TY - JOUR A1 - Gonnermann-Müller, Jana A1 - Haase, Jennifer A1 - Fackeldey, Konstantin A1 - Pokutta, Sebastian T1 - FACET: Teacher-Centred LLM-Based Multi-Agent Systems-Towards Personalized Educational Worksheets N2 - The increasing heterogeneity of student populations poses significant challenges for teachers, particularly in mathematics education, where cognitive, motivational, and emotional differences strongly influence learning outcomes. While AI-driven personalization tools have emerged, most remain performance-focused, offering limited support for teachers and neglecting broader pedagogical needs. This paper presents the FACET framework, a teacher-facing, large language model (LLM)-based multi-agent system designed to generate individualized classroom materials that integrate both cognitive and motivational dimensions of learner profiles. The framework comprises three specialized agents: (1) learner agents that simulate diverse profiles incorporating topic proficiency and intrinsic motivation, (2) a teacher agent that adapts instructional content according to didactical principles, and (3) an evaluator agent that provides automated quality assurance. We tested the system using authentic grade 8 mathematics curriculum content and evaluated its feasibility through a) automated agent-based assessment of output quality and b) exploratory feedback from K-12 in-service teachers. Results from ten internal evaluations highlighted high stability and alignment between generated materials and learner profiles, and teacher feedback particularly highlighted structure and suitability of tasks. The findings demonstrate the potential of multi-agent LLM architectures to provide scalable, context-aware personalization in heterogeneous classroom settings, and outline directions for extending the framework to richer learner profiles and real-world classroom trials. Y1 - 2025 ER - TY - JOUR A1 - Andrés Arcones, Daniel A1 - Weiser, Martin A1 - Koutsourelakis, Phaedon-Stelios A1 - Unger, Jörg F. T1 - Embedded Model Form Uncertainty Quantification with Measurement Noise for Bayesian Model Calibration JF - Data-Centric Engineering N2 - A key factor in ensuring the accuracy of computer simulations that model physical systems is the proper calibration of their parameters based on real-world observations or experimental data. Inevitably, uncertainties arise, and Bayesian methods provide a robust framework for quantifying and propagating these uncertainties to model predictions. Nevertheless, Bayesian methods paired with inexact models usually produce predictions unable to represent the observed datapoints. Additionally, the quantified uncertainties of these overconfident models cannot be propagated to other Quantities of Interest (QoIs) reliably. A promising solution involves embedding a model inadequacy term in the inference parameters, allowing the quantified model form uncertainty to influence non-observed QoIs. This paper introduces a more interpretable framework for embedding the model inadequacy compared to existing methods. To overcome the limitations of current approaches, we adapt the existing likelihood models to properly account for noise in the measurements and propose two new formulations designed to address their shortcomings. Moreover, we evaluate the performance of this inadequacy-embedding approach in the presence of discrepancies between measurements and model predictions, including noise and outliers. Particular attention is given to how the uncertainty associated with the model inadequacy term propagates to the QoIs, enabling a more comprehensive statistical analysis of prediction’s reliability. Finally, the proposed approach is applied to estimate the uncertainty in the predicted heat flux from a transient thermal simulation using temperature bservations. Y1 - 2026 U6 - https://doi.org/10.1017/dce.2025.10035 VL - 7 ER - TY - JOUR A1 - Agarwal, A. A1 - Greve, Nico A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - et al., T1 - Performance of the prototype Silicon Tracking System of the CBM experiment tested with heavy-ion beams at SIS18 JF - Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment Y1 - 2025 U6 - https://doi.org/10.1016/j.nima.2025.171059 SN - 0168-9002 N1 - This paper has 343 authors. For the complete list of authors use the DOI, please. VL - 1082 SP - 171059 PB - Elsevier BV ER - TY - JOUR A1 - Xie, Kunpeng A1 - Gruber, Lennart Johannes A1 - Crampen, Martin A1 - Li, Yao A1 - Ferreira, André A1 - Tappeiner, Elias A1 - Gillot, Maxime A1 - Schepers, Jan A1 - Xu, Jiangchang A1 - Pankert, Tobias A1 - Beyer, Michel A1 - Shahamiri, Negar A1 - ten Brink, Reinier A1 - Dot, Gauthier A1 - Weschke, Charlotte A1 - van Nistelrooij, Niels A1 - Verhelst, Pieter-Jan A1 - Guo, Yan A1 - Xu, Zhibin A1 - Bienzeisler, Jonas A1 - Rashad, Ashkan A1 - Flügge, Tabea A1 - Cotton, Ross A1 - Vinayahalingam, Shankeeth A1 - Ilesan, Robert A1 - Raith, Stefan A1 - Madsen, Dennis A1 - Seibold, Constantin A1 - Xi, Tong A1 - Bergé, Stefaan A1 - Nebelung, Sven A1 - Kodym, Oldřich A1 - Sundqvist, Osku A1 - Thieringer, Florian A1 - Lamecker, Hans A1 - Coppens, Antoine A1 - Potrusil, Thomas A1 - Kraeima, Joep A1 - Witjes, Max A1 - Wu, Guomin A1 - Chen, Xiaojun A1 - Lambrechts, Adriaan A1 - Cevidanes, Lucia H Soares A1 - Zachow, Stefan A1 - Hermans, Alexander A1 - Truhn, Daniel A1 - Alves, Victor A1 - Egger, Jan A1 - Röhrig, Rainer A1 - Hölzle, Frank A1 - Puladi, Behrus T1 - Beyond Benchmarks: Towards Robust Artificial Intelligence Bone Segmentation in Socio-Technical Systems JF - Expert Systems With Applications N2 - Despite the advances in automated medical image segmentation, AI models still underperform in various clinical settings, challenging real-world integration. In this multicenter evaluation, we analyzed 20 state-of-the-art mandibular segmentation models across 19,218 segmentations of 1,000 clinically resampled CT/CBCT scans. We show that segmentation accuracy varies by up to 25% depending on socio-technical factors such as voxel size, bone orientation, and patient conditions such as osteosynthesis or pathology. Higher sharpness, isotropic smaller voxels, and neutral orientation significantly improved results, while metallic osteosynthesis and anatomical complexity led to significant degradation. Our findings challenge the common view of AI models as “plug-and-play” tools and suggest evidence-based optimization recommendations for both clinicians and developers. This will in turn boost the integration of AI segmentation tools in routine healthcare. Y1 - 2025 UR - https://www.medrxiv.org/content/10.1101/2025.06.11.25329022v1 U6 - https://doi.org/10.1016/j.eswa.2025.130031 VL - 299 IS - Part D ER - TY - JOUR A1 - Sato, Mako A1 - Koch, Thorsten A1 - Le, Thi Thai T1 - Influence of frictional drag on Kelvin-Helmholtz instability in viscous fluids JF - Physics of Fluids N2 - The Kelvin-Helmholtz instability arises at the interface between two fluid layers with a tangential velocity discontinuity, significantly impacting the safety of systems in industrial applications. Despite extensive studies, many theoretical analyses neglect viscosity and frictional drag due to the complexity of solving the dispersion equation. However, including these effects is crucial, as viscosity alters the growth rate of the instability, while frictional drag influences energy dissipation and momentum transfer. In this study, these effects are incorporated into both finite and infinite flows. The assumption of a potential flow combined with a dissipation method is employed to derive the dispersion equation, providing a more tractable approach than direct calculation methods. The results indicate that, in the case of infinite flows, the frictional drag suppresses the growth of the instability for long waves (small wavenumber k) but enhances it for short waves (large k). In contrast, the surface tension dominates, while the frictional drag only slightly affects the growth rate in the case of finite flows bounded by solid