[{"citation":{"chicago":"Ibsen-Jensen, Rasmus, Krishnendu Chatterjee, and Martin Nowak. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1511366112\">https://doi.org/10.1073/pnas.1511366112</a>.","short":"R. Ibsen-Jensen, K. Chatterjee, M. Nowak, PNAS 112 (2015) 15636–15641.","ieee":"R. Ibsen-Jensen, K. Chatterjee, and M. Nowak, “Computational complexity of ecological and evolutionary spatial dynamics,” <i>PNAS</i>, vol. 112, no. 51. National Academy of Sciences, pp. 15636–15641, 2015.","ista":"Ibsen-Jensen R, Chatterjee K, Nowak M. 2015. Computational complexity of ecological and evolutionary spatial dynamics. PNAS. 112(51), 15636–15641.","ama":"Ibsen-Jensen R, Chatterjee K, Nowak M. Computational complexity of ecological and evolutionary spatial dynamics. <i>PNAS</i>. 2015;112(51):15636-15641. doi:<a href=\"https://doi.org/10.1073/pnas.1511366112\">10.1073/pnas.1511366112</a>","mla":"Ibsen-Jensen, Rasmus, et al. “Computational Complexity of Ecological and Evolutionary Spatial Dynamics.” <i>PNAS</i>, vol. 112, no. 51, National Academy of Sciences, 2015, pp. 15636–41, doi:<a href=\"https://doi.org/10.1073/pnas.1511366112\">10.1073/pnas.1511366112</a>.","apa":"Ibsen-Jensen, R., Chatterjee, K., &#38; Nowak, M. (2015). Computational complexity of ecological and evolutionary spatial dynamics. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1511366112\">https://doi.org/10.1073/pnas.1511366112</a>"},"scopus_import":1,"abstract":[{"text":"There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant)will take over a resident population?We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).","lang":"eng"}],"type":"journal_article","_id":"1559","quality_controlled":"1","publication_status":"published","publisher":"National Academy of Sciences","author":[{"first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Computational complexity of ecological and evolutionary spatial dynamics","department":[{"_id":"KrCh"}],"publist_id":"5612","language":[{"iso":"eng"}],"volume":112,"pmid":1,"date_created":"2018-12-11T11:52:43Z","day":"22","status":"public","publication":"PNAS","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697423/"}],"doi":"10.1073/pnas.1511366112","oa_version":"Submitted Version","date_published":"2015-12-22T00:00:00Z","month":"12","intvolume":"       112","date_updated":"2021-01-12T06:51:36Z","oa":1,"issue":"51","page":"15636 - 15641","external_id":{"pmid":["26644569"]},"year":"2015"},{"publist_id":"5611","department":[{"_id":"MiSi"}],"page":"338 - 340","year":"2015","language":[{"iso":"eng"}],"publisher":"Nature Publishing Group","month":"03","intvolume":"        16","date_published":"2015-03-19T00:00:00Z","issue":"4","title":"The lymph node filter revealed","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-6625-3348","last_name":"Hons","id":"4167FE56-F248-11E8-B48F-1D18A9856A87","first_name":"Miroslav","full_name":"Hons, Miroslav"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"}],"date_updated":"2021-01-12T06:51:36Z","publication_status":"published","doi":"10.1038/ni.3126","publication":"Nature Immunology","oa_version":"None","type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"Stromal cells in the subcapsular sinus of the lymph node 'decide' which cells and molecules are allowed access to the deeper parenchyma. The glycoprotein PLVAP is a crucial component of this selector function."}],"citation":{"apa":"Hons, M., &#38; Sixt, M. K. (2015). The lymph node filter revealed. <i>Nature Immunology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ni.3126\">https://doi.org/10.1038/ni.3126</a>","mla":"Hons, Miroslav, and Michael K. Sixt. “The Lymph Node Filter Revealed.” <i>Nature Immunology</i>, vol. 16, no. 4, Nature Publishing Group, 2015, pp. 338–40, doi:<a href=\"https://doi.org/10.1038/ni.3126\">10.1038/ni.3126</a>.","short":"M. Hons, M.K. Sixt, Nature Immunology 16 (2015) 338–340.","ista":"Hons M, Sixt MK. 2015. The lymph node filter revealed. Nature Immunology. 16(4), 338–340.","ieee":"M. Hons and M. K. Sixt, “The lymph node filter revealed,” <i>Nature Immunology</i>, vol. 16, no. 4. Nature Publishing Group, pp. 338–340, 2015.","ama":"Hons M, Sixt MK. The lymph node filter revealed. <i>Nature Immunology</i>. 2015;16(4):338-340. doi:<a href=\"https://doi.org/10.1038/ni.3126\">10.1038/ni.3126</a>","chicago":"Hons, Miroslav, and Michael K Sixt. “The Lymph Node Filter Revealed.” <i>Nature Immunology</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ni.3126\">https://doi.org/10.1038/ni.3126</a>."},"volume":16,"day":"19","quality_controlled":"1","status":"public","date_created":"2018-12-11T11:52:43Z","_id":"1560"},{"publisher":"Wiley","month":"06","intvolume":"        45","date_published":"2015-06-01T00:00:00Z","issue":"6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors","author":[{"first_name":"Klaus","last_name":"Heger","full_name":"Heger, Klaus"},{"full_name":"Kober, Maike","first_name":"Maike","last_name":"Kober"},{"full_name":"Rieß, David","first_name":"David","last_name":"Rieß"},{"full_name":"Drees, Christoph","last_name":"Drees","first_name":"Christoph"},{"id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"full_name":"Bertossi, Arianna","last_name":"Bertossi","first_name":"Arianna"},{"full_name":"Roers, Axel","first_name":"Axel","last_name":"Roers"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"first_name":"Marc","last_name":"Schmidt Supprian","full_name":"Schmidt Supprian, Marc"}],"date_updated":"2021-01-12T06:51:36Z","department":[{"_id":"MiSi"}],"publist_id":"5610","page":"1614 - 1620","year":"2015","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Replication-deficient recombinant adenoviruses are potent vectors for the efficient transient expression of exogenous genes in resting immune cells. However, most leukocytes are refractory to efficient adenoviral transduction as they lack expression of the coxsackie/adenovirus receptor (CAR). To circumvent this obstacle, we generated the R26/CAG-CARΔ1StopF (where R26 is ROSA26 and CAG is CMV early enhancer/chicken β actin promoter) knock-in mouse line. This strain allows monitoring of in situ Cre recombinase activity through expression of CARΔ1. Simultaneously, CARΔ1 expression permits selective and highly efficient adenoviral transduction of immune cell populations, such as mast cells or T cells, directly ex vivo in bulk cultures without prior cell purification or activation. Furthermore, we show that CARΔ1 expression dramatically improves adenoviral infection of in vitro differentiated conventional and plasmacytoid dendritic cells (DCs), basophils, mast cells, as well as Hoxb8-immortalized hematopoietic progenitor cells. This novel dual function mouse strain will hence be a valuable tool to rapidly dissect the function of specific genes in leukocyte physiology."}],"scopus_import":1,"citation":{"mla":"Heger, Klaus, et al. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” <i>European Journal of Immunology</i>, vol. 45, no. 6, Wiley, 2015, pp. 1614–20, doi:<a href=\"https://doi.org/10.1002/eji.201545457\">10.1002/eji.201545457</a>.","apa":"Heger, K., Kober, M., Rieß, D., Drees, C., de Vries, I., Bertossi, A., … Schmidt Supprian, M. (2015). A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. <i>European Journal of Immunology</i>. Wiley. <a href=\"https://doi.org/10.1002/eji.201545457\">https://doi.org/10.1002/eji.201545457</a>","chicago":"Heger, Klaus, Maike Kober, David Rieß, Christoph Drees, Ingrid de Vries, Arianna Bertossi, Axel Roers, Michael K Sixt, and Marc Schmidt Supprian. “A Novel Cre Recombinase Reporter Mouse Strain Facilitates Selective and Efficient Infection of Primary Immune Cells with Adenoviral Vectors.” <i>European Journal of Immunology</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/eji.201545457\">https://doi.org/10.1002/eji.201545457</a>.","ieee":"K. Heger <i>et al.