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  • Springer Science and Business Media LLC  (7)
  • 1
    Online Resource
    Online Resource
    QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis
    Springer Science and Business Media LLC ; 2021
    In:  BMC Bioinformatics Vol. 22, No. 1 ( 2021-12)
    Details
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 22, No. 1 ( 2021-12)
    Abstract: The technical development of imaging techniques in life sciences has enabled the three-dimensional recording of living samples at increasing temporal resolutions. Dynamic 3D data sets of developing organisms allow for time-resolved quantitative analyses of morphogenetic changes in three dimensions, but require efficient and automatable analysis pipelines to tackle the resulting Terabytes of image data. Particle image velocimetry (PIV) is a robust and segmentation-free technique that is suitable for quantifying collective cellular migration on data sets with different labeling schemes. This paper presents the implementation of an efficient 3D PIV package using the Julia programming language—quickPIV. Our software is focused on optimizing CPU performance and ensuring the robustness of the PIV analyses on biological data. Results QuickPIV is three times faster than the Python implementation hosted in openPIV, both in 2D and 3D. Our software is also faster than the fastest 2D PIV package in openPIV, written in C++. The accuracy evaluation of our software on synthetic data agrees with the expected accuracies described in the literature. Additionally, by applying quickPIV to three data sets of the embryogenesis of Tribolium castaneum , we obtained vector fields that recapitulate the migration movements of gastrulation, both in nuclear and actin-labeled embryos. We show normalized squared error cross-correlation to be especially accurate in detecting translations in non-segmentable biological image data. Conclusions The presented software addresses the need for a fast and open-source 3D PIV package in biological research. Currently, quickPIV offers efficient 2D and 3D PIV analyses featuring zero-normalized and normalized squared error cross-correlations, sub-pixel/voxel approximation, and multi-pass. Post-processing options include filtering and averaging of the resulting vector fields, extraction of velocity, divergence and collectiveness maps, simulation of pseudo-trajectories, and unit conversion. In addition, our software includes functions to visualize the 3D vector fields in Paraview.
    Type of Medium: Online Resource
    ISSN: 1471-2105
    URL: Article
    DOI: 10.1186/s12859-021-04474-0
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2041484-5
    SSG: 12
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  • 2
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    TTCA: an R package for the identification of differentially expressed genes in time course microarray data
    Springer Science and Business Media LLC ; 2017
    In:  BMC Bioinformatics Vol. 18, No. 1 ( 2017-12)
    Details
    In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 18, No. 1 ( 2017-12)
    Type of Medium: Online Resource
    ISSN: 1471-2105
    URL: Article
    DOI: 10.1186/s12859-016-1440-8
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2041484-5
    SSG: 12
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  • 3
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    An individual-based model for collective cancer cell migration explains speed dynamics and phenotype variability in response to growth factors
    Springer Science and Business Media LLC ; 2017
    In:  npj Systems Biology and Applications Vol. 3, No. 1 ( 2017-03-03)
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    In: npj Systems Biology and Applications, Springer Science and Business Media LLC, Vol. 3, No. 1 ( 2017-03-03)
    Abstract: Collective cell migration is a common phenotype in epithelial cancers, which is associated with tumor cell metastasis and poor patient survival. However, the interplay between physiologically relevant pro-migratory stimuli and the underlying mechanical cell–cell interactions are poorly understood. We investigated the migratory behavior of different collectively migrating non-small cell lung cancer cell lines in response to motogenic growth factors (e.g. epidermal growth factor) or clinically relevant small compound inhibitors. Depending on the treatment, we observed distinct behaviors in a classical lateral migration assay involving traveling fronts, finger-shapes or the development of cellular bridges. Particle image velocimetry analysis revealed characteristic speed dynamics (evolution of the average speed of all cells in a frame) in all experiments exhibiting initial acceleration and subsequent deceleration of the cell populations. To better understand the mechanical properties of individual cells leading to the observed speed dynamics and the phenotypic differences we developed a mathematical model based on a Langevin approach. This model describes intercellular forces, random motility, and stimulation of active migration by mechanical interaction between cells. Simulations show that the model is able to reproduce the characteristic spatio-temporal speed distributions as well as most migratory phenotypes of the studied cell lines. A specific strength of the proposed model is that it identifies a small set of mechanical features necessary to explain all phenotypic and dynamical features of the migratory response of non-small cell lung cancer cells to chemical stimulation/inhibition. Furthermore, all processes included in the model can be associated with potential molecular components, and are therefore amenable to experimental validation. Thus, the presented mathematical model may help to predict which mechanical aspects involved in non-small cell lung cancer cell migration are affected by the respective therapeutic treatment.