walls. Y1 - 2026 U6 - https://doi.org/10.1063/5.0306177 VL - 38 IS - 1 PB - AIP Publishing CY - Physics of Fluids ER - TY - JOUR A1 - Hu, Chenhao A1 - Tutika, Ravi A1 - Deng, Zhifei A1 - Jia, Zian A1 - Chen, Liuni A1 - Chen, Hongshun A1 - Geng, Yang A1 - Xiao, Xianghui A1 - Shevchenko, Pavel D. A1 - Pierre, Christoph A1 - Weaver, James C. A1 - Baum, Daniel A1 - Bartlett, Michael D. A1 - Li, Ling T1 - Mineralized sclerites in the gorgonian coral Leptogorgia chilensis as a natural jamming system JF - PNAS Y1 - 2025 U6 - https://doi.org/10.1073/pnas.2504541122 VL - 122 IS - 44 ER - TY - JOUR A1 - Zittel, Janina A1 - Petkovic, Milena A1 - Einck, Mathias T1 - Forecasting Hourly Gas Flows JF - Foresight - The International Journal of Applied Forecasting Y1 - 2025 UR - https://econpapers.repec.org/RePEc:for:ijafaa:y:2025:i:79:p:40-44 VL - 79 SP - 40 EP - 44 ER - TY - JOUR A1 - Kießling, David A1 - Leyffer, Sven A1 - Vanaret, Charlie T1 - A Unified Funnel Restoration SQP Algorithm JF - Mathematical Programming B N2 - We consider nonlinearly constrained optimization problems and discuss a generic double-loop framework consisting of basic algorithmic ingredients that unifies a broad range of nonlinear optimization solvers. This framework has been implemented in the open-source solver Uno, a Swiss Army knife-like C++ optimization framework that unifies many nonlinearly constrained nonconvex optimization solvers. We illustrate the framework with a sequential quadratic programming (SQP) algorithm that maintains an acceptable upper bound on the constraint violation, called a funnel, that is monotonically decreased to control the feasibility of the iterates. Infeasible quadratic subproblems are handled by a feasibility restoration strategy. Globalization is controlled by a line search or a trust-region method. We prove global convergence of the trust-region funnel SQP method, building on known results from filter methods. We implement the algorithm in Uno, and we provide extensive test results for the trust-region line-search funnel SQP on small CUTEst instances. Y1 - 2025 U6 - https://doi.org/10.1007/s10107-025-02284-3 ER - TY - JOUR A1 - Bartoli, Adrien A1 - Sengupta, Agniva T1 - Camera Pose in SfT and NRSfM under Isometric and Weaker Deformation Models JF - Computer Vision and Image Understanding N2 - Camera pose is a very natural concept in 3D vision in the rigid setting. It is however much more difficult to work with in deformable settings. Consequently, numerous deformable reconstruction methods simply ignore camera pose. We analyse the concept of pose in deformable settings and prove that it is unconstrained with the existing formulations, properly justifying the existing pose-less methods reconstructing structure only. We explain this result intuitively by the impossibility to define an intrinsic coordinate frame to a general deforming object. The proposed analysis uses the isometric deformation model and extends to the weaker models including conformality and equiareality. We propose a novel prior to rescue camera pose estimation in deformable settings, which attributes the deforming object’s dominant rigid-body motion to the camera. We show that adding this prior to any existing formulation fully constrains camera pose and leads to elegant two-step solution methods, involving deformable structure reconstruction using a base method in the first step, and absolute orientation or Procrustes analysis in the second step. We derive the proposed approach for the template-based and template-less settings, respectively implemented using Shape-from-Template (SfT) and Non-Rigid Structure-from-Motion (NRSfM) as base methods, and validate them experimentally, showing that the computed pose is qualitatively and quantitatively plausible. Y1 - 2025 U6 - https://doi.org/10.1016/j.cviu.2025.104488 VL - 261 ER - TY - JOUR A1 - Reuss, Joana A1 - Macdonald, Jan A1 - Becker, Simon A1 - Schultka, Konrad A1 - Richter, Lorenz A1 - Körner, Marco T1 - Meta-learning For Few-Shot Time Series Crop Type Classification: A Benchmark On The EuroCropsML Dataset N2 - Spatial imbalances in crop type data pose significant challenges for accurate classification in remote sensing applications. Algorithms aiming at transferring knowledge from data-rich to data-scarce tasks have thus surged in popularity. However, despite their effectiveness in previous evaluations, their performance in challenging real-world applications is unclear and needs to be evaluated. This study benchmarks transfer learning and several meta-learning algorithms, including (First-Order) Model-Agnostic Meta-Learning ((FO)-MAML), Almost No Inner Loop (ANIL), and Task-Informed Meta-Learning (TIML), on the real-world EuroCropsML time series dataset, which combines farmer-reported crop data with Sentinel-2 satellite observations from Estonia, Latvia, and Portugal. Our findings indicate that MAML-based meta-learning algorithms achieve slightly higher accuracy compared to simpler transfer learning methods when applied to crop type classification tasks in Estonia after pre-training on data from Latvia. However, this improvement comes at the cost of increased computational demands and training time. Moreover, we find that the transfer of knowledge between geographically disparate regions, such as Estonia and Portugal, poses significant challenges to all investigated algorithms. These insights underscore the trade-offs between accuracy and computational resource requirements in selecting machine learning methods for real-world crop type classification tasks and highlight the difficulties of transferring knowledge between different regions of the Earth. To facilitate future research in this domain, we present the first comprehensive benchmark for evaluating transfer and meta-learning methods for crop type classification under real-world conditions. The corresponding code is publicly available at this https URL. Y1 - 2025 ER - TY - JOUR A1 - Berner, Julius A1 - Richter, Lorenz A1 - Sendera, Marcin A1 - Rector-Brooks, Jarrid A1 - Malkin, Nikolay T1 - From discrete-time policies to continuous-time diffusion samplers: Asymptotic equivalences and faster training N2 - We study the problem of training neural stochastic differential equations, or diffusion models, to sample from a Boltzmann distribution without access to target samples. Existing methods for training such models enforce time-reversal of the generative and noising processes, using either differentiable simulation or off-policy reinforcement learning (RL). We prove equivalences between families of objectives in the limit of infinitesimal discretization steps, linking entropic RL methods (GFlowNets) with continuous-time objects (partial differential equations and path space measures). We further show that an appropriate choice of coarse time discretization during training allows greatly improved sample efficiency and the use of time-local objectives, achieving competitive performance on standard sampling benchmarks with reduced computational cost. Y1 - 2025 ER - TY - JOUR A1 - Blessing, Denis A1 - Berner, Julius A1 - Richter, Lorenz A1 - Domingo-Enrich, Carles A1 - Du, Yuanqi A1 - Vahdat, Arash A1 - Neumann, Gerhard T1 - Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inference N2 - Solving stochastic optimal control problems with quadratic control costs can be viewed as approximating a target path space measure, e.g. via gradient-based optimization. In practice, however, this optimization is challenging in particular if the target measure differs substantially from the prior. In this work, we therefore approach the problem by iteratively solving constrained problems incorporating trust regions that aim for approaching the target measure gradually in a systematic way. It turns out that this trust region based strategy can be understood as a geometric annealing from the prior to the target measure, where, however, the incorporated trust regions lead to a principled and educated way of choosing the time steps