspectral imaging (HSI) is an innovative, noninvasive technique that assesses tissue and organ perfusion and oxygenation. This study aimed to evaluate HSI as a predictive tool for early postoperative graft function and long-term outcomes in living donor (LD) and deceased donor (DD) kidney transplantation (KT).</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Patients and methods</jats:title>

            <jats:p>HSI of kidney allograft parenchyma from 19 LD and 51 DD kidneys was obtained intraoperatively 15 minutes after reperfusion. Using the dedicated HSI TIVITA Tissue System, indices of tissue oxygenation (StO<jats:sub>2</jats:sub>), perfusion (near-infrared [NIR]), organ hemoglobin (OHI), and tissue water (TWI) were calculated and then analyzed retrospectively.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Results</jats:title>

            <jats:p>LD kidneys had superior intraoperative HSI values of StO<jats:sub>2</jats:sub> (0.78 ± 0.13 versus 0.63 ± 0.24; <jats:italic>P</jats:italic> = 0.001) and NIR (0.67 ± 0.10 versus 0.56 ± 0.27; <jats:italic>P</jats:italic> = 0.016) compared to DD kidneys. Delayed graft function (DGF) was observed in 18 cases (26%), in which intraoperative HSI showed significantly lower values of StO<jats:sub>2</jats:sub> (0.78 ± 0.07 versus 0.35 ± 0.21; <jats:italic>P</jats:italic> < 0.001) and NIR (0.67 ± 0.11 versus 0.34 ± 0.32; <jats:italic>P</jats:italic> < 0.001). Receiver operating characteristic curve analysis demonstrated an excellent predictive value of HSI for the development of DGF, with an area under the curve of 0.967 for StO<jats:sub>2</jats:sub> and 0.801 for NIR. Kidney grafts with low StO<jats:sub>2</jats:sub> values (cut-off point 0.6) showed reduced renal function with a low glomerular filtration rate and elevated urea levels in the first two weeks after KT. Three years after KT, graft survival was also inferior in the group with initially low StO<jats:sub>2</jats:sub> values.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Conclusion</jats:title>

            <jats:p>HSI is a useful tool for predicting DGF in living and deceased KT and may assist in estimating short-term allograft function. However, further studies with expanded cohorts are needed to evaluate the association between HSI and long-term graft outcomes.</jats:p>

          </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Eissazadeh2025,

title = {Anti-Endoglin monoclonal antibody prevents the progression of liver sinusoidal endothelial inflammation and fibrosis in MASH},

author = {Samira Eissazadeh and Petra Fikrova and Jana Urbankova Rathouska and Ivana Nemeckova and Katarina Tripska and Martina Vasinova and Radim Havelek and SeyedehNiloufar Mohammadi and Ivone Cristina Igreja Sa and Charles Theuer and Matthias König and Stanislav Micuda and Petr Nachtigal},

doi = {10.1016/j.lfs.2025.123428},

issn = {0024-3205},

year  = {2025},

date = {2025-03-00},

urldate = {2025-03-00},

journal = {Life Sciences},

volume = {364},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mandl2025,

title = {Separable physics-informed DeepONet: Breaking the curse of dimensionality in physics-informed machine learning},

author = {Luis Mandl and Somdatta Goswami and Lena Lambers and Tim Ricken},

doi = {10.1016/j.cma.2024.117586},

issn = {0045-7825},

year  = {2025},

date = {2025-02-00},

urldate = {2025-02-00},

journal = {Computer Methods in Applied Mechanics and Engineering},

volume = {434},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Xu2024,

title = {The effects of saturated and unsaturated fatty acids on MASLD: a Mendelian randomization analysis and in vivo experiment},

author = {Fengming Xu and Mohamed Albadry and Annika Döding and Xinpei Chen and Olaf Dirsch and Ulrike Schulze-Späte and Uta Dahmen},

doi = {10.1007/s00394-024-03560-2},

issn = {1436-6215},

year  = {2025},

date = {2025-02-00},

urldate = {2025-02-00},

journal = {Eur J Nutr},

volume = {64},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

          <jats:sec>

            <jats:title>Background</jats:title>

            <jats:p>Excessive intake of fatty acids is a key factor contributing to metabolic dysfunction-associated steatotic liver disease (MASLD). However, the effects of saturated fatty acids (SFA) and unsaturated fatty acids (UFA) on the development of MASLD are uncertain. Therefore, we conducted two-sample Mendelian randomization studies and animal experiments to explore the effects of SFA, monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA) on the risk of developing MASLD.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Methods</jats:title>

