[{"citation":{"ieee":"N. Sen, R. Biswas, and P. Bhowmick, “On some local topological properties of naive discrete sphere,” in <i>Computational Topology in Image Context</i>, vol. 9667, Cham: Springer Nature, 2016, pp. 253–264.","ista":"Sen N, Biswas R, Bhowmick P. 2016.On some local topological properties of naive discrete sphere. In: Computational Topology in Image Context. LNCS, vol. 9667, 253–264.","chicago":"Sen, Nabhasmita, Ranita Biswas, and Partha Bhowmick. “On Some Local Topological Properties of Naive Discrete Sphere.” In <i>Computational Topology in Image Context</i>, 9667:253–64. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">https://doi.org/10.1007/978-3-319-39441-1_23</a>.","ama":"Sen N, Biswas R, Bhowmick P. On some local topological properties of naive discrete sphere. In: <i>Computational Topology in Image Context</i>. Vol 9667. Cham: Springer Nature; 2016:253-264. doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">10.1007/978-3-319-39441-1_23</a>","apa":"Sen, N., Biswas, R., &#38; Bhowmick, P. (2016). On some local topological properties of naive discrete sphere. In <i>Computational Topology in Image Context</i> (Vol. 9667, pp. 253–264). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">https://doi.org/10.1007/978-3-319-39441-1_23</a>","short":"N. Sen, R. Biswas, P. Bhowmick, in:, Computational Topology in Image Context, Springer Nature, Cham, 2016, pp. 253–264.","mla":"Sen, Nabhasmita, et al. “On Some Local Topological Properties of Naive Discrete Sphere.” <i>Computational Topology in Image Context</i>, vol. 9667, Springer Nature, 2016, pp. 253–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">10.1007/978-3-319-39441-1_23</a>."},"quality_controlled":"1","publication":"Computational Topology in Image Context","publication_status":"published","date_created":"2019-01-08T20:44:24Z","extern":"1","publication_identifier":{"isbn":["978-3-319-39440-4"],"eissn":["1611-3349"],"eisbn":["978-3-319-39441-1"],"issn":["0302-9743"]},"department":[{"_id":"HeEd"}],"oa_version":"None","conference":{"location":"Marseille, France","start_date":"2016-06-15","name":"CTIC: Computational Topology in Image Context","end_date":"2016-06-17"},"doi":"10.1007/978-3-319-39441-1_23","article_processing_charge":"No","page":"253-264","year":"2016","month":"06","publisher":"Springer Nature","date_published":"2016-06-02T00:00:00Z","volume":9667,"_id":"5805","alternative_title":["LNCS"],"title":"On some local topological properties of naive discrete sphere","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"02","intvolume":"      9667","abstract":[{"lang":"eng","text":"Discretization of sphere in the integer space follows a particular discretization scheme, which, in principle, conforms to some topological model. This eventually gives rise to interesting topological properties of a discrete spherical surface, which need to be investigated for its analytical characterization. This paper presents some novel results on the local topological properties of the naive model of discrete sphere. They follow from the bijection of each quadraginta octant of naive sphere with its projection map called f -map on the corresponding functional plane and from the characterization of certain jumps in the f-map. As an application, we have shown how these properties can be used in designing an efficient reconstruction algorithm for a naive spherical surface from an input voxel set when it is sparse or noisy."}],"author":[{"full_name":"Sen, Nabhasmita","first_name":"Nabhasmita","last_name":"Sen"},{"first_name":"Ranita","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","last_name":"Biswas"},{"last_name":"Bhowmick","full_name":"Bhowmick, Partha","first_name":"Partha"}],"type":"book_chapter","status":"public","language":[{"iso":"eng"}],"place":"Cham","date_updated":"2022-01-28T08:01:22Z"},{"publication_identifier":{"isbn":["978-3-319-32359-6"],"eisbn":["978-3-319-32360-2"],"issn":["0302-9743","1611-3349"]},"department":[{"_id":"HeEd"}],"oa_version":"None","article_processing_charge":"No","year":"2016","page":"256-267","conference":{"name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","end_date":"2016-04-20","start_date":"2016-04-18","location":"Nantes, France"},"doi":"10.1007/978-3-319-32360-2_20","publication_status":"published","citation":{"ista":"Biswas R, Bhowmick P. 2016. On functionality of quadraginta octants of naive sphere with application to circle drawing. Discrete Geometry for Computer Imagery. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 9647, 256–267.","ieee":"R. Biswas and P. Bhowmick, “On functionality of quadraginta octants of naive sphere with application to circle drawing,” in <i>Discrete Geometry for Computer Imagery</i>, Nantes, France, 2016, vol. 9647, pp. 256–267.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” In <i>Discrete Geometry for Computer Imagery</i>, 9647:256–67. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">https://doi.org/10.1007/978-3-319-32360-2_20</a>.","mla":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” <i>Discrete Geometry for Computer Imagery</i>, vol. 9647, Springer Nature, 2016, pp. 256–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">10.1007/978-3-319-32360-2_20</a>.","ama":"Biswas R, Bhowmick P. On functionality of quadraginta octants of naive sphere with application to circle drawing. In: <i>Discrete Geometry for Computer Imagery</i>. Vol 9647. Cham: Springer Nature; 2016:256-267. doi:<a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">10.1007/978-3-319-32360-2_20</a>","apa":"Biswas, R., &#38; Bhowmick, P. (2016). On functionality of quadraginta octants of naive sphere with application to circle drawing. In <i>Discrete Geometry for Computer Imagery</i> (Vol. 9647, pp. 256–267). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">https://doi.org/10.1007/978-3-319-32360-2_20</a>","short":"R. Biswas, P. Bhowmick, in:, Discrete Geometry for Computer Imagery, Springer Nature, Cham, 2016, pp. 256–267."},"quality_controlled":"1","publication":"Discrete Geometry for Computer Imagery","date_created":"2019-01-08T20:44:37Z","extern":"1","intvolume":"      9647","abstract":[{"lang":"eng","text":"Although the concept of functional plane for naive plane is studied and reported in the literature in great detail, no similar study is yet found for naive sphere. This article exposes the first study in this line, opening up further prospects of analyzing the topological properties of sphere in the discrete space. We show that each quadraginta octant Q of a naive sphere forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as the functional plane of Q, and hence gives rise to merely mono-jumps during back projection. The other two coordinate planes serve as para-functional and dia-functional planes for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds neither of the two. Owing to this, the quadraginta octants form symmetry groups and subgroups with equivalent jump conditions. We also show a potential application in generating a special class of discrete 3D circles based on back projection and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry, uniqueness, and bounded distance from the underlying real sphere and real plane."