Radiation Induced Chromatin Conformation Changes Analysed by Fluorescent Localization Microscopy, Statistical Physics, and Graph Theory
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{"title"=>"Radiation induced chromatin conformation changes analysed by fluorescent localization microscopy, statistical physics, and graph theory", "type"=>"journal", "authors"=>[{"first_name"=>"Yang", "last_name"=>"Zhang", "scopus_author_id"=>"54793887800"}, {"first_name"=>"Gabriell", "last_name"=>"Máté", "scopus_author_id"=>"36092941400"}, {"first_name"=>"Patrick", "last_name"=>"Müller", "scopus_author_id"=>"7403138456"}, {"first_name"=>"Sabina", "last_name"=>"Hillebrandt", "scopus_author_id"=>"56203739300"}, {"first_name"=>"Matthias", "last_name"=>"Krufczik", "scopus_author_id"=>"56708798400"}, {"first_name"=>"Margund", "last_name"=>"Bach", "scopus_author_id"=>"56708134700"}, {"first_name"=>"Rainer", "last_name"=>"Kaufmann", "scopus_author_id"=>"36094414900"}, {"first_name"=>"Michael", "last_name"=>"Hausmann", "scopus_author_id"=>"16207104500"}, {"first_name"=>"Dieter W.", "last_name"=>"Heermann", "scopus_author_id"=>"7006305687"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0128555", "scopus"=>"2-s2.0-84934900930", "issn"=>"19326203", "pui"=>"604911745", "sgr"=>"84934900930"}, "id"=>"0fd12e81-b114-3e24-8af1-738c2d0049ee", "abstract"=>"RESEARCHARTICLE Radiation Induced Chromatin Conformation Changes Analysed by Fluorescent Localization Microscopy, Statistical Physics, and Graph Theory Yang Zhang1☯, Gabriell Máté1☯*, Patrick Müller2, Sabina Hillebrandt2, Matthias Krufczik2, Margund Bach2, Rainer Kaufmann2¤, Michael Hausmann2, Dieter W. Heermann1 1 Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120, Heidelberg, Germany, 2 Kirchhoff-Institute for Physics, Heidelberg University, ImNeuenheimer Feld 227, 69120, Heidelberg, Germany ☯These authors contributed equally to this work. ¤ Current address: Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Department of Biochemistry, South Parks Road, Oxford University, Oxford, OX1 3QU, United Kingdom * g.mate@tphys.uni-heidelberg.de Abstract It has been well established that the architecture of chromatin in cell nuclei is not randombut functionally correlated.Chromatin damage caused by ionizing radiation raises complex repair machineries. This is accompanied by local chromatin rearrangements and structural changes whichmay for instance improve the accessibility of damaged sites for repair protein com- plexes.Using stably transfected HeLa cells expressing either green fluorescent protein (GFP) labelled histone H2B or yellow fluorescent protein (YFP) labelled histoneH2A,we in- vestigated the positioning of individual histone proteins in cell nuclei by means of high resolu- tion localization microscopy (Spectral PositionDetermination Microscopy = SPDM). The cells were exposed to ionizing radiation of different doses and aliquotswere fixed after different repair times for SPDMimaging. In addition to the repair dependent histone protein pattern, the positioning of antibodies specific for heterochromatin and euchromatin was separately re- corded by SPDM. The present paper aims to provide a quantitative description of structural changes of chromatin after irradiation and during repair. It introduces a novel approach to an- alyse SPDMimages bymeans of statistical physics and graph theory. Themethod is based on the calculation of the radial distribution functions as well as edge length distributions for graphs defined by a triangulation of themarker positions. The obtained results show that through the cell nucleus the different chromatin re-arrangements as detected by the fluores- cent nucleosomal pattern average themselves. In contrast heterochromatic regions alone in- dicate a relaxation after radiation exposure and re-condensation during repairwhereas euchromatin seemed to be unaffected or behave contrarily. SPDMin combinationwith the analysis techniques applied allows the systematic elucidation of chromatin re-arrangements after irradiation and during repair, if selected sub-regions of nuclei are investigated. PLOS", "link"=>"http://www.mendeley.com/research/radiation-induced-chromatin-conformation-changes-analysed-fluorescent-localization-microscopy-statis", "reader_count"=>16, "reader_count_by_academic_status"=>{"Librarian"=>1, "Researcher"=>3, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>3, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Librarian"=>1, "Researcher"=>3, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>6, "Student > Master"=>3, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Agricultural and Biological Sciences"=>6, "Philosophy"=>1, "Physics and Astronomy"=>5, "Chemistry"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Computer Science"=>{"Computer Science"=>2}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"France"=>1, "Germany"=>1, "Russia"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2095330"], "description"=>"<p>Panel A. The figure shows the radial radial distribution function for H3K4 antibodies representing euchromatin (methylated histone variants) for non-irradiated and irradiated cells. Error bars represent the standard deviation of the mean value after averaging over the sample of cells. The value for <i>g</i>(<i>r</i>) at small distances goes up to around 20, indicating the high marker densities during repair. The rapid drop off of the radial distribution function within a distance of about 50 nm shows that euchromatin forms small clustered areas. Upon exposure to 0.5 Gy γ-irradiation, a change in the correlation function can be observed in cells that were imaged after 30 min and 48 hrs. The value at small radial distances increases compared to non-irradiated cells. This indicates that the density in the euchromatic regions becomes on average higher in irradiated cells. Panel B. The distribution of edge lengths in the Delaunay triangulation of the markers confirms these observations. A sharp peak in the distribution at around 30 nm can be seen in untreated cells. In 48 h post-irradiation cells, the peak spreads slightly.