            <jats:p>The genetic summary data of exposures and outcome were retrieved from genome-wide association studies (GWASs) and used for five Mendelian randomization methods. A comprehensive sensitivity analysis was performed to verify the robustness of the results. Mice were subjected to different diets followed by assessment of severity of steatosis based on a histological score and determination of hepatic triglyceride levels to investigate the relationships between SFA, MUFA, PUFA and MASLD.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Results</jats:title>

            <jats:p>The Mendelian randomization results showed that MUFA (odds ratio: 1.441, 95% confidence interval: 1.078–1.927, <jats:italic>P =</jats:italic> 0.014) was causally associated with the incidence of MASLD. SFA and PUFA were not causally associated with the incidence of MASLD. Sensitivity analysis did not identify any significant bias in the results. The animal experiment results showed that a MUFA-enriched diet significantly contributed to the development of hepatic steatosis (<jats:italic>P <</jats:italic> 0.001).</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Conclusion</jats:title>

            <jats:p>SFA and PUFA did not have a significant causal effect on MASLD, but MUFA intake is a risk factor for MASLD. A MUFA-enriched diet increased the incidence of macrovesicular steatosis and the hepatic triglyceride levels. Therefore, replacing MUFA intake with a moderate intake of PUFA might help reduce the risk of MASLD.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Graphical Abstract</jats:title>

          </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Arasteh-Khoshbin2024,

title = {Comparing durability and compressive strength predictions of hyperoptimized random forests and artificial neural networks on a small dataset of concrete containing nano SiO2 and RHA},

author = {O. Arasteh-Khoshbin and S. M. Seyedpour and L. Mandl and L. Lambers and T. Ricken},

doi = {10.1080/19648189.2024.2393881},

issn = {2116-7214},

year  = {2025},

date = {2025-01-25},

urldate = {2025-01-25},

journal = {European Journal of Environmental and Civil Engineering},

volume = {29},

number = {2},

pages = {331--350},

publisher = {Informa UK Limited},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nogatz2024,

title = {MorphFlow: Estimating Motion in In-Situ Tests of Concrete},

author = {T. Nogatz and C. Redenbach and K. Schladitz},

doi = {10.1007/s11340-024-01104-7},

issn = {1741-2765},

year  = {2025},

date = {2025-01-00},

urldate = {2025-01-00},

journal = {Exp Mech},

volume = {65},

number = {1},

pages = {35--53},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title>

          <jats:sec>

            <jats:title>Background</jats:title>

            <jats:p>

              <jats:italic>In situ</jats:italic> Computed Tomography is a valuable tool to investigate failure mechanics of materials in 3D. For brittle materials with sudden fracture like concrete however, state-of-the-art methods such as Digital Volume Correlation fail to produce displacement fields that display the discontinuous behavior of load induced cracking correctly.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Objective</jats:title>

            <jats:p>The main objective is to develop an algorithm that calculates displacement fields for large-scale <jats:italic>in situ</jats:italic> experiments on concrete.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Methods</jats:title>

            <jats:p>The algorithm presented is based on a 3D Optical Flow method solved by a primal-dual procedure and equipped with a coarse-to-fine scheme based on morphological wavelets. The algorithm is publicly available. Our evaluation focuses on the beneficial use of morphological wavelets over classical ones, and on the ability to produce reliable results with limited data. Applying the primal-dual scheme to <jats:italic>in situ</jats:italic> tests and using morphological wavelets are novel contributions.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Results</jats:title>

            <jats:p>The results show that our algorithm cannot only cope with large volume images, but also produces discontinuous displacement fields that yield high strain in fractured regions. It does not only perform better than state-of-the-art methods, but also achieves sufficient results on reduced data. The morphological wavelets play a key role in this finding - they even allow to deduce cracks of widths less than a voxel.</jats:p>

          </jats:sec>

          <jats:sec>

            <jats:title>Conclusion</jats:title>

            <jats:p>Displacement calculation for <jats:italic>in situ</jats:italic> tests of brittle materials requires voxel-accurate displacement fields that allow for discontinuities. The presented algorithm fulfills these requirements and therefore is a powerful tool for future understanding of failure mechanics in concrete.</jats:p>

