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  1. Article: Models and Algorithms for the Refinement of Therapeutic Approaches for Retinal Diseases.

    Friedmann, Elfriede / Dörsam, Simon / Auffarth, Gerd U

    Diagnostics (Basel, Switzerland)

    2023  Volume 13, Issue 5

    Abstract: We are developing a Virtual Eye for in silico therapies to accelerate research and drug development. In this paper, we present a model for drug distribution in the vitreous body that enables personalized therapy in ophthalmology. The standard treatment ... ...

    Abstract We are developing a Virtual Eye for in silico therapies to accelerate research and drug development. In this paper, we present a model for drug distribution in the vitreous body that enables personalized therapy in ophthalmology. The standard treatment for age-related macular degeneration is anti-vascular endothelial growth factor (VEGF) drugs administered by repeated injections. The treatment is risky, unpopular with patients, and some of them are unresponsive with no alternative treatment. Much attention is paid to the efficacy of these drugs, and many efforts are being made to improve them. We are designing a mathematical model and performing long-term three-dimensional Finite Element simulations for drug distribution in the human eye to gain new insights in the underlying processes using computational experiments. The underlying model consists of a time-dependent convection-diffusion equation for the drug coupled with a steady-state Darcy equation describing the flow of aqueous humor through the vitreous medium. The influence of collagen fibers in the vitreous on drug distribution is included by anisotropic diffusion and the gravity via an additional transport term. The resulting coupled model was solved in a decoupled way: first the Darcy equation with mixed finite elements, then the convection-diffusion equation with trilinear Lagrange elements. Krylov subspace methods are used to solve the resulting algebraic system. To cope with the large time steps resulting from the simulations over 30 days (operation time of 1 anti-VEGF injection), we apply the strong A-stable fractional step theta scheme. Using this strategy, we compute a good approximation to the solution that converges quadratically in both time and space. The developed simulations were used for the therapy optimization, for which specific output functionals are evaluated. We show that the effect of gravity on drug distribution is negligible, that the optimal pair of injection angles is (50∘,50∘), that larger angles can result in 38% less drug at the macula, and that in the best case only 40% of the drug reaches the macula while the rest escapes, e.g., through the retina, that by using heavier drug molecules, more of the drug concentration reaches the macula in an average of 30 days. As a refined therapy, we have found that for longer-acting drugs, the injection should be made in the center of the vitreous, and for more intensive initial treatment, the drug should be injected even closer to the macula. In this way, we can perform accurate and efficient treatment testing, calculate the optimal injection position, perform drug comparison, and quantify the effectiveness of the therapy using the developed functionals. We describe the first steps towards virtual exploration and improvement of therapy for retinal diseases such as age-related macular degeneration.
    Language English
    Publishing date 2023-03-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662336-5
    ISSN 2075-4418
    ISSN 2075-4418
    DOI 10.3390/diagnostics13050975
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Models and Algorithms for the Refinement of Therapeutic Approaches for Retinal Diseases

    Elfriede Friedmann / Simon Dörsam / Gerd U. Auffarth

    Diagnostics, Vol 13, Iss 975, p

    2023  Volume 975

    Abstract: We are developing a Virtual Eye for in silico therapies to accelerate research and drug development. In this paper, we present a model for drug distribution in the vitreous body that enables personalized therapy in ophthalmology. The standard treatment ... ...