in the annealing path. We demonstrate in multiple optimal control applications that our novel method can improve performance significantly, including tasks in diffusion-based sampling, transition path sampling, and fine-tuning of diffusion models. Y1 - 2025 ER - TY - JOUR A1 - Reuss, Joana A1 - Macdonald, Jan A1 - Becker, Simon A1 - Richter, Lorenz A1 - Körner, Marco T1 - The EuroCropsML time series benchmark dataset for few-shot crop type classification in Europe JF - Scientific Data N2 - We introduce EuroCropsML, an analysis-ready remote sensing dataset based on the open-source EuroCrops collection, for machine learning (ML) benchmarking of time series crop type classification in Europe. It is the first time-resolved remote sensing dataset designed to benchmark transnational few-shot crop type classification algorithms that supports advancements in algorithmic development and research comparability. It comprises 706683 multi-class labeled data points across 176 crop classes. Each data point features a time series of per-parcel median pixel values extracted from Sentinel-2 L1C data and precise geospatial coordinates. EuroCropsML is publicly available on Zenodo. Y1 - 2025 U6 - https://doi.org/10.1038/s41597-025-04952-7 VL - 12 ER - TY - JOUR A1 - Eigen, Lennart A1 - Ladenburger, Pius A1 - Brence, Blaž A1 - Shubitidze, Ani A1 - Baum, Daniel A1 - Hildebrandt, Thomas A1 - Brecht, Michael T1 - Elephant trunk tip musculature reflects species differences in grasping behavior JF - Communications Biology N2 - Elephants use their trunks, muscular hydrostats, to perform a plethora of tasks. Trunk tip morphology as well as grasping behavior differ between elephant species. While African savanna elephants (Loxodonta africana) use their dorsal and ventral finger for pinching movements, Asian elephants (Elephas maximus) prefer to wrap around objects with their one dorsal finger and ventral bulb trunk tip lip. Moreover, E. maximus can flip their ventral bulb backwards to clamp objects behind the trunk tip. Whether trunk tip musculature differs between elephant species and muscle architecture is reflected by preferred grasping behavior is, however, not clear. In this study, we performed dense muscle fascicle reconstruction of three L. africana and three E. maximus hemi-trunk tips using a combination of manual and automated segmentation of high-resolution microfocus tomography (microCT) scans. We distinguish three types of muscle fascicles: longitudinal (bending and shortening), radial (elongating) and transversal muscle fascicles (elongating). We found that trunk tips of L. africana consist to one third of longitudinal and two thirds radial/transversal muscle fascicles, likely aiding in their grasping behavior, while E. maximus trunk tips consist to two thirds of longitudinal and one third radial/transversal muscle fascicles, which is advantageous for their wrapping and backward clamping behavior. Y1 - 2025 U6 - https://doi.org/10.1038/s42003-025-08998-6 VL - 8 ER - TY - JOUR A1 - Brence, Blaž A1 - Wandelt, Laura R. A1 - Walter, Sophie A1 - Sigrist, Stephan J. A1 - Petzoldt, Astrid G. A1 - Baum, Daniel T1 - Semi-automatic 3D-quantification of in-vivo synapse formation JF - ResearchSquare N2 - Background: Synapses, as specialised cell-cell contacts, allow for a faithful and controlled signal transmission between a neuron and a target cell. Presynapses, the sites of neurotransmitter release, form de novo throughout the development of an organism. Although this process is fundamental to the development and function of synaptic circuits, how developing neurons control number and distribution of individual synapses remains poorly understood. In-vivo imaging analysis of synapse formation at the neuromuscular junction of anaesthetised Drosophila third instar larvae allows for spatial and temporal resolution of the underlying molecular processes. However, high-throughput, comprehensive analysis are hampered by the manual and time-consuming imaging analysis methods applied hitherto. Here, we focus on the early presynaptic formation steps, that is, the presynaptic seeding, initiated by the formation of transient Liprin-a/SYD1 seeding sites, either stabilised or disintegrated over a time span of 30-90 min. Results: To investigate the dynamics of the Liprin-a/SYD1 seeding sites, we developed an automated analysis pipeline for 3D confocal images from in-vivo imaging at distinct time points to analyse fluorescently labelled presynaptic protein dynamics during early synapse formation. The workflow is realised in the data analysis software Amira, utilising the hierarchical watershed algorithm, and was designed for automatic processing with an option for manual proofreading. Compared to the previous 2D manual quantification, this automated approach provides a higher sensitivity in single Liprin-a seeding site detection in low-intensity areas and in regions of dense seeding sites.In addition, it substantially reduces the work time. To account for possible errors occurring in the automated processing, we implemented an additional proofreading step allowing for a manual correction of Liprin-a seeding site segmentation and assignment, thus greatly improving the analysis while only marginally increasing work time by 10% to a total work time reduction of 80% compared to the 2D manual analysis paradigm. Conclusion: The process of synaptogenesis underlies the general principles of locomotion, learning and memory formation. The developed fast and accurate semi-automated 3D workflow provides a substantial progress in the analysis of this molecular process and its application can be easily extended to other dynamic in-vivo research approaches across species. Y1 - 2025 U6 - https://doi.org/10.21203/rs.3.rs-6073150/v1 ER - TY - JOUR A1 - Brence, Blaž A1 - Brummer, Josephine A1 - Dercksen, Vincent J. A1 - Özel, Mehmet Neset A1 - Kulkarni, Abhishkek A1 - Wolterhoff, Neele A1 - Prohaska, Steffen A1 - Hiesinger, Peter Robin A1 - Baum, Daniel T1 - Semi-automatic Geometrical Reconstruction and Analysis of Filopodia Dynamics in 4D Two-Photon Microscopy Images JF - bioRxiv N2 - Background: Filopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells. Results: To address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal Drosophila brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the Amira software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing. Conclusion: To facilitate simple application within Amira or other frameworks, we share the source code, which is available athttps://github.com/zibamira/filopodia-tool. Y1 - 2025 U6 - https://doi.org/10.1101/2025.05.20.654789 ER - TY - JOUR A1 - Trepczynski, Adam A1 - Kneifel, Paul A1 - Heyland, Mark A1 - Leskovar, Marko A1 - Moewis, Philippe A1 - Damm, Philipp A1 - Taylor, William R. A1 - Zachow, Stefan A1 - Duda, Georg N. T1 - Impact of the external knee flexion moment on patello-femoral loading derived from in vivo loads and kinematics JF - Frontiers in Bioengineering and Biotechnology N2 - Introduction: Anterior knee pain and other patello-femoral (PF) complications frequently limit the success of total knee arthroplasty as the final treatment of end stage osteoarthritis. However, knowledge about the in-vivo loading conditions at the PF joint remains limited, as no direct measurements are available. We hypothesised that the external knee flexion moment (EFM) is highly predictive of the PF contact forces during activities with substantial flexion of the loaded knee. Materials and methods: Six patients (65–80 years, 67–101 kg) with total knee arthroplasty (TKA) performed two activities of daily living: sit-stand-sit and squat. Tibio-femoral (TF) contact forces were measured in vivo using instrumented tibial components, while synchronously internal TF and PF kinematics were captured with mobile fluoroscopy. The measurements were used to compute PF contact forces using patient specific musculoskeletal models. The relationship between the EFM and the PF contact force was