          </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Brodbeck2024,

title = {On the influence of non-linearity within two-phase poro-elasticity: Numerical examples and counterexamples},

author = {Maximilian Brodbeck and Franziska S. Egli and Marlon Suditsch and Seyed Morteza Seyedpour and Tim Ricken},

doi = {10.1016/j.exco.2024.100167},

issn = {2666-657X},

year  = {2024},

date = {2024-12-00},

urldate = {2024-12-00},

journal = {Examples and Counterexamples},

volume = {6},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Azhdari2024b,

title = {Refining thermal therapy: Temperature distribution modeling with distinct absorption in multi-layered skin tissue during infrared laser exposure},

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

doi = {10.1016/j.icheatmasstransfer.2024.107818},

issn = {0735-1933},

year  = {2024},

date = {2024-09-00},

urldate = {2024-09-00},

journal = {International Communications in Heat and Mass Transfer},

volume = {157},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Reisch2024,

title = {Building up a model family for inflammations},

author = {Cordula Reisch and Sandra Nickel and Hans-Michael Tautenhahn},

doi = {10.1007/s00285-024-02126-4},

issn = {1432-1416},

year  = {2024},

date = {2024-09-00},

urldate = {2024-09-00},

journal = {J. Math. Biol.},

volume = {89},

number = {3},

publisher = {Springer Science and Business Media LLC},

abstract = {<jats:title>Abstract</jats:title><jats:p>The paper presents an approach for overcoming modeling problems of typical life science applications with partly unknown mechanisms and lacking quantitative data: A model family of reaction–diffusion equations is built up on a mesoscopic scale and uses classes of feasible functions for reaction and taxis terms. The classes are found by translating biological knowledge into mathematical conditions and the analysis of the models further constrains the classes. Numerical simulations allow comparing single models out of the model family with available qualitative information on the solutions from observations. The method provides insight into a hierarchical order of the mechanisms. The method is applied to the clinics for liver inflammation such as metabolic dysfunction-associated steatohepatitis or viral hepatitis where reasons for the chronification of disease are still unclear and time- and space-dependent data is unavailable.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jäger2024,

title = {Cell seeding dynamics in a porous scaffold material designed for meniscus tissue regeneration},

author = {Henry Jäger and Elise Grosjean and Steffen Plunder and Claudia Redenbach and Alex Keilmann and Bernd Simeon and Christina Surulescu},

doi = {10.1002/pamm.202400133},

issn = {1617-7061},

year  = {2024},

date = {2024-08-00},

urldate = {2024-08-00},

journal = {Proc Appl Math and Mech},

volume = {24},

number = {2},

publisher = {Wiley},

abstract = {<jats:title>Abstract</jats:title><jats:p>We study the dynamics of a seeding experiment where a fibrous scaffold material is colonized by two types of cell populations. The specific application that we have in mind is related to the idea of meniscus tissue regeneration. In order to support the development of a promising replacement material, we discuss certain rate equations for the densities of human mesenchymal stem cells and chondrocytes and for the production of collagen‐containing extracellular matrix. For qualitative studies, we start with a system of ordinary differential equations and refine then the model to include spatial effects of the underlying nonwoven scaffold structure. Numerical experiments as well as a complete set of parameters for future benchmarking are provided.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pathak2024,

title = {Modeling freezing and BioGeoChemical processes in Antarctic sea ice},

author = {Raghav Pathak and Seyed Morteza Seyedpour and Bernd Kutschan and Andrea Thom and Silke Thoms and Tim Ricken},