    Type of Medium: Online Resource
    ISSN: 2056-7189
    URL: Article
    DOI: 10.1038/s41540-017-0006-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2017
    detail.hit.zdb_id: 2841868-2
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  • 4
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    New measurement criteria for studying alcohol drinking and relapse in rodents
    Springer Science and Business Media LLC ; 2013
    In:  In Silico Pharmacology Vol. 1, No. 1 ( 2013-11-01)
    Details
    In: In Silico Pharmacology, Springer Science and Business Media LLC, Vol. 1, No. 1 ( 2013-11-01)
    Abstract: Relapse to alcohol use is considered as one of the central features distinguishing dependence from controlled alcohol consumption. Relapse-like drinking in rodents is a transient episode of heavy drinking that follows a period of abstinence. This behaviour is called the alcohol deprivation effect (ADE). Not all animals develop behavioural changes that resemble relapse-like drinking behaviour. The purpose of our study was to develop a generalized quantitative criterion by which animals could be separated into two groups depending on their behaviour during a relapse-like situation (ADE vs. no-ADE). Methods An automated drinkometer system was used for data collection. This system measures fluid consumption by means of high-precision sensors attached to the drinking bottles in the home cage of the rat. We used a four bottle free choice paradigm with water 5, 10, and 20% ethanol solutions. For data analysis we developed a new measure of alcohol intake that quantifies net alcohol intake in relation to net consumption of water. This new measure is called water-penalized net ethanol intake. Results The new measure is more robust than commonly used measurements, such as alcohol preference and intake. It allows the comparison of alcohol intake between different groups of animals and different setups using an arbitrary number of bottles. Based on this new measure we developed a method to automatically select the threshold for the presence of ADE in individual animals. Conclusions Separating animals by their behavior during relapse-like situation could be used as one of the criteria for identification of alcohol addicted and non-addicted rats. A classification into presenting ADE or not is also essential to test the effectiveness of newly developed therapeutic drugs.
    Type of Medium: Online Resource
    ISSN: 2193-9616
    URL: Article
    DOI: 10.1186/2193-9616-1-13
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2013
    detail.hit.zdb_id: 2702993-1
    SSG: 15,3
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  • 5
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    Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis
    Springer Science and Business Media LLC ; 2021
    In:  BMC Biology Vol. 19, No. 1 ( 2021-02-24)
    Details
    In: BMC Biology, Springer Science and Business Media LLC, Vol. 19, No. 1 ( 2021-02-24)
    Abstract: Organoids are morphologically heterogeneous three-dimensional cell culture systems and serve as an ideal model for understanding the principles of collective cell behaviour in mammalian organs during development, homeostasis, regeneration, and pathogenesis. To investigate the underlying cell organisation principles of organoids, we imaged hundreds of pancreas and cholangiocarcinoma organoids in parallel using light sheet and bright-field microscopy for up to 7 days. Results We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation, and degeneration and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation, and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright-field microscopy analysis of entire cultures. Conclusion Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying the core regulatory principles of organoid morphogenesis.
    Type of Medium: Online Resource
    ISSN: 1741-7007
    URL: Article
    DOI: 10.1186/s12915-021-00958-w
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2133020-7
    SSG: 12
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  • 6
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    Structural analysis of functional connectivity related to memory reveals network changes in memory function over the life span
    Springer Science and Business Media LLC ; 2011
    In:  BMC Neuroscience Vol. 12, No. S1 ( 2011-12)
    Details
    In: BMC Neuroscience, Springer Science and Business Media LLC, Vol. 12, No. S1 ( 2011-12)
    Type of Medium: Online Resource
    ISSN: 1471-2202
    URL: Article
    DOI: 10.1186/1471-2202-12-S1-P71
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 2041344-0
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  • 7
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    Cell fate clusters in ICM organoids arise from cell fate heredity and division: a modelling approach
    Springer Science and Business Media LLC ; 2020
    In:  Scientific Reports Vol. 10, No. 1 ( 2020-12-29)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 10, No. 1 ( 2020-12-29)
    Abstract: During the mammalian preimplantation phase, cells undergo two subsequent cell fate decisions. During the first decision, the trophectoderm and the inner cell mass are formed. Subsequently, the inner cell mass segregates into the epiblast and the primitive endoderm. Inner cell mass organoids represent an experimental model system, mimicking the second cell fate decision. It has been shown that cells of the same fate tend to cluster stronger than expected for random cell fate decisions. Three major processes are hypothesised to contribute to the cell fate arrangements: (1) chemical signalling; (2) cell sorting; and (3) cell proliferation. In order to quantify the influence of cell proliferation on the observed cell lineage type clustering, we developed an agent-based model accounting for mechanical cell–cell interaction, i.e. adhesion and repulsion, cell division, stochastic cell fate decision and cell fate heredity. The model supports the hypothesis that initial cell fate acquisition is a stochastically driven process, taking place in the early development of inner cell mass organoids. Further, we show that the observed neighbourhood structures can emerge solely due to cell fate heredity during cell division.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-020-80141-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2615211-3
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