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  1. Book ; Online: Methods and Applications of Computational Immunology

    Greiff, Victor / Yaari, Gur / Textor, Johannes / Chain, Benny

    2020  

    Keywords Medicine ; Immunology ; systems immunology ; computational biology ; bioinformatics ; mathematical modeling ; innate and adaptive immune response
    Size 1 electronic resource (358 pages)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021231193
    ISBN 9782889633883 ; 2889633888
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Interpreting T-cell search "strategies" in the light of evolution under constraints.

    Wortel, Inge M N / Textor, Johannes

    PLoS computational biology

    2023  Volume 19, Issue 2, Page(s) e1010918

    Abstract: Two decades of in vivo imaging have revealed how diverse T-cell motion patterns can be. Such recordings have sparked the notion of search "strategies": T cells may have evolved ways to search for antigen efficiently depending on the task at hand. ... ...

    Abstract Two decades of in vivo imaging have revealed how diverse T-cell motion patterns can be. Such recordings have sparked the notion of search "strategies": T cells may have evolved ways to search for antigen efficiently depending on the task at hand. Mathematical models have indeed confirmed that several observed T-cell migration patterns resemble a theoretical optimum; for example, frequent turning, stop-and-go motion, or alternating short and long motile runs have all been interpreted as deliberately tuned behaviours, optimising the cell's chance of finding antigen. But the same behaviours could also arise simply because T cells cannot follow a straight, regular path through the tight spaces they navigate. Even if T cells do follow a theoretically optimal pattern, the question remains: which parts of that pattern have truly been evolved for search, and which merely reflect constraints from the cell's migration machinery and surroundings? We here employ an approach from the field of evolutionary biology to examine how cells might evolve search strategies under realistic constraints. Using a cellular Potts model (CPM), where motion arises from intracellular dynamics interacting with cell shape and a constraining environment, we simulate evolutionary optimization of a simple task: explore as much area as possible. We find that our simulated cells indeed evolve their motility patterns. But the evolved behaviors are not shaped solely by what is functionally optimal; importantly, they also reflect mechanistic constraints. Cells in our model evolve several motility characteristics previously attributed to search optimisation-even though these features are not beneficial for the task given here. Our results stress that search patterns may evolve for other reasons than being "optimal". In part, they may be the inevitable side effects of interactions between cell shape, intracellular dynamics, and the diverse environments T cells face in vivo.
    MeSH term(s) T-Lymphocytes ; Models, Theoretical ; Cell Movement
    Language English
    Publishing date 2023-02-27
    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.1010918
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: pgmpy

    Ankan, Ankur / Textor, Johannes

    A Python Toolkit for Bayesian Networks

    2023  

    Abstract: Bayesian Networks (BNs) are used in various fields for modeling, prediction, and decision making. pgmpy is a python package that provides a collection of algorithms and tools to work with BNs and related models. It implements algorithms for structure ... ...

    Abstract Bayesian Networks (BNs) are used in various fields for modeling, prediction, and decision making. pgmpy is a python package that provides a collection of algorithms and tools to work with BNs and related models. It implements algorithms for structure learning, parameter estimation, approximate and exact inference, causal inference, and simulations. These implementations focus on modularity and easy extensibility to allow users to quickly modify/add to existing algorithms, or to implement new algorithms for different use cases. pgmpy is released under the MIT License; the source code is available at: https://github.com/pgmpy/pgmpy, and the documentation at: https://pgmpy.org.
    Keywords Computer Science - Machine Learning ; Statistics - Methodology
    Publishing date 2023-04-17
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Identifiability of causal effects in test-negative design studies.

    Shrier, Ian / Stovitz, Steven D / Textor, Johannes

    International journal of epidemiology

    2023  Volume 52, Issue 6, Page(s) 1968–1974

    Abstract: Causal directed acyclic graphs (DAGs) are often used to select variables in a regression model to identify causal effects. Outcome-based sampling studies, such as the 'test-negative design' used to assess vaccine effectiveness, present unique challenges ... ...