doi = {10.1002/pamm.202400047},

issn = {1617-7061},

year  = {2024},

date = {2024-08-00},

urldate = {2024-08-00},

journal = {Proc Appl Math and Mech},

volume = {24},

number = {2},

publisher = {Wiley},

abstract = {<jats:title>Abstract</jats:title><jats:p>The Antarctic sea ice, which undergoes annual freezing and melting, plays a significant role in the global climate cycle. Since satellite observations in the Antarctic region began, 2023 saw a historically unprecedented decrease in the extent of sea ice. Further ocean warming and future environmental conditions in the Southern Ocean will influence the extent and amount of ice in the Marginal Ice Zones (MIZ), the BioGeoChemical (BGC) cycles, and their interconnected relationships. The so‐called pancake floes are a composition of a porous sea ice matrix with interstitial brine, nutrients, and biological communities inside the pores. The ice formation and salinity are both dependent on the ambient temperature. To realistically model these multiphasic and multicomponent coupled processes, the extended Theory of Porous Media (eTPM) is used to develop Partial Differential Equations (PDEs) based high‐fidelity models capable of simulating the different seasonal variations in the region. All critical variables like salinity, ice volume fraction, and temperature, among others, are considered and have their equations of state. The phase transition phenomenon is approached through a micro‐macro linking scheme. In this paper, a phase‐field solidification model [4] coupled with salinity is used to model the microscale freezing processes and up‐scaled to the macroscale eTPM model. The evolution equations for the phase field model are derived following Landau‐Ginzburg order parameter gradient dynamics and mass conservation of salt allowing to model the salt trapped inside the pores. A BGC flux model for sea ice is set up to simulate the algal species present in the sea ice matrix. Ordinary differential equations (ODE) are employed to represent the diverse environmental factors involved in the growth and loss of distinct BGC components. Processes like photosynthesis are dependent on temperature and salinity, which are derived through an ODE‐PDE coupling with the eTPM model. Academic simulations and results are presented as validation for the mathematical model. These high‐fidelity models eventually lead to their incorporation into large‐scale global climate models.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Assessment of intracranial aneurysm neck deformation after contour deployment},

author = {Iam Lena Spitz and Jana Korte and Franziska Gaidzik and Naomi Larsen and Bernhard Preim and Sylvia Saalfeld},

url = {https://link.springer.com/article/10.1007/s11548-024-03189-w},

doi = {https://doi.org/10.1007/s11548-024-03189-w},

year  = {2024},

date = {2024-05-31},

urldate = {2024-05-31},

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

volume = {1},

pages = {1:8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Albadry2024,

title = {Cross-species variability in lobular geometry and cytochrome P450 hepatic zonation: insights into CYP1A2, CYP2D6, CYP2E1 and CYP3A4},

author = {Mohamed Albadry and Jonas Küttner 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 König and Uta Dahmen},

doi = {10.3389/fphar.2024.1404938},

issn = {1663-9812},

year  = {2024},

date = {2024-05-16},

urldate = {2024-05-16},

journal = {Front. Pharmacol.},

volume = {15},

publisher = {Frontiers Media SA},

abstract = {<jats:p>There is a lack of systematic research exploring cross-species variation in liver lobular geometry and zonation patterns of critical drug-metabolizing enzymes, a knowledge gap essential for translational studies. This study investigated the critical interplay between lobular geometry and key cytochrome P450 (CYP) zonation in four species: mouse, rat, pig, and human. We developed an automated pipeline based on whole slide images (WSI) of hematoxylin-eosin-stained liver sections and immunohistochemistry. This pipeline allows accurate quantification of both lobular geometry and zonation patterns of essential CYP proteins. Our analysis of CYP zonal expression shows that all CYP enzymes (besides CYP2D6 with panlobular expression) were observed in the pericentral region in all species, but with distinct differences. Comparison of normalized gradient intensity shows a high similarity between mice and humans, followed by rats. Specifically, CYP1A2 was expressed throughout the pericentral region in mice and humans, whereas it was restricted to a narrow pericentral rim in rats and showed a panlobular pattern in pigs. Similarly, CYP3A4 is present in the pericentral region, but its extent varies considerably in rats and appears panlobular in pigs. CYP2D6 zonal expression consistently shows a panlobular pattern in all species, although the intensity varies. CYP2E1 zonal expression covered the entire pericentral region with extension into the midzone in all four species, suggesting its potential for further cross-species analysis. Analysis of lobular geometry revealed an increase in lobular size with increasing species size, whereas lobular compactness was similar. Based on our results, zonated CYP expression in mice is most similar to humans. Therefore, mice appear to be the most appropriate species for drug metabolism studies unless larger species are required for other purposes, e.g., surgical reasons. CYP selection should be based on species, with CYP2E1 and CYP2D6 being the most preferable to compare four species. CYP1A2 could be considered as an additional CYP for rodent versus human comparisons, and CYP3A4 for mouse/human comparisons. In conclusion, our image analysis pipeline together with suggestions for species and CYP selection can serve to improve future cross-species and translational drug metabolism studies.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Danesini2024,