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"09","place":"Cham","date_updated":"2022-01-28T08:10:11Z","author":[{"first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"status":"public","type":"conference","language":[{"iso":"eng"}],"month":"04","publisher":"Springer Nature","alternative_title":["LNCS"],"_id":"5806","title":"On functionality of quadraginta octants of naive sphere with application to circle drawing","date_published":"2016-04-09T00:00:00Z","volume":9647},{"title":"On the connectivity and smoothness of discrete spherical circles","_id":"5809","date_created":"2019-01-08T20:45:19Z","extern":"1","date_published":"2016-01-06T00:00:00Z","volume":9448,"publication_status":"published","month":"01","publisher":"Springer Nature","citation":{"mla":"Biswas, Ranita, et al. “On the Connectivity and Smoothness of Discrete Spherical Circles.” <i>Combinatorial Image Analysis</i>, vol. 9448, Springer Nature, 2016, pp. 86–100, doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>.","ama":"Biswas R, Bhowmick P, Brimkov VE. On the connectivity and smoothness of discrete spherical circles. In: <i>Combinatorial Image Analysis</i>. Vol 9448. Cham: Springer Nature; 2016:86-100. doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2016, pp. 86–100.","apa":"Biswas, R., Bhowmick, P., &#38; Brimkov, V. E. (2016). On the connectivity and smoothness of discrete spherical circles. In <i>Combinatorial image analysis</i> (Vol. 9448, pp. 86–100). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>","ista":"Biswas R, Bhowmick P, Brimkov VE. 2016.On the connectivity and smoothness of discrete spherical circles. In: Combinatorial image analysis. vol. 9448, 86–100.","ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the connectivity and smoothness of discrete spherical circles,” in <i>Combinatorial image analysis</i>, vol. 9448, Cham: Springer Nature, 2016, pp. 86–100.","chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Connectivity and Smoothness of Discrete Spherical Circles.” In <i>Combinatorial Image Analysis</i>, 9448:86–100. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>."},"quality_controlled":"1","publication":"Combinatorial image analysis","article_processing_charge":"No","place":"Cham","date_updated":"2022-01-28T08:13:03Z","page":"86-100","year":"2016","author":[{"orcid":"0000-0002-5372-7890","last_name":"Biswas","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita"},{"last_name":"Bhowmick","full_name":"Bhowmick, Partha","first_name":"Partha"},{"first_name":"Valentin E.","full_name":"Brimkov, Valentin E.","last_name":"Brimkov"}],"status":"public","type":"book_chapter","conference":{"location":"Kolkata, India","start_date":"2015-11-24","end_date":"2015-11-27","name":"IWCIA: International Workshop on Combinatorial Image Analysis"},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-26145-4_7","intvolume":"      9448","abstract":[{"text":"A discrete spherical circle is a topologically well-connected 3D circle in the integer space, which belongs to a discrete sphere as well as a discrete plane. It is one of the most important 3D geometric primitives, but has not possibly yet been studied up to its merit. This paper is a maiden exposition of some of its elementary properties, which indicates a sense of its profound theoretical prospects in the framework of digital geometry. We have shown how different types of discretization can lead to forbidden and admissible classes, when one attempts to define the discretization of a spherical circle in terms of intersection between a discrete sphere and a discrete plane. Several fundamental theoretical results have been presented, the algorithm for construction of discrete spherical circles has been discussed, and some test results have been furnished to demonstrate its practicality and usefulness.","lang":"eng"}],"publication_identifier":{"eisbn":["978-3-319-26145-4"],"issn":["0302-9743"],"isbn":["978-3-319-26144-7"],"eissn":["1611-3349"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"HeEd"}],"oa_version":"None","day":"06"},{"publisher":"Public Library of Science","month":"12","citation":{"ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>","mla":"Roux, Camille, et al. <i>Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>."},"related_material":{"record":[{"id":"1158","status":"public","relation":"used_in_publication"}]},"title":"Simulation study to test the robustness of ABC in face of recent times of divergence","_id":"9862","date_created":"2021-08-10T08:20:17Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa_version":"Published Version","day":"27","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","article_processing_charge":"No","date_updated":"2025-09-22T09:55:08Z","doi":"10.1371/journal.pbio.2000234.s016","author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"full_name":"Anciaux, Youann","first_name":"Youann","last_name":"Anciaux"},{"last_name":"Galtier","full_name":"Galtier, Nicolas","first_name":"Nicolas"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"status":"public","type":"research_data_reference"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","day":"27","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2025-09-22T09:55:09Z","article_processing_charge":"No","year":"2016","type":"research_data_reference","status":"public","author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"last_name":"Galtier","full_name":"Galtier, Nicolas","first_name":"Nicolas"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"doi":"10.1371/journal.pbio.2000234.s017","month":"12","publisher":"Public Library of Science","citation":{"ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>.","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>"},"_id":"9863","title":"Accessions of surveyed individuals, geographic locations and summary statistics","related_material":{"record":[{"status":"public","id":"1158","relation":"used_in_publication"}]},"date_created":"2021-08-10T08:22:52Z"},{"article_processing_charge":"No","date_updated":"2025-07-10T11:49:59Z","year":"2016","author":[{"first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo"},{"first_name":"Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"de Vladar, Harold","last_name":"de Vladar","orcid":"0000-0002-5985-7653"},{"last_name":"Włodarski","full_name":"Włodarski, Tomasz","first_name":"Tomasz"},{"orcid":"0000-0002-4624-4612","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}],"type":"research_data_reference","status":"public","doi":"10.6084/m9.figshare.4315652.v1","abstract":[{"lang":"eng","text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"day":"14","oa_version":"Published Version","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","_id":"9864","related_material":{"record":[{"status":"public","id":"1077","relation":"used_in_publication"}]},"date_created":"2021-08-10T08:29:47Z","date_published":"2016-12-14T00:00:00Z","month":"12","publisher":"The Royal Society","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"citation":{"ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>."