[{"status":"public","intvolume":"        45","language":[{"iso":"eng"}],"citation":{"short":"G. Graff, P. Pilarczyk, Topological Methods in Nonlinear Analysis 45 (2015) 273–286.","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>.","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.","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>","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>.","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.","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>"},"issue":"1","publication_status":"published","doi":"10.12775/TMNA.2015.014","date_published":"2015-03-01T00:00:00Z","quality_controlled":"1","publisher":"Juliusz Schauder Center for Nonlinear Studies","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"year":"2015","publication":"Topological Methods in Nonlinear Analysis","_id":"1563","scopus_import":1,"author":[{"full_name":"Graff, Grzegorz","last_name":"Graff","first_name":"Grzegorz"},{"last_name":"Pilarczyk","first_name":"Pawel","full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"}],"page":"273 - 286","date_updated":"2021-01-12T06:51:37Z","abstract":[{"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/}.","lang":"eng"}],"day":"01","type":"journal_article","oa_version":"None","month":"03","title":"An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds","volume":45,"date_created":"2018-12-11T11:52:44Z","publist_id":"5608"},{"status":"public","intvolume":"         9","citation":{"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>","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>.","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.","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>","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.","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>.","short":"M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015)."},"oa":1,"publication_status":"published","has_accepted_license":"1","ddc":["570"],"date_published":"2015-11-30T00:00:00Z","year":"2015","_id":"1564","oa_version":"Published Version","month":"11","type":"journal_article","date_updated":"2021-01-12T06:51:37Z","volume":9,"date_created":"2018-12-11T11:52:45Z","file_date_updated":"2020-07-14T12:45:02Z","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"issue":"11","language":[{"iso":"eng"}],"pubrep_id":"479","doi":"10.3389/fncom.2015.00145","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Frontiers Research Foundation","department":[{"_id":"GaTk"}],"publication":"Frontiers in Computational Neuroscience","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":1,"ec_funded":1,"author":[{"full_name":"Gilson, Matthieu","first_name":"Matthieu","last_name":"Gilson"},{"last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","full_name":"Savin, Cristina"},{"full_name":"Zenke, Friedemann","last_name":"Zenke","first_name":"Friedemann"}],"file":[{"file_size":187038,"relation":"main_file","content_type":"application/pdf","creator":"system","file_name":"IST-2016-479-v1+1_fncom-09-00145.pdf","date_created":"2018-12-12T10:12:09Z","access_level":"open_access","file_id":"4927","date_updated":"2020-07-14T12:45:02Z","checksum":"cea73b6d3ef1579f32da10b82f4de4fd"}],"day":"30","article_number":"145","title":"Editorial: Emergent neural computation from the interaction of different forms of plasticity","publist_id":"5607"},{"publist_id":"5606","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","day":"15","author":[{"full_name":"Gavello, Daniela","last_name":"Gavello","first_name":"Daniela"},{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","first_name":"David H"},{"full_name":"Gosso, Sara","first_name":"Sara","last_name":"Gosso"},{"full_name":"Carbone, Emilio","last_name":"Carbone","first_name":"Emilio"},{"last_name":"Carabelli","first_name":"Valentina","full_name":"Carabelli, Valentina"}],"scopus_import":1,"publication":"Journal of Physiology","department":[{"_id":"PeJo"}],"pmid":1,"publisher":"Wiley-Blackwell","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1113/JP271078","issue":"22","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:52:45Z","volume":593,"oa_version":"Submitted Version","type":"journal_article","month":"11","date_updated":"2021-01-12T06:51:38Z","abstract":[{"lang":"eng","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."