title = {Endomysium determines active and passive force production in muscle fibers},

author = {Paolo Carlo Danesini and Maximilian Heim and André Tomalka and Tobias Siebert and Filiz Ates},

editor = {Journal Biomechanics},

url = {https://www.sciencedirect.com/science/article/pii/S0021929024002124?via%3Dihub},

doi = {https://doi.org/10.1016/j.jbiomech.2024.112134},

year  = {2024},

date = {2024-05-03},

urldate = {2024-05-03},

journal = {Journal of Biomechanics},

volume = {Volume 168},

issue = {May 2024},

abstract = {Connective tissues can be recognized as an important structural support element in muscles. Recent studies have also highlighted its importance in active force generation and transmission between muscles, particularly through the epimysium. In the present study, we aimed to investigate the impact of the endomysium, the connective tissue surrounding muscle fibers, on both passive and active force production. Pairs of skeletal muscle fibers were extracted from the extensor digitorum longus muscles of rats and, after chemical skinning, their passive and active force–length relationships were measured under two conditions: (i) with the endomysium between muscle fibers intact, and (ii) after its dissection. We found that the dissection of the endomysium caused force to significantly decrease in both active (by 22.2 % when normalized to the maximum isometric force; p < 0.001) and passive conditions (by 25.9 % when normalized to the maximum isometric force; p = 0.034). These findings indicate that the absence of endomysium compromises muscle fiber’s not only passive but also active force production. This effect may be attributed to increased heterogeneity in sarcomere lengths, enhanced lattice spacing between myofilaments, or a diminished role of trans-sarcolemmal proteins due to dissecting the endomysium. Future investigations into the underlying mechanisms and their implications for various extracellular matrix-related diseases are warranted.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Höpfl2024b,

title = {Bayesian modelling of time series data (BayModTS)—a FAIR workflow to process sparse and highly variable data},

author = {Sebastian Höpfl and Mohamed Albadry and Uta Dahmen and Karl-Heinz Herrmann and Eva Marie Kindler and Matthias König and Jürgen Rainer Reichenbach and Hans-Michael Tautenhahn and Weiwei Wei and Wan-Ting Zhao and Nicole Erika Radde},

editor = {Anthony Mathelier},

doi = {10.1093/bioinformatics/btae312},

issn = {1367-4811},

year  = {2024},

date = {2024-05-02},

urldate = {2024-05-02},

volume = {40},

number = {5},

publisher = {Oxford University Press (OUP)},

abstract = {<jats:title>Abstract</jats:title>

               <jats:sec>

                  <jats:title>Motivation</jats:title>

                  <jats:p>Systems biology aims to better understand living systems through mathematical modelling of experimental and clinical data. A pervasive challenge in quantitative dynamical modelling is the integration of time series measurements, which often have high variability and low sampling resolution. Approaches are required to utilize such information while consistently handling uncertainties.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Results</jats:title>

                  <jats:p>We present BayModTS (Bayesian modelling of time series data), a new FAIR (findable, accessible, interoperable, and reusable) workflow for processing and analysing sparse and highly variable time series data. BayModTS consistently transfers uncertainties from data to model predictions, including process knowledge via parameterized models. Further, credible differences in the dynamics of different conditions can be identified by filtering noise. To demonstrate the power and versatility of BayModTS, we applied it to three hepatic datasets gathered from three different species and with different measurement techniques: (i) blood perfusion measurements by magnetic resonance imaging in rat livers after portal vein ligation, (ii) pharmacokinetic time series of different drugs in normal and steatotic mice, and (iii) CT-based volumetric assessment of human liver remnants after clinical liver resection.</jats:p>

               </jats:sec>

               <jats:sec>

                  <jats:title>Availability and implementation</jats:title>

                  <jats:p>The BayModTS codebase is available on GitHub at https://github.com/Systems-Theory-in-Systems-Biology/BayModTS. The repository contains a Python script for the executable BayModTS workflow and a widely applicable SBML (systems biology markup language) model for retarded transient functions. In addition, all examples from the paper are included in the repository. Data and code of the application examples are stored on DaRUS: https://doi.org/10.18419/darus-3876. The raw MRI ROI voxel data were uploaded to DaRUS: https://doi.org/10.18419/darus-3878. The steatosis metabolite data are published on FairdomHub: 10.15490/fairdomhub.1.study.1070.1.</jats:p>