</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436365, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g009", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_for_cells_exposed_to_0_5_Gy_radiation_/1436365", "title"=>"Results for cells exposed to 0.5 Gy radiation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2095329"], "description"=>"<p>Panel A. The panel shows the conditional probability distribution <i>p</i>(<i>r</i>|<i>r</i>′) of the edge lengths calculated for the positions of the antibodies marking heterochromatic regions before irradiation. Panel B. The panel shows the conditional probability for the heterochromatin markers 30 min after irradiation. Panel C. The panel shows the conditional probability for the heterochromatin markers 48 h after irradiation. In all three cases the diagonal is emphasized indicating preferential spatial distribution of the edges. This may stem from the clustering of the heterochromatin markers. Note that although shades along the diagonal are darker in panel C, the value of the corresponding probabilities are very close to the probabilities along the diagonal of panel A except for small radii. Panel D. The panel shows the difference in the conditional probability distribution <i>p</i>(<i>r</i>|<i>r</i>′) before irradiation and 30 min after irradiation. A red shade of the color-map means that the probability is higher before irradiation while a blue shade means that it is higher after irradiation. The panel indicates a slightly stronger change along the diagonal indicating a more homogeneous system after irradiation. However, the change is almost independent of the value of the condition <i>r</i>′. Panel E. The panel shows the difference of the conditional probability distribution calculated for samples before and 48 h after irradiation. Shades of red indicate higher probabilities for the samples recorded before irradiation while shades of blue indicate higher probabilities in samples recorded after irradiation. Panel F. The panel illustrates the difference of the conditional probability distribution 30 min and 48 h after irradiation. Red shades correspond to higher probabilities 30 min post-irradiation while shades of blue indicate larger values 48 h after irradiation. The difference between structures observed 30 min after irradiation and 48 h after irradiation indicate a reversed trend compared to panel D.</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436364, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g008", "stats"=>{"downloads"=>4, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conditional_Probability_Distribution_of_the_Edge_Lengths_for_Heterochromatin_Markers_/1436364", "title"=>"Conditional Probability Distribution of the Edge Lengths for Heterochromatin Markers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2095325"], "description"=>"<p>Panel A. Shown is the density distribution of the localized markers in a cell prior to irradiation. Small, very bright spots where markers are agglomerated can be seen. This means that heterochromatin is mainly organized in coarse areas. Panel B. Shown is the segmented image of the not irradiated cell that is used for subsequent analysis of the marker distribution. Panel C. The density distribution of a cell at 30 min after irradiation with 0.5 Gy is shown here. Differences between this cell and the not irradiated cell can be made out by visual inspection. We observe that the density has much less agglomerated and bright spots and is instead much more homogeneous. Panel D. This effect can also be seen by visual inspection of the heterochromatin markers directly. Marker positions are visibly more spread out and less strongly clustered together. Heterochromatin clearly undergoes structural changes upon irradiation.</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436360, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g006", "stats"=>{"downloads"=>2, "page_views"=>37, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_Localization_Microscopy_Images_of_Heterochromatin_Markers_/1436360", "title"=>"Examples of Localization Microscopy Images of Heterochromatin Markers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2095319"], "description"=>"<p>Panel A. Radial pair correlation functions determined at different repair times after exposure to 0.5 Gy radiation dose. The radial pair correlation function <i>g</i>(<i>r</i>) shows that correlations between the positions of labeled H2B histones exist up to a distance of roughly 300 nm. Marker and thus chromatin densities in the surroundings of each marker are elevated compared to the average density of markers in the cell nucleus. Above 300 