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  1. Article ; Online: Agent-based modeling in cancer biomedicine: applications and tools for calibration and validation.

    Cogno, Nicolò / Axenie, Cristian / Bauer, Roman / Vavourakis, Vasileios

    Cancer biology & therapy

    2024  Volume 25, Issue 1, Page(s) 2344600

    Abstract: Computational models are not just appealing because they can simulate and predict the development of biological phenomena across multiple spatial and temporal scales, but also because they can integrate information from well- ... ...

    Abstract Computational models are not just appealing because they can simulate and predict the development of biological phenomena across multiple spatial and temporal scales, but also because they can integrate information from well-established
    MeSH term(s) Humans ; Neoplasms ; Calibration ; Computer Simulation ; Animals ; Models, Biological
    Language English
    Publishing date 2024-04-28
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2146305-0
    ISSN 1555-8576 ; 1538-4047
    ISSN (online) 1555-8576
    ISSN 1538-4047
    DOI 10.1080/15384047.2024.2344600
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5887: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Book ; Online: 500 ans de Suisse romande protestante

    Bauer, Olivier

    2020  

    Keywords Histoire ; protestantisme ; Suisse romande ; Réforme
    Size 1 Online-Ressource
    Publisher Éditions Livreo-Alphil
    Publishing place Neuchâtel
    Document type Book ; Online
    Note French ; Open Access
    HBZ-ID HT021050513
    ISBN 9782889500413 ; 2889500411
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Article ; Online: Mechanistic model of radiotherapy-induced lung fibrosis using coupled 3D agent-based and Monte Carlo simulations.

    Cogno, Nicolò / Bauer, Roman / Durante, Marco

    Communications medicine

    2024  Volume 4, Issue 1, Page(s) 16

    Abstract: Background: Mechanistic modelling of normal tissue toxicities is unfolding as an alternative to the phenomenological normal tissue complication probability models. The latter, currently used in the clinics, rely exclusively on limited patient data and ... ...

    Abstract Background: Mechanistic modelling of normal tissue toxicities is unfolding as an alternative to the phenomenological normal tissue complication probability models. The latter, currently used in the clinics, rely exclusively on limited patient data and neglect spatial dose distribution information. Among the various approaches, agent-based models are appealing as they provide the means to include patient-specific parameters and simulate long-term effects in complex systems. However, Monte Carlo tools remain the state-of-the-art for modelling radiation transport and provide measurements of the delivered dose with unmatched precision.
    Methods: In this work, we develop and characterize a coupled 3D agent-based - Monte Carlo model that mechanistically simulates the onset of the radiation-induced lung fibrosis in an alveolar segment. To the best of our knowledge, this is the first such model.
    Results: Our model replicates extracellular matrix patterns, radiation-induced lung fibrosis severity indexes and functional subunits survivals that show qualitative agreement with experimental studies and are consistent with our past results. Moreover, in accordance with experimental results, higher functional subunits survival and lower radiation-induced lung fibrosis severity indexes are achieved when a 5-fractions treatment is simulated. Finally, the model shows increased sensitivity to more uniform protons dose distributions with respect to more heterogeneous ones from photon irradiation.
    Conclusions: This study lays thus the groundwork for further investigating the effects of different radiotherapeutic treatments on the onset of radiation-induced lung fibrosis via mechanistic modelling.
    Language English
    Publishing date 2024-02-09
    Publishing country England
    Document type Journal Article
    ISSN 2730-664X
    ISSN (online) 2730-664X
    DOI 10.1038/s43856-024-00442-w
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  4. Article ; Online: Historical trauma and polysubstance use in Black young adults: The role of contemporary racism.

    Ebrahimi, Chantel T / Polanco-Roman, Lillian / Saraiya, Tanya C / Bauer, Alexandria G / Hien, Denise

    Psychological trauma : theory, research, practice and policy

    2024  

    Abstract: Objectives: The legacy of slavery renders Black individuals vulnerable to the harmful effects of historical trauma which may interact with contemporary racism-related experiences to increase substance use. We examined the associations between historical ...

    Abstract Objectives: The legacy of slavery renders Black individuals vulnerable to the harmful effects of historical trauma which may interact with contemporary racism-related experiences to increase substance use. We examined the associations between historical and contemporary racism-related experiences (i.e., historical loss thinking, major racial discrimination events, racial microaggressions, and internalized racism) and polysubstance use in a group of Black young adults.
    Method: Black young adults (
    Results: Historical loss thinking (
    Conclusions: Findings suggest an association between substance use and historical and contemporary-related experiences among Black young adults. This may suggest that experiences with racism contextualized within historical and contemporary manifestations may impact risk for polysubstance use among Black young adults. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
    Language English
    Publishing date 2024-02-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2497028-1
    ISSN 1942-969X ; 1942-9681
    ISSN (online) 1942-969X
    ISSN 1942-9681
    DOI 10.1037/tra0001652
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Development of the foregut and the formation of the trachea and esophagus in rat embryos. A symphony of confusion.