}],"page":"4835 - 4853","_id":"1565","year":"2015","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.","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650409/","open_access":"1"}],"date_published":"2015-11-15T00:00:00Z","publication_status":"published","oa":1,"citation":{"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.","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>.","short":"D. Gavello, D.H. Vandael, S. Gosso, E. Carbone, V. Carabelli, Journal of Physiology 593 (2015) 4835–4853.","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>","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>.","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.","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>"},"intvolume":"       593","status":"public","external_id":{"pmid":["26282459"]}},{"language":[{"iso":"eng"}],"issue":"10","doi":"10.1371/journal.pcbi.1004541","quality_controlled":"1","pubrep_id":"478","publication":"PLoS Computational Biology","scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","department":[{"_id":"CaHe"}],"title":"An exploration of the universe of polyglutamine structures","article_number":"e1004541","publist_id":"5605","author":[{"full_name":"Gómez Sicilia, Àngel","first_name":"Àngel","last_name":"Gómez Sicilia"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","full_name":"Sikora, Mateusz K","first_name":"Mateusz K","last_name":"Sikora"},{"first_name":"Marek","last_name":"Cieplak","full_name":"Cieplak, Marek"},{"last_name":"Carrión Vázquez","first_name":"Mariano","full_name":"Carrión Vázquez, Mariano"}],"file":[{"checksum":"8b67d729be663bfc9af04bfd94459655","file_id":"5207","date_updated":"2020-07-14T12:45:02Z","access_level":"open_access","date_created":"2018-12-12T10:16:21Z","file_name":"IST-2016-478-v1+1_journal.pcbi.1004541.pdf","creator":"system","file_size":1412511,"relation":"main_file","content_type":"application/pdf"}],"day":"23","intvolume":"        11","related_material":{"record":[{"relation":"research_data","id":"9714","status":"public"}]},"citation":{"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.","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>.","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.","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>.","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>","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>"},"status":"public","ddc":["570"],"date_published":"2015-10-23T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1","_id":"1566","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. ","year":"2015","volume":11,"file_date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-11T11:52:45Z","date_updated":"2023-02-23T14:05:55Z","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."}],"type":"journal_article","month":"10","oa_version":"Published Version"},{"volume":9411,"title":"Shape, homology, persistence, and stability","date_created":"2018-12-11T11:52:46Z","publist_id":"5604","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"}],"day":"01","date_updated":"2022-01-28T08:25:00Z","abstract":[{"lang":"eng","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."}],"month":"01","type":"conference","oa_version":"None","publication":"23rd International Symposium","_id":"1567","scopus_import":"1","article_processing_charge":"No","publisher":"Springer Nature","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"HeEd"}],"year":"2015","date_published":"2015-01-01T00:00:00Z","quality_controlled":"1","publication_status":"published","intvolume":"      9411","conference":{"location":"Los Angeles, CA, United States","name":"GD: Graph Drawing and Network Visualization","start_date":"2015-09-24","end_date":"2015-09-26"},"language":[{"iso":"eng"}],"citation":{"chicago":"Edelsbrunner, Herbert. “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.","short":"H. Edelsbrunner, in:, 23rd International Symposium, Springer Nature, 2015.","ama":"Edelsbrunner H. Shape, homology, persistence, and stability. In: <i>23rd International Symposium</i>. Vol 9411. Springer Nature; 2015.","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.","ista":"Edelsbrunner H. 2015. Shape, homology, persistence, and stability. 23rd International Symposium. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411."},"alternative_title":["LNCS"],"status":"public"},{"status":"public","related_material":{"record":[{"status":"public","id":"1289","relation":"later_version"}]},"conference":{"name":"SYNASC: Symbolic and Numeric Algorithms for Scientific Computing","location":"Timisoara, Romania","start_date":"2014-09-22","end_date":"2014-09-25"},"language":[{"iso":"eng"}],"citation":{"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.","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.","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>","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>.","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.","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>"},"publication_status":"published","doi":"10.1109/SYNASC.2014.81","date_published":"2015-02-05T00:00:00Z","quality_controlled":"1","publisher":"IEEE","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This research is supported by the project No. 477 of P.G. Demidov Yaroslavl State University within State Assignment for Research.","department":[{"_id":"HeEd"}],"year":"2015","publication":"Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing","_id":"1568","scopus_import":1,"page":"7034731","author":[{"last_name":"Dunaeva","first_name":"Olga","full_name":"Dunaeva, Olga"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Lukyanov, Anton","last_name":"Lukyanov","first_name":"Anton"},{"full_name":"Machin, Michael","first_name":"Michael","last_name":"Machin"},{"full_name":"Malkova, Daria","last_name":"Malkova","first_name":"Daria"}],"date_updated":"2023-02-21T16:57:29Z","day":"05","abstract":[{"lang":"eng","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."