    Abstract Causal directed acyclic graphs (DAGs) are often used to select variables in a regression model to identify causal effects. Outcome-based sampling studies, such as the 'test-negative design' used to assess vaccine effectiveness, present unique challenges that are not addressed by the common back-door criterion. Here we discuss intuitive, graphical approaches to explain why the common back-door criterion cannot be used for identification of population average causal effects with outcome-based sampling studies. We also describe graphical rules that can be used instead in outcome-based sampling studies when the objective is limited to determining if the causal odds ratio is identifiable, and illustrate recent changes to the free online software Dagitty which incorporate these principles.
    MeSH term(s) Humans ; Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; Causality ; Software
    Language English
    Publishing date 2023-07-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 187909-1
    ISSN 1464-3685 ; 0300-5771
    ISSN (online) 1464-3685
    ISSN 0300-5771
    DOI 10.1093/ije/dyad102
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 893: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser.

    Wortel, Inge Mn / Textor, Johannes

    eLife

    2021  Volume 10

    Abstract: The cellular Potts model (CPM) is a powerful in silico method for simulating biological processes at tissue scale. Their inherently graphical nature makes CPMs very accessible in theory, but in practice, they are mostly implemented in specialised ... ...

    Abstract The cellular Potts model (CPM) is a powerful in silico method for simulating biological processes at tissue scale. Their inherently graphical nature makes CPMs very accessible in theory, but in practice, they are mostly implemented in specialised frameworks users need to master before they can run simulations. We here present Artistoo (Artificial Tissue Toolbox), a JavaScript library for building 'explorable' CPM simulations where viewers can change parameters interactively, exploring their effects in real time. Simulations run directly in the web browser and do not require third-party software, plugins, or back-end servers. The JavaScript implementation imposes no major performance loss compared to frameworks written in C++; Artistoo remains sufficiently fast for interactive, real-time simulations. Artistoo provides an opportunity to unlock CPM models for a broader audience: interactive simulations can be shared via a URL in a
    MeSH term(s) Animals ; Cell Physiological Phenomena ; Computational Biology ; Computer Simulation ; Humans ; Models, Biological ; Programming Languages ; Software Design ; Time Factors ; Web Browser
    Language English
    Publishing date 2021-04-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.61288
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: A Simple Unified Approach to Testing High-Dimensional Conditional Independences for Categorical and Ordinal Data

    Ankan, Ankur / Textor, Johannes

    2022  

    Abstract: Conditional independence (CI) tests underlie many approaches to model testing and structure learning in causal inference. Most existing CI tests for categorical and ordinal data stratify the sample by the conditioning variables, perform simple ... ...

    Abstract Conditional independence (CI) tests underlie many approaches to model testing and structure learning in causal inference. Most existing CI tests for categorical and ordinal data stratify the sample by the conditioning variables, perform simple independence tests in each stratum, and combine the results. Unfortunately, the statistical power of this approach degrades rapidly as the number of conditioning variables increases. Here we propose a simple unified CI test for ordinal and categorical data that maintains reasonable calibration and power in high dimensions. We show that our test outperforms existing baselines in model testing and structure learning for dense directed graphical models while being comparable for sparse models. Our approach could be attractive for causal model testing because it is easy to implement, can be used with non-parametric or parametric probability models, has the symmetry property, and has reasonable computational requirements.
    Keywords Statistics - Machine Learning ; Computer Science - Machine Learning
    Subject code 310
    Publishing date 2022-06-09
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Flow rate resonance of actively deforming particles.

    Parisi, Daniel R / Wiebke, Lucas E / Mandl, Judith N / Textor, Johannes

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 9455

    Abstract: Lymphoid organs are unusual multicellular tissues: they are densely packed, but the lymphocytes trafficking through them are actively moving. We hypothesize that the intriguing ability of lymphocytes to avoid jamming and clogging is in part attributable ... ...