    Abstract We are developing a Virtual Eye for in silico therapies to accelerate research and drug development. In this paper, we present a model for drug distribution in the vitreous body that enables personalized therapy in ophthalmology. The standard treatment for age-related macular degeneration is anti-vascular endothelial growth factor (VEGF) drugs administered by repeated injections. The treatment is risky, unpopular with patients, and some of them are unresponsive with no alternative treatment. Much attention is paid to the efficacy of these drugs, and many efforts are being made to improve them. We are designing a mathematical model and performing long-term three-dimensional Finite Element simulations for drug distribution in the human eye to gain new insights in the underlying processes using computational experiments. The underlying model consists of a time-dependent convection-diffusion equation for the drug coupled with a steady-state Darcy equation describing the flow of aqueous humor through the vitreous medium. The influence of collagen fibers in the vitreous on drug distribution is included by anisotropic diffusion and the gravity via an additional transport term. The resulting coupled model was solved in a decoupled way: first the Darcy equation with mixed finite elements, then the convection-diffusion equation with trilinear Lagrange elements. Krylov subspace methods are used to solve the resulting algebraic system. To cope with the large time steps resulting from the simulations over 30 days (operation time of 1 anti-VEGF injection), we apply the strong A-stable fractional step theta scheme. Using this strategy, we compute a good approximation to the solution that converges quadratically in both time and space. The developed simulations were used for the therapy optimization, for which specific output functionals are evaluated. We show that the effect of gravity on drug distribution is negligible, that the optimal pair of injection angles is <math xmlns="http://www.w3.org/1998/Math/MathML" ...<br />
    Keywords numerical modeling ; AMD treatment ; drug distribution ; drug diffusion ; free convection ; partial differential equations ; Medicine (General) ; R5-920
    Subject code 510
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: PDE/ODE modeling and simulation to determine the role of diffusion in long-term and -range cellular signaling.

    Friedmann, Elfriede

    BMC biophysics

    2015  Volume 8, Page(s) 10

    Abstract: Background: We study the relevance of diffusion for the dynamics of signaling pathways. Mathematical modeling of cellular diffusion leads to a coupled system of differential equations with Robin boundary conditions which requires a substantial knowledge ...

    Abstract Background: We study the relevance of diffusion for the dynamics of signaling pathways. Mathematical modeling of cellular diffusion leads to a coupled system of differential equations with Robin boundary conditions which requires a substantial knowledge in mathematical theory. Using our new developed analytical and numerical techniques together with modern experiments, we analyze and quantify various types of diffusive effects in intra- and inter-cellular signaling. The complexity of these models necessitates suitable numerical methods to perform the simulations precisely and within an acceptable period of time.
    Methods: The numerical methods comprise a Galerkin finite element space discretization, an adaptive time stepping scheme and either an iterative operator splitting method or fully coupled multilevel algorithm as solver.
    Results: The simulation outcome allows us to analyze different biological aspects. On the scale of a single cell, we showed the high cytoplasmic concentration gradients in irregular geometries. We found an 11 % maximum relative total STAT5-concentration variation in a fibroblast and a 70 % maximum relative pSTAT5-concentration variation in a fibroblast with an irregular cell shape. For pSMAD2 the maximum relative variation was 18 % in a hepatocyte with a box shape and 70 % in an irregular geometry. This result can be also obtained in a cell with a box shape if the molecules diffuse slowly (with D=1 μm(2)/s instead of D=15 μm(2)/s). On a scale of cell system in the lymph node, our simulations showed an inhomogeneous IL-2 pattern with an amount over three orders of magnitude (10(-3)-1 pM) and high gradients in face of its fast diffusivity. We observed that 20 out of 125 cells were activated after 9 h and 33 in the steady state. Our in-silico experiments showed that the insertion of 31 regulatory T cells in our cell system can completely downregulate the signal.
    Conclusions: We quantify the concentration gradients evolving from the diffusion of the molecules in several signaling pathways. For intracellular signaling pathways with nuclear accumulation the size of cytoplasmic gradients does not indicate the change in gene expression which has to be analyzed separately in future. For intercellular signaling the high cytokine concentration gradients play an essential role in the regulation of the molecular mechanism of the immune response. Furthermore, our simulation results can give the information on which signaling pathway diffusion may play a role. We conclude that a PDE model has to be considered for cells with an irregular shape or for slow diffusing molecules. Also the high gradients inside a cell or in a cell system can play an essential role in the regulation of the molecular mechanisms.
    Language English
    Publishing date 2015-10-14
    Publishing country England
    Document type Journal Article
    ISSN 2046-1682
    ISSN 2046-1682
    DOI 10.1186/s13628-015-0024-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online ; Thesis: Modeling and Simulation of the Aqueous Humor Flow for Healthy, Glaucomatous and Treated Eyes with Stokes and Darcy Equations

    Olkhovskiy, Vladislav [Verfasser] / Friedmann, Elfriede [Akademischer Betreuer]

    2020  

    Author's details Vladislav Olkhovskiy ; Betreuer: Elfriede Friedmann
    Keywords Medizin, Gesundheit ; Medicine, Health
    Subject code sg610
    Language English
    Publisher Universitätsbibliothek Heidelberg
    Publishing place Heidelberg
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

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  5. Article ; Online: Quantitative evaluation of microvacuole formation in five intraocular lens models made of different hydrophobic materials.

