@article{Klink2026,

title = {Solving approximation tasks with greedy deep kernel methods},

author = {Marian Klink and Tobias Ehring and Robin Herkert and Robin Lautenschlager and Dominik Göddeke and Bernard Haasdonk},

url = {https://link.springer.com/article/10.1007/s44207-026-00012-z#citeas},

doi = {https://doi.org/10.1007/s44207-026-00012-z},

year  = {2026},

date = {2026-06-25},

urldate = {2026-06-25},

journal = {Computational Science and Engineering},

volume = {3},

issue = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mohan2026,

title = {Global existence of weak solutions to a cell migration and (de)differentiation model with double haptotaxis in the context of tissue regeneration},

author = {Nishith Mohan and Christina Surulescu },

editor = {Elsevier },

url = {https://www.sciencedirect.com/science/article/pii/S1468121825001981},

doi = {https://doi.org/10.1016/j.nonrwa.2025.104516},

issn = {1468-1218},

year  = {2026},

date = {2026-06-15},

urldate = {2026-06-15},

journal = {Nonlinear Analysis: Real World Applications},

volume = {89},

number = {104516},

abstract = {We study a model for the spread and (de)differentiation of mesenchymal stem cells and chondrocytes in a scaffold whose fibers are coated with hyaluron. The chondrocytes produce new extracellular matrix, which, together with hyaluron, serves as a haptotactic cue for the stem cell migration. We prove global existence of weak solutions of the corresponding cross-diffusion system with double haptotaxis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Surulescu2026,

title = {An in-silico approach to meniscus tissue regeneration: Modeling, numerical simulation, and experimental analysis},

author = {Christina Surulescu and Elise Grosjean and Martin Dauner and Michael Doser and Henry Jäger and Alex Keilmann and Carsten Linti and Shimi Chettiparambil Mohanan and Graciosa Quelhas Teixeira and Claudia Redenbach and Luisa de Roy and Andreas Martin Seitz and Bernd Simeon},

editor = {Elsevier },

url = {https://www.sciencedirect.com/science/article/pii/S0307904X25006092},

doi = {https://doi.org/10.48550/arXiv.2403.05909},

issn = {0307-904X},

year  = {2026},

date = {2026-03-31},

urldate = {2026-03-31},

journal = {Applied Mathematical Modelling},

volume = {151 Part B},

number = {116535},

abstract = {We develop a model the dynamics of human mesenchymal stem cells (hMSCs) and chondrocytes evolving in a nonwoven polyethylene terephtalate (PET) scaffold impregnated with hyaluron and supplied with a differentiation medium. The scaffold and the cells are assumed to be contained in a bioreactor with fluid perfusion. The differentiation of hMSCs into chondrocytes favors the production of extracellular matrix (ECM) and is influenced by fluid stress. The model takes deformations of ECM and PET scaffold into account. The scaffold structure is explicitly included by statistical assessment of the fibre distribution from CT images. The effective macroscopic equations are obtained by appropriate upscaling from dynamics on lower (microscopic and mesoscopic) scales and feature in the motility terms an explicit cell diffusion tensor encoding the assessed anisotropic scaffold structure. Numerical simulations show its influence on the overall cell and tissue dynamics. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Braun2026,

title = {Step count as a digital mobility outcome in orthopedics and orthopedic trauma surgery: a scoping review },

author = {Benedikt J. Braun and Bernd Grimm and Meir T. Marmor and Georg Osterhoff and David A. Back and Maximilian M. Menger and Carolina Vogel and Tina Histing and Dannik Haas and AO Trauma Digital Expert Group and Digital Working Group pf the DGOU},

editor = {EFORT Open Review },

url = {https://doi.org/10.1530/EOR-2025-0165},

doi = {https://doi.org/10.1530/EOR-2025-0165},

issn = {2058-5241},

year  = {2026},

date = {2026-02-04},

urldate = {2026-02-04},

journal = {EFORT Open Reviews},

volume = {11},

issue = {2},

pages = {85-95},

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{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{Ranno2025,

title = {A computational model of coronary arteries with in-stent restenosis coupling hemodynamics and pharmacokinetics with growth mechanics. },

