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Item does not contain fulltext, Fibrillar collagen is an abundant extracellular matrix (ECM) component of interstitial tissues which supports the structure of many organs, including the skin and breast. Many different physiological processes, but also pathological processes such as metastatic cancer invasion, involve interstitial cell migration. Often, cell movement takes place through small ECM gaps and pores and depends upon the ability of the cell and its stiff nucleus to deform. Such nuclear deformation during cell migration may impact nuclear integrity, such as of chromatin or the nuclear envelope, and therefore the morphometric analysis of nuclear shapes can provide valuable insight into a broad variety of biological processes. Here, we describe a protocol on how to generate a cell-collagen model in vitro and how to use confocal microscopy for the static and dynamic visualization of labeled nuclei in single migratory cells. We developed, and here provide, two scripts that (Fidler, Nat Rev Cancer 3(6):453-458, 2003) enable the semi-automated and fast quantification of static single nuclear shape descriptors, such as aspect ratio or circularity, and the nuclear irregularity index that forms a combination of four distinct shape descriptors, as well as (Frantz et al., J Cell Sci 123 (Pt 24):4195-4200, 2010) a quantification of their changes over time. Finally, we provide quantitative measurements on nuclear shapes from cells that migrated through collagen either in the presence or the absence of an inhibitor of collagen degradation, showing the distinctive power of this approach. This pipeline can also be applied to cell migration studied in different assays, ranging from 3D microfluidics to migration in the living organism.

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Contains fulltext : 293806.pdf (Publisher’s version ) (Open Access), High-content image-based cell phenotyping provides fundamental insights into a broad variety of life science disciplines. Striving for accurate conclusions and meaningful impact demands high reproducibility standards, with particular relevance for high-quality open-access data sharing and meta-analysis. However, the sources and degree of biological and technical variability, and thus the reproducibility and usefulness of meta-analysis of results from live-cell microscopy, have not been systematically investigated. Here, using high-content data describing features of cell migration and morphology, we determine the sources of variability across different scales, including between laboratories, persons, experiments, technical repeats, cells, and time points. Significant technical variability occurred between laboratories and, to lesser extent, between persons, providing low value to direct meta-analysis on the data from different laboratories. However, batch effect removal markedly improved the possibility to combine image-based datasets of perturbation experiments. Thus, reproducible quantitative high-content cell image analysis of perturbation effects and meta-analysis depend on standardized procedures combined with batch correction.

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Contains fulltext : 249325.pdf (Publisher’s version ) (Open Access)

Contains fulltext : 282583.pdf (Publisher’s version ) (Open Access), In skeletal muscles, niche factors stimulate satellite cells to activate and induce muscle regeneration after injury. In vitro, matrigel is widely used for myoblast differentiation, however, is unsuitable for clinical applications. Therefore, this study aimed to analyze attachment and differentiation of satellite cells into myotubes on fibrin coatings with selected niche components. The attachment of satellite cells to fibrin alone and fibrin with niche components (laminin, collagen-IV, laminin-entactin complex [LEC]) were compared to matrigel. Only on matrigel and fibrin with LEC, Pax7-positive cells attached well. Then, LEC was selected to analyze proliferation, differentiation, and fusion indices. The proliferation index at day 1 on fibrin-LEC (22.5%, SD 9.1%) was similar to that on matrigel (30.8% [SD 11.1%]). The differentiation index on fibrin-LEC (28.7% [SD 6.1%] at day 5 and 32.8% [SD 6.7%] at day 7) was similar to that on matrigel (40.1% [5.1%] at day 5 and 27.1% [SD 4.3%] at day 7). On fibrin-LEC, the fusion index at day 9 (26.9% [SD 11.5%]) was similar to that on matrigel (25.5% [SD 4.7%]). Our results showed that the addition of LEC enhances the formation of myotubes on fibrin. Fibrin with LEC might be suitable to enhance muscle regeneration after surgery such as cleft palate repair and other muscle defects.

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Contains fulltext : 237723.pdf (Publisher’s version ) (Open Access)

Second International Workshop, UHDL 2019, 10 oktober 2019, Contains fulltext : 283353.pdf (Publisher’s version ) (Closed access), In this paper, we present our work on semantic deep mapping at scale by combining information from various sources and disciplines to study historical Amsterdam. We model our data according to semantic web standards and ground them in space and time such that we can investigate what happened at a particular time and place from a linguistics, socio-economic and urban historical perspective. In a small use case we test the spatio-temporal infrastructure for research on entertainment culture in Amsterdam around the turn of the 20th century. We explain the bottlenecks we encountered for integrating information from different disciplines and sources and how we resolved or worked around them. Finally, we present a set of recommendations and best practices for adapting semantic deep mapping to other settings.