               </jats:sec>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Maier2024,

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

author = {Benjamin Maier and Dominik Göddeke and Felix Huber and Thomas Klotz and Oliver Röhrle 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 – 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 Göddeke and Oliver Röhrle 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{Gerhäusser2024,

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

author = {Steffen Gerhäusser and Lena Lambers and Luis Mandl and Julian Franquinet and Tim Ricken and Matthias König},

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{nokeyb,

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 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{nokeyc,

title = {Verification Study of In Silico Computed Intracardiac Blood Flow With 4D Flow MRI},

author = {Lukas Obermeier and M. Wiegand and F. Hellmeier and C. Manini and Titus Kuehne and Leonid Goubergrits},

editor = {IEEE},

url = {https://ieeexplore.ieee.org/document/10478556},

doi = {10.1109/TBME.2024.3381212},

year  = {2024},

date = {2024-03-25},

urldate = {2024-03-25},

journal = {IEEE Transactions on Biomedical Engineering},

volume = {71},

issue = {9},

pages = {2568 - 2579},

abstract = {Objective: Major challenges for clinical applications of in silico medicine are limitations in time and computational resources. Computational approaches should therefore be tailored to specific applications with relatively low complexity and must be verified and validated against clinical gold standards. Methods: This study performed computational fluid dynamics simulations of left ventricular hemodynamics of different complexity based on shape reconstruction from steady state gradient echo magnetic resonance imaging (MRI) data. Computed flow results of a rigid wall model (RWM) and a prescribed motion fluid-structure interaction (PM-FSI) model were compared against phase-contrast MRI measurements for three healthy subjects. Results: Extracted boundary conditions from the steady state MRI sequences as well as computed metrics, such as flow rate, valve velocities, and kinetic energy show good agreement with in vivo flow measurements. Regional flow analysis reveals larger differences. Conclusion: Basic flow structures are well captured with RWM and PM-FSI. For the computation of further biomarkers like washout or flow efficiency, usage of PM-FSI is required. Regarding boundary-near flow, more accurate anatomical models are inevitable. Significance: These results delineate areas of application of both methods and lay a foundation for larger validation studies and sensitivity analysis for healthy and diseased cases, being an essential step upon clinical translations.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokeyd,

title = {Experiments meet simulations: Understanding skeletal muscle mechanics to address clinical problems},

author = {Filiz Ates and Oliver Roehrle},

editor = {Wiley-VCH GmbH},

url = {https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/gamm.202370012},

doi = {https://doi.org/10.1002/gamm.202370012},

year  = {2024},

date = {2024-03-15},

urldate = {2024-03-15},

journal = {GAMM Mitteilungen},

volume = {2024},

abstract = {This article aims to present some novel experimental approaches and compu- 

tational methods providing detailed insights into the mechanical behavior of 

skeletal muscles relevant to clinical problems associated with managing and 

treating musculoskeletal diseases. The mechanical characterization of skele- 

tal muscles in vivo is crucial for better understanding of, prevention of, or 

intervention in movement alterations due to exercise, aging, or pathologies 

related to neuromuscular diseases. To achieve this, we suggest an intraoperative 

experimental method including direct measurements of human muscle forces 

supported by computational methodologies. A set of intraoperative experiments 

indicated the major role of extracellular matrix (ECM) in spastic cerebral palsy. 

The force data linked to joint function are invaluable and irreplaceable for eval- 

uating individual muscles however, they are not feasible in many situations. 