    Yildirim, Timur M / Schickhardt, Sonja K / Wang, Qiang / Friedmann, Elfriede / Khoramnia, Ramin / Auffarth, Gerd U

    PloS one

    2021  Volume 16, Issue 4, Page(s) e0250860

    Abstract: In this laboratory study, we assessed the resistance to microvacuole (glistening) formation in hydrophobic intraocular lenses (IOLs). Glistenings were induced in five lenses each of five different hydrophobic acrylic IOL models, using an established in ... ...

    Abstract In this laboratory study, we assessed the resistance to microvacuole (glistening) formation in hydrophobic intraocular lenses (IOLs). Glistenings were induced in five lenses each of five different hydrophobic acrylic IOL models, using an established in vitro laboratory model: 800C (Rayner, Worthing, UK), AcrySof SN60WF (Alcon, Fort Worth, USA), Tecnis ZCB00 (Johnson & Johnson Vision, Santa Ana, USA), Vivinex XY1 (Hoya, Tokyo, Japan) and CT Lucia 611P (Zeiss, Oberkochen, Germany). We evaluated the number of microvacuoles per square millimeter (MV/mm2) in the central part of each IOL. Results were analyzed statistically, and mean glistening numbers were ranked, with the highest in the SN60WF which had 66.0 (±45.5) MVs/mm, followed by the 611P with 30.7 (±8.4) MVs/mm2. The 800C and XY1 showed comparable values of 2.0 (±3.6) and 2.7 (±2.4) MVs/mm2, respectively. ZCB00 had the lowest number with 0.9 (±0.6) MVs/mm2. This study shows that the resistance to glistening formation differs depending on the hydrophobic acrylic copolymer composition of the IOL material. Some IOLs from current clinical use are still prone to develop glistenings whereas others, including the ZCB00, 800C and XY1 show high resistance to microvacuole formation.
    MeSH term(s) Acrylic Resins/chemistry ; Humans ; Hydrophobic and Hydrophilic Interactions ; In Vitro Techniques ; Lenses, Intraocular ; Polymers/chemistry ; Stress, Mechanical ; Temperature
    Chemical Substances Acrylic Resins ; Polymers
    Language English
    Publishing date 2021-04-30
    Publishing country United States
    Document type Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0250860
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online ; Thesis: Riblets in the viscous sublayer

    Friedmann, Elfriede

    optimal shape design of microstructures

    2006  

    Author's details vorgelegt von Elfriede Friedmann
    Language English
    Size Online-Ressource
    Document type Book ; Online ; Thesis
    Thesis / German Habilitation thesis Univ., Diss--Heidelberg, 2005
    Database Former special subject collection: coastal and deep sea fishing

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  7. Article ; Online: Quantitative evaluation of microvacuole formation in five intraocular lens models made of different hydrophobic materials.

    Timur M Yildirim / Sonja K Schickhardt / Qiang Wang / Elfriede Friedmann / Ramin Khoramnia / Gerd U Auffarth

    PLoS ONE, Vol 16, Iss 4, p e

    2021  Volume 0250860

    Abstract: In this laboratory study, we assessed the resistance to microvacuole (glistening) formation in hydrophobic intraocular lenses (IOLs). Glistenings were induced in five lenses each of five different hydrophobic acrylic IOL models, using an established in ... ...