Contains fulltext : 220755.pdf (publisher's version ) (Open Access), Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.

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Contains fulltext : 212364.pdf (publisher's version ) (Open Access)

WHiSe 2017, Item does not contain fulltext

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Contains fulltext : 94566.pdf (publisher's version ) (Open Access), The natural history domain is rich in information. For hundreds of years, biodiversity researchers have collected specimens and samples, and meticulously recorded the how, what, and where of these objects of research. To retrace this information, however, deep knowledge of the collection and patience is necessary. Whereas traditional access methods (e.g., analysing paper logs of specimen finds) can be used for smaller collections, the sheer size of most current natural history collections prohibits this. At the same time, information technology has advanced to the point where it is able to capture the intricacies of biodiversity collection information and provide the first steps towards full digital access. The need for collection information access is dire, as lack of access impairs our ability to answer questions about species biodiversity, diversity and change through time (Scoble, 2010). Examples from the young field of biodiversity informatics stress that in order to assess and tackle problems such as predicting a species’ reaction to changing environment or prioritisation of preservation policies, digitisation of and access to (large) collection databases is imperative (Guralnick & Hill, 2009; Johnson, 2007; Raes, 2009; Soberón & Peterson, 2004). Although much progress has been made, for example with the Global Biodiversity Data Portal (Berendsohn et al., 2010), many collections have not yet been (fully) digitised. In this contribution, we first present a new approach to collection digitisation, as well as a novel collection registration management system (CRS) as implemented at the Netherlands Centre for Biodiversity (NCB Naturalis). The new approach to digitisation at NCB Naturalis implements a cascaded digitisation approach: in parts of the collection that have not yet been digitised, first a shelf or drawer is assigned a unique ID in the CRS, along with a description of the specimens contained within it. Whenever the shelf or drawer is revisited, the new policy

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Contains fulltext : 64393.pdf (publisher's version ) (Open Access), This paper describes a semi-automated procedure for the verification of a large human-labeled data set containing online handwriting. A number of classifiers trained on the UNIPEN "trainset" is employed for detecting anomalies in the labels of the UNIPEN "devset". Multiple classifiers with different feature sets are used to increase the robustness of the automated procedure and to ensure that the number of false accepts is kept to a minimum. The rejected samples are manually categorized into four classes: (i) recoverable segmentation errors, (ii) incorrect (recoverable) labels, (iii) well-segmented but ambiguous cases and (iv) unrecoverable segments that should be removed. As a result of the verification procedure, a well-labeled data set is currently being generated, which will be made available to the handwriting recognition community.

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11th IGS conference: 2-5 Nov. 2003 Scottsdale, Arizona, USA. (IGS2003), Contains fulltext : 63661.pdf (preprint version ) (Open Access)

Proceedings 3rd International Conference on Hybrid Intelligent Systems (HIS03), Item does not contain fulltext, This paper presents the WANDA Workbench, which is an open framework for electronic data processing. The framework provides generic interfaces for ’plugin’ applications for graphical user interfaces (client desktop with client plug-ins) and processing modules (server with server plug-ins). The applied plug-in concept allows for the functional extension of the workbench without changing the framework. Moreover, for data modeling, messaging and system configuration the eXtensible Markup Language (XML) is implemented, which supports the interoperability with existing applications and allows for continuous adaptations to the evolving state of technology. The current application domain of the framework is writer identification and handwriting examination as frequently used in crime investigation and prosecution. Dedicated plug-ins using digital image processing and pattern recognition establish objective measurements and feature extraction to promote reproducible analysis results. Moreover, based on domain knowledge, which was collected from forensic document examiners, the data standard WANDAXML was designed that allows for the annotation, processing, journaling and storage of digitized questioned handwriting documents. In the following, we detail the adopted design philosophy, provide pointers for employing the data model, and sketch the realized framework and current plug-ins. The generic framework with appositive plug-in programmer handbooks as well as the data standard will be made available to the research community through the Internet http://pentel.ipk.fhg.de/wanda.

Item does not contain fulltext, In the majority of cases, a properly trained classifier or ensemble of classifiers may yield acceptable recognition results. However, in some cases, recognition will fail due to typical conflicts that are encountered, like the confusion between [A] and [H] or [U] and [V]. In this paper, two architectures for the recognition of handwritten text are described. The key issue for each of these systems is to detect the event of a possible conflict and subsequently attempt to solve that particular problem. Both systems exploit a two-stage classification method. In the event that the first-stage classifiers are not certain about the result, the second-stage system engages a set of support vector classifiers for refining the output hypothesis.

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