Three-dimensional, continuum-mechanical models provide a way to predict the 

exerted muscle forces. To obtain, however, realistic predictions, it is important 

to investigate the muscle not by itself, but embedded within the respective mus- 

culoskeletal system, for example, a 6-muscle upper arm model, and the ability 

to obtain non-invasively, or at least, minimally invasively material parameters 

for continuum-mechanical skeletal muscle models, for example, by presently 

proposed homogenization methodologies. Botulinum toxin administration as a 

treatment option for spasticity is exemplified by combining experiments with 

modeling to find out the mechanical outcomes of altered ECM and the contro- 

versial effects of the toxin. The potentials and limitations of both experimental 

and modeling approaches and how they need each other are discussed.},

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 Matérn-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 Matérn-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{Han2024,

title = {Janus microparticles-based targeted and spatially-controlled piezoelectric neural stimulation via low-intensity focused ultrasound},

author = {Mertcan Han and Erdost Yildiz and Ugur Bozuyuk and Asli Aydin and Yan Yu and Aarushi Bhargava and Selcan Karaz and Metin Sitti},

editor = {Nature Publishing Group UK London},

url = {https://www.nature.com/articles/s41467-024-46245-4#citeas},

doi = {https://doi.org/10.1038/s41467-024-46245-4},

year  = {2024},

date = {2024-03-05},

journal = {Nature Communications},

volume = {15},

issue = {1},

pages = {2013},

abstract = {Electrical stimulation is a fundamental tool in studying neural circuits, treating neurological diseases, and advancing regenerative medicine. Injectable, free-standing piezoelectric particle systems have emerged as non-genetic and wireless alternatives for electrode-based tethered stimulation systems. However, achieving cell-specific and high-frequency piezoelectric neural stimulation remains challenging due to high-intensity thresholds, non-specific diffusion, and internalization of particles. Here, we develop cell-sized 20 μm-diameter silica-based piezoelectric magnetic Janus microparticles (PEMPs), enabling clinically-relevant high-frequency neural stimulation of primary neurons under low-intensity focused ultrasound. Owing to its functionally anisotropic design, half of the PEMP acts as a piezoelectric electrode via conjugated barium titanate nanoparticles to induce electrical stimulation, while the nickel-gold nanofilm-coated magnetic half provides spatial and orientational control on neural stimulation via external uniform rotating magnetic fields. Furthermore, surface functionalization with targeting antibodies enables cell-specific binding/targeting and stimulation of dopaminergic neurons. Taking advantage of such functionalities, the PEMP design offers unique features towards wireless neural stimulation for minimally invasive treatment of neurological diseases.},

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 König 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{nokeye,

title = {Computational Flow Diverter Implantation—A 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{Villota-Narvaez2024,

title = {Data sharing in modeling and simulation of biomechanical systems in interdisciplinary environments},

author = {Yesid Villota-Narvaez and Christian Bleiler and Oliver Roehrle},

editor = {GAMM Mitteilungen},

url = {https://onlinelibrary.wiley.com/doi/10.1002/gamm.202370006},

doi = {https://doi.org/10.1002/gamm.202370006},

year  = {2024},

date = {2024-02-22},

urldate = {2024-02-22},

journal = {GAMM Mitteilungen},

volume = {47},

issue = {2},

abstract = {All digital objects that result from the modeling and simulation field are valid sets of research data. In general, research data are the result of intense intellectual activity that is worth communicating. This communication is an essential research practice that, whether with the aim of understanding, critiquing or further developing results, smoothly leads to collaboration, which not only involves discussions, and sharing institutional resources, but also the sharing of data and information at several stages of the research process. Data sharing is intended to improve and facilitate collaboration but quickly introduces challenges like reproducibility, reusability, interoperability, and standardization. These challenges are deeply rooted in an apparent reproducibility standard, about which there is a debate worth considering before emphasizing how the modeling and simulation workflow commonly occurs. Although that workflow is almost natural for practitioners, the sharing practices still require special attention because the principles (known as FAIR principles) that guide research practices towards data sharing also guide the requirements for machine actionable results. The FAIR principles, however, do not address the actual implementation of the data sharing process. This implementation requires careful consideration of characteristics of the sharing platforms for benefiting the most of the data sharing activity. This article serves as an invitation to integrate data sharing practices into the established routines of researchers and elaborates on the perspectives, and guidelines surrounding data sharing implementation.},