</i>, “A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors,” <i>European Journal of Immunology</i>, vol. 45, no. 6. Wiley, pp. 1614–1620, 2015.","ista":"Heger K, Kober M, Rieß D, Drees C, de Vries I, Bertossi A, Roers A, Sixt MK, Schmidt Supprian M. 2015. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. European Journal of Immunology. 45(6), 1614–1620.","short":"K. Heger, M. Kober, D. Rieß, C. Drees, I. de Vries, A. Bertossi, A. Roers, M.K. Sixt, M. Schmidt Supprian, European Journal of Immunology 45 (2015) 1614–1620.","ama":"Heger K, Kober M, Rieß D, et al. A novel Cre recombinase reporter mouse strain facilitates selective and efficient infection of primary immune cells with adenoviral vectors. <i>European Journal of Immunology</i>. 2015;45(6):1614-1620. doi:<a href=\"https://doi.org/10.1002/eji.201545457\">10.1002/eji.201545457</a>"},"volume":45,"status":"public","quality_controlled":"1","day":"01","date_created":"2018-12-11T11:52:44Z","_id":"1561","doi":"10.1002/eji.201545457","publication_status":"published","publication":"European Journal of Immunology","oa_version":"None"},{"status":"public","day":"01","date_created":"2018-12-11T11:52:44Z","volume":66,"ec_funded":1,"oa_version":"None","publication":"Journal of Experimental Botany","doi":"10.1093/jxb/erv177","issue":"16","date_updated":"2023-02-23T10:04:26Z","acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG- 20101109-PSDP to JF); the European Social Fund and the state budget of the Czech Republic [the project ‘Employment of Newly Graduated Doctors of Science for Scientific Excellence’ (CZ.1.07/2.3.00/30.0009) to TN]; the Czech Science Foundation (GACR) [project 13-40637S to JF].","date_published":"2015-08-01T00:00:00Z","intvolume":"        66","month":"08","year":"2015","page":"5055 - 5065","quality_controlled":"1","_id":"1562","scopus_import":1,"abstract":[{"text":"The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor.","lang":"eng"}],"type":"journal_article","citation":{"mla":"Grones, Peter, et al. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” <i>Journal of Experimental Botany</i>, vol. 66, no. 16, Oxford University Press, 2015, pp. 5055–65, doi:<a href=\"https://doi.org/10.1093/jxb/erv177\">10.1093/jxb/erv177</a>.","apa":"Grones, P., Chen, X., Simon, S., Kaufmann, W., De Rycke, R., Nodzyński, T., … Friml, J. (2015). Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erv177\">https://doi.org/10.1093/jxb/erv177</a>","chicago":"Grones, Peter, Xu Chen, Sibu Simon, Walter Kaufmann, Riet De Rycke, Tomasz Nodzyński, Eva Zažímalová, and Jiří Friml. “Auxin-Binding Pocket of ABP1 Is Crucial for Its Gain-of-Function Cellular and Developmental Roles.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/jxb/erv177\">https://doi.org/10.1093/jxb/erv177</a>.","short":"P. Grones, X. Chen, S. Simon, W. Kaufmann, R. De Rycke, T. Nodzyński, E. Zažímalová, J. Friml, Journal of Experimental Botany 66 (2015) 5055–5065.","ista":"Grones P, Chen X, Simon S, Kaufmann W, De Rycke R, Nodzyński T, Zažímalová E, Friml J. 2015. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. Journal of Experimental Botany. 66(16), 5055–5065.","ieee":"P. Grones <i>et al.</i>, “Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles,” <i>Journal of Experimental Botany</i>, vol. 66, no. 16. Oxford University Press, pp. 5055–5065, 2015.","ama":"Grones P, Chen X, Simon S, et al. Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles. <i>Journal of Experimental Botany</i>. 2015;66(16):5055-5065. doi:<a href=\"https://doi.org/10.1093/jxb/erv177\">10.1093/jxb/erv177</a>"},"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"title":"Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Grones, Peter","last_name":"Grones","id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Xu"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"first_name":"Tomasz","last_name":"Nodzyński","full_name":"Nodzyński, Tomasz"},{"full_name":"Zažímalová, Eva","first_name":"Eva","last_name":"Zažímalová"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"publisher":"Oxford University Press","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"publist_id":"5609"},{"citation":{"chicago":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” <i>Topological Methods in Nonlinear Analysis</i>. Juliusz Schauder Center for Nonlinear Studies, 2015. <a href=\"https://doi.org/10.12775/TMNA.2015.014\">https://doi.org/10.12775/TMNA.2015.014</a>.","ama":"Graff G, Pilarczyk P. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. <i>Topological Methods in Nonlinear Analysis</i>. 2015;45(1):273-286. doi:<a href=\"https://doi.org/10.12775/TMNA.2015.014\">10.12775/TMNA.2015.014</a>","ista":"Graff G, Pilarczyk P. 2015. An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. Topological Methods in Nonlinear Analysis. 45(1), 273–286.","short":"G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015) 273–286.","ieee":"G. Graff and P. Pilarczyk, “An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds,” <i>Topological Methods in Nonlinear Analysis</i>, vol. 45, no. 1. Juliusz Schauder Center for Nonlinear Studies, pp. 273–286, 2015.","mla":"Graff, Grzegorz, and Pawel Pilarczyk. “An Algorithmic Approach to Estimating the Minimal Number of Periodic Points for Smooth Self-Maps of Simply-Connected Manifolds.” <i>Topological Methods in Nonlinear Analysis</i>, vol. 45, no. 1, Juliusz Schauder Center for Nonlinear Studies, 2015, pp. 273–86, doi:<a href=\"https://doi.org/10.12775/TMNA.2015.014\">10.12775/TMNA.2015.014</a>.","apa":"Graff, G., &#38; Pilarczyk, P. (2015). An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds. <i>Topological Methods in Nonlinear Analysis</i>. Juliusz Schauder Center for Nonlinear Studies. <a href=\"https://doi.org/10.12775/TMNA.2015.014\">https://doi.org/10.12775/TMNA.2015.014</a>"},"volume":45,"type":"journal_article","abstract":[{"lang":"eng","text":"For a given self-map $f$ of $M$, a closed smooth connected and simply-connected manifold of dimension $m\\geq 4$, we provide an algorithm for estimating the values of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic points in the smooth homotopy class of $f$. Our results are based on the combinatorial scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm programmed in C++ is publicly available at {\\tt http://www.pawelpilarczyk.com/combtop/}."