    Abstract In this laboratory study, we assessed the resistance to microvacuole (glistening) formation in hydrophobic intraocular lenses (IOLs). Glistenings were induced in five lenses each of five different hydrophobic acrylic IOL models, using an established in vitro laboratory model: 800C (Rayner, Worthing, UK), AcrySof SN60WF (Alcon, Fort Worth, USA), Tecnis ZCB00 (Johnson & Johnson Vision, Santa Ana, USA), Vivinex XY1 (Hoya, Tokyo, Japan) and CT Lucia 611P (Zeiss, Oberkochen, Germany). We evaluated the number of microvacuoles per square millimeter (MV/mm2) in the central part of each IOL. Results were analyzed statistically, and mean glistening numbers were ranked, with the highest in the SN60WF which had 66.0 (±45.5) MVs/mm, followed by the 611P with 30.7 (±8.4) MVs/mm2. The 800C and XY1 showed comparable values of 2.0 (±3.6) and 2.7 (±2.4) MVs/mm2, respectively. ZCB00 had the lowest number with 0.9 (±0.6) MVs/mm2. This study shows that the resistance to glistening formation differs depending on the hydrophobic acrylic copolymer composition of the IOL material. Some IOLs from current clinical use are still prone to develop glistenings whereas others, including the ZCB00, 800C and XY1 show high resistance to microvacuole formation.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Three-Dimensional Gradients of Cytokine Signaling between T Cells.

    Thurley, Kevin / Gerecht, Daniel / Friedmann, Elfriede / Höfer, Thomas

    PLoS computational biology

    2015  Volume 11, Issue 4, Page(s) e1004206

    Abstract: Immune responses are regulated by diffusible mediators, the cytokines, which act at sub-nanomolar concentrations. The spatial range of cytokine communication is a crucial, yet poorly understood, functional property. Both containment of cytokine action in ...

    Abstract Immune responses are regulated by diffusible mediators, the cytokines, which act at sub-nanomolar concentrations. The spatial range of cytokine communication is a crucial, yet poorly understood, functional property. Both containment of cytokine action in narrow junctions between immune cells (immunological synapses) and global signaling throughout entire lymph nodes have been proposed, but the conditions under which they might occur are not clear. Here we analyze spatially three-dimensional reaction-diffusion models for the dynamics of cytokine signaling at two successive scales: in immunological synapses and in dense multicellular environments. For realistic parameter values, we observe local spatial gradients, with the cytokine concentration around secreting cells decaying sharply across only a few cell diameters. Focusing on the well-characterized T-cell cytokine interleukin-2, we show how cytokine secretion and competitive uptake determine this signaling range. Uptake is shaped locally by the geometry of the immunological synapse. However, even for narrow synapses, which favor intrasynaptic cytokine consumption, escape fluxes into the extrasynaptic space are expected to be substantial (≥20% of secretion). Hence paracrine signaling will generally extend beyond the synapse but can be limited to cellular microenvironments through uptake by target cells or strong competitors, such as regulatory T cells. By contrast, long-range cytokine signaling requires a high density of cytokine producers or weak consumption (e.g., by sparsely distributed target cells). Thus in a physiological setting, cytokine gradients between cells, and not bulk-phase concentrations, are crucial for cell-to-cell communication, emphasizing the need for spatially resolved data on cytokine signaling.
    MeSH term(s) Animals ; Cells, Cultured ; Computer Simulation ; Diffusion ; Humans ; Immunological Synapses/chemistry ; Immunological Synapses/immunology ; Models, Immunological ; Paracrine Communication/immunology ; Receptors, Cytokine/chemistry ; Receptors, Cytokine/immunology ; T-Lymphocytes/chemistry ; T-Lymphocytes/immunology
    Chemical Substances Receptors, Cytokine
    Language English
    Publishing date 2015-04-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1004206
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Mathematical Models in the Description of Pregnane X Receptor (PXR)-Regulated Cytochrome P450 Enzyme Induction.

    Tebbens, Jurjen Duintjer / Azar, Malek / Friedmann, Elfriede / Lanzendörfer, Martin / Pávek, Petr

    International journal of molecular sciences

    2018  Volume 19, Issue 6

    Abstract: The pregnane X receptor (PXR) is a drug/xenobiotic-activated transcription factor of crucial importance for major cytochrome P450 xenobiotic-metabolizing enzymes (CYP) expression and regulation in the liver and the intestine. One of the major target ... ...