}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"AnKi"}],"day":"09","oa_version":"Published Version","article_processing_charge":"No","date_updated":"2025-09-22T09:53:16Z","year":"2016","author":[{"first_name":"Marcin P","full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","last_name":"Zagórski"},{"last_name":"Burda","first_name":"Zdzisław","full_name":"Burda, Zdzisław"},{"last_name":"Wacław","first_name":"Bartłomiej","full_name":"Wacław, Bartłomiej"}],"type":"research_data_reference","status":"public","doi":"10.1371/journal.pcbi.1005218.s009","month":"12","publisher":"Public Library of Science","citation":{"chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived Directory Containing All Data and Computer Programs.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>.","ista":"Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all data and computer programs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing all data and computer programs.” Public Library of Science, 2016.","apa":"Zagórski, M. P., Burda, Z., &#38; Wacław, B. (2016). ZIP-archived directory containing all data and computer programs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>","short":"M.P. Zagórski, Z. Burda, B. Wacław, (2016).","ama":"Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data and computer programs. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>","mla":"Zagórski, Marcin P., et al. <i>ZIP-Archived Directory Containing All Data and Computer Programs</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>."},"_id":"9866","title":"ZIP-archived directory containing all data and computer programs","related_material":{"record":[{"status":"public","id":"1167","relation":"used_in_publication"}]},"date_created":"2021-08-10T08:37:20Z","date_published":"2016-12-09T00:00:00Z"},{"author":[{"first_name":"Christian","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"full_name":"Hagel, Kristin","first_name":"Kristin","last_name":"Hagel"},{"full_name":"Milinski, Manfred","first_name":"Manfred","last_name":"Milinski"}],"status":"public","type":"research_data_reference","doi":"10.1371/journal.pone.0163867.s008","article_processing_charge":"No","date_updated":"2025-09-22T08:27:00Z","year":"2016","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"KrCh"}],"day":"04","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German."}],"date_created":"2021-08-10T08:42:00Z","title":"Experimental game instructions","_id":"9867","related_material":{"record":[{"status":"public","id":"1322","relation":"used_in_publication"}]},"citation":{"ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public Library of Science, 2016.","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game Instructions.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>.","mla":"Hilbe, Christian, et al. <i>Experimental Game Instructions</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","ama":"Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental game instructions. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>"},"month":"10","publisher":"Public Library of Science"},{"year":"2016","date_updated":"2025-09-22T08:27:00Z","article_processing_charge":"No","doi":"10.1371/journal.pone.0163867.s009","type":"research_data_reference","status":"public","author":[{"last_name":"Hilbe","orcid":"0000-0001-5116-955X","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","first_name":"Christian"},{"last_name":"Hagel","full_name":"Hagel, Kristin","first_name":"Kristin"},{"full_name":"Milinski, Manfred","first_name":"Manfred","last_name":"Milinski"}],"abstract":[{"text":"The raw data file containing the experimental decisions of all our study subjects.","lang":"eng"}],"oa_version":"Published Version","day":"04","department":[{"_id":"KrCh"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"relation":"used_in_publication","id":"1322","status":"public"}]},"title":"Experimental data","_id":"9868","date_published":"2016-10-04T00:00:00Z","date_created":"2021-08-10T08:45:00Z","publisher":"Public Library of Science","month":"10","citation":{"chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>.","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of Science, 2016.","mla":"Hilbe, Christian, et al. <i>Experimental Data</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental data. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>","ama":"Hilbe C, Hagel K, Milinski M. Experimental data. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>"}},{"date_updated":"2025-09-22T08:46:14Z","article_processing_charge":"No","year":"2016","status":"public","type":"research_data_reference","author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"last_name":"Gerland","full_name":"Gerland, Ulrich","first_name":"Ulrich"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"doi":"10.1371/journal.pone.0163628.s001","abstract":[{"lang":"eng","text":"A lower bound on the error of a positional estimator with limited positional information is derived."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","day":"27","department":[{"_id":"GaTk"}],"title":"Error bound on an estimator of position","_id":"9869","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"date_created":"2021-08-10T08:53:48Z","date_published":"2016-09-27T00:00:00Z","month":"09","publisher":"Public Library of Science","citation":{"ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","mla":"Hillenbrand, Patrick, et al. <i>Error Bound on an Estimator of Position</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>."