}],"scopus_import":1,"date_created":"2018-12-11T11:52:44Z","_id":"1563","status":"public","day":"01","quality_controlled":"1","doi":"10.12775/TMNA.2015.014","publication_status":"published","publication":"Topological Methods in Nonlinear Analysis","oa_version":"None","month":"03","intvolume":"        45","date_published":"2015-03-01T00:00:00Z","publisher":"Juliusz Schauder Center for Nonlinear Studies","date_updated":"2021-01-12T06:51:37Z","issue":"1","author":[{"full_name":"Graff, Grzegorz","last_name":"Graff","first_name":"Grzegorz"},{"full_name":"Pilarczyk, Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds","page":"273 - 286","publist_id":"5608","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"year":"2015"},{"issue":"11","oa":1,"date_updated":"2021-01-12T06:51:37Z","article_number":"145","intvolume":"         9","month":"11","date_published":"2015-11-30T00:00:00Z","year":"2015","status":"public","day":"30","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_created":"2018-12-11T11:52:45Z","volume":9,"oa_version":"Published Version","ec_funded":1,"doi":"10.3389/fncom.2015.00145","publication":"Frontiers in Computational Neuroscience","file":[{"creator":"system","file_size":187038,"content_type":"application/pdf","file_id":"4927","checksum":"cea73b6d3ef1579f32da10b82f4de4fd","access_level":"open_access","relation":"main_file","file_name":"IST-2016-479-v1+1_fncom-09-00145.pdf","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:12:09Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Matthieu","last_name":"Gilson","full_name":"Gilson, Matthieu"},{"last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina"},{"full_name":"Zenke, Friedemann","first_name":"Friedemann","last_name":"Zenke"}],"title":"Editorial: Emergent neural computation from the interaction of different forms of plasticity","publisher":"Frontiers Research Foundation","has_accepted_license":"1","pubrep_id":"479","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"publist_id":"5607","quality_controlled":"1","_id":"1564","type":"journal_article","file_date_updated":"2020-07-14T12:45:02Z","scopus_import":1,"citation":{"mla":"Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” <i>Frontiers in Computational Neuroscience</i>, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:<a href=\"https://doi.org/10.3389/fncom.2015.00145\">10.3389/fncom.2015.00145</a>.","apa":"Gilson, M., Savin, C., &#38; Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. <i>Frontiers in Computational Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncom.2015.00145\">https://doi.org/10.3389/fncom.2015.00145</a>","chicago":"Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” <i>Frontiers in Computational Neuroscience</i>. Frontiers Research Foundation, 2015. <a href=\"https://doi.org/10.3389/fncom.2015.00145\">https://doi.org/10.3389/fncom.2015.00145</a>.","ama":"Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. <i>Frontiers in Computational Neuroscience</i>. 2015;9(11). doi:<a href=\"https://doi.org/10.3389/fncom.2015.00145\">10.3389/fncom.2015.00145</a>","ista":"Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.","ieee":"M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” <i>Frontiers in Computational Neuroscience</i>, vol. 9, no. 11. Frontiers Research Foundation, 2015.","short":"M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015)."},"publication_status":"published","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"publication_status":"published","quality_controlled":"1","_id":"1565","abstract":[{"text":"Leptin is an adipokine produced by the adipose tissue regulating body weight through its appetite-suppressing effect. Besides being expressed in the hypothalamus and hippocampus, leptin receptors (ObRs) are also present in chromaffin cells of the adrenal medulla. In the present study, we report the effect of leptin on mouse chromaffin cell (MCC) functionality, focusing on cell excitability and catecholamine secretion. Acute application of leptin (1 nm) on spontaneously firing MCCs caused a slowly developing membrane hyperpolarization followed by complete blockade of action potential (AP) firing. This inhibitory effect at rest was abolished by the BK channel blocker paxilline (1 μm), suggesting the involvement of BK potassium channels. Single-channel recordings in 'perforated microvesicles' confirmed that leptin increased BK channel open probability without altering its unitary conductance. BK channel up-regulation was associated with the phosphoinositide 3-kinase (PI3K) signalling cascade because the PI3K specific inhibitor wortmannin (100 nm) fully prevented BK current increase. We also tested the effect of leptin on evoked AP firing and Ca2+-driven exocytosis. Although leptin preserves well-adapted AP trains of lower frequency, APs are broader and depolarization-evoked exocytosis is increased as a result of the larger size of the ready-releasable pool and higher frequency of vesicle release. The kinetics and quantal size of single secretory events remained unaltered. Leptin had no effect on firing and secretion in db-/db- mice lacking the ObR gene, confirming its specificity. In conclusion, leptin exhibits a dual action on MCC activity. It dampens AP firing at rest but preserves AP firing and increases catecholamine secretion during sustained stimulation, highlighting the importance of the adipo-adrenal axis in the leptin-mediated increase of sympathetic tone and catecholamine release.","lang":"eng"}],"scopus_import":1,"type":"journal_article","citation":{"mla":"Gavello, Daniela, et al. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” <i>Journal of Physiology</i>, vol. 593, no. 22, Wiley-Blackwell, 2015, pp. 4835–53, doi:<a href=\"https://doi.org/10.1113/JP271078\">10.1113/JP271078</a>.","apa":"Gavello, D., Vandael, D. H., Gosso, S., Carbone, E., &#38; Carabelli, V. (2015). Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. <i>Journal of Physiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1113/JP271078\">https://doi.org/10.1113/JP271078</a>","chicago":"Gavello, Daniela, David H Vandael, Sara Gosso, Emilio Carbone, and Valentina Carabelli. “Dual Action of Leptin on Rest-Firing and Stimulated Catecholamine Release via Phosphoinositide 3-Kinase-Riven BK Channel up-Regulation in Mouse Chromaffin Cells.” <i>Journal of Physiology</i>. Wiley-Blackwell, 2015. <a href=\"https://doi.org/10.1113/JP271078\">https://doi.org/10.1113/JP271078</a>.","ama":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. <i>Journal of Physiology</i>. 2015;593(22):4835-4853. doi:<a href=\"https://doi.org/10.1113/JP271078\">10.1113/JP271078</a>","ista":"Gavello D, Vandael DH, Gosso S, Carbone E, Carabelli V. 2015. Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells. Journal of Physiology. 593(22), 4835–4853.","short":"D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853.","ieee":"D. Gavello, D. H. Vandael, S. Gosso, E. Carbone, and V. Carabelli, “Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells,” <i>Journal of Physiology</i>, vol. 593, no. 22. Wiley-Blackwell, pp. 4835–4853, 2015."},"language":[{"iso":"eng"}],"publist_id":"5606","department":[{"_id":"PeJo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Daniela","last_name":"Gavello","full_name":"Gavello, Daniela"},{"orcid":"0000-0001-7577-1676","last_name":"Vandael","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H"},{"full_name":"Gosso, Sara","last_name":"Gosso","first_name":"Sara"},{"full_name":"Carbone, Emilio","last_name":"Carbone","first_name":"Emilio"},{"first_name":"Valentina","last_name":"Carabelli","full_name":"Carabelli, Valentina"}],"title":"Dual action of leptin on rest-firing and stimulated catecholamine release via phosphoinositide 3-kinase-riven BK channel up-regulation in mouse chromaffin cells","publisher":"Wiley-Blackwell","oa_version":"Submitted Version","publication":"Journal of Physiology","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/","open_access":"1"}],"doi":"10.1113/JP271078","status":"public","day":"15","date_created":"2018-12-11T11:52:45Z","volume":593,"pmid":1,"year":"2015","external_id":{"pmid":["26282459"]},"page":"4835 - 4853","oa":1,"issue":"22","date_updated":"2021-01-12T06:51:38Z","acknowledgement":"This work was supported by the Compagnia di San Paolo Foundation ‘Neuroscience Program’ to VC and ‘Progetto di Ateneo 2011-13’ to EC.