}],"month":"02","oa_version":"None","type":"conference","title":"The classification of endoscopy images with persistent homology","date_created":"2018-12-11T11:52:46Z","publist_id":"5603"},{"doi":"10.1073/pnas.1424856112","quality_controlled":"1","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"language":[{"iso":"eng"}],"issue":"7","author":[{"last_name":"Doyle","first_name":"Siamsa","full_name":"Doyle, Siamsa"},{"full_name":"Haegera, Ash","first_name":"Ash","last_name":"Haegera"},{"full_name":"Vain, Thomas","last_name":"Vain","first_name":"Thomas"},{"first_name":"Adeline","last_name":"Rigala","full_name":"Rigala, Adeline"},{"full_name":"Viotti, Corrado","first_name":"Corrado","last_name":"Viotti"},{"first_name":"Małgorzata","last_name":"Łangowskaa","full_name":"Łangowskaa, Małgorzata"},{"last_name":"Maa","first_name":"Qian","full_name":"Maa, Qian"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Raikhel, Natasha","last_name":"Raikhel","first_name":"Natasha"},{"full_name":"Hickse, Glenn","last_name":"Hickse","first_name":"Glenn"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"}],"day":"17","title":"An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana","publist_id":"5602","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"publication":"PNAS","ec_funded":1,"scopus_import":1,"oa":1,"publication_status":"published","date_published":"2015-02-17T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/"}],"status":"public","intvolume":"       112","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>","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>.","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.","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>.","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."},"page":"E806 - E815","date_updated":"2021-01-12T06:51:39Z","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","month":"02","type":"journal_article","volume":112,"date_created":"2018-12-11T11:52:46Z","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.). ","year":"2015","_id":"1569"},{"title":"Novel plasticity rule can explain the development of sensorimotor intelligence","publist_id":"5601","author":[{"full_name":"Der, Ralf","first_name":"Ralf","last_name":"Der"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","first_name":"Georg S","last_name":"Martius"}],"day":"10","publication":"PNAS","ec_funded":1,"scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","pmid":1,"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"doi":"10.1073/pnas.1508400112","quality_controlled":"1","language":[{"iso":"eng"}],"issue":"45","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"volume":112,"date_created":"2018-12-11T11:52:47Z","page":"E6224 - E6232","date_updated":"2021-01-12T06:51:40Z","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"}],"month":"11","type":"journal_article","oa_version":"Submitted Version","_id":"1570","year":"2015","date_published":"2015-11-10T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/"}],"oa":1,"publication_status":"published","intvolume":"       112","citation":{"ista":"Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232.","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>.","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>","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>","short":"R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232.","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.","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>."},"status":"public","external_id":{"pmid":["26504200"]}},{"publication":"PNAS","_id":"1571","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","department":[{"_id":"ToBo"}],"year":"2015","title":"Breaking evolutionary constraint with a tradeoff ratchet","volume":112,"publist_id":"5600","date_created":"2018-12-11T11:52:47Z","author":[{"first_name":"Marjon","last_name":"De Vos","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","full_name":"De Vos, Marjon"},{"full_name":"Dawid, Alexandre","last_name":"Dawid","first_name":"Alexandre"},{"full_name":"Šunderlíková, Vanda","first_name":"Vanda","last_name":"Šunderlíková"},{"full_name":"Tans, Sander","first_name":"Sander","last_name":"Tans"}],"page":"14906 - 14911","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."}],"date_updated":"2021-01-12T06:51:40Z","day":"01","month":"12","type":"journal_article","oa_version":"None","intvolume":"       112","language":[{"iso":"eng"}],"citation":{"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>","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>.","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>","short":"M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911.","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."