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- Bandaru, Manoj Kumar, et al.
(författare)
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Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis
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Tidskriftsartikel (refereegranskat)abstract
- Background: Hundreds of loci have been robustly associated with circulating lipids, atherosclerosis and coronary artery disease; but for most loci the causal genes and mechanisms remain uncharacterized.Methods: We developed a semi-automated experimental pipeline for systematic, quantitative, large-scale characterization of mechanisms, drugs and genes associated with dyslipidemia and atherosclerosis in a zebrafish model system. We validated our pipeline using a dietary (n>2000), drug treatment (n>1000), and genetic intervention (n=384).Results: Our results show that five days of overfeeding and cholesterol supplementation had independent pro-atherogenic effects, which could be diminished by concomitant treatment with atorvastatin and ezetimibe. CRISPR-Cas9-induced mutations in orthologues of proof-of-concept genes resulted in higher LDL cholesterol levels (apoea), and more early stage atherosclerosis (apobb.1).Conclusions: In summary, our pipeline facilitates systematic, in vivo characterization of drugs and candidate genes to increase our understanding of disease etiology, and can likely help identify novel targets for therapeutic intervention.
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| 2. |
- Erlandsson, Fredrik, et al.
(författare)
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A detailed analysis of cyclin A accumulation at the G1/S border in normal and transformed cells.
- 2000
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Ingår i: Experimental Cell Research. - 0014-4827. ; 256, s. 86-95
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Tidskriftsartikel (refereegranskat)abstract
- Automatic cell segmentation has various applications in cytometry, and while thenucleus is often very distinct and easy to identify, the cytoplasm provides a lotmore challenge. A new combination of image analysis algorithms forsegmentation of cells imaged by fluorescence microscopy is presented. Thealgorithm consists of an image pre-processing step, a general segmentationand merging step followed by a segmentation quality measurement. The qualitymeasurement consists of a statistical analysis of a number of shape descriptivefeatures. Objects that have features that differ to that of correctly segmentedsingle cells can be further processed by a splitting step. By statistical analysiswe therefore get a feedback system for separation of clustered cells. After thesegmentation is completed, the quality of the final segmentation is evaluated. Bytraining the algorithm on a representative set of training images, the algorithmis made fully automatic for subsequent images created under similar conditions.Automatic cytoplasm segmentation was tested on CHO-cells stained withcalcein. The fully automatic method showed between 89% and 97% correctsegmentation as compared to manual segmentation.
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| 7. |
- Kleywegt, Gerard J, et al.
(författare)
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The Uppsala Electron-Density Server
- 2004
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Ingår i: Acta Crystallographica Section D. - 0907-4449 .- 1399-0047. ; 60:Pt 12 Pt 1, s. 2240-2249
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Tidskriftsartikel (refereegranskat)abstract
- The Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) is a web-based facility that provides access to electron-density maps and statistics concerning the fit of crystal structures and their maps. Maps are available for approximately 87% of the crystallographic Protein Data Bank (PDB) entries for which structure factors have been deposited and for which straightforward map calculations succeed in reproducing the published R value to within five percentage points. Here, an account is provided of the methods that are used to generate the information contained in the server. Some of the problems that are encountered in the map-generation process as well as some spin-offs of the project are also discussed.
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| 8. |
- Matuszewski, Damian J., et al.