\r\nWe thank Dr Claudio Franchino for cell preparation and for providing excellent technical support.","date_published":"2015-11-15T00:00:00Z","month":"11","intvolume":"       593"},{"language":[{"iso":"eng"}],"pubrep_id":"478","department":[{"_id":"CaHe"}],"publist_id":"5605","file":[{"date_created":"2018-12-12T10:16:21Z","date_updated":"2020-07-14T12:45:02Z","file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","access_level":"open_access","relation":"main_file","checksum":"8b67d729be663bfc9af04bfd94459655","content_type":"application/pdf","file_id":"5207","creator":"system","file_size":1412511}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An exploration of the universe of polyglutamine structures","author":[{"last_name":"Gómez Sicilia","first_name":"Àngel","full_name":"Gómez Sicilia, Àngel"},{"full_name":"Sikora, Mateusz K","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora"},{"first_name":"Marek","last_name":"Cieplak","full_name":"Cieplak, Marek"},{"full_name":"Carrión Vázquez, Mariano","last_name":"Carrión Vázquez","first_name":"Mariano"}],"has_accepted_license":"1","publisher":"Public Library of Science","publication_status":"published","_id":"1566","quality_controlled":"1","citation":{"ama":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of the universe of polyglutamine structures. <i>PLoS Computational Biology</i>. 2015;11(10). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">10.1371/journal.pcbi.1004541</a>","short":"À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational Biology 11 (2015).","ieee":"À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration of the universe of polyglutamine structures,” <i>PLoS Computational Biology</i>, vol. 11, no. 10. Public Library of Science, 2015.","ista":"Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration of the universe of polyglutamine structures. PLoS Computational Biology. 11(10), e1004541.","chicago":"Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” <i>PLoS Computational Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">https://doi.org/10.1371/journal.pcbi.1004541</a>.","apa":"Gómez Sicilia, À., Sikora, M. K., Cieplak, M., &#38; Carrión Vázquez, M. (2015). An exploration of the universe of polyglutamine structures. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">https://doi.org/10.1371/journal.pcbi.1004541</a>","mla":"Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine Structures.” <i>PLoS Computational Biology</i>, vol. 11, no. 10, e1004541, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1004541\">10.1371/journal.pcbi.1004541</a>."},"type":"journal_article","file_date_updated":"2020-07-14T12:45:02Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease."}],"year":"2015","date_updated":"2023-02-23T14:05:55Z","issue":"10","oa":1,"month":"10","intvolume":"        11","date_published":"2015-10-23T00:00:00Z","article_number":"e1004541","acknowledgement":"We acknowledge the support by the EU Joint Programme in Neurodegenerative Diseases (JPND AC14/00037) project. The project is supported through the following funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland, National Science Centre; and Spain, ISCIII. ","related_material":{"record":[{"status":"public","relation":"research_data","id":"9714"}]},"oa_version":"Published Version","doi":"10.1371/journal.pcbi.1004541","publication":"PLoS Computational Biology","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:52:45Z","status":"public","day":"23","volume":11},{"date_created":"2018-12-11T11:52:46Z","_id":"1567","day":"01","quality_controlled":"1","status":"public","citation":{"apa":"Edelsbrunner, H. (2015). Shape, homology, persistence, and stability. In <i>23rd International Symposium</i> (Vol. 9411). Los Angeles, CA, United States: Springer Nature.","mla":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” <i>23rd International Symposium</i>, vol. 9411, Springer Nature, 2015.","ama":"Edelsbrunner H. Shape, homology, persistence, and stability. In: <i>23rd International Symposium</i>. Vol 9411. Springer Nature; 2015.","ieee":"H. Edelsbrunner, “Shape, homology, persistence, and stability,” in <i>23rd International Symposium</i>, Los Angeles, CA, United States, 2015, vol. 9411.","ista":"Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411.","short":"H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015.","chicago":"Edelsbrunner, Herbert. “Shape, Homology, Persistence, and Stability.” In <i>23rd International Symposium</i>, Vol. 9411. Springer Nature, 2015."},"volume":9411,"type":"conference","abstract":[{"text":"My personal journey to the fascinating world of geometric forms started more than 30 years ago with the invention of alpha shapes in the plane. It took about 10 years before we generalized the concept to higher dimensions, we produced working software with a graphics interface for the three-dimensional case. At the same time, we added homology to the computations. Needless to say that this foreshadowed the inception of persistent homology, because it suggested the study of filtrations to capture the scale of a shape or data set. Importantly, this method has fast algorithms. The arguably most useful result on persistent homology is the stability of its diagrams under perturbations.","lang":"eng"}],"scopus_import":"1","oa_version":"None","publication_status":"published","publication":"23rd International Symposium","date_updated":"2022-01-28T08:25:00Z","author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"title":"Shape, homology, persistence, and stability","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"01","intvolume":"      9411","date_published":"2015-01-01T00:00:00Z","alternative_title":["LNCS"],"publisher":"Springer Nature","language":[{"iso":"eng"}],"year":"2015","article_processing_charge":"No","conference":{"start_date":"2015-09-24","end_date":"2015-09-26","name":"GD: Graph Drawing and Network Visualization","location":"Los Angeles, CA, United States"},"department":[{"_id":"HeEd"}],"publist_id":"5604"},{"title":"The classification of endoscopy images with persistent homology","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Dunaeva, Olga","last_name":"Dunaeva","first_name":"Olga"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"last_name":"Lukyanov","first_name":"Anton","full_name":"Lukyanov, Anton"},{"full_name":"Machin, Michael","first_name":"Michael","last_name":"Machin"},{"full_name":"Malkova, Daria","first_name":"Daria","last_name":"Malkova"}],"date_updated":"2023-02-21T16:57:29Z","acknowledgement":"This research is supported by the project No. 477 of P.G. Demidov Yaroslavl State University within State Assignment for Research.","publisher":"IEEE","month":"02","date_published":"2015-02-05T00:00:00Z","year":"2015","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publist_id":"5603","conference":{"name":"SYNASC: Symbolic and Numeric Algorithms for Scientific Computing","start_date":"2014-09-22","end_date":"2014-09-25","location":"Timisoara, Romania"},"page":"7034731","status":"public","day":"05","quality_controlled":"1","date_created":"2018-12-11T11:52:46Z","_id":"1568","type":"conference","abstract":[{"text":"Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI) magnifying endoscopy (ME) images of the stomach, we combine methods from image processing, computational topology, and machine learning to classify patterns into normal, tubular, vessel. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.","lang":"eng"}],"scopus_import":1,"citation":{"mla":"Dunaeva, Olga, et al. “The Classification of Endoscopy Images with Persistent Homology.” <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>, IEEE, 2015, p. 7034731, doi:<a href=\"https://doi.org/10.1109/SYNASC.2014.81\">10.1109/SYNASC.2014.81</a>.","apa":"Dunaeva, O., Edelsbrunner, H., Lukyanov, A., Machin, M., &#38; Malkova, D. (2015). The classification of endoscopy images with persistent homology. In <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i> (p. 7034731). Timisoara, Romania: IEEE. <a href=\"https://doi.org/10.1109/SYNASC.2014.81\">https://doi.org/10.1109/SYNASC.2014.81</a>","chicago":"Dunaeva, Olga, Herbert Edelsbrunner, Anton Lukyanov, Michael Machin, and Daria Malkova. “The Classification of Endoscopy Images with Persistent Homology.” In <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>, 7034731. IEEE, 2015. <a href=\"https://doi.org/10.1109/SYNASC.2014.81\">https://doi.org/10.1109/SYNASC.2014.81</a>.","short":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, D. Malkova, in:, Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing, IEEE, 2015, p. 7034731.","ieee":"O. Dunaeva, H. Edelsbrunner, A. Lukyanov, M. Machin, and D. Malkova, “The classification of endoscopy images with persistent homology,” in <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>, Timisoara, Romania, 2015, p. 7034731.","ista":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. 2015. The classification of endoscopy images with persistent homology. Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing. SYNASC: Symbolic and Numeric Algorithms for Scientific Computing, 7034731.","ama":"Dunaeva O, Edelsbrunner H, Lukyanov A, Machin M, Malkova D. The classification of endoscopy images with persistent homology. In: <i>Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing</i>. IEEE; 2015:7034731. doi:<a href=\"https://doi.org/10.1109/SYNASC.2014.81\">10.1109/SYNASC.2014.81</a>"},"oa_version":"None","related_material":{"record":[{"id":"1289","status":"public","relation":"later_version"}]},"publication_status":"published","doi":"10.1109/SYNASC.2014.81","publication":"Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing"},{"department":[{"_id":"JiFr"}],"publist_id":"5602","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","author":[{"full_name":"Doyle, Siamsa","last_name":"Doyle","first_name":"Siamsa"},{"first_name":"Ash","last_name":"Haegera","full_name":"Haegera, Ash"},{"full_name":"Vain, Thomas","first_name":"Thomas","last_name":"Vain"},{"full_name":"Rigala, Adeline","last_name":"Rigala","first_name":"Adeline"},{"first_name":"Corrado","last_name":"Viotti","full_name":"Viotti, Corrado"},{"last_name":"Łangowskaa","first_name":"Małgorzata","full_name":"Łangowskaa, Małgorzata"},{"first_name":"Qian","last_name":"Maa","full_name":"Maa, Qian"},{"full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"Natasha","last_name":"Raikhel","full_name":"Raikhel, Natasha"},{"last_name":"Hickse","first_name":"Glenn","full_name":"Hickse, Glenn"},{"full_name":"Robert, Stéphanie","first_name":"Stéphanie","last_name":"Robert"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","project":[{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","citation":{"ama":"Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. <i>PNAS</i>. 2015;112(7):E806-E815. doi:<a href=\"https://doi.org/10.1073/pnas.1424856112\">10.1073/pnas.1424856112</a>","ista":"Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815.","ieee":"S. Doyle <i>et al.</i>, “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” <i>PNAS</i>, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015.","short":"S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815.","chicago":"Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1424856112\">https://doi.org/10.1073/pnas.1424856112</a>.","apa":"Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1424856112\">https://doi.org/10.1073/pnas.1424856112</a>","mla":"Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” <i>PNAS</i>, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:<a href=\"https://doi.org/10.1073/pnas.1424856112\">10.1073/pnas.1424856112</a>."},"abstract":[{"text":"Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.","lang":"eng"}],"scopus_import":1,"type":"journal_article","_id":"1569","quality_controlled":"1","page":"E806 - E815","year":"2015","date_published":"2015-02-17T00:00:00Z","month":"02","intvolume":"       112","acknowledgement":"This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ","date_updated":"2021-01-12T06:51:39Z","oa":1,"issue":"7","publication":"PNAS","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/"}],"doi":"10.1073/pnas.1424856112","oa_version":"Published Version","ec_funded":1,"volume":112,"date_created":"2018-12-11T11:52:46Z","status":"public","day":"17"},{"ec_funded":1,"oa_version":"Submitted Version","publication":"PNAS","doi":"10.1073/pnas.1508400112","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/","open_access":"1"}],"date_created":"2018-12-11T11:52:47Z","day":"10","status":"public","volume":112,"pmid":1,"year":"2015","page":"E6224 - E6232","external_id":{"pmid":["26504200"]},"date_updated":"2021-01-12T06:51:40Z","oa":1,"issue":"45","date_published":"2015-11-10T00:00:00Z","month":"11","intvolume":"       112","project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"publication_status":"published","_id":"1570","quality_controlled":"1","citation":{"ama":"Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. <i>PNAS</i>. 2015;112(45):E6224-E6232. doi:<a href=\"https://doi.org/10.1073/pnas.1508400112\">10.1073/pnas.1508400112</a>","ieee":"R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” <i>PNAS</i>, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015.","short":"R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.","ista":"Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.","chicago":"Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1508400112\">https://doi.org/10.1073/pnas.1508400112</a>.","apa":"Der, R., &#38; Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1508400112\">https://doi.org/10.1073/pnas.1508400112</a>","mla":"Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” <i>PNAS</i>, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:<a href=\"https://doi.org/10.1073/pnas.1508400112\">10.1073/pnas.1508400112</a>."