nm, however, histone positions are uncorrelated and the marked histones can be viewed as being positioned randomly relative to each other. Furthermore, the radial pair correlation function for cells exposed to 0.5 Gy γ-irradiation apparently does not differ from the one of untreated cells, regardless of the time passed after irradiation. Panel B. Rescaled distribution of the length of edges in a Delaunay triangulation of the H2B marker positions after different repair times post 0.5 Gy irradiation. The inset shows the original distributions for the different images. The differences in the edge length distributions are due to the different marker densities in the images. Therefore a rescaling of the distributions was performed with respect to the point density to clear out this effect. The rescaled distributions can be seen in the main panel and show that the distributions belong to the same family.</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436354, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_for_cells_exposed_to_0_5_Gy_radiation_/1436354", "title"=>"Results for cells exposed to 0.5 Gy radiation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2095332"], "description"=>"<p>The analysis was performed on non-irradiated samples, and on samples fixed 6 h and 24 h post irradiation, respectively. <b>Panel A</b> present the behaviour of heterochromatic regions irradiated with 0.5 Gy and 3.5 Gy. We observe a decrease in the ratio of the clustered points 6 h after irradiation for both doses. 24 h after irradiation these changes are reverted. This means that a few hours after irradiation the heterochromatin decondenses and after one day the decondensation is reverted. <b>Panel B</b> shows the cluster analysis result for euchromatin. These regions behave differently, compared to heterochromatin. For 0.5 Gy, the number of clustered points is increased after 6 h, and the trend continues at the 24 h timestamp. However, for 3.5 Gy, after the initial increase in the percentage of clustered points at 6 h, the ratio drops again in the 24 h measurements. The interpretation of the increase/decrease in the number of clustered points is similar in this case: when the ratio increases, the studied domains condense, when the ratio decreases, the domains relax. This means, that heterochromatin and euchromatin react to irradiation in an opposite way: This analysis, in accordance with the other results, indicates that while heterochromatin opens up soon after irradiation, euchromatin condensates. Given enough time, these processes are reverted in both cases.</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436367, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g010", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cluster_analysis_of_the_spatial_distribution_of_heterochromatin_and_euchromatin_after_irradiation_with_0_5_Gy_and_3_5_Gy_/1436367", "title"=>"Cluster analysis of the spatial distribution of heterochromatin and euchromatin after irradiation with 0.5 Gy and 3.5 Gy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2095327"], "description"=>"<p>Panel A. The figure shows the radial radial distribution function for H4K20 antibodies representing heterochromatin (methylated histone variants) for non-irradiated and irradiated cells. Error bars represent the standard deviation of the mean value after averaging over the sample of cells. The value for <i>g</i>(<i>r</i>) at small distances goes up to around 20, indicating the high marker densities in regions where heterochromatin is located. The rapid drop off of the radial distribution function within a distance of less than 100 nm shows that heterochromatin forms small clustered areas that are spread throughout the cell nucleus. Upon exposure to 0.5 Gy γ-irradiation, a dramatic change in the correlation function can be observed in cells that were imaged after 30 min. The value at small radial distances drops to around 6, or around 70% smaller than in non-irradiated cells. This indicates that the density in the heterochromatic regions becomes on average much lower in irradiated cells. In cells measured 48 h after irradiation, the correlation function have recovered again and the value at small <i>r</i> is at around 14, only 30% less than in unirradiated cells. Panel B. The distribution of edge lengths in the Delaunay triangulation of the markers confirms these observations. A sharp peak in the distribution at around 30 nm can be seen in untreated cells. In 30 min post-irradiation cells the peak vanishes and a spread distribution can be seen. In 48 h post-irradiation cells however, the peak reappears again but less pronounced than in untreated cells.</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436362, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g007", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_for_cells_exposed_to_0_5_Gy_radiation_/1436362", "title"=>"Results for cells exposed to 0.5 Gy radiation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2095306"], "description"=>"<p>The Delaunay triangulation and its dual, the Voronoi tessellation for a random set of points. The blue lines are the segments of the Voronoi tessellation, the red ones are the edges of the Delaunay graph (triangulation).