author = {Anna Ranno and Kiran Manjunatha and Thore Koritzius and Ivo Steinbrecher and Norbert Hosters and Maximilian Nachtsheim and Pakhwan Nilcham and Nicole Schaaps and Anne Turoni-Glitz and Janina Datz and Alexander Popp and Kevin Linka and Felix Vogt and Marek Behr },

url = {https://www.nature.com/articles/s41598-025-22291-w#citeas},

doi = {https://doi.org/10.1038/s41598-025-22291-w},

issn = {2045-2322 (online) },

year  = {2025},

date = {2025-11-10},

urldate = {2025-11-10},

journal = {Scientific Reports},

volume = {15},

number = {39229},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Elias2025,

title = {A digital twin of glimepiride for personalized and stratified diabetes treatment},

author = {Michelle Elias and Matthias König},

doi = {https://doi.org/10.3389/fphar.2025.1686415},

issn = {1663-9812},

year  = {2025},

date = {2025-10-08},

urldate = {2025-10-08},

journal = {Front. Pharmacol.},

volume = {16},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Andres2025,

title = {Predicting the effect of individual weight-bearing on tibial load and fracture healing after tibial plateau fractures–introduction of a biomechanical simulation model},

author = {Annchristin Andres and Michael Roland and Kerstin Wickert and Stefan Diebels and Daniel Truhn and Tina Histing and Benedikt Braun},

editor = {Front. Bioeng. Biotechnol. },

url = {https://doi.org/10.3389/fbioe.2025.1659029},

doi = {https://doi.org/10.3389/fbioe.2025.1659029},

year  = {2025},

date = {2025-09-25},

urldate = {2025-09-25},

journal = {Front. Bioeng. Biotechnol. Sec. Biomechanics},

number = {1659029},

issue = {13 - 2025},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Klotz2025,

title = {Revisiting convolutive blind source separation for identifying spiking motor neuron activity: from theory to practice},

author = {Thomas Klotz and Robin Rohlén},

editor = {IOP Publishing Ltd },

url = {https://iopscience.iop.org/article/10.1088/1741-2552/adf886},

doi = {DOI 10.1088/1741-2552/adf886},

year  = {2025},

date = {2025-08-26},

urldate = {2025-08-26},

journal = {Journal of Neural Engineering},

volume = {22},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sesa2025,

title = {A comprehensive framework for computational modeling of growth and remodeling in tissue-engineered soft collagenous materials},

author = {Mahmoud Sesa and H. Holthusen and C. Böhm and S. Jockenhövel and Stefanie Reese and Kevin Linka},

editor = {Springer nature },

url = {https://link.springer.com/article/10.1007/s10237-025-01988-x},

doi = {https://doi.org/10.1007/s10237-025-01988-x},

year  = {2025},

date = {2025-07-23},

urldate = {2025-07-23},

journal = { Biomechanics and Modeling in Mechanobiology},

volume = {24},

pages = {1687–1711},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Braun2025b,

title = {Towards a comprehensive digital wearable tracking system of the patient recovery journey after extremity trauma: a narrative review},

author = { Benedikt J Braun and Maximilian M Menger and Tina Histing and Meir T Marmor and Bernd Grimm ad Felix Fischer and Conrad Harrison and Alexander Joeris and Simon Lambert and AO Upper Extremity Global Expert Committee* and AO Trauma Digital Expert Group* and BG Tübingen Digital Outcome Assessment Group*









BG Tübingen Digital Outcome Assessment Group},

editor = {EFORT Open Review},

url = {https://doi.org/10.1530/EOR-2024-0154},

doi = {10.1530/EOR-2024-0154},

issn = {2058-5241},

year  = {2025},

date = {2025-07-01},

urldate = {2025-07-01},

journal = {General Orthopaedics},

volume = {10},

issue = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Andres2025d,

title = {From Injury to Full Recovery: Monitoring Patient Progress Through Advanced Sensor and Motion Capture Technology},

author = {Annchristin Andres and Michael Roland and Marcel Orth and Stefan Diebels},