    Ginzel, Marco / Huber, Nana / Bauer, Leopold / Kluth, Dietrich / Metzger, Roman

    Frontiers in cell and developmental biology

    2023  Volume 11, Page(s) 1092753

    Abstract: Introduction: ...

    Abstract Introduction:
    Language English
    Publishing date 2023-02-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2023.1092753
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Retinal self-organization: a model of retinal ganglion cells and starburst amacrine cells mosaic formation.

    de Montigny, Jean / Sernagor, Evelyne / Bauer, Roman

    Open biology

    2023  Volume 13, Issue 4, Page(s) 220217

    Abstract: Individual retinal cell types exhibit semi-regular spatial patterns called retinal mosaics. Retinal ganglion cells (RGCs) and starburst amacrine cells (SACs) are known to exhibit such layouts. Mechanisms responsible for the formation of mosaics are not ... ...

    Abstract Individual retinal cell types exhibit semi-regular spatial patterns called retinal mosaics. Retinal ganglion cells (RGCs) and starburst amacrine cells (SACs) are known to exhibit such layouts. Mechanisms responsible for the formation of mosaics are not well understood but follow three main principles: (i) homotypic cells prevent nearby cells from adopting the same type, (ii) cell tangential migration and (iii) cell death. Alongside experiments in mouse, we use BioDynaMo, an agent-based simulation framework, to build a detailed and mechanistic model of mosaic formation. We investigate the implications of the three theories for RGC's mosaic formation. We report that the cell migration mechanism yields the most regular mosaics. In addition, we propose that low-density RGC type mosaics exhibit on average low regularities, and thus we question the relevance of regular spacing as a criterion for a group of RGCs to form a RGC type. We investigate SAC mosaics formation and interactions between the ganglion cell layer (GCL) and inner nuclear layer (INL) populations. We propose that homotypic interactions between the GCL and INL populations during mosaics creation are required to reproduce the observed SAC mosaics' characteristics. This suggests that the GCL and INL populations of SACs might not be independent during retinal development.
    MeSH term(s) Mice ; Animals ; Retinal Ganglion Cells/metabolism ; Amacrine Cells/metabolism ; Retina ; Software ; Computer Simulation
    Language English
    Publishing date 2023-04-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2630944-0
    ISSN 2046-2441 ; 2046-2441
    ISSN (online) 2046-2441
    ISSN 2046-2441
    DOI 10.1098/rsob.220217
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Retinal self-organization

    Jean de Montigny / Evelyne Sernagor / Roman Bauer

    Open Biology, Vol 13, Iss

    a model of retinal ganglion cells and starburst amacrine cells mosaic formation

    2023  Volume 4

    Abstract: Individual retinal cell types exhibit semi-regular spatial patterns called retinal mosaics. Retinal ganglion cells (RGCs) and starburst amacrine cells (SACs) are known to exhibit such layouts. Mechanisms responsible for the formation of mosaics are not ... ...

    Abstract Individual retinal cell types exhibit semi-regular spatial patterns called retinal mosaics. Retinal ganglion cells (RGCs) and starburst amacrine cells (SACs) are known to exhibit such layouts. Mechanisms responsible for the formation of mosaics are not well understood but follow three main principles: (i) homotypic cells prevent nearby cells from adopting the same type, (ii) cell tangential migration and (iii) cell death. Alongside experiments in mouse, we use BioDynaMo, an agent-based simulation framework, to build a detailed and mechanistic model of mosaic formation. We investigate the implications of the three theories for RGC's mosaic formation. We report that the cell migration mechanism yields the most regular mosaics. In addition, we propose that low-density RGC type mosaics exhibit on average low regularities, and thus we question the relevance of regular spacing as a criterion for a group of RGCs to form a RGC type. We investigate SAC mosaics formation and interactions between the ganglion cell layer (GCL) and inner nuclear layer (INL) populations. We propose that homotypic interactions between the GCL and INL populations during mosaics creation are required to reproduce the observed SAC mosaics' characteristics. This suggests that the GCL and INL populations of SACs might not be independent during retinal development.
    Keywords self-organization ; retinal mosaic ; computational modelling ; retinal ganglion cells ; starburst amacrine cells ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher The Royal Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: An Agent-Based Model of Radiation-Induced Lung Fibrosis.

    Cogno, Nicolò / Bauer, Roman / Durante, Marco

    International journal of molecular sciences

    2022  Volume 23, Issue 22

    Abstract: Early- and late-phase radiation-induced lung injuries, namely pneumonitis and lung fibrosis (RILF), severely constrain the maximum dose and irradiated volume in thoracic radiotherapy. As the most radiosensitive targets, epithelial cells respond to ... ...