</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436344, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g001", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sketch_of_a_Delaunay_Triangulation_/1436344", "title"=>"Sketch of a Delaunay Triangulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2095322"], "description"=>"<p>Panel A. The panel shows the conditional probability distribution <i>p</i>(<i>r</i>|<i>r</i>′) of the edge lengths for the H2B markers before irradiation. The relatively prominent diagonal indicates locally a varying density. Panel B. The panel shows the conditional probability for the H2B markers 30 minutes after irradiation. Panel C. The panel shows the conditional probability for the H2B markers 48 h after irradiation. Panel D. The panel shows the difference of the conditional probabilities <i>p</i>(<i>r</i>|<i>r</i>′) measured for structures recorded before irradiation and for structures registered 30 min after irradiation. Shades towards red indicate values which are larger in the samples before irradiation, while values towards the shades of blue indicate probabilities which are larger in images registered 30 min after irradiation. The plot indicates slightly increased values along the diagonal after irradiation. This might mean a slightly increased clustering of the points. Panel E. The panel shows the differences of the conditional probability before irradiation and 48 h after irradiation. Entries in shades of red are larger in samples recorded before irradiation, while entries in shades of blue are larger in the samples recorded 48 h after irradiation. The trend is similar to that observed in panel D, however differences are less prominent. Panel F. The panel shows the differences if the conditional probability measured 30 min and 48 h after irradiation respectively. The red shades indicate larger probabilities in samples recorded 30 min after irradiation while blue shades indicate larger probabilities in samples registered 48 h after irradiation. Here a reversed trend compared to panel D was observed.</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436357, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g005", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conditional_Probability_Distribution_of_the_Edge_Lengths_/1436357", "title"=>"Conditional Probability Distribution of the Edge Lengths.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2095317"], "description"=>"<p>Panel A. Widefield image of a cell nucleus, as usually obtained by standard microscopy. Panel B. Pointilist image obtained after merging the acquired time series of SPDM images. Each point represents a detected blinking process during image acquisition. The green insert shows an area with a low average density, which could correspond to euchromatin and the blue area corresponds to an area with high point density, possibly belonging to heterochromatin. Panel C. This panel shows the calculated density distribution of the localized markers using a Gaussian kernel density estimation with a uniform Gaussian kernels. Panel D. The figure shows the localized points of the image. From the points, areas with very low point density, possibly corresponding to nucleoli, can clearly be made out visually. Panel E. Shown is the segmented image where only the area of interest is kept for the analysis. The segmentation was based on the density distribution; areas below a threshold density were discarded for analysis.</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436353, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Localization_Microscopy_Images_/1436353", "title"=>"Localization Microscopy Images.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/2095315"], "description"=>"<p>The figures illustrate how the <i>p</i>(<i>r</i>|<i>r</i>′) conditional probability looks for randomly generated point positions. Panel A. Conditional probability of points with coordinates generated according to a uniform distribution. Panel B. Conditional probability of points with coordinates generated according to a mixture of uniform distribution and clusters of Gaussian distributions. In the latter example an emphasized diagonal is observed which is the result of the Gaussian clusters. Tightly packed points tend to produce short edges, while points from the edges of the clusters mostly have longer edges.</p>", "links"=>[], "tags"=>["histone H 2B", "histone H 2A", "Radiation Induced Chromatin Conformation Changes Analysed", "edge length distributions", "stably transfected HeLa cells", "chromatin", "Spectral Position Determination Microscopy", "contrast heterochromatic regions", "cell nuclei", "analyse SPDM images", "histone protein pattern", "resolution localization microscopy", "repair protein complexes", "Fluorescent Localization Microscopy", "radiation", "yfp", "gfp"], "article_id"=>1436351, "categories"=>["Biological Sciences"], "users"=>["Yang Zhang", "Gabriell Máté", "Patrick Müller", "Sabina Hillebrandt", "Matthias Krufczik", "Margund Bach", "Rainer Kaufmann", "Michael Hausmann", "Dieter W. Heermann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0128555.g002", "stats"=>{"downloads"=>2, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conditional_Probabilities_of_Edge_Lengths_for_Random_Data_/1436351", "title"=>"Conditional Probabilities of Edge Lengths for Random Data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-04 02:52:56"}

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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