url = {https://doi.org/10.3390/s25133853 },

doi = {https://doi.org/10.3390/s25133853 },

year  = {2025},

date = {2025-06-20},

urldate = {2025-06-20},

journal = {Sensors},

number = {3853},

issue = {25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Andres2025c,

title = {Advantages of digital twin technology in orthopedic trauma Surgery – Exploring different clinical use cases},

author = {Annchristin Andres and Michael Roland and Kerstin Wickert and Stefan Diebels and Johannes Stöckl and Stefan Herrmann and Frank Reinauer and Ralf Leibinger and Atanas Pavlov and Lutz Schuppener and Daniel Schäfer and Tina Histing and Benedikt J. Braun },

url = {https://doi.org/10.1038/s41598-025-04792-w},

doi = {https://doi.org/10.1038/s41598-025-04792-w},

year  = {2025},

date = {2025-06-06},

urldate = {2025-06-06},

journal = {Sci Rep},

volume = {15},

number = {19987 (2025)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Obermeier2025,

title = {Impact of surgical ventricular restoration on intracardiac hemodynamics: An in silico study using CCT data},

author = {Lukas Obermeier and Moritz Wiegand and Titus Kuehne and Volkmar Falk and Christoph Knosalla and Natalia Solowjowa and Leonid Goubergrits and Katharina Vellguth},

doi = {10.1016/j.compbiomed.2025.110227},

issn = {0010-4825},

year  = {2025},

date = {2025-06-00},

urldate = {2025-06-00},

journal = {Computers in Biology and Medicine},

volume = {192},

publisher = {Elsevier BV},

abstract = {Surgical ventricular restoration (SVR) excludes scarred myocardium after myocardial infarction to restore shape and contractility of dilated, aneurysmal left ventricles (LVs). Detailed changes in intracardiac hemodynamics following the surgery are not fully investigated. In this study, digital replicas of the patient’s LV were used to study the hemodynamic impact of successful SVR. The digital replicas were built based on pre-operative and post-operative cardiac computed tomography data of nine patients (3 females, 60 ± 13 years) who underwent successful SVR (significant reduction in heart failure symptoms). The computational framework was used to calculate LV morphology, dynamics, and intracardiac hemodynamics using image-based computational fluid dynamics (CFD). SVR successfully reduced the LV volumes. Morphological analysis showed restoration of myocardial wall thickness in aneurysmal regions (5.5 ± 2.0 vs. 8.6 ± 3.0 mm) and an increased end-diastolic sphericity (sphericity index 0.39 ± 0.07 vs. 0.46 ± 0.07). No distinct flow alterations could be linked thereto. CFD revealed a higher post-operative kinetic energy level (diastolic maximum 10.0 ± 7.6 vs. 16.8 ± 9.1 mJ) and an improved global washout (29.5 ± 9.7 vs. 10.3 ± 6.4% after five cycles), which correlated to increases in volume-curve-derived diastolic energy gain and ejection fraction, respectively. Flow efficiency improved by means of an increased end-diastolic surface-averaged vortex strength (16.2 ± 5.1 vs. 30.0 ± 15.0 1/s) and a decreased normed diastolic energy loss (18.9 ± 3.9 vs. 15.0 ± 3.7%). The hemodynamic filling forces in diastole were aligned with the LV long axis before and after surgery and correlated with LV contractility. In summary, the digital patient replicas facilitated a detailed analysis and showed favorable flow changes with successful SVR.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Andres2025b,

title = {Simulation of a Custom-Made Temporomandibular Joint—An Academic View on an Industrial Workflow },

author = {Annchristin Andres and Kerstin Wickert and Elena Gneiting and Franziska Binmoeller and Stefan Diebels and Michael Roland},

url = {https://doi.org/10.3390/bioengineering12050545},

doi = {https://doi.org/10.3390/bioengineering12050545},

year  = {2025},

date = {2025-05-20},

urldate = {2025-05-20},

journal = {Bioengineering},

volume = {5},

pages = {545},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Braun2025,

title = {Patient Recruitment Characteristics for Wearable-Sensor-Based Outcome Assessment in Trauma Surgery },

author = {Benedikt J. Braun and Kira Hofmann and Chiara N. Meierhofer and Maximilian M. Menger and Tanja C. Maisenbacher and Carolina Vogel and Dannik Haas and Meir T. Marmor and Tina Histing and Eva-Marie Braun and The AO Smart Digital Solutions Task Force