    Abstract The pregnane X receptor (PXR) is a drug/xenobiotic-activated transcription factor of crucial importance for major cytochrome P450 xenobiotic-metabolizing enzymes (CYP) expression and regulation in the liver and the intestine. One of the major target genes regulated by PXR is the cytochrome P450 enzyme (CYP3A4), which is the most important human drug-metabolizing enzyme. In addition, PXR is supposed to be involved both in basal and/or inducible expression of many other CYPs, such as CYP2B6, CYP2C8, 2C9 and 2C19, CYP3A5, CYP3A7, and CYP2A6. Interestingly, the dynamics of PXR-mediated target genes regulation has not been systematically studied and we have only a few mechanistic mathematical and biologically based models describing gene expression dynamics after PXR activation in cellular models. Furthermore, few indirect mathematical PKPD models for prediction of CYP3A metabolic activity in vivo have been built based on compartmental models with respect to drug⁻drug interactions or hormonal crosstalk. Importantly, several negative feedback loops have been described in PXR regulation. Although current mathematical models propose these adaptive mechanisms, a comprehensive mathematical model based on sufficient experimental data is still missing. In the current review, we summarize and compare these models and address some issues that should be considered for the improvement of PXR-mediated gene regulation modelling as well as for our better understanding of the quantitative and spatial dynamics of CYPs expression.
    MeSH term(s) Animals ; Cytochrome P-450 Enzyme System/genetics ; Cytochrome P-450 Enzyme System/metabolism ; Feedback, Physiological ; Gene Regulatory Networks ; Humans ; Models, Theoretical ; Receptors, Steroid/genetics ; Receptors, Steroid/metabolism
    Chemical Substances Receptors, Steroid ; pregnane X receptor ; Cytochrome P-450 Enzyme System (9035-51-2)
    Language English
    Publishing date 2018-06-15
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms19061785
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Three-Dimensional Gradients of Cytokine Signaling between T Cells.

    Kevin Thurley / Daniel Gerecht / Elfriede Friedmann / Thomas Höfer

    PLoS Computational Biology, Vol 11, Iss 4, p e

    2015  Volume 1004206

    Abstract: Immune responses are regulated by diffusible mediators, the cytokines, which act at sub-nanomolar concentrations. The spatial range of cytokine communication is a crucial, yet poorly understood, functional property. Both containment of cytokine action in ...

    Abstract Immune responses are regulated by diffusible mediators, the cytokines, which act at sub-nanomolar concentrations. The spatial range of cytokine communication is a crucial, yet poorly understood, functional property. Both containment of cytokine action in narrow junctions between immune cells (immunological synapses) and global signaling throughout entire lymph nodes have been proposed, but the conditions under which they might occur are not clear. Here we analyze spatially three-dimensional reaction-diffusion models for the dynamics of cytokine signaling at two successive scales: in immunological synapses and in dense multicellular environments. For realistic parameter values, we observe local spatial gradients, with the cytokine concentration around secreting cells decaying sharply across only a few cell diameters. Focusing on the well-characterized T-cell cytokine interleukin-2, we show how cytokine secretion and competitive uptake determine this signaling range. Uptake is shaped locally by the geometry of the immunological synapse. However, even for narrow synapses, which favor intrasynaptic cytokine consumption, escape fluxes into the extrasynaptic space are expected to be substantial (≥20% of secretion). Hence paracrine signaling will generally extend beyond the synapse but can be limited to cellular microenvironments through uptake by target cells or strong competitors, such as regulatory T cells. By contrast, long-range cytokine signaling requires a high density of cytokine producers or weak consumption (e.g., by sparsely distributed target cells). Thus in a physiological setting, cytokine gradients between cells, and not bulk-phase concentrations, are crucial for cell-to-cell communication, emphasizing the need for spatially resolved data on cytokine signaling.
    Keywords Biology (General) ; QH301-705.5
    Subject code 610
    Language English
    Publishing date 2015-04-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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