}},{"year":"2016","date_updated":"2025-09-22T08:46:14Z","article_processing_charge":"No","doi":"10.1371/journal.pone.0163628.s002","status":"public","type":"research_data_reference","author":[{"last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick","first_name":"Patrick"},{"last_name":"Gerland","full_name":"Gerland, Ulrich","first_name":"Ulrich"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"abstract":[{"lang":"eng","text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined."}],"oa_version":"Published Version","day":"27","department":[{"_id":"GaTk"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"id":"1270","status":"public","relation":"used_in_publication"}]},"_id":"9870","title":"Computation of positional information in an Ising model","date_published":"2016-09-27T00:00:00Z","date_created":"2021-08-10T09:23:45Z","publisher":"Public Library of Science","month":"09","citation":{"ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>.","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in an Ising Model</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>."}},{"status":"public","type":"research_data_reference","author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455"}],"doi":"10.1371/journal.pone.0163628.s003","date_updated":"2025-09-22T08:46:14Z","article_processing_charge":"No","year":"2016","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","day":"27","department":[{"_id":"GaTk"}],"abstract":[{"text":"The positional information in a discrete morphogen field with Gaussian noise is computed.","lang":"eng"}],"date_created":"2021-08-10T09:27:35Z","title":"Computation of positional information in a discrete morphogen field","_id":"9871","related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"citation":{"chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in a Discrete Morphogen Field</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>.","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>"},"month":"09","publisher":"Public Library of Science"},{"year":"2016","article_processing_charge":"No","date_updated":"2025-09-22T09:10:03Z","doi":"10.1371/journal.pgen.1005974.s015","author":[{"full_name":"Boehm, Alex","first_name":"Alex","last_name":"Boehm"},{"full_name":"Arnoldini, Markus","first_name":"Markus","last_name":"Arnoldini"},{"full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller"},{"full_name":"Röösli, Thomas","first_name":"Thomas","last_name":"Röösli"},{"last_name":"Bigosch","first_name":"Colette","full_name":"Bigosch, Colette"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"}],"status":"public","type":"research_data_reference","department":[{"_id":"CaGu"}],"oa_version":"Published Version","day":"19","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"relation":"used_in_publication","id":"1250","status":"public"}]},"_id":"9873","title":"Quantification of the growth rate reduction as a consequence of age-specific mortality","date_created":"2021-08-10T09:42:34Z","publisher":"Public Library of Science","month":"04","citation":{"ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Quantification of the growth rate reduction as a consequence of age-specific mortality, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>.","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Quantification of the growth rate reduction as a consequence of age-specific mortality.” Public Library of Science, 2016.","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">https://doi.org/10.1371/journal.pgen.1005974.s015</a>.","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 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Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>."}},{"publication_status":"published","month":"02","publisher":"Springer Nature","citation":{"mla":"Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–45, doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>.","ama":"Harada H, Shigemoto R. High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: <i>Receptor and Ion Channel Detection in the Brain</i>. Neuromethods. Springer Nature; 2016:233-245. doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>","apa":"Harada, H., &#38; Shigemoto, R. (2016). High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In <i>Receptor and Ion Channel Detection in the Brain</i> (pp. 233–245). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>","short":"H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Springer Nature, 2016, pp. 233–245.","ieee":"H. Harada and R. Shigemoto, “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL),” in <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–245.","ista":"Harada H, Shigemoto R. 2016.High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). 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Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>."},"corr_author":"1","quality_controlled":"1","publication":"Receptor and Ion Channel Detection in the Brain","title":"High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL)","_id":"19990","date_created":"2025-07-10T13:56:06Z","date_published":"2016-02-02T00:00:00Z","acknowledgement":"We thank Mitsuru Ikeda for preparing replica images used in Fig. 2.","abstract":[{"text":"Visualizing molecular localization at high resolution contributes to understanding of their functions and roles in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study high-resolution two-dimensional distribution of transmembrane proteins and their tightly associated proteins on platinum-carbon replica. During treatment with SDS, unfixed proteins and intracellular organelle are dissolved and integral membrane proteins captured and stabilized by carbon and platinum deposition are denatured, retaining most of their antigenicity, and exposed on exoplasmic and protoplasmic surfaces of lipid monolayers. The exposure of these antigens on the surface of replica facilitates the accessibility of antibodies and therefore provides higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples and an additional procedure for fluorescence-guided electron microscopy for replica immunolabeling.","lang":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["0893-2336"],"eisbn":["9781493930647"],"eissn":["1940-6045"],"isbn":["9781493930630"]},"department":[{"_id":"RySh"}],"day":"02","oa_version":"None","article_processing_charge":"No","date_updated":"2026-04-07T08:32:03Z","series_title":"Neuromethods","page":"233-245","year":"2016","author":[{"last_name":"Harada","orcid":"0000-0001-7429-7896","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harada, Harumi"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"}],"status":"public","type":"book_chapter","OA_type":"closed access","language":[{"iso":"eng"}],"doi":"10.1007/978-1-4939-3064-7_17"},{"ec_funded":1,"file":[{"access_level":"open_access","file_name":"IST-2016-664-v1+1_acs.nanolett.6b02715.pdf","date_created":"2018-12-12T10:14:04Z","date_updated":"2020-07-14T12:44:44Z","relation":"main_file","file_size":535121,"file_id":"5053","content_type":"application/pdf","creator":"system","checksum":"b63feece90d7b620ece49ca632e34ff3"}],"ddc":["539"],"scopus_import":"1","department":[{"_id":"GeKa"}],"oa":1,"oa_version":"Published Version","page":"6879 - 6885","year":"2016","article_processing_charge":"No","doi":"10.1021/acs.nanolett.6b02715","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_status":"published","publication":"Nano Letters","corr_author":"1","citation":{"short":"H. Watzinger, C. Kloeffel, L. Vukušić, M. Rossell, V. Sessi, J. Kukucka, R. Kirchschlager, E. Lausecker, A. Truhlar, M. Glaser, A. Rastelli, A. Fuhrer, D. Loss, G. Katsaros, Nano Letters 16 (2016) 6879–6885.","apa":"Watzinger, H., Kloeffel, C., Vukušić, L., Rossell, M., Sessi, V., Kukucka, J., … Katsaros, G. (2016). Heavy-hole states in germanium hut wires. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">https://doi.org/10.1021/acs.nanolett.6b02715</a>","ama":"Watzinger H, Kloeffel C, Vukušić L, et al. Heavy-hole states in germanium hut wires. <i>Nano Letters</i>. 2016;16(11):6879-6885. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">10.1021/acs.nanolett.6b02715</a>","mla":"Watzinger, Hannes, et al. “Heavy-Hole States in Germanium Hut Wires.” <i>Nano Letters</i>, vol. 16, no. 11, American Chemical Society, 2016, pp. 6879–85, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">10.1021/acs.nanolett.6b02715</a>.","chicago":"Watzinger, Hannes, Christoph Kloeffel, Lada Vukušić, Marta Rossell, Violetta Sessi, Josip Kukucka, Raimund Kirchschlager, et al. “Heavy-Hole States in Germanium Hut Wires.” <i>Nano Letters</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acs.nanolett.6b02715\">https://doi.org/10.1021/acs.nanolett.6b02715</a>.","ista":"Watzinger H, Kloeffel C, Vukušić L, Rossell M, Sessi V, Kukucka J, Kirchschlager R, Lausecker E, Truhlar A, Glaser M, Rastelli A, Fuhrer A, Loss D, Katsaros G. 2016. Heavy-hole states in germanium hut wires. Nano Letters. 16(11), 6879–6885.","ieee":"H. Watzinger <i>et al.</i>, “Heavy-hole states in germanium hut wires,” <i>Nano Letters</i>, vol. 16, no. 11. American Chemical Society, pp. 6879–6885, 2016."},"quality_controlled":"1","related_material":{"record":[{"relation":"popular_science","id":"7977"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"issue":"11","pubrep_id":"664","date_created":"2018-12-11T11:51:24Z","abstract":[{"lang":"eng","text":"Hole spins have gained considerable interest in the past few years due to their potential for fast electrically controlled qubits. Here, we study holes confined in Ge hut wires, a so-far unexplored type of nanostructure. Low-temperature magnetotransport measurements reveal a large anisotropy between the in-plane and out-of-plane g-factors of up to 18. Numerical simulations verify that this large anisotropy originates from a confined wave function of heavy-hole character. A light-hole admixture of less than 1% is estimated for the states of lowest energy, leading to a surprisingly large reduction of the out-of-plane g-factors compared with those for pure heavy holes. Given this tiny light-hole contribution, the spin lifetimes are expected to be very long, even in isotopically nonpurified samples."}],"acknowledgement":"The work was supported by the EC FP7 ICT project SiSPIN no. 323841, the EC FP7 ICT project PAMS no. 610446, the ERC Starting Grant no. 335497, the FWF-I-1190-N20 project, and the Swiss NSF. We acknowledge F. Schäffler for fruitful discussions related to the hut wire growth and for giving us access to the molecular beam epitaxy system, M. Schatzl for her support in electron beam lithography, and V. Jadris ̌ko for helping us with the COMSOL simulations. Finally, we thank G. Bauer for his continuous support. ","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires","call_identifier":"FP7"}],"intvolume":"        16","day":"22","file_date_updated":"2020-07-14T12:44:44Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"5941","date_updated":"2026-04-08T07:27:13Z","has_accepted_license":"1","language":[{"iso":"eng"}],"author":[{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","full_name":"Watzinger, Hannes","first_name":"Hannes","last_name":"Watzinger"},{"last_name":"Kloeffel","full_name":"Kloeffel, Christoph","first_name":"Christoph"},{"first_name":"Lada","full_name":"Vukusic, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","last_name":"Vukusic"},{"last_name":"Rossell","full_name":"Rossell, Marta","first_name":"Marta"},{"full_name":"Sessi, Violetta","first_name":"Violetta","last_name":"Sessi"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","first_name":"Josip","last_name":"Kukucka"},{"last_name":"Kirchschlager","first_name":"Raimund","full_name":"Kirchschlager, Raimund"},{"last_name":"Lausecker","first_name":"Elisabeth","full_name":"Lausecker, Elisabeth","id":"33662F76-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alisha","full_name":"Truhlar, Alisha","id":"49CBC780-F248-11E8-B48F-1D18A9856A87","last_name":"Truhlar"},{"full_name":"Glaser, Martin","first_name":"Martin","last_name":"Glaser"},{"last_name":"Rastelli","first_name":"Armando","full_name":"Rastelli, Armando"},{"first_name":"Andreas","full_name":"Fuhrer, Andreas","last_name":"Fuhrer"},{"first_name":"Daniel","full_name":"Loss, Daniel","last_name":"Loss"},{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X"}],"external_id":{"isi":["000387625000025"]},"status":"public","type":"journal_article","publisher":"American Chemical Society","month":"09","_id":"1328","title":"Heavy-hole states in germanium hut wires","date_published":"2016-09-22T00:00:00Z","volume":16},{"title":"Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification","_id":"1346","date_published":"2016-06-08T00:00:00Z","volume":7,"publisher":"Nature Publishing Group","month":"06","publist_id":"5906","date_updated":"2026-04-08T13:54:44Z","language":[{"iso":"eng"}],"has_accepted_license":"1","type":"journal_article","external_id":{"isi":["000377899800001"]},"status":"public","author":[{"last_name":"Dejonghe","first_name":"Wim","full_name":"Dejonghe, Wim"},{"full_name":"Kuenen, Sabine","first_name":"Sabine","last_name":"Kuenen"},{"last_name":"Mylle","full_name":"Mylle, Evelien","first_name":"Evelien"},{"last_name":"Vasileva","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","full_name":"Vasileva, Mina K","first_name":"Mina K"},{"full_name":"Keech, Olivier","first_name":"Olivier","last_name":"Keech"},{"last_name":"Viotti","full_name":"Viotti, Corrado","first_name":"Corrado"},{"full_name":"Swerts, Jef","first_name":"Jef","last_name":"Swerts"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"first_name":"Fausto","full_name":"Ortiz