},

url = {https://doi.org/10.3390/jcm14030805},

doi = {10.3390/jcm14030805},

year  = {2025},

date = {2025-05-14},

urldate = {2025-05-14},

journal = {Journal of Clinical Medicine},

volume = {14},

number = {3},

pages = {803},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Baier2025,

title = {Contactless measurement of muscle fiber conduction velocity—a novel approach using optically pumped magnetometers},

author = {Lukas Baier and Tim Brümmer and Burak Senay and Markus Siegel and Ahmet Doğukan Keleş and Oliver Röhrle and Thomas Klotz and Nima Noury and Justus Marquetand},

editor = {IOP Publishing Ltd },

url = {https://iopscience.iop.org/article/10.1088/1741-2552/adc83b},

doi = {doi: 10.1088/1741-2552/adc83b},

year  = {2025},

date = {2025-04-16},

urldate = {2025-04-16},

journal = {Journal of Neural Engineering},

volume = {22},

issue = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Andres2025e,

title = {Individual postoperative and preoperative workflow for patients with fractures of the lower extremities},

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

url = {https://doi.org/10.1016/j.clinbiomech.2025.106503},

doi = {https://doi.org/10.1016/j.clinbiomech.2025.106503},

issn = {0268-0033},

year  = {2025},

date = {2025-03-22},

urldate = {2025-03-22},

journal = {Clinical Biomechanics},

number = {106503},

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{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{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{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{Stengel2024,

title = {Enriched and Discontinuous Galerkin Discretizations for a Cardiac Mechanics Benchmark Problem},

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

url = {https://cinc.org/archives/2024/pdf/CinC2024-299.pdf},

doi = {doi.org/10.22489/CinC.2024.299},

year  = {2024},

date = {2024-12-31},

urldate = {2024-12-31},

abstract = {Computer models of the human heart enhance understanding of cardiac function but require a compromise between computational cost and numerical accuracy for clinical use. Due to the high mathematical complexity of the underlying model, the commonly used finite element discretization may not achieve the optimal balance between efficiency, reliability, and accuracy. To investigate the impact of different spatial discretization schemes on cardiac mechanics, we realized a benchmark configuration, which considers the hyper-elastic problem of inflating and ac-

tively contracting an idealized left ventricle with transversely isotropic and nearly incompressible properties. Comparing linear and quadratic conforming Galerkin, discontinuous Galerkin and enriched Galerkin elements, we found that enriched and discontinuous Galerkin methods reduced locking phenomena but with higher numbers of degrees of freedom and computational costs, particularly for the discontinuous Galerkin approach. However, enriched Galerkin demonstrated comparable robustness to discontinuous Galerkin with substantially fewer degrees of freedom, presenting a favorable compromise between computational efficiency and numerical robustness.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Duhme2024,

title = {Modeling Human Ventricular Cardiomyocyte Force-Frequency Relationship},

author = {Jan-Erik Duhme and Jonathan Krauß and Axel Loewe},

editor = {De Gruyter Bril},

url = {https://www.degruyterbrill.com/document/doi/10.1515/cdbme-2024-2051/html},

doi = {doi.org/10.1515/cdbme-2024-2051},

year  = {2024},

date = {2024-12-19},

urldate = {2024-12-19},

journal = {Current Directions in Biomedical Engineering},

volume = {10},

issue = {4},

pages = {212-215},

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{Stengel2024b,

title = {Enriched and Discontinuous Galerkin Discretizations for a Cardiac Mechanics Benchmark Problem},