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{nokeyf,

title = {Unveiling rupture risk and clinical outcomes in midline aneurysms: A matched cohort analysis investigating the impact of localization within the anterior or posterior circulation},

author = {Vanessa M Swiatek and Amir Amini and Celina E Sandalcioglu Ortuño and Lena Spitz and Karl Hartmann and Ali Rashidi and Klaus-Peter Stein and Sylvia Saalfeld and I Erol Sandalcioglu and Belal Neyazi},

url = {https://link.springer.com/article/10.1007/s10143-024-02310-6},

doi = {https://doi.org/10.1007/s10143-024-02310-6},

year  = {2024},

date = {2024-02-07},

journal = {Neurosurgical Review},

volume = {47},

issue = {76},

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{Braun2024,

title = {Wearable activity data can predict functional recovery after musculoskeletal injury: Feasibility of a machine learning approach},

author = {Benedikt J Braun and Tina Histing and Maximilian M Menger and Steven C Herath and Gustav A Mueller-Franzes and Bernd Grimm and Meir T Marmor and Daniel Truhn},

doi = {10.1016/j.injury.2023.111254},

issn = {0020-1383},

year  = {2024},

date = {2024-02-00},

urldate = {2024-02-00},

journal = {Injury},

volume = {55},

number = {2},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schwer2024,

title = {The biomechanical properties of human menisci: A systematic review},

author = {Jonas Schwer and Anita Ignatius and Andreas Martin Seitz},

doi = {10.1016/j.actbio.2023.12.010},

issn = {1742-7061},

year  = {2024},

date = {2024-02-00},

urldate = {2024-02-00},

journal = {Acta Biomaterialia},

volume = {175},

pages = {1--26},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tautenhahn2024,

title = {SimLivA–Modeling 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 Bütow and Steffen Gerhäusser and Lena Lambers and Xinpei Chen and Elina Lehmann and Olaf Dirsch and Matthias König},

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—all 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{nokeyg,

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},

urldate = {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 Röhrle and Randall K. Powers and Francesco Negro and Utku Ş. 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{nokeyh,

title = {Fusiform versus Saccular Intracranial Aneurysms—Hemodynamic 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 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{nokeyi,

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{Fröhlich2024,

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

author = {Jonathan Fröhlich and Tobias Gerach and Jonathan Krauß and Axel Loewe and Laura Stengel and Christian Wieners},

editor = {Gesellschaft 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{Yildiz2024,

title = {Experimental model for strain-induced mechanical neurostimulation on human progenitor neurons},

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

editor = {Science Communications World Wide},

url = {https://www.world-wide.org/fens-24/experimental-model-strain-induced-mechanical-5cbdf455/},

doi = {https://doi.org/10.57736/a03c-08e1},

year  = {2024},

date = {2024-01-01},

journal = {Science Communications World Wide},

abstract = {Aim: Although non-invasive, such as focused ultrasound stimulation, and invasive, such as neural interface implantations, neurological interventions on the brain are increasing in the clinics nowadays, there is no detailed experimental model of these mechanical effects on neurons. In this study, we built an experimental model to mimic mechanical strain stress on neurons and compared the experimental model's effectiveness with the existing literature. Methods: In this study, we designed unidirectional, bidirectional, and omnidirectional strain setups integrated with a high-speed camera. Neural membrane potentials and intracellular calcium levels were calculated with a custom algorithm based on the calcium signal collected with Fluo-4 from RenCell human progenitor neurons, which was strained up to 20%. During this analysis, confounding effects of motion, strain, and background were removed with a custom-made algorithm. Results: In these experiments, human progenitor neurons subjected to instantaneous omnidirectional strain stress application above 15% generate action potential responses. While the action potential generation behavior is related to fast intracellular calcium influx, slow internal calcium increase due to strain application is not associated with action potential propagation. Conclusion: In this study, we have produced an experimental model for reproducible omnidirectional strain stress application and determined the threshold strain-stress values of action potential propagation behavior in human progenitor neurons. These results from this experimental model can be combined with theoretical models, such as the Hodgkin & Huxley model, and can be an effective simulation tool for future clinical applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{shi2024a,

title = {A physics-informed deep learning framework for modeling of coronary in-stent restenosis},

author = {Jianye Shi and Kiran Manjunatha and Marek Behr and Felix Vogt and Stefanie Reese},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Biomechanics and Modeling in Mechanobiology},

volume = {23},

number = {2},

pages = {615–629},

publisher = {Springer},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{shi2024data,

title = {Data-driven reduced order surrogate modeling for coronary in-stent restenosis},

author = {Jianye Shi and Kiran Manjunatha and Felix Vogt and Stefanie Reese},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Computer Methods and Programs in Biomedicine},

pages = {108466},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}