Morea, Fausto","last_name":"Ortiz Morea"},{"full_name":"Mishev, Kiril","first_name":"Kiril","last_name":"Mishev"},{"last_name":"Delang","full_name":"Delang, Simon","first_name":"Simon"},{"last_name":"Scholl","first_name":"Stefan","full_name":"Scholl, Stefan"},{"full_name":"Zarza, Xavier","first_name":"Xavier","last_name":"Zarza"},{"last_name":"Heilmann","full_name":"Heilmann, Mareike","first_name":"Mareike"},{"last_name":"Kourelis","full_name":"Kourelis, Jiorgos","first_name":"Jiorgos"},{"first_name":"Jaroslaw","full_name":"Kasprowicz, Jaroslaw","last_name":"Kasprowicz"},{"last_name":"Nguyen","full_name":"Nguyen, Le","first_name":"Le"},{"first_name":"Andrzej","full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki"},{"last_name":"Van Houtte","full_name":"Van Houtte, Isabelle","first_name":"Isabelle"},{"full_name":"Szatmári, Anna","first_name":"Anna","last_name":"Szatmári"},{"first_name":"Mateusz","full_name":"Majda, Mateusz","last_name":"Majda"},{"last_name":"Baisa","full_name":"Baisa, Gary","first_name":"Gary"},{"first_name":"Sebastian","full_name":"Bednarek, Sebastian","last_name":"Bednarek"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"first_name":"Dominique","full_name":"Audenaert, Dominique","last_name":"Audenaert"},{"last_name":"Testerink","full_name":"Testerink, Christa","first_name":"Christa"},{"last_name":"Munnik","full_name":"Munnik, Teun","first_name":"Teun"},{"last_name":"Van Damme","first_name":"Daniël","full_name":"Van Damme, Daniël"},{"last_name":"Heilmann","first_name":"Ingo","full_name":"Heilmann, Ingo"},{"first_name":"Karin","full_name":"Schumacher, Karin","last_name":"Schumacher"},{"full_name":"Winne, Johan","first_name":"Johan","last_name":"Winne"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Patrik","full_name":"Verstreken, Patrik","last_name":"Verstreken"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}],"abstract":[{"lang":"eng","text":"ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane."}],"intvolume":"         7","project":[{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We thank Yvon Jaillais, Ikuko Hara-Nishimura, Akihiko Nakano, Takashi Ueda and Jinxing Lin for providing materials, Natasha Raikhel, Glenn Hicks, Steffen Vanneste, and Ricardo Tejos for useful suggestions, Patrick Callaerts for providing S2 Drosophila cell cultures, Michael Sixt for providing HeLa cells, Annick Bleys for literature searches, VIB Bio Imaging Core for help with imaging conditions and Martine De Cock for help in preparing the article. This work was supported by the Agency for Innovation by Science\r\nand Technology for a pre-doctoral fellowship to W.D.; the Research fund KU Leuven\r\n(GOA), a Methusalem grant of the Flemish government and VIB to S.K., J.K. and P.V.;\r\nby the Netherlands Organisation for Scientific Research (NWO) for ALW grants\r\n846.11.002 (C.T.) and 867.15.020 (T.M.); the European Research Council (project\r\nERC-2011-StG-20101109 PSDP) (to J.F.); a European Research Council (ERC) Starting\r\nGrant (grant 260678) (to P.V.), the Research Foundation-Flanders (grants G.0747.09,\r\nG094011 and G095511) (to P.V.), the Hercules Foundation, an Interuniversity Attraction\r\nPoles Poles Program, initiated by the Belgian State, Science Policy Office (to P.V.),\r\nthe Swedish VetenskapsRådet grant to O.K., the Ghent University ‘Bijzonder\r\nOnderzoek Fonds’ (BOF) for a predoctoral fellowship to F.A.O.-M., the Research\r\nFoundation-Flanders (FWO) to K.M. and E.R.","day":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:44:45Z","related_material":{"record":[{"relation":"dissertation_contains","id":"7172","status":"public"}]},"pubrep_id":"653","date_created":"2018-12-11T11:51:30Z","isi":1,"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_number":"11710","publication":"Nature Communications","quality_controlled":"1","citation":{"chicago":"Dejonghe, Wim, Sabine Kuenen, Evelien Mylle, Mina K Vasileva, Olivier Keech, Corrado Viotti, Jef Swerts, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11710\">https://doi.org/10.1038/ncomms11710</a>.","ista":"Dejonghe W, Kuenen S, Mylle E, Vasileva MK, Keech O, Viotti C, Swerts J, Fendrych M, Ortiz Morea F, Mishev K, Delang S, Scholl S, Zarza X, Heilmann M, Kourelis J, Kasprowicz J, Nguyen L, Drozdzecki A, Van Houtte I, Szatmári A, Majda M, Baisa G, Bednarek S, Robert S, Audenaert D, Testerink C, Munnik T, Van Damme D, Heilmann I, Schumacher K, Winne J, Friml J, Verstreken P, Russinova E. 2016. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. Nature Communications. 7, 11710.","ieee":"W. Dejonghe <i>et al.</i>, “Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","mla":"Dejonghe, Wim, et al. “Mitochondrial Uncouplers Inhibit Clathrin-Mediated Endocytosis Largely through Cytoplasmic Acidification.” <i>Nature Communications</i>, vol. 7, 11710, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11710\">10.1038/ncomms11710</a>.","short":"W. Dejonghe, S. Kuenen, E. Mylle, M.K. Vasileva, O. Keech, C. Viotti, J. Swerts, M. Fendrych, F. Ortiz Morea, K. Mishev, S. Delang, S. Scholl, X. Zarza, M. Heilmann, J. Kourelis, J. Kasprowicz, L. Nguyen, A. Drozdzecki, I. Van Houtte, A. Szatmári, M. Majda, G. Baisa, S. Bednarek, S. Robert, D. Audenaert, C. Testerink, T. Munnik, D. Van Damme, I. Heilmann, K. Schumacher, J. Winne, J. Friml, P. Verstreken, E. Russinova, Nature Communications 7 (2016).","apa":"Dejonghe, W., Kuenen, S., Mylle, E., Vasileva, M. K., Keech, O., Viotti, C., … Russinova, E. (2016). Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11710\">https://doi.org/10.1038/ncomms11710</a>","ama":"Dejonghe W, Kuenen S, Mylle E, et al. Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11710\">10.1038/ncomms11710</a>"},"year":"2016","article_processing_charge":"No","doi":"10.1038/ncomms11710","ec_funded":1,"ddc":["570"],"file":[{"creator":"system","content_type":"application/pdf","file_size":3532505,"file_id":"5369","checksum":"e8dc81b3e44db5a7718d7f1501ce1aa7","date_created":"2018-12-12T10:18:47Z","file_name":"IST-2016-653-v1+1_ncomms11710_1_.pdf","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:44:45Z"}],"scopus_import":"1","oa_version":"Published Version","oa":1,"department":[{"_id":"JiFr"}]},{"scopus_import":"1","file":[{"date_updated":"2020-07-14T12:44:46Z","relation":"main_file","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","date_created":"2018-12-12T10:12:01Z","access_level":"open_access","checksum":"fe3f3a1526d180b29fe691ab11435b78","creator":"system","file_id":"4919","file_size":861805,"content_type":"application/pdf"},{"relation":"main_file","date_updated":"2020-07-14T12:44:46Z","date_created":"2018-12-12T10:12:02Z","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","access_level":"open_access","checksum":"164864a1a675f3ad80e9917c27aba07f","creator":"system","content_type":"application/pdf","file_size":1084703,"file_id":"4920"}],"ddc":["576"],"ec_funded":1,"oa":1,"department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"oa_version":"Published Version","article_processing_charge":"No","year":"2016","doi":"10.1038/ncomms12307","publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_number":"12307","isi":1,"citation":{"chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>."