54 results match your criteria: "Zuse Institute Berlin (ZIB)[Affiliation]"
Bull Math Biol
November 2024
Zuse Institute Berlin (ZIB), Takustrasse 7, 14195, Berlin, Germany.
The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different resolutions on lattices for biochemical species with different diffusion constants, the mgRDME approach improves both accuracy and efficiency of compartment-based reaction-diffusion simulations. The mgRDME framework is examined through its application to morphogen gradient formation in stochastic reaction-diffusion scenarios, using both an analytically tractable first-order reaction network and a model with a second-order reaction.
View Article and Find Full Text PDFAdv Sci (Weinh)
December 2024
Max Planck Institute of Colloids and Interfaces, Potsdam Science Park, Am Mühlenberg 1 OT Golm, 14476, Potsdam, Germany.
The skeletons of sharks and rays, fashioned from cartilage, and armored by a veneer of mineralized tiles (tesserae) present a mathematical challenge: How can the continuous covering be maintained as the skeleton expands? This study, using microCT and custom visual data analyses of growing stingray skeletons, systematically examines tessellation patterns and morphologies of the many thousand interacting tesserae covering the hyomandibula (a skeletal element critical to feeding), over a two-fold developmental change in hyomandibula length. The number of tesserae remains surprisingly constant, even as the hyomandibula expands isometrically, with all hyomandibulae displaying self-similar distributions of tesserae shapes/sizes. Although the distribution of tesserae geometries largely agrees with the rules for polyhedra tiling of complex surfaces-dominated by hexagons and a minor fraction of pentagons and heptagons, but very few other polygons-the agreement with Euler's classic mathematical laws is not perfect.
View Article and Find Full Text PDFBackground: Collaborative comparisons and combinations of epidemic models are used as policy-relevant evidence during epidemic outbreaks. In the process of collecting multiple model projections, such collaborations may gain or lose relevant information. Typically, modellers contribute a probabilistic summary at each time-step.
View Article and Find Full Text PDFPhys Chem Chem Phys
February 2024
Thin film Physics Division, Department of Physics, Chemistry and Biology (IFM), Linköping University, SE 581 83 Linköping, Sweden.
Int J Implant Dent
September 2023
Department of Oral and Maxillofacial Surgery, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Augustenburger Platz 1, 13353, Berlin, Germany.
Purpose: To investigate the influence of teeth and dental restorations on the facial skeleton's gray value distributions in cone-beam computed tomography (CBCT).
Methods: Gray value selection for the upper and lower jaw segmentation was performed in 40 patients. In total, CBCT data of 20 maxillae and 20 mandibles, ten partial edentulous and ten fully edentulous in each jaw, respectively, were evaluated using two different gray value selection procedures: manual lower threshold selection and automated lower threshold selection.
Sci Rep
December 2022
Institute of Biomechanics and Orthopaedics, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany.
Sci Rep
October 2022
Institute of Biomechanics and Orthopaedics, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany.
Alternative treatment methods for knee osteoarthritis (OA) are in demand, to delay the young (< 50 Years) patient's need for osteotomy or knee replacement. Novel interpositional knee spacers shape based on statistical shape model (SSM) approach and made of polyurethane (PU) were developed to present a minimally invasive method to treat medial OA in the knee. The implant should be supposed to reduce peak strains and pain, restore the stability of the knee, correct the malalignment of a varus knee and improve joint function and gait.
View Article and Find Full Text PDFNat Methods
February 2022
Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
Computational trajectory inference enables the reconstruction of cell state dynamics from single-cell RNA sequencing experiments. However, trajectory inference requires that the direction of a biological process is known, largely limiting its application to differentiating systems in normal development. Here, we present CellRank ( https://cellrank.
View Article and Find Full Text PDFViruses
December 2021
Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
Background: We evaluated how plasma proteomic signatures in patients with suspected COVID-19 can unravel the pathophysiology, and determine kinetics and clinical outcome of the infection.
Methods: Plasma samples from patients presenting to the emergency department (ED) with symptoms of COVID-19 were stratified into: (1) patients with suspected COVID-19 that was not confirmed ( = 44); (2) non-hospitalized patients with confirmed COVID-19 ( = 44); (3) hospitalized patients with confirmed COVID-19 ( = 53) with variable outcome; and (4) patients presenting to the ED with minor diseases unrelated to SARS-CoV-2 infection ( = 20). Besides standard of care diagnostics, 177 circulating proteins related to inflammation and cardiovascular disease were analyzed using proximity extension assay (PEA, Olink) technology.
Brain Sci
December 2021
Neuroscience Research Flanders (NERF), Interuniversity Microelectronics Centre (IMEC), Kapeldreef 75, 3001 Leuven, Belgium.
Image segmentation still represents an active area of research since no universal solution can be identified. Traditional image segmentation algorithms are problem-specific and limited in scope. On the other hand, machine learning offers an alternative paradigm where predefined features are combined into different classifiers, providing pixel-level classification and segmentation.
View Article and Find Full Text PDFInt J Comput Assist Radiol Surg
May 2021
Zuse Institute Berlin (ZIB), Berlin, Germany.
Purpose: Segmentation of surgical instruments in endoscopic video streams is essential for automated surgical scene understanding and process modeling. However, relying on fully supervised deep learning for this task is challenging because manual annotation occupies valuable time of the clinical experts.
Methods: We introduce a teacher-student learning approach that learns jointly from annotated simulation data and unlabeled real data to tackle the challenges in simulation-to-real unsupervised domain adaptation for endoscopic image segmentation.