},"issue":"48","status":"public","doi":"10.1073/pnas.1510282112","date_published":"2015-12-01T00:00:00Z","quality_controlled":"1","publication_status":"published"},{"date_published":"2015-06-23T00:00:00Z","doi":"10.1007/s00220-015-2402-0","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1312.7873"}],"publication_status":"published","oa":1,"intvolume":"       339","issue":"1","language":[{"iso":"eng"}],"citation":{"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.","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>","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>","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.","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>."},"status":"public","volume":339,"title":"Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet","publist_id":"5599","date_created":"2018-12-11T11:52:47Z","page":"279 - 307","author":[{"first_name":"Michele","last_name":"Correggi","full_name":"Correggi, Michele"},{"last_name":"Giuliani","first_name":"Alessandro","full_name":"Giuliani, Alessandro"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert"}],"month":"06","oa_version":"Preprint","type":"journal_article","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"}],"day":"23","date_updated":"2021-01-12T06:51:41Z","_id":"1572","publication":"Communications in Mathematical Physics","scopus_import":1,"publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"year":"2015"},{"status":"public","intvolume":"        68","citation":{"short":"T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884.","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>.","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.","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>","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.","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>.","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>"},"publication_status":"published","oa":1,"date_published":"2015-10-01T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1307.3168","open_access":"1"}],"year":"2015","_id":"1573","page":"1845 - 1884","abstract":[{"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.","lang":"eng"}],"date_updated":"2021-01-12T06:51:41Z","month":"10","type":"journal_article","oa_version":"Preprint","volume":68,"date_created":"2018-12-11T11:52:48Z","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"language":[{"iso":"eng"}],"issue":"10","doi":"10.1002/cpa.21552","quality_controlled":"1","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"publication":"Communications on Pure and Applied Mathematics","scopus_import":1,"author":[{"last_name":"Chen","first_name":"Thomas","full_name":"Chen, Thomas"},{"full_name":"Hainzl, Christian","last_name":"Hainzl","first_name":"Christian"},{"full_name":"Pavlović, Nataša","first_name":"Nataša","last_name":"Pavlović"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"day":"01","title":"Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti","publist_id":"5598"},{"author":[{"full_name":"Chen, Qian","last_name":"Chen","first_name":"Qian"},{"last_name":"Liu","first_name":"Yang","full_name":"Liu, Yang"},{"full_name":"Maere, Steven","last_name":"Maere","first_name":"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","first_name":"Wei","last_name":"Xuan"},{"full_name":"Lucas, Jessica","first_name":"Jessica","last_name":"Lucas"},{"first_name":"Valya","last_name":"Vassileva","full_name":"Vassileva, Valya"},{"last_name":"Kitakura","first_name":"Saeko","full_name":"Kitakura, Saeko"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","full_name":"Marhavy, Peter","first_name":"Peter","last_name":"Marhavy"},{"first_name":"Krzysztof T","last_name":"Wabnik","full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7263-0560"},{"full_name":"Geldner, Niko","last_name":"Geldner","first_name":"Niko"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"full_name":"Le, Jie","last_name":"Le","first_name":"Jie"},{"last_name":"Fukaki","first_name":"Hidehiro","full_name":"Fukaki, Hidehiro"},{"full_name":"Grotewold, Erich","first_name":"Erich","last_name":"Grotewold"},{"last_name":"Li","first_name":"Chuanyou","full_name":"Li, Chuanyou"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml"},{"last_name":"Sack","first_name":"Fred","full_name":"Sack, Fred"},{"last_name":"Beeckman","first_name":"Tom","full_name":"Beeckman, Tom"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"}],"file":[{"creator":"system","content_type":"application/pdf","relation":"main_file","file_size":1701815,"file_name":"IST-2016-477-v1+1_ncomms9821.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:32Z","checksum":"8ff5c108899b548806e1cb7a302fe76d","date_updated":"2020-07-14T12:45:02Z","file_id":"5085"}],"day":"18","title":"A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development","article_number":"8821","publist_id":"5597","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"publication":"Nature Communications","scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"pubrep_id":"477","doi":"10.1038/ncomms9821","quality_controlled":"1","language":[{"iso":"eng"}],"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."