    Abstract Lymphoid organs are unusual multicellular tissues: they are densely packed, but the lymphocytes trafficking through them are actively moving. We hypothesize that the intriguing ability of lymphocytes to avoid jamming and clogging is in part attributable to the dynamic shape changes that cells undergo when they move. In this work, we test this hypothesis by investigating an idealized system, namely, the flow of self-propelled, oscillating particles passing through a narrow constriction in two dimensions (2D), using numerical simulations. We found that deformation allows particles with these properties to flow through a narrow constriction in conditions when non-deformable particles would not be able to do so. Such a flowing state requires the amplitude and frequency of oscillations to exceed threshold values. Moreover, a resonance leading to the maximum flow rate was found when the oscillation frequency matched the natural frequency of the particle related to its elastic stiffness. To our knowledge, this phenomenon has not been described previously. Our findings could have important implications for understanding and controlling flow in a variety of systems in addition to lymphoid organs, such as granular flows subjected to vibration.
    MeSH term(s) Vibration ; Lymphocytes/cytology ; Cell Shape ; Models, Biological
    Language English
    Publishing date 2023-06-10
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-36182-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Reply to "Comment on 'Inverse Square Lévy Walks are not Optimal Search Strategies for d≥2"'.

    Levernier, Nicolas / Textor, Johannes / Bénichou, Olivier / Voituriez, Raphaël

    Physical review letters

    2021  Volume 126, Issue 4, Page(s) 48902

    MeSH term(s) Animals ; Behavior, Animal ; Movement
    Language English
    Publishing date 2021-02-12
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.126.048902
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

    Z 4' 58/153: Show issues

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  9. Article ; Online: Testing Graphical Causal Models Using the R Package "dagitty".

    Ankan, Ankur / Wortel, Inge M N / Textor, Johannes

    Current protocols

    2021  Volume 1, Issue 2, Page(s) e45

    Abstract: Causal diagrams such as directed acyclic graphs (DAGs) are used in several scientific fields to help design and analyze studies that aim to infer causal effects from observational data; for example, DAGs can help identify suitable strategies to reduce ... ...

    Abstract Causal diagrams such as directed acyclic graphs (DAGs) are used in several scientific fields to help design and analyze studies that aim to infer causal effects from observational data; for example, DAGs can help identify suitable strategies to reduce confounding bias. However, DAGs can be difficult to design, and the validity of any DAG-derived strategy hinges on the validity of the postulated DAG itself. Researchers should therefore check whether the assumptions encoded in the DAG are consistent with the data before proceeding with the analysis. Here, we explain how the R package 'dagitty', based on the web tool dagitty.net, can be used to test the statistical implications of the assumptions encoded in a given DAG. We hope that this will help researchers discover model specification errors, avoid erroneous conclusions, and build better models. © 2021 The Authors. Basic Protocol 1: Constructing and importing DAG models from the dagitty web interface Support Protocol 1: Installing R, RStudio, and the dagitty package Basic Protocol 2: Testing DAGs against categorical data Basic Protocol 3: Testing DAGs against continuous data Support Protocol 2: Testing DAGs against continuous data with non-linearities Basic Protocol 4: Testing DAGs against a combination of categorical and continuous data.
    MeSH term(s) Bias ; Causality ; Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; Models, Theoretical
    Language English
    Publishing date 2021-02-25
    Publishing country United States
    Document type Journal Article
    ISSN 2691-1299
    ISSN (online) 2691-1299
    DOI 10.1002/cpz1.45
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online: A parallelized cellular Potts model that enables simulations at tissue scale

    Sultan, Shabaz / Devi, Sapna / Mueller, Scott N. / Textor, Johannes

    2023  

    Abstract: The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide use, CPM ... ...

    Abstract The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide use, CPM simulations are considered too computationally intensive for three-dimensional (3D) models at organ scale. CPMs have been difficult to parallelise because of their inherently sequential update scheme. Here, we present a Graphical Processing Unit (GPU)-based parallelisation scheme that preserves local update statistics and is up to 3-4 orders of magnitude faster than serial implementations. We show several examples where our scheme preserves simulation behaviors that are drastically altered by existing parallelisation methods. We use our framework to construct tissue-scale models of liver and lymph node environments containing millions of cells that are directly based on microscopy-imaged tissue structures. Thus, our GPU-based CPM framework enables in silico studies of multicellular systems of unprecedented scale.

    Comment: 29 pages, 11 figures, 3 tables
    Keywords Quantitative Biology - Tissues and Organs
    Publishing date 2023-12-14
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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