quantified using linear regression. Results: Mean peak TF contact forces of 1.97–3.24 times body weight (BW) were found while peak PF forces reached 1.75 to 3.29 times body weight (BW). The peak EFM ranged from 3.2 to 5.9 %BW times body height, and was a good predictor of the PF contact force (R2 = 0.95 and 0.88 for sit-stand-sit and squat, respectively). Discussion: The novel combination of in vivo TF contact forces and internal patellar kinematics enabled a reliable assessment of PF contact forces. The results of the regression analysis suggest that PF forces can be estimated based solely on the EFM from quantitative gait analysis. Our study also demonstrates the relevance of PF contact forces, which reach magnitudes similar to TF forces during activities of daily living. Y1 - 2024 U6 - https://doi.org/10.3389/fbioe.2024.1473951 SN - 2296-4185 VL - 12/2024 PB - Frontiers Media SA ER - TY - JOUR A1 - Rong, Guoyang A1 - Chen, Ying A1 - Ma, Feicheng A1 - Koch, Thorsten T1 - Exploring Interdisciplinary Research Trends through Critical Years for Interdisciplinary Citation JF - Journal of Informetrics Y1 - 2025 U6 - https://doi.org/10.1016/j.joi.2025.101726 VL - 19 IS - 4 ER - TY - JOUR A1 - Shinano, Yuji A1 - Fujii, Koichi T1 - Introduction to Quadratic Programming Solvers JF - Journal of The Society of Instrument and Control Engineers Y1 - 2025 U6 - https://doi.org/10.11499/sicejl.64.532 VL - 64 IS - 8 SP - 532 EP - 540 ER - TY - JOUR A1 - Bauer, Wolfgang A1 - Galtung, Noa A1 - Geserick, Peter A1 - Friedrich, Katharina A1 - Weber, Marcus A1 - Somasundaram, Rajan A1 - Diehl-Wiesenecker, Eva A1 - Kappert, Kai T1 - Pentraxin-3, MyD88, GLP-1, and PD-L1: Performance assessment and composite algorithmic analysis for sepsis identification JF - Journal of Infection N2 - This study examines nine emerging biomarkers as possible indicators for diagnosing sepsis in emergency department patient. Y1 - 2025 U6 - https://doi.org/10.1016/j.jinf.2025.106599 VL - 91 IS - 3 SP - 106599 ER - TY - JOUR A1 - Kourov, Mikhail N. A1 - Samoilova, Anna E. A1 - Straube, Arthur T1 - Dynamics of a chain of interacting magnetic particles in a one-dimensional periodic energy landscape JF - Bull. Russ. Acad. Sci. Phys. N2 - We explore the dynamics of a one-dimensional chain of paramagnetic colloidal particles in a periodic potential. The model accounts for a constant external force, along with magnetic dipolar attraction and hard-core repulsive interactions between particles. Numerical simulations reveal the emergence of a traveling kink – a chain defect propagating along the chain. We show that the kink emerges beyond a critical force threshold and identify parameter regimes corresponding to distinct dynamic modes such as a pinned kink, a running kink, a cluster kink, and chain drift. Y1 - 2025 U6 - https://doi.org/10.1134/S1062873825711742 SN - 1062-8738 VL - 89 IS - 7 SP - 1086 EP - 1092 ER - TY - JOUR A1 - Straube, Arthur A1 - Olicón Méndez, Guillermo A1 - Winkelmann, Stefanie A1 - Höfling, Felix A1 - Engel, Maximilian T1 - Unfolding the geometric structure and multiple timescales of the urea-urease pH oscillator N2 - We study a two-variable dynamical system modeling pH oscillations in the urea–urease reaction within giant lipid vesicles – a problem that intrinsically contains multiple, well-separated timescales. Building on an existing, deterministic formulation via ordinary differential equations, we resolve different orders of magnitude within a small parameter and analyze the system's limit cycle behavior using geometric singular perturbation theory (GSPT). By introducing two different coordinate scalings – each valid in a distinct region of the phase space – we resolve the local dynamics near critical fold points, using the extension of GSPT through such singular points due to Krupa and Szmolyan. This framework enables a geometric decomposition of the periodic orbits into slow and fast segments and yields closed-form estimates for the period of oscillation. In particular, we link the existence of such oscillations to an underlying biochemical asymmetry, namely, the differential transport across the vesicle membrane. Y1 - 2025 ER - TY - JOUR A1 - Binkowski, Felix A1 - Koulas-Simos, Aris A1 - Betz, Fridtjof A1 - Plock, Matthias A1 - Sekulic, Ivan A1 - Manley, Phillip A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Munkhbat, Battulga A1 - Reitzenstein, Stephan A1 - Burger, Sven T1 - High Purcell enhancement in all-TMDC nanobeam resonator designs with active monolayers for nanolasers JF - Phys. Rev. B Y1 - 2025 U6 - https://doi.org/10.1103/nxh9-dhvx VL - 112 SP - 235410 ER - TY - JOUR A1 - Weimann, Kuba A1 - Conrad, Tim T1 - Self-supervised pre-training with joint-embedding predictive architecture boosts ECG classification performance JF - Computers in Biology and Medicine N2 - Accurate diagnosis of heart arrhythmias requires the interpretation of electrocardiograms (ECG), which capture the electrical activity of the heart. Automating this process through machine learning is challenging due to the need for large annotated datasets, which are difficult and costly to collect. To address this issue, transfer learning is often employed, where models are pre-trained on large datasets and fine-tuned for specific ECG classification tasks with limited labeled data. Self-supervised learning has become a widely adopted pre-training method, enabling models to learn meaningful representations from unlabeled datasets. In this work, we explore the joint-embedding predictive architecture (JEPA) for self-supervised learning from ECG data. Unlike invariance-based methods, JEPA does not rely on hand-crafted data augmentations, and unlike generative methods, it predicts latent features rather than reconstructing input data. We create a large unsupervised pre-training dataset by combining ten public ECG databases, amounting to over one million records. We pre-train Vision Transformers using JEPA on this dataset and fine-tune them on various PTB-XL benchmarks. Our results show that JEPA outperforms existing invariance-based and generative approaches, achieving an AUC of 0.945 on the PTB-XL all statements task. JEPA consistently learns the highest quality representations, as demonstrated in frozen evaluations, and proves advantageous for pre-training even in the absence of additional data. Y1 - 2025 U6 - https://doi.org/10.1016/j.compbiomed.2025.110809 SN - 0010-4825 VL - 196 PB - Elsevier BV ER - TY - JOUR A1 - Klus, Stefan A1 - Gelß, Patrick T1 - Continuous optimization methods for the graph isomorphism problem JF - Information and Inference: A Journal of the IMA Y1 - 2025 U6 - https://doi.org/10.1093/imaiai/iaaf011 VL - 14 IS - 2 ER - TY - JOUR A1 - Gelß, Patrick A1 - Klein, Rupert A1 - Matera, Sebastian A1 - Schmidt, Burkhard T1 - Quantum dynamics of coupled excitons and phonons in chain-like systems: tensor train approaches and higher-order propagators JF - The Journal of Chemical Physics Y1 - 2025 U6 - https://doi.org/10.1063/5.0258904 VL - 162 ER - TY - JOUR A1 - Wirth, Elias A1 - Peña, Javier A1 - Pokutta, Sebastian T1 - Fast convergence of Frank-Wolfe algorithms on polytopes JF - INFORMS Journal on Mathematics of Operations Research Y1 - 2025 U6 - https://doi.org/10.1287/moor.2024.0580 ER - TY - JOUR A1 - Ramos, Alejandro A1 - Fischer, Eric W. A1 - Saalfrank, Peter A1 - Kühn, Oliver T1 - Shaping the laser control landscape of a hydrogen transfer reaction by vibrational strong coupling. A direct optimal control approach JF - The Journal of Chemical Physics Y1 - 2024 ER - TY - JOUR A1 - Halbig, Katrin A1 - Hoen, Alexander A1 - Gleixner, Ambros A1 - Witzig, Jakob A1 - Weninger, Dieter T1 - A diving heuristic for mixed-integer problems with unbounded semi-continuous variables JF - EURO Journal on Computational Optimization Y1 - 2025 U6 - https://doi.org/10.1016/j.ejco.2025.100107 VL - 13 ER - TY - JOUR A1 - Ramos, Alejandro A1 - Kühn, Oliver T1 - Manipulating the dynamics of a Fermi resonance with light. A direct optimal