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  • 1
    Language: English
    In: PLoS ONE, 01 January 2015, Vol.10(12), p.e0144959
    Description: Tracking motile cells in time-lapse series is challenging and is required in many biomedical applications. Cell tracks can be mathematically represented as acyclic oriented graphs. Their vertices describe the spatio-temporal locations of individual cells, whereas the edges represent temporal...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 2
    Language: English
    In: Review of Scientific Instruments, September 2011, Vol.82(9)
    Description: With the development of novel fluorescence techniques, high resolution light microscopy has become a challenging technique for investigations of the three-dimensional (3D) micro-cosmos in cells and sub-cellular components. So far, all fluorescence microscopes applied for 3D imaging in biosciences show a spatially anisotropic point spread function resulting in an anisotropic optical resolution or point localization precision. To overcome this shortcoming, micro axial tomography was suggested which allows object tilting on the microscopic stage and leads to an improvement in localization precision and spatial resolution. Here, we present a miniaturized device which can be implemented in a motor driven microscope stage. The footprint of this device corresponds to a standard microscope slide. A special glass fiber can manually be adjusted in the object space of the microscope lens. A stepwise fiber rotation can be controlled by a miniaturized stepping motor incorporated into the device. By means of a special mounting device, test particles were fixed onto glass fibers, optically localized with high precision, and automatically rotated to obtain views from different perspective angles under which distances of corresponding pairs of objects were determined. From these angle dependent distance values, the real 3D distance was calculated with a precision in the ten nanometer range (corresponding here to an optical resolution of 10–30 nm) using standard microscopic equipment. As a proof of concept, the spindle apparatus of a mature mouse oocyte was imaged during metaphase II meiotic arrest under different perspectives. Only very few images registered under different rotation angles are sufficient for full 3D reconstruction. The results indicate the principal advantage of the micro axial tomography approach for many microscopic setups therein and also those of improved resolutions as obtained by high precision localization determination.
    Keywords: Articles
    ISSN: 0034-6748
    E-ISSN: 1089-7623
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  • 3
    Language: English
    In: PLoS ONE, 01 January 2012, Vol.7(12), p.e52555
    Description: miRNA cluster miR-17-92 is known as oncomir-1 due to its potent oncogenic function. miR-17-92 is a polycistronic cluster that encodes 6 miRNAs, and can both facilitate and inhibit cell proliferation. Known targets of miRNAs encoded by this cluster are largely regulators of cell cycle progression...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 4
    Language: English
    In: BMC Bioinformatics, Dec 20, 2011, Vol.12, p.485
    Description: Background High-content, high-throughput RNA interference (RNAi) offers unprecedented possibilities to elucidate gene function and involvement in biological processes. Microscopy based screening allows phenotypic observations at the level of individual cells. It was recently shown that a cell's population context significantly influences results. However, standard analysis methods for cellular screens do not currently take individual cell data into account unless this is important for the phenotype of interest, i.e. when studying cell morphology. Results We present a method that normalizes and statistically scores microscopy based RNAi screens, exploiting individual cell information of hundreds of cells per knockdown. Each cell's individual population context is employed in normalization. We present results on two infection screens for hepatitis C and dengue virus, both showing considerable effects on observed phenotypes due to population context. In addition, we show on a non-virus screen that these effects can be found also in RNAi data in the absence of any virus. Using our approach to normalize against these effects we achieve improved performance in comparison to an analysis without this normalization and hit scoring strategy. Furthermore, our approach results in the identification of considerably more significantly enriched pathways in hepatitis C virus replication than using a standard analysis approach. Conclusions Using a cell-based analysis and normalization for population context, we achieve improved sensitivity and specificity not only on a individual protein level, but especially also on a pathway level. This leads to the identification of new host dependency factors of the hepatitis C and dengue viruses and higher reproducibility of results.
    Keywords: Genes -- Identification And Classification ; Genetic Testing -- Methods ; Genetic Testing -- Research ; Rna Interference -- Physiological Aspects ; Rna Interference -- Usage
    ISSN: 1471-2105
    Source: Cengage Learning, Inc.
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  • 5
    Language: English
    In: BMC Bioinformatics, Dec 20, 2011, Vol.12, p.485
    Description: Background High-content, high-throughput RNA interference (RNAi) offers unprecedented possibilities to elucidate gene function and involvement in biological processes. Microscopy based screening allows phenotypic observations at the level of individual cells. It was recently shown that a cell's population context significantly influences results. However, standard analysis methods for cellular screens do not currently take individual cell data into account unless this is important for the phenotype of interest, i.e. when studying cell morphology. Results We present a method that normalizes and statistically scores microscopy based RNAi screens, exploiting individual cell information of hundreds of cells per knockdown. Each cell's individual population context is employed in normalization. We present results on two infection screens for hepatitis C and dengue virus, both showing considerable effects on observed phenotypes due to population context. In addition, we show on a non-virus screen that these effects can be found also in RNAi data in the absence of any virus. Using our approach to normalize against these effects we achieve improved performance in comparison to an analysis without this normalization and hit scoring strategy. Furthermore, our approach results in the identification of considerably more significantly enriched pathways in hepatitis C virus replication than using a standard analysis approach. Conclusions Using a cell-based analysis and normalization for population context, we achieve improved sensitivity and specificity not only on a individual protein level, but especially also on a pathway level. This leads to the identification of new host dependency factors of the hepatitis C and dengue viruses and higher reproducibility of results.
    Keywords: Genes -- Identification And Classification ; Genetic Testing -- Methods ; Genetic Testing -- Research ; Rna Interference -- Physiological Aspects ; Rna Interference -- Usage
    ISSN: 1471-2105
    Source: Cengage Learning, Inc.