},"corr_author":"1","quality_controlled":"1","publication":"Nature Communications","related_material":{"record":[{"id":"6071","status":"public","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:51:34Z","pubrep_id":"627","intvolume":"         7","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27"}],"abstract":[{"lang":"eng","text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements."}],"file_date_updated":"2020-07-14T12:44:46Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"04","date_updated":"2026-04-08T13:54:24Z","publist_id":"5887","author":[{"last_name":"Friedlander","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","first_name":"Roshan","last_name":"Prizak"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"}],"external_id":{"isi":["000380858400001"]},"status":"public","type":"journal_article","has_accepted_license":"1","language":[{"iso":"eng"}],"month":"08","publisher":"Nature Publishing Group","title":"Intrinsic limits to gene regulation by global crosstalk","_id":"1358","volume":7,"date_published":"2016-08-04T00:00:00Z"},{"page":"493 - 506","year":"2016","article_processing_charge":"No","doi":"10.1016/j.devcel.2016.05.024","scopus_import":"1","department":[{"_id":"CaHe"}],"oa_version":"None","related_material":{"record":[{"relation":"part_of_dissertation","id":"7186","status":"public"}]},"issue":"6","date_created":"2018-12-11T11:50:07Z","isi":1,"publication_status":"published","publication":"Developmental Cell","citation":{"chicago":"Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and Carl-Philipp J Heisenberg. “Actin Rings of Power.” <i>Developmental Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">https://doi.org/10.1016/j.devcel.2016.05.024</a>.","ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","ieee":"C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg, “Actin rings of power,” <i>Developmental Cell</i>, vol. 37, no. 6. Cell Press, pp. 493–506, 2016.","mla":"Schwayer, Cornelia, et al. “Actin Rings of Power.” <i>Developmental Cell</i>, vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">10.1016/j.devcel.2016.05.024</a>.","apa":"Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., &#38; Heisenberg, C.-P. J. (2016). Actin rings of power. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">https://doi.org/10.1016/j.devcel.2016.05.024</a>","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506.","ama":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings of power. <i>Developmental Cell</i>. 2016;37(6):493-506. doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">10.1016/j.devcel.2016.05.024</a>"},"quality_controlled":"1","publist_id":"6279","date_updated":"2026-04-08T13:55:28Z","language":[{"iso":"eng"}],"author":[{"last_name":"Schwayer","orcid":"0000-0001-5130-2226","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia"},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","last_name":"Sikora"},{"id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","full_name":"Slovakova, Jana","first_name":"Jana","last_name":"Slovakova"},{"last_name":"Kardos","first_name":"Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"status":"public","type":"journal_article","external_id":{"isi":["000378204200005"]},"intvolume":"        37","day":"20","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Actin rings of power","_id":"1096","volume":37,"date_published":"2016-06-20T00:00:00Z","publisher":"Cell Press","month":"06"},{"doi":"10.1007/978-3-319-39555-5_16","conference":{"location":"Guildford, UK","start_date":"2016-06-19","name":"ACNS: Applied Cryptography and Network Security","end_date":"2016-06-22"},"article_processing_charge":"No","page":"285 - 303","year":"2016","oa":1,"department":[{"_id":"KrPi"}],"oa_version":"Submitted Version","scopus_import":"1","file":[{"file_name":"IST-2017-765-v1+1_838.pdf","date_created":"2018-12-12T10:17:20Z","access_level":"open_access","date_updated":"2020-07-14T12:44:39Z","relation":"main_file","creator":"system","file_id":"5273","file_size":515000,"content_type":"application/pdf","checksum":"34fa9ce681da845a1ba945ba3dc57867"}],"ddc":["005","600"],"ec_funded":1,"date_created":"2018-12-11T11:50:50Z","pubrep_id":"765","related_material":{"record":[{"status":"public","id":"83","relation":"dissertation_contains"}]},"citation":{"ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Offline witness encryption. ACNS: Applied Cryptography and Network Security, LNCS, vol. 9696, 285–303.","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Offline witness encryption,” presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK, 2016, vol. 9696, pp. 285–303.","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Offline Witness Encryption,” 9696:285–303. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>.","mla":"Abusalah, Hamza M., et al. <i>Offline Witness Encryption</i>. Vol. 9696, Springer, 2016, pp. 285–303, doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>.","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Offline witness encryption. In: Vol 9696. Springer; 2016:285-303. doi:<a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">10.1007/978-3-319-39555-5_16</a>","apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Offline witness encryption (Vol. 9696, pp. 285–303). Presented at the ACNS: Applied Cryptography and Network Security, Guildford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-39555-5_16\">https://doi.org/10.1007/978-3-319-39555-5_16</a>","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 285–303."