control theory approach JF - Chemical Physics Y1 - 2022 ER - TY - JOUR A1 - Widler, Valeria A1 - Kaminska, Barbara A1 - Martins, Andre C. R. A1 - Puga-Gonzalez, Ivan T1 - An Investigation into the Causal Mechanism of Political Opinion Dynamics: A Model of Hierarchical Coarse-Graining with Community-Bounded Social Influence JF - Computational Social Science of Social Cohesion and Polarization N2 - The increasing polarization in democratic societies is an emergent outcome of political opinion dynamics. Yet, the fundamental mechanisms behind the formation of political opinions, from individual beliefs to collective consensus, remain unknown. Understanding that a causal mechanism must account for both bottom-up and top-down influences, we conceptualize political opinion dynamics as hierarchical coarse-graining, where microscale opinions integrate into a macro-scale state variable. Using the CODA (Continuous Opinions Discrete Actions) model, we simulate Bayesian opinion updating, social identity-based information integration, and migration between social identity groups to represent higher-level connectivity. This results in coarse-graining across micro, meso, and macro levels. Our findings show that higher-level connectivity shapes information integration, yielding three regimes: independent (disconnected, local convergence), parallel (fast, global convergence), and iterative (slow, stepwise convergence). In the iterative regime, low connectivity fosters transient diversity, indicating an informed consensus. In all regimes, time-scale separation leads to downward causation, where agents converge on the aggregate majority choice, driving consensus. Critically, any degree of coherent higher-level information integration can overcome misalignment via global downward causation. The results highlight how emergent properties of the causal mechanism, such as downward causation, are essential for consensus and may inform more precise investigations into polarized political discourse. Y1 - 2026 U6 - https://doi.org/10.1007/978-3-032-01373-6_10 SP - 225 EP - 256 PB - Springer, Cham. ET - Computational Social Science of Social Cohesion and Polarization ER - TY - JOUR A1 - Sterzik, Anna A1 - Krone, Michael A1 - Baum, Daniel A1 - Cunningham, Douglas W. A1 - Lawonn, Kai T1 - Uncertainty Visualization for Biomolecular Structures: An Empirical Evaluation JF - IEEE Transactions on Visualization and Computer Graphics N2 - Uncertainty is an intrinsic property of almost all data, regardless of the data being measured, simulated, or generated. It can significantly influence the results and reliability of subsequent analysis steps. Clearly communicating uncertainties is crucial for informed decision-making and understanding, especially in biomolecular data, where uncertainty is often difficult to infer. Uncertainty visualization (UV) is a powerful tool for this purpose. However, previously proposed UV methods lack sufficient empirical evaluation. We collected and categorized visualization methods for portraying positional uncertainty in biomolecular structures. We then organized the methods into metaphorical groups and extracted nine representatives: color, clouds, ensemble, hulls, sausages, contours, texture, waves, and noise. We assessed their strengths and weaknesses in a twofold approach: expert assessments with six domain experts and three perceptual evaluations involving 1,756 participants. Through the expert assessments, we aimed to highlight the advantages and limitations of the individual methods for the application domain and discussed areas for necessary improvements. Through the perceptual evaluation, we investigated whether the visualizations are intuitively associated with uncertainty and whether the directionality of the mapping is perceived as intended. We also assessed the accuracy of inferring uncertainty values from the visualizations. Based on our results, we judged the appropriateness of the metaphors for encoding uncertainty and suggest further areas for improvement. Y1 - 2025 U6 - https://doi.org/10.1109/TVCG.2025.3596385 VL - 31 IS - 12 SP - 10296 EP - 10310 ER - TY - JOUR A1 - van Lieshout, Rolf A1 - Lindner, Niels T1 - A Compact Cycle Formulation for the Multiperiodic Event Scheduling Problem N2 - The Periodic Event Scheduling Problem (PESP) is a fundamental model in periodic timetabling for public transport systems, assuming a common period across all events. However, real-world networks often feature heterogeneous service frequencies. This paper studies the Multiperiodic Event Scheduling Problem (MPESP), a generalization of PESP that allows each event to recur at its own individual period. While more expressive, MPESP presents new modeling challenges due to the loss of a global period. We present a cycle-based formulation for MPESP that extends the strongest known formulation for PESP and, in contrast to existing approaches, is valid for any MPESP instance. Crucially, the formulation requires a cycle basis derived from a spanning tree satisfying specific structural properties, which we formalize and algorithmically construct, extending the concept of sharp spanning trees to rooted instances. We further prove a multiperiodic analogue of the cycle periodicity property. Our new formulation solves nearly all tested instances, including several large-scale real-world public transport networks, to optimality or with small optimality gaps, dramatically outperforming existing arc-based models. The results demonstrate the practical potential of MPESP in capturing heterogeneous frequencies without resorting to artificial event duplication. Y1 - 2025 ER - TY - JOUR A1 - Coomber, Celvic A1 - Chewle, Surahit A1 - Secker, Christopher A1 - Fackeldey, Konstantin A1 - Weber, Marcus A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - Investigating Endogenous Opioids Unravels the Mechanisms Behind Opioid-Induced Constipation, a Mathematical Modeling Approach JF - International Journal of Molecular Sciences N2 - Endogenous opioids, such as Endomorphin-2, are not typically associated with severe constipation, unlike pharmaceutical opioids, which induce opioid-induced constipation (OIC) by activating μ-opioid receptors in the gastrointestinal tract. In this study, we present a mathematical model, which integrates the serotonergic and opioid pathways, simulating the interaction between serotonin and opioid signaling within the enteric nervous system (ENS). The model explores the mechanisms underlying OIC, with a focus on the change in adenylyl cyclase (AC) activity, cAMP accumulation, and the distinct functionalities of Endomorphin-2 compared to commonly used pharmaceutical opioids. We study the effects of Morphine, Fentanyl, and Methadone and contrast them with Endomorphin-2. Our findings reveal that opioids do not perturb the signaling of serotonin, but only the activity of AC, suggesting that serotonin levels have no influence on improving opioid-induced constipation. Furthermore, this study reveals that the primary difference between endogenous and pharmaceutical opioids is their degradation rates. This finding shows that modulating opioid degradation rates significantly improves cAMP recovery. In conclusion, our insights steer towards exploring opioid degrading enzymes, localized to the gut, as a strategy for mitigating OIC. Y1 - 2025 U6 - https://doi.org/10.3390/ijms26136207 VL - 26 IS - 13 ER - TY - JOUR A1 - Vohra, Sumit Kumar A1 - Eberle, Maren A1 - Boulanger-Weill, Jonathan A1 - Petkova, Mariela D. A1 - Schuhknecht, Gregor F. P. A1 - Herrera, Kristian J. A1 - Kämpf, Florian A1 - Ruetten, Virginia M. S. A1 - Lichtman, Jeff W. A1 - Engert, Florian A1 - Randlett, Owen A1 - Bahl, Armin A1 - Isoe, Yasuko A1 - Hege, Hans-Christian A1 - Baum, Daniel T1 - Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish JF - bioRxiv N2 - Understanding how neural circuits give rise to behavior requires comprehensive knowledge of neuronal morphology, connectivity, and function. Atlas platforms play a critical