}],"date_updated":"2021-01-12T06:51:42Z","type":"journal_article","month":"11","oa_version":"Published Version","volume":6,"file_date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-11T11:52:48Z","acknowledgement":"of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ","year":"2015","_id":"1574","publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["580"],"date_published":"2015-11-18T00:00:00Z","status":"public","intvolume":"         6","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>.","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.","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).","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>","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>","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>.","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."}},{"author":[{"last_name":"Chabaud","first_name":"Mélanie","full_name":"Chabaud, Mélanie"},{"first_name":"Mélina","last_name":"Heuzé","full_name":"Heuzé, Mélina"},{"last_name":"Bretou","first_name":"Marine","full_name":"Bretou, Marine"},{"first_name":"Pablo","last_name":"Vargas","full_name":"Vargas, Pablo"},{"full_name":"Maiuri, Paolo","last_name":"Maiuri","first_name":"Paolo"},{"first_name":"Paola","last_name":"Solanes","full_name":"Solanes, Paola"},{"first_name":"Mathieu","last_name":"Maurin","full_name":"Maurin, Mathieu"},{"first_name":"Emmanuel","last_name":"Terriac","full_name":"Terriac, Emmanuel"},{"first_name":"Maël","last_name":"Le Berre","full_name":"Le Berre, Maël"},{"first_name":"Danielle","last_name":"Lankar","full_name":"Lankar, Danielle"},{"full_name":"Piolot, Tristan","first_name":"Tristan","last_name":"Piolot"},{"last_name":"Adelstein","first_name":"Robert","full_name":"Adelstein, Robert"},{"first_name":"Yingfan","last_name":"Zhang","full_name":"Zhang, Yingfan"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Jacobelli, Jordan","last_name":"Jacobelli","first_name":"Jordan"},{"last_name":"Bénichou","first_name":"Olivier","full_name":"Bénichou, Olivier"},{"full_name":"Voituriez, Raphaël","first_name":"Raphaël","last_name":"Voituriez"},{"last_name":"Piel","first_name":"Matthieu","full_name":"Piel, Matthieu"},{"full_name":"Lennon Duménil, Ana","first_name":"Ana","last_name":"Lennon Duménil"}],"file":[{"date_updated":"2020-07-14T12:45:02Z","file_id":"4915","checksum":"bae12e86be2adb28253f890b8bba8315","date_created":"2018-12-12T10:11:58Z","access_level":"open_access","file_name":"IST-2016-476-v1+1_ncomms8526.pdf","content_type":"application/pdf","relation":"main_file","file_size":4530215,"creator":"system"}],"day":"25","article_number":"7526","title":"Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells","publist_id":"5596","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","department":[{"_id":"MiSi"}],"publication":"Nature Communications","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":1,"pubrep_id":"476","doi":"10.1038/ncomms8526","quality_controlled":"1","language":[{"iso":"eng"}],"month":"06","type":"journal_article","oa_version":"Published Version","date_updated":"2021-01-12T06:51:42Z","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."}],"volume":6,"file_date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-11T11:52:48Z","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).","year":"2015","_id":"1575","publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2015-06-25T00:00:00Z","ddc":["570"],"status":"public","intvolume":"         6","citation":{"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>","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>","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.","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>.","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>.","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.","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)."}},{"publication_status":"published","oa":1,"date_published":"2015-12-08T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1504.05716","open_access":"1"}],"status":"public","related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"intvolume":"       115","citation":{"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>.","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>","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>","ista":"Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101.","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>."},"date_updated":"2023-09-07T12:55:21Z","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."