},"abstract":[{"text":"Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.","lang":"eng"}],"scopus_import":1,"type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publist_id":"5601","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"},{"last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","full_name":"Martius, Georg S"}],"title":"Novel plasticity rule can explain the development of sensorimotor intelligence","publisher":"National Academy of Sciences"},{"page":"14906 - 14911","publist_id":"5600","department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"year":"2015","intvolume":"       112","month":"12","date_published":"2015-12-01T00:00:00Z","publisher":"National Academy of Sciences","acknowledgement":"This work is part of the research program of the Foundation for Fundamental Research on Matter, which is part of the Netherlands Organization for Scientific Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences (ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão, J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for discussions and suggestions on the Markov computation. Furthermore, we thank F. J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial version of the manuscript.","date_updated":"2021-01-12T06:51:40Z","issue":"48","title":"Breaking evolutionary constraint with a tradeoff ratchet","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"De Vos","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","first_name":"Marjon","full_name":"De Vos, Marjon"},{"first_name":"Alexandre","last_name":"Dawid","full_name":"Dawid, Alexandre"},{"full_name":"Šunderlíková, Vanda","first_name":"Vanda","last_name":"Šunderlíková"},{"first_name":"Sander","last_name":"Tans","full_name":"Tans, Sander"}],"doi":"10.1073/pnas.1510282112","publication_status":"published","publication":"PNAS","oa_version":"None","citation":{"mla":"de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” <i>PNAS</i>, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11, doi:<a href=\"https://doi.org/10.1073/pnas.1510282112\">10.1073/pnas.1510282112</a>.","apa":"de Vos, M., Dawid, A., Šunderlíková, V., &#38; Tans, S. (2015). Breaking evolutionary constraint with a tradeoff ratchet. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1510282112\">https://doi.org/10.1073/pnas.1510282112</a>","chicago":"Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1510282112\">https://doi.org/10.1073/pnas.1510282112</a>.","ieee":"M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary constraint with a tradeoff ratchet,” <i>PNAS</i>, vol. 112, no. 48. National Academy of Sciences, pp. 14906–14911, 2015.","short":"M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.","ista":"de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 112(48), 14906–14911.","ama":"de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint with a tradeoff ratchet. <i>PNAS</i>. 2015;112(48):14906-14911. doi:<a href=\"https://doi.org/10.1073/pnas.1510282112\">10.1073/pnas.1510282112</a>"},"volume":112,"type":"journal_article","abstract":[{"lang":"eng","text":"Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance."}],"scopus_import":1,"date_created":"2018-12-11T11:52:47Z","_id":"1571","quality_controlled":"1","status":"public","day":"01"},{"month":"06","intvolume":"       339","date_published":"2015-06-23T00:00:00Z","publisher":"Springer","date_updated":"2021-01-12T06:51:41Z","issue":"1","title":"Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Correggi, Michele","first_name":"Michele","last_name":"Correggi"},{"last_name":"Giuliani","first_name":"Alessandro","full_name":"Giuliani, Alessandro"},{"full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"oa":1,"page":"279 - 307","department":[{"_id":"RoSe"}],"publist_id":"5599","language":[{"iso":"eng"}],"year":"2015","citation":{"mla":"Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” <i>Communications in Mathematical Physics</i>, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:<a href=\"https://doi.org/10.1007/s00220-015-2402-0\">10.1007/s00220-015-2402-0</a>.","apa":"Correggi, M., Giuliani, A., &#38; Seiringer, R. (2015). Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-015-2402-0\">https://doi.org/10.1007/s00220-015-2402-0</a>","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” <i>Communications in Mathematical Physics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00220-015-2402-0\">https://doi.org/10.1007/s00220-015-2402-0</a>.","ama":"Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. <i>Communications in Mathematical Physics</i>. 2015;339(1):279-307. doi:<a href=\"https://doi.org/10.1007/s00220-015-2402-0\">10.1007/s00220-015-2402-0</a>","ista":"Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 339(1), 279–307.","short":"M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics 339 (2015) 279–307.","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet,” <i>Communications in Mathematical Physics</i>, vol. 339, no. 1. Springer, pp. 279–307, 2015."},"volume":339,"type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.\r\n"}],"date_created":"2018-12-11T11:52:47Z","_id":"1572","quality_controlled":"1","status":"public","day":"23","doi":"10.1007/s00220-015-2402-0","main_file_link":[{"url":"http://arxiv.org/abs/1312.7873","open_access":"1"}],"publication_status":"published","publication":"Communications in Mathematical Physics","oa_version":"Preprint"},{"publisher":"Wiley","title":"Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chen, Thomas","last_name":"Chen","first_name":"Thomas"},{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"full_name":"Pavlović, Nataša","last_name":"Pavlović","first_name":"Nataša"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert"}],"publist_id":"5598","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"citation":{"mla":"Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” <i>Communications on Pure and Applied Mathematics</i>, vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:<a href=\"https://doi.org/10.1002/cpa.21552\">10.1002/cpa.21552</a>.","apa":"Chen, T., Hainzl, C., Pavlović, N., &#38; Seiringer, R. (2015). Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. <i>Communications on Pure and Applied Mathematics</i>. Wiley. <a href=\"https://doi.org/10.1002/cpa.21552\">https://doi.org/10.1002/cpa.21552</a>","chicago":"Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” <i>Communications on Pure and Applied Mathematics</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/cpa.21552\">https://doi.org/10.1002/cpa.21552</a>.","ama":"Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. <i>Communications on Pure and Applied Mathematics</i>. 2015;68(10):1845-1884. doi:<a href=\"https://doi.org/10.1002/cpa.21552\">10.1002/cpa.21552</a>","short":"T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884.","ieee":"T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti,” <i>Communications on Pure and Applied Mathematics</i>, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015.","ista":"Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 68(10), 1845–1884."},"type":"journal_article","abstract":[{"lang":"eng","text":"We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau."}],"scopus_import":1,"_id":"1573","quality_controlled":"1","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","intvolume":"        68","month":"10","date_published":"2015-10-01T00:00:00Z","date_updated":"2021-01-12T06:51:41Z","issue":"10","oa":1,"page":"1845 - 1884","year":"2015","volume":68,"date_created":"2018-12-11T11:52:48Z","status":"public","day":"01","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3168"}],"doi":"10.1002/cpa.21552","publication":"Communications on Pure and Applied Mathematics","oa_version":"Preprint"},{"file":[{"content_type":"application/pdf","file_id":"5085","file_size":1701815,"creator":"system","relation":"main_file","checksum":"8ff5c108899b548806e1cb7a302fe76d","access_level":"open_access","file_name":"IST-2016-477-v1+1_ncomms9821.pdf","date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:14:32Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chen","first_name":"Qian","full_name":"Chen, Qian"},{"full_name":"Liu, Yang","last_name":"Liu","first_name":"Yang"},{"last_name":"Maere","first_name":"Steven","full_name":"Maere, Steven"},{"full_name":"Lee, Eunkyoung","last_name":"Lee","first_name":"Eunkyoung"},{"full_name":"Van Isterdael, Gert","first_name":"Gert","last_name":"Van Isterdael"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"full_name":"Xuan, Wei","last_name":"Xuan","first_name":"Wei"},{"last_name":"Lucas","first_name":"Jessica","full_name":"Lucas, Jessica"},{"last_name":"Vassileva","first_name":"Valya","full_name":"Vassileva, Valya"},{"first_name":"Saeko","last_name":"Kitakura","full_name":"Kitakura, Saeko"},{"orcid":"0000-0001-5227-5741","last_name":"Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Marhavy, Peter"},{"id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T","last_name":"Wabnik","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T"},{"first_name":"Niko","last_name":"Geldner","full_name":"Geldner, Niko"},{"full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","last_name":"Benková"},{"full_name":"Le, Jie","first_name":"Jie","last_name":"Le"},{"full_name":"Fukaki, Hidehiro","first_name":"Hidehiro","last_name":"Fukaki"},{"first_name":"Erich","last_name":"Grotewold","full_name":"Grotewold, Erich"},{"last_name":"Li","first_name":"Chuanyou","full_name":"Li, Chuanyou"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"},{"full_name":"Sack, Fred","first_name":"Fred","last_name":"Sack"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"}],"title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","publisher":"Nature Publishing Group","has_accepted_license":"1","pubrep_id":"477","language":[{"iso":"eng"}],"publist_id":"5597","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"quality_controlled":"1","_id":"1574","type":"journal_article","file_date_updated":"2020-07-14T12:45:02Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level."}],"citation":{"chicago":"Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms9821\">https://doi.org/10.1038/ncomms9821</a>.","ama":"Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms9821\">10.1038/ncomms9821</a>","ieee":"Q. Chen <i>et al.</i>, “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","ista":"Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821.","short":"Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015).","mla":"Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” <i>Nature Communications</i>, vol. 6, 8821, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms9821\">10.1038/ncomms9821</a>.","apa":"Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms9821\">https://doi.org/10.1038/ncomms9821</a>"},"publication_status":"published","oa":1,"date_updated":"2021-01-12T06:51:42Z","article_number":"8821","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","intvolume":"         6","month":"11","date_published":"2015-11-18T00:00:00Z","year":"2015","day":"18","status":"public","date_created":"2018-12-11T11:52:48Z","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["580"],"volume":6,"oa_version":"Published Version","doi":"10.1038/ncomms9821","publication":"Nature Communications"},{"volume":6,"status":"public","day":"25","ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:52:48Z","doi":"10.1038/ncomms8526","publication":"Nature Communications","oa_version":"Published Version","article_number":"7526","acknowledgement":"M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie).","month":"06","intvolume":"         6","date_published":"2015-06-25T00:00:00Z","oa":1,"date_updated":"2021-01-12T06:51:42Z","year":"2015","type":"journal_article","file_date_updated":"2020-07-14T12:45:02Z","abstract":[{"lang":"eng","text":"The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space."}],"scopus_import":1,"citation":{"chicago":"Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms8526\">https://doi.org/10.1038/ncomms8526</a>.","ama":"Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms8526\">10.1038/ncomms8526</a>","ieee":"M. Chabaud <i>et al.</i>, “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","ista":"Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526.","short":"M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015).","mla":"Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” <i>Nature Communications</i>, vol. 6, 7526, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms8526\">10.1038/ncomms8526</a>.","apa":"Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms8526\">https://doi.org/10.1038/ncomms8526</a>"},"quality_controlled":"1","_id":"1575","publication_status":"published","publisher":"Nature Publishing Group","has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-12T10:11:58Z","file_name":"IST-2016-476-v1+1_ncomms8526.pdf","access_level":"open_access","checksum":"bae12e86be2adb28253f890b8bba8315","relation":"main_file","content_type":"application/pdf","file_id":"4915","creator":"system","file_size":4530215}],"title":"Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells","author":[{"full_name":"Chabaud, Mélanie","first_name":"Mélanie","last_name":"Chabaud"},{"first_name":"Mélina","last_name":"Heuzé","full_name":"Heuzé, Mélina"},{"last_name":"Bretou","first_name":"Marine","full_name":"Bretou, Marine"},{"full_name":"Vargas, Pablo","last_name":"Vargas","first_name":"Pablo"},{"first_name":"Paolo","last_name":"Maiuri","full_name":"Maiuri, Paolo"},{"full_name":"Solanes, Paola","last_name":"Solanes","first_name":"Paola"},{"full_name":"Maurin, Mathieu","last_name":"Maurin","first_name":"Mathieu"},{"full_name":"Terriac, Emmanuel","last_name":"Terriac","first_name":"Emmanuel"},{"first_name":"Maël","last_name":"Le Berre","full_name":"Le Berre, Maël"},{"last_name":"Lankar","first_name":"Danielle","full_name":"Lankar, Danielle"},{"last_name":"Piolot","first_name":"Tristan","full_name":"Piolot, Tristan"},{"full_name":"Adelstein, Robert","last_name":"Adelstein","first_name":"Robert"},{"last_name":"Zhang","first_name":"Yingfan","full_name":"Zhang, Yingfan"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K"},{"last_name":"Jacobelli","first_name":"Jordan","full_name":"Jacobelli, Jordan"},{"last_name":"Bénichou","first_name":"Olivier","full_name":"Bénichou, Olivier"},{"last_name":"Voituriez","first_name":"Raphaël","full_name":"Voituriez, Raphaël"},{"first_name":"Matthieu","last_name":"Piel","full_name":"Piel, Matthieu"},{"full_name":"Lennon Duménil, Ana","first_name":"Ana","last_name":"Lennon Duménil"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5596","department":[{"_id":"MiSi"}],"pubrep_id":"476","language":[{"iso":"eng"}]},{"year":"2015","date_published":"2015-12-08T00:00:00Z","month":"12","intvolume":"       115","article_number":"248101","date_updated":"2023-09-07T12:55:21Z","oa":1,"issue":"24","publication":"Physical Review Letters","doi":"10.1103/PhysRevLett.115.248101","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1504.05716"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6473"}]},"oa_version":"Preprint","ec_funded":1,"volume":115,"date_created":"2018-12-11T11:52:49Z","day":"08","status":"public","department":[{"_id":"GaTk"}],"publist_id":"5595","language":[{"iso":"eng"}],"publisher":"American Physical Society","title":"Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation","author":[{"full_name":"Cepeda Humerez, Sarah A","last_name":"Cepeda Humerez","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A"},{"last_name":"Rieckh","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"publication_status":"published","citation":{"apa":"Cepeda Humerez, S. A., Rieckh, G., &#38; Tkačik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.115.248101\">https://doi.org/10.1103/PhysRevLett.115.248101</a>","mla":"Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” <i>Physical Review Letters</i>, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.115.248101\">10.1103/PhysRevLett.115.248101</a>.","ista":"Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101.","ieee":"S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” <i>Physical Review Letters</i>, vol. 115, no. 24. American Physical Society, 2015.","short":"S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015).","ama":"Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. <i>Physical Review Letters</i>. 