role in enabling the visualization, exploration, and dissemination of such information. Here, we present FishExplorer, an interactive and expandable community platform designed to integrate and analyze multimodal brain data from larval zebrafish. FishExplorer supports datasets acquired through light microscopy (LM), electron microscopy (EM), and X-ray imaging, all co-registered within a unified spatial coordinate system which enables seamless comparison of neuronal morphologies and synaptic connections. To further assist circuit analysis, FishExplorer includes a suite of tools for querying and visualizing connectivity at the whole-brain scale. By integrating data from recent large-scale EM reconstructions (presented in companion studies), FishExplorer enables researchers to validate circuit models, explore wiring principles, and generate new hypotheses. As a continuously evolving resource, FishExplorer is designed to facilitate collaborative discovery and serve the growing needs of the teleost neuroscience community. Y1 - 2025 U6 - https://doi.org/10.1101/2025.07.14.664689 ER - TY - JOUR A1 - Petkovic, Milena A1 - Zittel, Janina T1 - Leveraging Transfer Learning to Overcome Data Limitations in Czochralski Crystal Growth JF - Advanced Theory and Simulations Y1 - 2025 U6 - https://doi.org/10.1002/adts.202500677 VL - 8 IS - 11 ER - TY - JOUR A1 - Shewarega, Michael A1 - Troidl, Jakob A1 - Alvarado Rodriguez, Oliver A1 - Dindoost, Mohammad A1 - Harth, Philipp A1 - Haberkern, Hannah A1 - Stegmaier, Johannes A1 - Bader, David A1 - Pfister, Hanspeter T1 - MoMo - Combining Neuron Morphology and Connectivity for Interactive Motif Analysis in Connectomes JF - IEEE Transactions on Visualization and Computer Graphics N2 - Connectomics, a subfield of neuroscience, reconstructs structural and functional brain maps at synapse-level resolution. These complex spatial maps consist of tree-like neurons interconnected by synapses. Motif analysis is a widely used method for identifying recurring subgraph patterns in connectomes. These motifs, thus, potentially represent fundamental units of information processing. However, existing computational tools often oversimplify neurons as mere nodes in a graph, disregarding their intricate morphologies. In this paper, we introduce MoMo, a novel interactive visualization framework for analyzing neuron morphology-aware motifs in large connectome graphs. First, we propose an advanced graph data structure that integrates both neuronal morphology and synaptic connectivity. This enables highly efficient, parallel subgraph isomorphism searches, allowing for interactive morphological motif queries. Second, we develop a sketch-based interface that facilitates the intuitive exploration of morphology-based motifs within our new data structure. Users can conduct interactive motif searches on state-of-the-art connectomes and visualize results as interactive 3D renderings. We present a detailed goal and task analysis for motif exploration in connectomes, incorporating neuron morphology. Finally, we evaluate MoMo through case studies with four domain experts, who asses the tool’s usefulness and effectiveness in motif exploration, and relevance to real-world neuroscience research. The source code for MoMo is available here: https://github.com/VCG/momo. Y1 - 2025 U6 - https://doi.org/10.1109/TVCG.2025.3634808 ER - TY - JOUR A1 - Deppe, Dominik A1 - Gabriele, Matteo A1 - Mazzoleni, Manuel Giovanni A1 - Ordas-Bayon, Alejandro A1 - Fidanza, Andrea A1 - Rozhko, Yuriy A1 - Şimşek, Ekin Kaya A1 - Keltz, Eran A1 - Osterhoff, Georg A1 - Damm, Philipp A1 - Duda, Georg N. A1 - Leskovar, Marko A1 - Zachow, Stefan A1 - Trepczynski, Adam A1 - Heyland, Mark T1 - Interobserver Reliability of the Modified Radiographic Union Score (mRUST) for Tibial and Femoral Fractures JF - Journal of Orthopaedic Trauma N2 - OBJECTIVES: To evaluate the reliability of the modified Radiographic Union Score for Tibial fractures (mRUST) as a reliable tool for monitoring lower limb fractures (femur, tibia) treated with various modalities (nail, plate). METHODS: Design: Retrospective analysis. Setting: Single center academic hospital in Germany. Patient Selection Criteria: Adult patients (≥18 years) with extra-articular long bone fractures of the lower extremities treated surgically between January 2005 and April 2022, requiring radiographs in two perpendicular planes and at least one follow-up visit, were included. Exclusion criteria were critical clinical conditions, inability to consent, joint articulation fractures, inadequate documentation, or insufficient imaging quality. Outcome Measures and Comparisons: Six international investigators (five orthopedic surgeons, one radiologist) independently assessed fracture line and callus growth per cortex (mRUST) at individualized follow-up time points based on clinical practice. To evaluate interrater reliability, intraclass correlation coefficients were calculated for the overall dataset, and for subsets of rated images, that were defined based on anatomical location (femur/tibia), treatment type (plate/nail fixation), and treatment combinations across locations. RESULTS: A total of 166 patients (63 femur fractures, 103 tibia fractures; 32.5% female, mean age 43.4 (18–84)) with 1136 follow-up time points were analyzed. Overall interrater reliability for mRUST was good (intraclass correlation coefficient 0.77), consistent across fixation methods (nail/plate fixation, 0.79) and anatomical locations (tibia, 0.78; femur, 0.81). Cortex-specific reliability varied, with highest agreement for the medial cortex (0.70–0.74) and lowest for the posterior cortex (0.65–0.74). CONCLUSIONS: The mRUST (radiographic score) demonstrated reliability for monitoring fracture healing in the femur and tibia, irrespective of fixation method, supporting its use as a generalizable tool across lower limb fractures. LEVEL OF EVIDENCE: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence. Y1 - 2025 U6 - https://doi.org/10.1097/BOT.0000000000003032 SN - 0890-5339 VL - 39 IS - 10 SP - 557 EP - 563 ER - TY - JOUR A1 - Petkova, Mariela D. A1 - Januszewski, Michał A1 - Blakely, Tim A1 - Herrera, Kristian J. A1 - Schuhknecht, Gregor F.P. A1 - Tiller, Robert A1 - Choi, Jinhan A1 - Schalek, Richard L. A1 - Boulanger-Weill, Jonathan A1 - Peleg, Adi A1 - Wu, Yuelong A1 - Wang, Shuohong A1 - Troidl, Jakob A1 - Vohra, Sumit Kumar A1 - Wei, Donglai A1 - Lin, Zudi A1 - Bahl, Armin A1 - Tapia, Juan Carlos A1 - Iyer, Nirmala A1 - Miller, Zachary T. A1 - Hebert, Kathryn B. A1 - Pavarino, Elisa C. A1 - Taylor, Milo A1 - Deng, Zixuan A1 - Stingl, Moritz A1 - Hockling, Dana A1 - Hebling, Alina A1 - Wang, Ruohong C. A1 - Zhang, Lauren L. A1 - Dvorak, Sam A1 - Faik, Zainab A1 - King, Jr., Kareem I. A1 - Goel, Pallavi A1 - Wagner-Carena, Julian A1 - Aley, David A1 - Chalyshkan, Selimzhan A1 - Contreas, Dominick A1 - Li, Xiong A1 - Muthukumar, Akila V. A1 - Vernaglia, Marina S. A1 - Carrasco, Teodoro Tapia A1 - Melnychuck, Sofia A1 - Yan, TingTing A1 - Dalal, Ananya A1 - DiMartino, James A1 - Brown, Sam A1 - Safo-Mensa, Nana A1 - Greenberg, Ethan A1 - Cook, Michael A1 - Finley, Samantha A1 - Flynn, Miriam A. A1 - Hopkins, Gary Patrick A1 - Kovalyak, Julie A1 - Leonard, Meghan A1 - Lohff, Alanna A1 - Ordish, Christopher A1 - Scott, Ashley L. A1 - Takemura, Satoko A1 - Smith, Claire A1 - Walsh, John J. A1 - Berger, Daniel R. A1 - Pfister, Hanspeter A1 - Berg, Stuart A1 - Knecht, Christopher A1 - Meissner, Geoffrey W. A1 - Korff, Wyatt A1 - Ahrens, Misha B A1 - Jain, Viren A1 - Lichtman, Jeff W. A1 - Engert, Florian T1 - A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain JF - bioRxiv N2 - We present a correlated light and electron microscopy (CLEM) dataset from a 7-day-old larval zebrafish, integrating confocal imaging of genetically labeled excitatory (vglut2a) and inhibitory (gad1b) neurons with nanometer-resolution serial section EM. The dataset spans the brain and anterior spinal cord, capturing >180,000 