Front Endocrinol (Lausanne)
December 2021
Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
New approaches to ovarian stimulation protocols, such as luteal start, random start or double stimulation, allow for flexibility in ovarian stimulation at different phases of the menstrual cycle. It has been proposed that the success of these methods is based on the continuous growth of multiple cohorts ("waves") of follicles throughout the menstrual cycle which leads to the availability of ovarian follicles for ovarian controlled stimulation at several time points. Though several preliminary studies have been published, their scientific evidence has not been considered as being strong enough to integrate these results into routine clinical practice.
View Article and Find Full Text PDFiScience
February 2021
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
ChemRxiv
July 2020
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of July 7th, 2020, almost seven months into the outbreak, there are no approved vaccines and few treatments available. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics.
View Article and Find Full Text PDFJ Chem Phys
September 2020
Zuse Institute Berlin (ZIB), Takustr. 7, 14195 Berlin, Germany.
Sci Rep
February 2020
Institute for Imaging Science and Computational Modelling in Cardiovascular Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany.
This study's objective was the generation of a standardized geometry of the healthy nasal cavity. An average geometry of the healthy nasal cavity was generated using a statistical shape model based on 25 symptom-free subjects. Airflow within the average geometry and these geometries was calculated using fluid simulations.
View Article and Find Full Text PDFBiophys J
September 2019
Department of Physics, Berlin, Germany. Electronic address:
Based on experimental drug concentration profiles in healthy as well as tape-stripped ex vivo human skin, we model the penetration of the antiinflammatory drug dexamethasone into the skin layers by the one-dimensional generalized diffusion equation. We estimate the position-dependent free-energy and diffusivity profiles by solving the conjugated minimization problem, in which the only inputs are concentration profiles of dexamethasone in skin at three consecutive penetration times. The resulting free-energy profiles for damaged and healthy skin show only minor differences.
View Article and Find Full Text PDFBMC Bioinformatics
May 2019
Max Planck Institute for Molecular Genetics, Berlin, Ihnestraße 63-73, Berlin, 14195, Germany.
Background: Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them have unknown function. Recent evidence has shown the importance of both lncRNAs and chromatin interactions in transcriptional regulation. Although network-based methods, mainly exploiting gene-lncRNA co-expression, have been applied to characterize lncRNA of unknown function by means of 'guilt-by-association', no strategy exists so far which identifies mRNA-lncRNA functional modules based on the 3D chromatin interaction graph.
View Article and Find Full Text PDFJ Chem Phys
May 2019
Zuse Institute Berlin (ZIB), Takustr. 7, 14195 Berlin, Germany.
Markov state models are to date the gold standard for modeling molecular kinetics since they enable the identification and analysis of metastable states and related kinetics in a very instructive manner. The state-of-the-art Markov state modeling methods and tools are very well developed for the modeling of reversible processes in closed equilibrium systems. On the contrary, they are largely not well suited to deal with nonreversible or even nonautonomous processes of nonequilibrium systems.
View Article and Find Full Text PDFChaos
January 2019
Zuse Institute Berlin (ZIB), Takustrasse 7, 14195 Berlin, Germany.
Given a time-dependent stochastic process with trajectories x(t) in a space Ω, there may be sets such that the corresponding trajectories only very rarely cross the boundaries of these sets. We can analyze such a process in terms of metastability or coherence. Metastable setsM are defined in space M⊂Ω, and coherent setsM(t)⊂Ω are defined in space and time.
View Article and Find Full Text PDFJ Biomech
February 2019
University of Southampton, School of Engineering, Southampton SO17 1BJ, United Kingdom.
Accurate determination of joint axes is essential for understanding musculoskeletal function. Whilst numerous algorithms to compute such axes exist, the conditions under which each of the methods performs best remain largely unknown. Typically, algorithms are evaluated for specific conditions only limiting the external validity of conclusions regarding their performance.
View Article and Find Full Text PDFJ Comput Chem
August 2018
Zuse Institute Berlin (ZIB), Takustr. 7, 14195, Berlin, Germany.
Time- and frequency-resolved optical signals provide insights into the properties of light-harvesting molecular complexes, including excitation energies, dipole strengths and orientations, as well as in the exciton energy flow through the complex. The hierarchical equations of motion (HEOM) provide a unifying theory, which allows one to study the combined effects of system-environment dissipation and non-Markovian memory without making restrictive assumptions about weak or strong couplings or separability of vibrational and electronic degrees of freedom. With increasing system size the exact solution of the open quantum system dynamics requires memory and compute resources beyond a single compute node.
View Article and Find Full Text PDFJ Chem Theory Comput
July 2018
University of Kassel, Institute of Physics, Theoretical Physics II , Heinrich-Plett-Str. 40 , 34132 Kassel , Germany.
Markov state models (MSMs) have received an unabated increase in popularity in recent years, as they are very well suited for the identification and analysis of metastable states and related kinetics. However, the state-of-the-art Markov state modeling methods and tools enforce the fulfillment of a detailed balance condition, restricting their applicability to equilibrium MSMs. To date, they are unsuitable to deal with general dominant data structures including cyclic processes, which are essentially associated with nonequilibrium systems.
View Article and Find Full Text PDFEntropy (Basel)
May 2018
Institut für Mathematik, Freie Universität Berlin and Zuse Institute Berlin (ZIB), Takustr. 7, D-14195 Berlin-Dahlem, Germany.
Stimulation of renal collecting duct principal cells with antidiuretic hormone (arginine-vasopressin, AVP) results in inhibition of the small GTPase RhoA and the enrichment of the water channel aquaporin-2 (AQP2) in the plasma membrane. The membrane insertion facilitates water reabsorption from primary urine and fine-tuning of body water homeostasis. Rho guanine nucleotide exchange factors (GEFs) interact with RhoA, catalyze the exchange of GDP for GTP and thereby activate the GTPase.
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