    Abstract Early- and late-phase radiation-induced lung injuries, namely pneumonitis and lung fibrosis (RILF), severely constrain the maximum dose and irradiated volume in thoracic radiotherapy. As the most radiosensitive targets, epithelial cells respond to radiation either by undergoing apoptosis or switching to a senescent phenotype that triggers the immune system and damages surrounding healthy cells. Unresolved inflammation stimulates mesenchymal cells' proliferation and extracellular matrix (ECM) secretion, which irreversibly stiffens the alveolar walls and leads to respiratory failure. Although a thorough understanding is lacking, RILF and idiopathic pulmonary fibrosis share multiple pathways and would mutually benefit from further insights into disease progression. Furthermore, current normal tissue complication probability (NTCP) models rely on clinical experience to set tolerance doses for organs at risk and leave aside mechanistic interpretations of the undergoing processes. To these aims, we implemented a 3D agent-based model (ABM) of an alveolar duct that simulates cell dynamics and substance diffusion following radiation injury. Emphasis was placed on cell repopulation, senescent clearance, and intra/inter-alveolar bystander senescence while tracking ECM deposition. Our ABM successfully replicates early and late fibrotic response patterns reported in the literature along with the ECM sigmoidal dose-response curve. Moreover, surrogate measures of RILF severity via a custom indicator show qualitative agreement with published fibrosis indices. Finally, our ABM provides a fully mechanistic alveolar survival curve highlighting the need to include bystander damage in lung NTCP models.
    MeSH term(s) Humans ; Lung Injury/pathology ; Lung/pathology ; Radiation Injuries/etiology ; Radiation Injuries/pathology ; Idiopathic Pulmonary Fibrosis/metabolism ; Thorax ; Radiation Fibrosis Syndrome
    Language English
    Publishing date 2022-11-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms232213920
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Development of the foregut and the formation of the trachea and esophagus in rat embryos. A symphony of confusion

    Marco Ginzel / Nana Huber / Leopold Bauer / Dietrich Kluth / Roman Metzger

    Frontiers in Cell and Developmental Biology, Vol

    2023  Volume 11

    Abstract: Introduction: During embryonic development, the trachea emerges from an area of the foregut, which is often referred to as “anterior” or “common” foregut tube or simply foregut. To explain this process of differentiation, four competing models exist to ... ...

    Abstract Introduction: During embryonic development, the trachea emerges from an area of the foregut, which is often referred to as “anterior” or “common” foregut tube or simply foregut. To explain this process of differentiation, four competing models exist to date. The outgrowth and watershed models propose a foregut that remains constant in length. In the outgrowth model, the trachea buds off and elongates from the foregut, while in the watershed model, a mesenchymal wedge splits the growing foregut into the trachea and esophagus. In contrast, the septation model proposes a cranial splitting and thus a shortening of the “common” foregut tube into the trachea and esophagus by an emerging septum. Finally, the splitting and extension model describes an interaction of cranial splitting of the foregut and simultaneous caudal tracheal and esophageal growth.Methods: Here we examine the development of the undifferentiated foregut by micro computed tomography, which allows precise measurements.Results: Our results show that this area of the foregut transforms into the larynx, a process, which is independent from tracheal and esophageal development.Discussion: These observations are only consistent with the outgrowth model.
    Keywords foregut development ; micro computed tomography ; μCT ; embryology ; tracheal development ; esophageal development ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Online: Recipes for calibration and validation of agent-based models in cancer biomedicine

    Cogno, Nicolò / Axenie, Cristian / Bauer, Roman / Vavourakis, Vasileios

    2023  

    Abstract: Computational models and simulations are not just appealing because of their intrinsic characteristics across spatiotemporal scales, scalability, and predictive power, but also because the set of problems in cancer biomedicine that can be addressed ... ...

    Abstract Computational models and simulations are not just appealing because of their intrinsic characteristics across spatiotemporal scales, scalability, and predictive power, but also because the set of problems in cancer biomedicine that can be addressed computationally exceeds the set of those amenable to analytical solutions. Agent-based models and simulations are especially interesting candidates among computational modelling strategies in cancer research due to their capabilities to replicate realistic local and global interaction dynamics at a convenient and relevant scale. Yet, the absence of methods to validate the consistency of the results across scales can hinder adoption by turning fine-tuned models into black boxes. This review compiles relevant literature to explore strategies to leverage high-fidelity simulations of multi-scale, or multi-level, cancer models with a focus on validation approached as simulation calibration. We argue that simulation calibration goes beyond parameter optimization by embedding informative priors to generate plausible parameter configurations across multiple dimensions.
    Keywords Quantitative Biology - Tissues and Organs ; Computer Science - Multiagent Systems
    Subject code 006
    Publishing date 2023-10-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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