segmented soma, >40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the dataset’s utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain. Y1 - 2025 U6 - https://doi.org/10.1101/2025.06.10.658982 ER - TY - JOUR A1 - Groussin, Olivier A1 - Jorda, L. A1 - Attree, N. A1 - Birch, S.P.D. A1 - Bürger, Johanna A1 - Gutiérrez, Pedro A1 - Jindal, Abhinav S. A1 - Keller, H.U. A1 - Kramer, Tobias A1 - Lasagni Manghi, Riccardo A1 - Läuter, Matthias A1 - Markkanen, J. A1 - Marschall, R. A1 - Schuckart, C. T1 - Thermal environment and erosion of comet 67P/Churyumov-Gerasimenko JF - Astronomy and Astrophysics N2 - Aims. This paper focuses on how insolation affects the nucleus of comet 67P/Churyumov-Gerasimenko over its current orbit. We aim to better understand the thermal environment of the nucleus, in particular its surface temperature variations, erosion, relationship with topography, and how insolation affects the interior temperature for the location of volatile species (H2O and CO2). Methods. We have developed two thermal models to calculate the surface and subsurface temperatures of 67P over its 6.45-year orbit. The first model, with high resolution (300 000 facets), calculates surface temperatures, taking shadows and self-heating into account but ignoring thermal conductivity. The second model, with lower resolution (10 000 facets), includes thermal conductivity to estimate temperatures down to ∼3 m below the surface. Results. The thermal environment of 67P is strongly influenced by its large obliquity (52◦), which causes significant seasonal effects and polar nights. The northern hemisphere is the coldest region, with temperatures of 210–300 K. H2O is found in the first few centimetres, while CO2 is found deeper (∼2 m) except during polar night around perihelion, when CO2 accumulates near the surface. Cliffs erode 3–5 times faster than plains, forming terraces. The equatorial region receives maximum solar energy (8.5×109 J m−2 per orbit), with maximum surface temperatures of 300–350 K. On the plains, H2O is found in the first few centimetres, while CO2 is found deeper (∼2 m) and never accumulates near the surface. In the southern hemisphere, a brief intense perihelion heating raises temperatures to 350–400 K, which is followed by a 5-year polar night when surface temperatures drop to 55 K. Here H2O remains in the first few centimetres, while CO2 accumulates shallowly during polar night, enriching the region. Erosion is maximal in the southern hemisphere and concentrated on the plains, which explains the observed overall flatness of this hemisphere compared to the northern one. Over one orbit, the total energy from self-heating is 17% of the total energy budget, and 34% for thermal conduction. Our study contributes to a better understanding of the surface changes observed on 67P. Y1 - 2025 U6 - https://doi.org/10.1051/0004-6361/202452260 VL - 694 SP - A21 ER - TY - JOUR A1 - Abdel, Dilara A1 - Relle, Jacob A1 - Kirchartz, Thomas A1 - Jaap, Patrick A1 - Fuhrmann, Jürgen A1 - Burger, Sven A1 - Becker, Christiane A1 - Jäger, Klaus A1 - Farrell, Patricio T1 - How nanotextured interfaces influence the electronics in perovskite solar cells JF - EES Sol. Y1 - 2026 U6 - https://doi.org/10.1039/D5EL00208G ER - TY - JOUR A1 - Ernst, Ariane A1 - Bankowski, Anastasia A1 - Jusyte, Meida A1 - Okunola, Toluwani A1 - Petrov, Tino A1 - Walter, Alexander A1 - Winkelmann, Stefanie T1 - Parameter Optimization for a Neurotransmission Recovery Model JF - Bulletin of Mathematical Biology N2 - We assess the empirical applicability of a simplified model for neurotransmitter release that incorporates maturation, fusion, and recovery of both release sites and vesicles. Model parameters are optimized by fitting the model to experimental data obtained from neuromuscular junction synapses of 3rd-instar Drosophila melanogaster larvae. In particular, the mean-squared error between the local extrema of the simulated total junction current and its experimental counterpart is minimized. We compare three estimation approaches, differing in the choice of optimized parameters and the fusion rate function. Despite the model’s minimalistic structure, it demonstrates a compelling ability to replicate experimental data, yielding plausible parameter estimates for five different animals. An additional identifiability analysis based on the profile likelihood reveals practical non-identifiabilities for several parameters, highlighting the need for additional constraints or data to improve estimation accuracy. Y1 - 2025 U6 - https://doi.org/10.1007/s11538-025-01486-2 VL - 87 PB - Bulletin of Mathematical Biology ER - TY - JOUR A1 - Yousefian, Maryam A1 - Frank, Anne-Simone A1 - Weber, Marcus A1 - Röblitz, Susanna T1 - Efficient construction of Markov state models for stochastic gene regulatory networks by domain decomposition JF - BMC Bioinformatics N2 - The dynamics of many gene regulatory networks (GRNs) is characterized by the occurrence of metastable phenotypes and stochastic phenotype switches. The chemical master equation (CME) is the most accurate description to model such stochastic dynamics, whereby the long-time dynamics of the system is encoded in the spectral properties of the CME operator. Markov State Models (MSMs) provide a general framework for analyzing and visualizing stochastic multistability and state transitions based on these spectral properties. Until now, however, this approach is either limited to low-dimensional systems or requires the use of high-performance computing facilities, thus limiting its usability. Y1 - 2025 U6 - https://doi.org/10.1186/s12859-025-06174-5 VL - 26 IS - 147 ER - TY - JOUR A1 - Vu, Thi Huong A1 - Litzel, Ida A1 - Koch, Thorsten T1 - Similarity-based fuzzy clustering scientific articles: potentials and challenges from mathematical and computational perspectives JF - Journal of Nonlinear and Variational Analysis N2 - Fuzzy clustering, which allows an article to belong to multiple clusters with soft membership degrees, plays a vital role in analyzing publication data. This problem can be formulated as a constrained optimization model, where the goal is to minimize the discrepancy between the similarity observed from data and the similarity derived from a predicted distribution. While this approach benefits from leveraging state-of-the-art optimization algorithms, tailoring them to work with real, massive databases like OpenAlex or Web of Science - containing about 70 million articles and a billion citations - poses significant challenges. We analyze potentials and challenges of the approach from both mathematical and computational perspectives. Among other things, second-order optimality conditions are established, providing new theoretical insights, and practical solution methods are proposed by exploiting the structure of the problem. Specifically, we accelerate the gradient projection method using GPU-based parallel computing to efficiently handle large-scale data. Y1 - 2026 U6 - https://doi.org/https://doi.org/10.23952/jnva.10.2026.2.8 VL - 10 IS - 2 SP - 381 EP - 401 PB - Biemdas ER - TY - JOUR A1 - Läuter, Matthias A1 - Kramer, Tobias T1 - Rotation dynamics and torque efficiency of cometary nuclei JF - Astronomy & Astrophysics N2 - The dynamics of a rigid cometary nucleus is described by the evolutions of its center-of-mass and of its rotation state. Solar irradiation that reaches the surface of a cometary nucleus causes the sublimation of volatiles that form the coma around the nucleus. The sublimation process transfers linear momentum and rotational angular momentum from the nucleus to the surrounding space, and thus affects the dynamics via nongravitational forces and nongravitational torques. With the exception of close approaches to planets, these torques exert the dominant influence on the rotation states of cometary nuclei. The Rosetta mission 2014-2016 accompanying comet 67P/Churyumov-Gerasimenko provides the longest continuous observational data to track its rotation