}],"oa_version":"Preprint","month":"12","type":"journal_article","volume":115,"date_created":"2018-12-11T11:52:49Z","year":"2015","_id":"1576","doi":"10.1103/PhysRevLett.115.248101","quality_controlled":"1","project":[{"grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"issue":"24","author":[{"full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","last_name":"Cepeda Humerez"},{"id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg","first_name":"Georg","last_name":"Rieckh"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"}],"day":"08","title":"Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation","article_number":"248101","publist_id":"5595","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"American Physical Society","department":[{"_id":"GaTk"}],"publication":"Physical Review Letters","scopus_import":1,"ec_funded":1},{"publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BeVi"}],"pmid":1,"publication":"PNAS","article_type":"original","scopus_import":1,"article_processing_charge":"No","author":[{"last_name":"Carvalho","first_name":"Antonio","full_name":"Carvalho, Antonio"},{"first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Russo, Claudia","last_name":"Russo","first_name":"Claudia"},{"full_name":"Swenor, Bonnielin","first_name":"Bonnielin","last_name":"Swenor"},{"full_name":"Clark, Andrew","last_name":"Clark","first_name":"Andrew"}],"day":"06","title":"Birth of a new gene on the Y chromosome of Drosophila melanogaster","publist_id":"5594","issue":"40","language":[{"iso":"eng"}],"doi":"10.1073/pnas.1516543112","quality_controlled":"1","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.","year":"2015","_id":"1577","page":"12450 - 12455","oa_version":"Published Version","type":"journal_article","month":"10","date_updated":"2021-01-12T06:51:43Z","abstract":[{"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.","lang":"eng"}],"volume":112,"date_created":"2018-12-11T11:52:49Z","external_id":{"pmid":["26385968"]},"status":"public","intvolume":"       112","citation":{"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>.","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.","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>","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.","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."},"oa":1,"publication_status":"published","date_published":"2015-10-06T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/"}]},{"title":"Triangulations from topologically correct digital Voronoi diagrams","volume":48,"date_created":"2018-12-11T11:52:49Z","publist_id":"5593","page":"507 - 519","author":[{"full_name":"Cao, Thanhtung","first_name":"Thanhtung","last_name":"Cao"},{"last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"full_name":"Tan, Tiowseng","last_name":"Tan","first_name":"Tiowseng"}],"oa_version":"None","type":"journal_article","month":"08","abstract":[{"lang":"eng","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."}],"date_updated":"2021-01-12T06:51:43Z","day":"01","_id":"1578","publication":"Computational Geometry","scopus_import":1,"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","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2015","department":[{"_id":"HeEd"}],"date_published":"2015-08-01T00:00:00Z","doi":"10.1016/j.comgeo.2015.04.001","quality_controlled":"1","publication_status":"published","intvolume":"        48","issue":"7","language":[{"iso":"eng"}],"citation":{"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>","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>.","ista":"Cao T, Edelsbrunner H, Tan T. 2015. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 48(7), 507–519.","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>.","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.","short":"T. Cao, H. Edelsbrunner, T. Tan, Computational Geometry 48 (2015) 507–519."},"status":"public"},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.4280"}],"date_published":"2015-06-01T00:00:00Z","oa":1,"publication_status":"published","citation":{"ama":"Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert problems of lines are at least alternating. <i>Transactions of the American Mathematical Society</i>. 2015;367(6):4183-4206. doi:<a href=\"https://doi.org/10.1090/S0002-9947-2014-06192-8\">10.1090/S0002-9947-2014-06192-8</a>","apa":"Brooks, C., Martin del Campo Sanchez, A., &#38; Sottile, F. (2015). Galois groups of Schubert problems of lines are at least alternating. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/S0002-9947-2014-06192-8\">https://doi.org/10.1090/S0002-9947-2014-06192-8</a>","mla":"Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” <i>Transactions of the American Mathematical Society</i>, vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:<a href=\"https://doi.org/10.1090/S0002-9947-2014-06192-8\">10.1090/S0002-9947-2014-06192-8</a>.","ista":"Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 367(6), 4183–4206.","chicago":"Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2015. <a href=\"https://doi.org/10.1090/S0002-9947-2014-06192-8\">https://doi.org/10.1090/S0002-9947-2014-06192-8</a>.","ieee":"C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of Schubert problems of lines are at least alternating,” <i>Transactions of the American Mathematical Society</i>, vol. 367, no. 6. American Mathematical Society, pp. 4183–4206, 2015.","short":"C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American Mathematical Society 367 (2015) 4183–4206."