2015;115(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.115.248101\">10.1103/PhysRevLett.115.248101</a>","chicago":"Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” <i>Physical Review Letters</i>. American Physical Society, 2015. <a href=\"https://doi.org/10.1103/PhysRevLett.115.248101\">https://doi.org/10.1103/PhysRevLett.115.248101</a>."},"scopus_import":1,"abstract":[{"lang":"eng","text":"Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect regulatory crosstalk: the possibility that noncognate TFs could initiate transcription, with potentially disastrous effects for the cell. Here, we estimate the importance of crosstalk, suggest that its avoidance strongly constrains equilibrium models of TF binding, and propose an alternative nonequilibrium scheme that implements kinetic proofreading to suppress erroneous initiation. This proposal is consistent with the observed covalent modifications of the transcriptional apparatus and predicts increased noise in gene expression as a trade-off for improved specificity. Using information theory, we quantify this trade-off to find when optimal proofreading architectures are favored over their equilibrium counterparts. Such architectures exhibit significant super-Poisson noise at low expression in steady state."}],"type":"journal_article","_id":"1576","quality_controlled":"1"},{"pmid":1,"volume":112,"status":"public","day":"06","date_created":"2018-12-11T11:52:49Z","doi":"10.1073/pnas.1516543112","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/","open_access":"1"}],"publication":"PNAS","oa_version":"Published Version","acknowledgement":"This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript.","month":"10","intvolume":"       112","date_published":"2015-10-06T00:00:00Z","issue":"40","oa":1,"date_updated":"2021-01-12T06:51:43Z","page":"12450 - 12455","external_id":{"pmid":["26385968"]},"year":"2015","type":"journal_article","abstract":[{"lang":"eng","text":"Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes."}],"scopus_import":1,"citation":{"chicago":"Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1516543112\">https://doi.org/10.1073/pnas.1516543112</a>.","short":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455.","ieee":"A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” <i>PNAS</i>, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015.","ista":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455.","ama":"Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. <i>PNAS</i>. 2015;112(40):12450-12455. doi:<a href=\"https://doi.org/10.1073/pnas.1516543112\">10.1073/pnas.1516543112</a>","mla":"Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” <i>PNAS</i>, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:<a href=\"https://doi.org/10.1073/pnas.1516543112\">10.1073/pnas.1516543112</a>.","apa":"Carvalho, A., Vicoso, B., Russo, C., Swenor, B., &#38; Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1516543112\">https://doi.org/10.1073/pnas.1516543112</a>"},"quality_controlled":"1","_id":"1577","publication_status":"published","publisher":"National Academy of Sciences","author":[{"first_name":"Antonio","last_name":"Carvalho","full_name":"Carvalho, Antonio"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"},{"last_name":"Russo","first_name":"Claudia","full_name":"Russo, Claudia"},{"first_name":"Bonnielin","last_name":"Swenor","full_name":"Swenor, Bonnielin"},{"full_name":"Clark, Andrew","first_name":"Andrew","last_name":"Clark"}],"title":"Birth of a new gene on the Y chromosome of Drosophila melanogaster","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"}],"publist_id":"5594","article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}]},{"_id":"1578","date_created":"2018-12-11T11:52:49Z","status":"public","day":"01","quality_controlled":"1","citation":{"apa":"Cao, T., Edelsbrunner, H., &#38; Tan, T. (2015). Triangulations from topologically correct digital Voronoi diagrams. <i>Computational Geometry</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2015.04.001\">https://doi.org/10.1016/j.comgeo.2015.04.001</a>","mla":"Cao, Thanhtung, et al. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” <i>Computational Geometry</i>, vol. 48, no. 7, Elsevier, 2015, pp. 507–19, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2015.04.001\">10.1016/j.comgeo.2015.04.001</a>.","ama":"Cao T, Edelsbrunner H, Tan T. Triangulations from topologically correct digital Voronoi diagrams. <i>Computational Geometry</i>. 2015;48(7):507-519. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2015.04.001\">10.1016/j.comgeo.2015.04.001</a>","short":"T. Cao, H. Edelsbrunner, T. Tan, Computational Geometry 48 (2015) 507–519.","ista":"Cao T, Edelsbrunner H, Tan T. 2015. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 48(7), 507–519.","ieee":"T. Cao, H. Edelsbrunner, and T. Tan, “Triangulations from topologically correct digital Voronoi diagrams,” <i>Computational Geometry</i>, vol. 48, no. 7. Elsevier, pp. 507–519, 2015.","chicago":"Cao, Thanhtung, Herbert Edelsbrunner, and Tiowseng Tan. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” <i>Computational Geometry</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.comgeo.2015.04.001\">https://doi.org/10.1016/j.comgeo.2015.04.001</a>."},"volume":48,"type":"journal_article","abstract":[{"text":"We prove that the dual of the digital Voronoi diagram constructed by flooding the plane from the data points gives a geometrically and topologically correct dual triangulation. This provides the proof of correctness for recently developed GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional Delaunay triangulations.","lang":"eng"}],"scopus_import":1,"oa_version":"None","doi":"10.1016/j.comgeo.2015.04.001","publication_status":"published","publication":"Computational Geometry","date_updated":"2021-01-12T06:51:43Z","issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Triangulations from topologically correct digital Voronoi diagrams","author":[{"last_name":"Cao","first_name":"Thanhtung","full_name":"Cao, Thanhtung"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"first_name":"Tiowseng","last_name":"Tan","full_name":"Tan, Tiowseng"}],"intvolume":"        48","month":"08","date_published":"2015-08-01T00:00:00Z","acknowledgement":"The research of the second author is partially supported by NSF under grant DBI-0820624 and by DARPA under grants HR011-05-1-0057 and HR0011-09-006\r\n","publisher":"Elsevier","language":[{"iso":"eng"}],"year":"2015","page":"507 - 519","publist_id":"5593","department":[{"_id":"HeEd"}]}]