state. In particular, the data set encompasses the direction of the angular velocity, denoted by ω, and the angular frequency |ω|over a time period of approximately 700 days. The observed change of the rotation state is not explained by a low heat conductivity thermophysical model in combination with a homogeneous surface ice coverage of comet 67P. Spatially and/or temporally varying weights for effective active fraction with respect to a prescribed set of surface regions provide a potential solution to this problem. Here, we present a methodology for classifying the surface based on vectorial efficiency of the torque. On any cometary surface without geometric symmetry, the methodology highlights the decomposition into eight characteristic regions that encode the signs of torque efficiency with respect to all vector components. This decomposition is divided into two subsets of four regions each of which is located in one of both hemispheric regions. We analyze in detail rotation states close to lowest energy and different thermophysical models, and we discuss how the uncertainties of observations affect the model parameters. We study the occurrence of these regions for an oblate ellipsoid, a nearprolate ellipsoid, a bilobed shape, and a shape model analogous to that of comet 67P. The sensitivity analysis for comet 67P indicates that the observations constrain only one of the eight weights uniquely. The other directions are poorly constrained and show the limitation of the rotational data to determine the regional activity on comet 67P. Y1 - 2025 U6 - https://doi.org/10.1051/0004-6361/202553845 VL - 699 SP - A75 ER - TY - JOUR A1 - Khatri, Vinod A1 - Boback, Nico A1 - Abdelwahab, Hassan A1 - Niemeyer, Daniela A1 - Palmer, Tahlia M. A1 - Sahoo, Anil Kumar A1 - Kerkhoff, Yannic A1 - Ludwig, Kai A1 - Balci, Dilara A1 - Trimpert, Jakob A1 - Haag, Rainer A1 - Povolotsky, Tatyana L. A1 - Netz, Roland R. A1 - Drosten, Christian A1 - Lauster, Daniel C. A1 - Bhatia, Sumati T1 - Polysialosides outperform sulfated analogs for the inhibition of SARS-CoV-2 JF - Small N2 - Both polysialosides and polysulfates are known to interact with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. However, a comprehensive site by site analysis of their binding affinities and potential synergistic antiviral effects have not been performed. Here, we report on the synthesis of polysialosides with nanomolar binding affinities to spike proteins of SARS-CoV-2 in solution using microscale thermophoresis (MST). The dendritic polyglycerol based polysialosides dPG500(SA)0.55 and dPG500(SA)0.25, with a dissociation constant Kd of 4.78 nM and 10.85 nM, respectively, bind ~500 times stronger than the high density polysulfated analog dPG500(OSO3Na)0.55, to intact SARS-CoV-2 virus particles or isolated spike protein. In fact, the presence of sulfate groups in a heteromultivalent compound dPG500(SA)0.20(OSO3Na)0.20 weakens the binding to spike proteins. A polycarboxylated analog does not bind to SARS-CoV-2, ruling out that the interaction of polysialoside is simply driven by electrostatic interactions. Furthermore, we found potent nanomolar binding of dPG500(SA)0.55 to SARS-CoV-2 variant B.1.617 (Delta) and B.1.1.529 (Omicron) RBD. Using explicit-solvent all-atom molecular dynamics (MD) simulations and docking studies, we obtain atomistic details on the interaction of different functional groups with the SARS-CoV-2 RBD and their binding affinities. Our data support the conclusion that sialosides interact stronger with RBD than sulfates. Notably, our most affine binder dPG500(SA)0.55 inhibits SARS-CoV-2 (WT, D614G) replication up to 98.6% at low nanomolar concentrations. Y1 - 2025 UR - https://doi.org/10.26434/chemrxiv-2024-8b0gb U6 - https://doi.org/10.1002/smll.202500719 VL - 21 IS - 34 ER - TY - JOUR A1 - Fricke, Mackenzie S. A1 - Frometa, Magalee R. A1 - Kerkhoff, Yannic A1 - Bernhard, Samuel P. A1 - Tahir, Ramat S. A1 - Quaas, Elisa A1 - Totten, William H. A1 - Haag, Rainer A1 - Achazi, Katharina A1 - Cloninger, Mary J. T1 - The toxicity, uptake, and impact on galectin-3 mediated apoptosis of lactose functionalized PAMAM dendrimers JF - Materials Advances N2 - Poly(amidoamine) (PAMAM) dendrimers functionalized with ligands that are designed to interact with biological receptors are important macromolecules for the elucidation and mediation of biological recognition processes. Specifically, carbohydrate functionalized dendrimers are useful synthetic multivalent systems for the study of multivalent protein–carbohydrate interactions. For example, lactose functionalized glycodendrimers can be used to discern the function of galectins, galactoside-binding proteins that are often over-expressed during cancer progression. In order to effectively interpret cancer cellular assays using glycodendrimers, however, their properties in the presence of cells must first be assessed. Macromolecules that are taken up by cells would be expected to have access to many different cell signaling pathways and modes of action that solely extracellular macromolecules cannot utilize. In addition, macromolecules that display cellular toxicity could not be used as drug delivery vehicles. Here, we report fundamental studies of cellular toxicity, viability, and uptake with four generations of lactose functionalized PAMAM dendrimers. In all cases, the dendrimers are readily taken up by the cells but do not display any significant cellular toxicity. The glycodendrimers also increase cellular apoptosis, suggesting that they may abrogate the antiapoptotic protections afforded by galectin-3 to cancer cells. The results reported here indicate that appropriately functionalized PAMAM dendrimers can be used as nontoxic tools for the study and mediation of both extra and intracellular cancer processes. Y1 - 2025 U6 - https://doi.org/10.1039/D4MA00782D VL - 6 SP - 3171 EP - 3184 ER - TY - JOUR A1 - Chen, Ying A1 - Koch, Thorsten A1 - Peng, Hanqui A1 - Zhang, Hongrui T1 - Benchmarking of Quantum and Classical Computing in Large-Scale Dynamic Portfolio Optimization Under Market Frictions N2 - Quantum computing is poised to transform the financial industry, yet its advantages over traditional methods have not been evidenced. As this technology rapidly evolves, benchmarking is essential to fairly evaluate and compare different computational strategies. This study presents a challenging yet solvable problem of large-scale dynamic portfolio optimization under realistic market conditions with frictions. We frame this issue as a Quadratic Unconstrained Binary Optimization (QUBO) problem, compatible with digital computing and ready for quantum computing, to establish a reliable benchmark. By applying the latest solvers to real data, we release benchmarks that help verify true advancements in dynamic trading strategies, either quantum or digital computing, ensuring that reported improvements in portfolio optimization are based on robust, transparent, and comparable metrics. Y1 - 2025 ER - TY - JOUR A1 - Hawthorne, Felipe A1 - Raulino, Paulo R. E. A1 - Rodrigues Pelá, Ronaldo A1 - Woellner, Cristiano F. T1 - Efficient and Accurate Machine Learning Interatomic Potential for Graphene: Capturing Stress–Strain and Vibrational Properties JF - The Journal of Physical Chemistry C Y1 - 2025 U6 - https://doi.org/10.1021/acs.jpcc.5c03470 VL - 129 SP - 16319 EP - 16326 ER - TY - JOUR A1 - Rossi, Thomas A1 - Qiao, Lu A1 - Dykstra, Conner P. A1 - Rodrigues Pelá, Ronaldo A1 - Gnewkow, Richard A1 - Wallick, Rachel F. A1 - Burke, John H. A1 - Nicholas, Erin A1 - March, Anne-Marie A1 - Doumy, Gilles A1 - Buchholz, D. Bruce A1 - Deparis, Christiane A1 - Zuñiga-Pérez, Jesus A1 - Weise, Michael A1 - Ellmer, Klaus A1 - Fondell, Mattis A1 - Draxl, Claudia A1 - van der Veen, Renske T1 - Dynamic control of X-ray core-exciton resonances by Coulomb screening in photoexcited semiconductors JF - Communications Materials Y1 - 2025 U6 - https://doi.org/10.1038/s43246-025-00909-w VL - 6 SP - 191 ER -