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

url = {https://www.cinc.org/archives/2024/pdf/CinC2024-299.pdf},

doi = {doi.org/10.22489/CinC.2024.299},

isbn = {2325-887X },

year  = {2024},

date = {2024-10-28},

urldate = {2024-10-28},

journal = {Computing in Cardiology },

volume = {51},

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{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{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{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{Ranno2024,

title = {In-silico Analysis of Hemodynamic Indicators in Idealized Stented Coronary Arteries for Varying Stent Indentation},

author = {A. Ranno and K. Manjunatha and A. Glitz and N. Schaaps and S. Reese and F. Vogt and M. Behr},

editor = {Cornell University},

url = {https://www.tandfonline.com/doi/citedby/10.1080/10255842.2024.2382819?scroll=top&needAccess=true},

doi = {https://doi.org/10.1080/10255842.2024.2382819},

year  = {2024},

date = {2024-07-31},

urldate = {2024-07-31},

journal = {Computer Methods in Biomechanics and Biomedical Engineering},

volume = {29},

number = {1},

pages = {167-188},

abstract = {In this work, we investigate the effects of stent indentation on hemodynamic indicators in stented coronary arteries. Our aim is to assess in-silico risk factors for in-stent restenosis (ISR) and thrombosis after stent implantation. The proposed model is applied to an idealized artery with Xience V stent for four indentation percentages and three mesh refinements. We analyze the patterns of hemodynamic indicators arising from different stent indentations and propose an empirical frequency analysis of time-averaged WSS (TAWSS), oscillatory shear index (OSI), and relative residence time (RRT). We observe that higher indentations display higher frequency of critically low TAWSS and non-physiological OSI and RRT. Furthermore, an appropriate mesh refinement is needed for accurate representation of hemodynamics in the stent vicinity. The results provide physics-based evidence for the correlation between high indentation and ISR.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Roland2024,

title = {Finite element simulations of smart fracture plates capable of cyclic shortening and lengthening: which stroke for which fracture?},

author = {Michael Roland and Stefan Diebels and Kerstin Wickert and Tim Pohlemann and Bergita Ganse},

editor = {Front. Bioeng. Biotechnol.},

url = {https://www.frontiersin.org/articles/10.3389/fbioe.2024.1420047/full},

doi = {10.3389/fbioe.2024.1420047},

year  = {2024},

date = {2024-07-23},

urldate = {2024-07-23},

journal = {Front. Bioeng. Biotechnol.},

volume = {Sec. Biomechanics},

issue = {12-2024},

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{Manjunatha2024b,

title = {In Silico Reproduction of the Pathophysiology of In-Stent Restenosis},

author = {K. Manjunatha and A. Ranno and J. Shi and N. Schaaps and R. Florescu and P. Nilcham and A. Cornelissen and M. Behr and S. Reese},

editor = {Cornell University},

url = {https://arxiv.org/abs/2401.03961},

doi = {10.48550/arXiv.2401.03961},

year  = {2024},

date = {2024-05-07},

urldate = {2024-05-07},

abstract = {The occurrence of in-stent restenosis following percutaneous coronary intervention highlights the need for the creation of computational tools that can extract pathophysiological insights and optimize interventional procedures on a patient-specific basis. In light of this, a comprehensive framework encompassing multiple physical phenomena is introduced in this work. This framework effectively captures the intricate interplay of chemical, mechanical, and biological factors. In addition, computational approaches for the extraction of hemodynamic indicators that modulate the severity of the restenotic process are devised. Thus, this marks a significant stride towards facilitating computer-assisted clinical methodologies.},

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},

urldate = {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{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},

urldate = {2024-03-29},

journal = {Journal of Neurosurgery},

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{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{Ates2024,

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},

urldate = {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{Wickert2024,

title = {Experimental and virtual testing of bone-implant systems equipped with the AO Fracture Monitor with regard to interfragmentary movement },

author = {Kerstin Wickert and Michael Roland and Annchristin Andres and Stefan Diebels and Bergita Ganse and Dorothea Kerner and Felix Frenzel and Thomas Tschernig and Manuela Ernst and Markus Windolf and Max Müller an Tim Pohlemann and Marcel Orth},

editor = {Front. Bioeng. Biotechnol.},

url = {https://doi.org/10.3389/fbioe.2024.1370837},

doi = {10.3389/fbioe.2024.1370837},

year  = {2024},

date = {2024-03-06},

urldate = {2024-03-06},

journal = {Front. Bioeng. Biotechnol.},

volume = {Sec. Biomechanics},

issue = {12-2024},

keywords = {},

pubstate = {published},

tppubtype = {article}

}