},"quality_controlled":"1","publication_status":"published","isi":1,"author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M","first_name":"Hamza M","last_name":"Abusalah"},{"id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg","first_name":"Georg","last_name":"Fuchsbauer"},{"orcid":"0000-0002-9139-1654","last_name":"Pietrzak","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"type":"conference","status":"public","external_id":{"isi":["000386324500016"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"date_updated":"2026-04-08T14:10:21Z","publist_id":"6105","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:44:39Z","day":"09","acknowledgement":"Research  supported  by  the  European  Research  Council,  ERC  starting  grant (259668-PSPC) and ERC consolidator grant (682815 - TOCNeT).","project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","grant_number":"682815"}],"intvolume":"      9696","abstract":[{"lang":"eng","text":"Witness encryption (WE) was introduced by Garg et al. [GGSW13]. A WE scheme is defined for some NP language L and lets a sender encrypt messages relative to instances x. A ciphertext for x can be decrypted using w witnessing x ∈ L, but hides the message if x ∈ L. Garg et al. construct WE from multilinear maps and give another construction [GGH+13b] using indistinguishability obfuscation (iO) for circuits. Due to the reliance on such heavy tools, WE can cur- rently hardly be implemented on powerful hardware and will unlikely be realizable on constrained devices like smart cards any time soon. We construct a WE scheme where encryption is done by simply computing a Naor-Yung ciphertext (two CPA encryptions and a NIZK proof). To achieve this, our scheme has a setup phase, which outputs public parameters containing an obfuscated circuit (only required for decryption), two encryption keys and a common reference string (used for encryption). This setup need only be run once, and the parame- ters can be used for arbitrary many encryptions. Our scheme can also be turned into a functional WE scheme, where a message is encrypted w.r.t. a statement and a function f, and decryption with a witness w yields f (m, w). Our construction is inspired by the functional encryption scheme by Garg et al. and we prove (selective) security assuming iO and statistically simulation-sound NIZK. We give a construction of the latter in bilinear groups and combining it with ElGamal encryption, our ciphertexts are of size 1.3 kB at a 128-bit security level and can be computed on a smart card."}],"volume":9696,"date_published":"2016-06-09T00:00:00Z","alternative_title":["LNCS"],"_id":"1229","title":"Offline witness encryption","month":"06","publisher":"Springer"},{"file_date_updated":"2020-07-14T12:44:41Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"02","project":[{"grant_number":"259668","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"intvolume":"      9610","acknowledgement":"Supported by the European Research Council, ERC Starting Grant (259668-PSPC).","abstract":[{"text":"A constrained pseudorandom function F: K × X → Y for a family T ⊆ 2X of subsets of X is a function where for any key k ∈ K and set S ∈ T one can efficiently compute a constrained key kS which allows to evaluate F (k, ·) on all inputs x ∈ S, while even given this key, the outputs on all inputs x ∉ S look random. At Asiacrypt’13 Boneh and Waters gave a construction which supports the most general set family so far. Its keys kc are defined for sets decided by boolean circuits C and enable evaluation of the PRF on any x ∈ X where C(x) = 1. In their construction the PRF input length and the size of the circuits C for which constrained keys can be computed must be fixed beforehand during key generation. We construct a constrained PRF that has an unbounded input length and whose constrained keys can be defined for any set recognized by a Turing machine. The only a priori bound we make is on the description size of the machines. We prove our construction secure assuming publiccoin differing-input obfuscation. As applications of our constrained PRF we build a broadcast encryption scheme where the number of potential receivers need not be fixed at setup (in particular, the length of the keys is independent of the number of parties) and the first identity-based non-interactive key exchange protocol with no bound on the number of parties that can agree on a shared key.","lang":"eng"}],"status":"public","external_id":{"isi":["000374102500024"]},"type":"conference","author":[{"last_name":"Abusalah","first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M"},{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"},{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","date_updated":"2026-04-08T14:10:21Z","publist_id":"6097","month":"02","publisher":"Springer","date_published":"2016-02-02T00:00:00Z","volume":9610,"alternative_title":["LNCS"],"_id":"1236","title":"Constrained PRFs for unbounded inputs","oa_version":"Submitted Version","department":[{"_id":"KrPi"}],"oa":1,"scopus_import":"1","ec_funded":1,"ddc":["005","600"],"file":[{"file_size":495176,"file_id":"4664","content_type":"application/pdf","creator":"system","checksum":"3851cee49933ae13b1272e516f213e13","access_level":"open_access","file_name":"IST-2017-764-v1+1_279.pdf","date_created":"2018-12-12T10:08:05Z","date_updated":"2020-07-14T12:44:41Z","relation":"main_file"}],"conference":{"start_date":"2016-02-29","location":"San Francisco, CA, USA","end_date":"2016-03-04","name":"CT-RSA: Topics in Cryptology"},"doi":"10.1007/978-3-319-29485-8_24","article_processing_charge":"No","year":"2016","page":"413 - 428","quality_controlled":"1","citation":{"ista":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. 2016. Constrained PRFs for unbounded inputs. CT-RSA: Topics in Cryptology, LNCS, vol. 9610, 413–428.","ieee":"H. M. Abusalah, G. Fuchsbauer, and K. Z. Pietrzak, “Constrained PRFs for unbounded inputs,” presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA, 2016, vol. 9610, pp. 413–428.","chicago":"Abusalah, Hamza M, Georg Fuchsbauer, and Krzysztof Z Pietrzak. “Constrained PRFs for Unbounded Inputs,” 9610:413–28. Springer, 2016. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>.","ama":"Abusalah HM, Fuchsbauer G, Pietrzak KZ. Constrained PRFs for unbounded inputs. In: Vol 9610. Springer; 2016:413-428. doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>","apa":"Abusalah, H. M., Fuchsbauer, G., &#38; Pietrzak, K. Z. (2016). Constrained PRFs for unbounded inputs (Vol. 9610, pp. 413–428). Presented at the CT-RSA: Topics in Cryptology, San Francisco, CA, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">https://doi.org/10.1007/978-3-319-29485-8_24</a>","short":"H.M. Abusalah, G. Fuchsbauer, K.Z. Pietrzak, in:, Springer, 2016, pp. 413–428.","mla":"Abusalah, Hamza M., et al. <i>Constrained PRFs for Unbounded Inputs</i>. Vol. 9610, Springer, 2016, pp. 413–28, doi:<a href=\"https://doi.org/10.1007/978-3-319-29485-8_24\">10.1007/978-3-319-29485-8_24</a>."},"publication_status":"published","isi":1,"date_created":"2018-12-11T11:50:52Z","pubrep_id":"764","related_material":{"record":[{"status":"public","id":"83","relation":"dissertation_contains"}]}}]