(författare)
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A short feature vector for image matching : The Log-Polar Magnitude feature descriptor
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12:11
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Tidskriftsartikel (refereegranskat)abstract
- The choice of an optimal feature detector-descriptor combination for image matching often depends on the application and the image type. In this paper, we propose the Log-Polar Magnitude feature descriptor—a rotation, scale, and illumination invariant descriptor that achieves comparable performance to SIFT on a large variety of image registration problems but with much shorter feature vectors. The descriptor is based on the Log-Polar Transform followed by a Fourier Transform and selection of the magnitude spectrum components. Selecting different frequency components allows optimizing for image patterns specific for a particular application. In addition, by relying only on coordinates of the found features and (optionally) feature sizes our descriptor is completely detector independent. We propose 48- or 56-long feature vectors that potentially can be shortened even further depending on the application. Shorter feature vectors result in better memory usage and faster matching. This combined with the fact that the descriptor does not require a time-consuming feature orientation estimation (the rotation invariance is achieved solely by using the magnitude spectrum of the Log-Polar Transform) makes it particularly attractive to applications with limited hardware capacity. Evaluation is performed on the standard Oxford dataset and two different microscopy datasets; one with fluorescence and one with transmission electron microscopy images. Our method performs better than SURF and comparable to SIFT on the Oxford dataset, and better than SIFT on both microscopy datasets indicating that it is particularly useful in applications with microscopy images.
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| 13. |
- Wählby, Carolina, et al.
(författare)
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Multiple tissue antigen analysis by sequential immunofluorescence staining and multi-dimensional image analysis
- 2001
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Ingår i: Proceedings of SCIA-01 (Scandinavian Conference on Image Analysis). ; , s. 25-31
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Konferensbidrag (refereegranskat)abstract
- This paper presents a novel method for sequential immunofluorescence staining, which, in combination with 3D image registration and segmentation, can be used to increase the number of antigens that can be observed simultaneously in single cells in tissue sections. Visualization of more than one antigen by multicolor immunostaining is often desirable or even necessary, both for quantitative studies and to explore spatial relationships of functional significance. Sequential staining, meaning repeated application and removal of fluorescence markers, greatly increases the number of different antigens that can be visualized and quantified in single cells using digital imaging fluorescence microscopy. Quantification and efficient objective analysis of the image data requires digital image analysis. A method for 3D image registration combined with 2D and 3D segmentation and 4D extraction of data is described.
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| 15. |
- Wählby, Carolina, et al.
(författare)
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Sequential immunofluorescence staining and image analysis for detection of large numbers of antigens in individual cell nuclei
- 2002
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Ingår i: Cytometry. - 0196-4763. ; 47:1, s. 32-41
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundVisualization of more than one antigen by multicolor immunostaining is often desirable or even necessary to explore spatial and temporal relationships of functional significance. Previously presented staining protocols have been limited to the visualization of three or four antigens.MethodsImmunofluorescence staining was performed both on slices of formalin-fixed tissue and on cells microscopy. The primary and secondary antibodies, as well as the fluorophores, were thereafter removed using a combination of denaturation and elution techniques. After removal of the fluorescence stain, a new immunofluorescence staining was performed, visualizing a new set of antigens. The procedure was repeated up to three times. A method for image registration combined with segmentation, extraction of data, and cell classification was developed for efficient and objective analysis of the image data.ResultsThe results show that immunofluorescence stains in many cases can be repeatedly removed without major effects on the antigenicity of the sample.ConclusionsThe concentration of at least six different antigens in each cell can thus be measured semiquantitatively using sequential immunofluorescence staining and the described image analysis techniques. The number of antigens that can be visualized in a single sample is considerably increased by the presented protocol.
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| 19. |
- Zhang, Hanqian, et al.
(författare)
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Quantitative image analysis of protein expression and colocalisation in skin sections
- 2018
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Ingår i: Experimental dermatology. - : Wiley. - 0906-6705 .- 1600-0625. ; 27:2, s. 196-199
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Tidskriftsartikel (refereegranskat)abstract
- Immunofluorescence (IF) and in situ proximity ligation assay (isPLA) are techniques that are used for in situ protein expression and colocalisation analysis, respectively. However, an efficient quantitative method to analyse both IF and isPLA staining on skin sections is lacking. Therefore, we developed a new method for semi-automatic quantitative layer-by-layer measurement of protein expression and colocalisation in skin sections using the free open-source software CellProfiler. As a proof of principle, IF and isPLA of ichthyosis-related proteins TGm-1 and SDR9C7 were examined. The results indicate that this new method can be used for protein expression and colocalisation analysis in skin sections.
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