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  • 6
    In: Cytometry Part A, August 2015, Vol.87(8), pp.759-772
    Description: Reliable 3D detection of diffraction‐limited spots in fluorescence microscopy images is an important task in subcellular observation. Generally, fluorescence microscopy images are heavily degraded by noise and non‐specifically stained background, making reliable detection a challenging task. In this work, we have studied the performance and parameter sensitivity of eight recent methods for 3D spot detection. The study is based on both 3D synthetic image data and 3D real confocal microscopy images. The synthetic images were generated using a simulator modeling the complete imaging setup, including the optical path as well as the image acquisition process. We studied the detection performance and parameter sensitivity under different noise levels and under the influence of uneven background signal. To evaluate the parameter sensitivity, we propose a novel measure based on the gradient magnitude of the score. We measured the success rate of the individual methods for different types of the image data and found that the type of image degradation is an important factor. Using the score and the newly proposed sensitivity measure, we found that the parameter sensitivity is not necessarily proportional to the success rate of a method. This also provided an explanation why the best performing method for synthetic data was outperformed by other methods when applied to the real microscopy images. On the basis of the results obtained, we conclude with the recommendation of the HDome method for data with relatively low variations in quality, or the Sorokin method for image sets in which the quality varies more. We also provide alternative recommendations for high‐quality images, and for situations in which detailed parameter tuning might be deemed expensive. © 2015 International Society for Advancement of Cytometry
    Keywords: Fluorescence Microscopy ; 3d Imaging ; Diffraction‐Limited Spot Detection ; Parameter Sensitivity
    ISSN: 1552-4922
    E-ISSN: 1552-4930
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  • 7
    Language: English
    In: BMC Bioinformatics, 01 December 2011, Vol.12(1), p.485
    Description: Abstract Background High-content, high-throughput RNA interference (RNAi) offers unprecedented possibilities to elucidate gene function and involvement in biological processes. Microscopy based screening allows phenotypic observations at the...
    Keywords: Biology
    ISSN: 1471-2105
    E-ISSN: 1471-2105
    Source: Directory of Open Access Journals (DOAJ)
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  • 8
    Language: English
    In: Journal of Real-Time Image Processing, 2015, Vol.10(1), pp.27-41
    Description: Linear morphological openings and closings are important non-linear operators from mathematical morphology. In practical applications, many different orientations of digital line segments must typically be considered. In this paper, we (1) review efficient sequential as well as parallel algorithms for the computation of linear openings and closings; (2) compare the performance of CPU implementations of four state-of-the-art algorithms; (3) describe GPU implementations of two recent efficient algorithms allowing arbitrary orientation of the line segments; (4) propose, as the main contribution, an efficient and optimized GPU implementation of linear openings; and (5) compare the performance of all implementations on real images from various applications. From our experimental results, it turned out that the proposed GPU implementation is suitable for applications with large, industrial images, running under severe timing constraints.
    Keywords: Morphology ; Opening ; Closing ; Linear ; 1-D SE ; Parallel ; Efficient ; Algorithm ; Implementation ; GPU
    ISSN: 1861-8200
    E-ISSN: 1861-8219
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  • 9
    Language: English
    In: BBA - Molecular Basis of Disease, May 2015, Vol.1852(5), pp.839-850
    Description: Aberrant fibroblast growth factor (FGF) signaling disturbs chondrocyte differentiation in skeletal dysplasia, but the mechanisms underlying this process remain unclear. Recently, FGF was found to activate canonical WNT/β-catenin pathway in chondrocytes via Erk MAP kinase-mediated phosphorylation of WNT co-receptor Lrp6. Here, we explore the cellular consequences of such a signaling interaction. WNT enhanced the FGF-mediated suppression of chondrocyte differentiation in mouse limb bud micromass and limb organ cultures, leading to inhibition of cartilage nodule formation in micromass cultures, and suppression of growth in cultured limbs. Simultaneous activation of the FGF and WNT/β-catenin pathways resulted in loss of chondrocyte extracellular matrix, expression of genes typical for mineralized tissues and alteration of cellular shape. WNT enhanced the FGF-mediated downregulation of chondrocyte proteoglycan and collagen extracellular matrix via inhibition of matrix synthesis and induction of proteinases involved in matrix degradation. Expression of genes regulating RhoA GTPase pathway was induced by FGF in cooperation with WNT, and inhibition of the RhoA signaling rescued the FGF/WNT-mediated changes in chondrocyte cellular shape. Our results suggest that aberrant FGF signaling cooperates with WNT/β-catenin in suppression of chondrocyte differentiation.
    Keywords: Fibroblast Growth Factor Receptor ; Fgfr3 ; Wnt ; Chondrocyte ; Differentiation ; Cartilage ; Biology ; Chemistry
    ISSN: 0925-4439
    E-ISSN: 1879-260X
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  • 10
    Language: English
    In: Multimedia Tools and Applications, 11/17/2018
    Description: We present an approach for the human face reconstruction from a single frontal image for the use in forensic anthropology when the subject’s age and gender is known. In our approach we build a database of several depth images per each age and gender group...
    Keywords: Algorithms ; Age ; Landmarks ; Data Bases ; Algorithms ; Image Reconstruction ; Forensic Anthropology ; Databases ; Anthropology ; Artificial Neural Networks ; Gender ; Three Dimensional Models ; Face Reconstruction ; Single Photo Reconstruction ; Depth Image Database ; Frontal Image ; Forensic Anthropology;
    ISSN: 1380-7501
    E-ISSN: 1573-7721
    Source: Springer (via CrossRef)
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