},"intvolume":"       367","status":"public","date_created":"2018-12-11T11:52:50Z","volume":367,"oa_version":"Preprint","month":"06","type":"journal_article","date_updated":"2021-01-12T06:51:43Z","abstract":[{"lang":"eng","text":"We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality."}],"page":"4183 - 4206","_id":"1579","year":"2015","acknowledgement":"This research was supported in part by NSF grant DMS-915211 and the Institut Mittag-Leffler.\r\n","quality_controlled":"1","doi":"10.1090/S0002-9947-2014-06192-8","issue":"6","language":[{"iso":"eng"}],"publist_id":"5592","title":"Galois groups of Schubert problems of lines are at least alternating","day":"01","author":[{"last_name":"Brooks","first_name":"Christopher","full_name":"Brooks, Christopher"},{"full_name":"Martin Del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","last_name":"Martin Del Campo Sanchez","first_name":"Abraham"},{"full_name":"Sottile, Frank","first_name":"Frank","last_name":"Sottile"}],"article_processing_charge":"No","scopus_import":1,"publication":"Transactions of the American Mathematical Society","department":[{"_id":"CaUh"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"American Mathematical Society"},{"citation":{"ama":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. <i>Neuroscience</i>. 2015;311:430-443. doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2015.10.046\">10.1016/j.neuroscience.2015.10.046</a>","mla":"Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” <i>Neuroscience</i>, vol. 311, Elsevier, 2015, pp. 430–43, doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2015.10.046\">10.1016/j.neuroscience.2015.10.046</a>.","ista":"Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 311, 430–443.","apa":"Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., &#38; Ghirardi, M. (2015). Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. <i>Neuroscience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuroscience.2015.10.046\">https://doi.org/10.1016/j.neuroscience.2015.10.046</a>","ieee":"O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons,” <i>Neuroscience</i>, vol. 311. Elsevier, pp. 430–443, 2015.","chicago":"Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” <i>Neuroscience</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuroscience.2015.10.046\">https://doi.org/10.1016/j.neuroscience.2015.10.046</a>.","short":"O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience 311 (2015) 430–443."},"intvolume":"       311","status":"public","date_published":"2015-12-17T00:00:00Z","ddc":["570"],"has_accepted_license":"1","oa":1,"publication_status":"published","_id":"1580","year":"2015","file_date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-11T11:52:50Z","volume":311,"abstract":[{"lang":"eng","text":"Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs."}],"date_updated":"2021-01-12T06:51:44Z","oa_version":"Submitted Version","month":"12","type":"journal_article","page":"430 - 443","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1016/j.neuroscience.2015.10.046","article_processing_charge":"No","scopus_import":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","publication":"Neuroscience","department":[{"_id":"PeJo"}],"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5591","title":"Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons","day":"17","file":[{"date_created":"2020-05-15T06:50:20Z","access_level":"open_access","file_id":"7849","date_updated":"2020-07-14T12:45:02Z","checksum":"af2c4c994718c7be417eba0dc746aac9","file_size":5563015,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_name":"2015_Neuroscience_Brenes.pdf"}],"author":[{"full_name":"Brenes, Oscar","last_name":"Brenes","first_name":"Oscar"},{"last_name":"Vandael","first_name":"David H","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Carbone, Emilio","first_name":"Emilio","last_name":"Carbone"},{"last_name":"Montarolo","first_name":"Pier","full_name":"Montarolo, Pier"},{"full_name":"Ghirardi, Mirella","last_name":"Ghirardi","first_name":"Mirella"}]},{"intvolume":"       161","issue":"3","citation":{"apa":"Bollenbach, M. T., &#38; Heisenberg, C.-P. J. (2015). Gradients are shaping up. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.04.009\">https://doi.org/10.1016/j.cell.2015.04.009</a>","mla":"Bollenbach, Mark Tobias, and Carl-Philipp J. Heisenberg. “Gradients Are Shaping Up.” <i>Cell</i>, vol. 161, no. 3, Cell Press, 2015, pp. 431–32, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.04.009\">10.1016/j.cell.2015.04.009</a>.","ista":"Bollenbach MT, Heisenberg C-PJ. 2015. Gradients are shaping up. Cell. 161(3), 431–432.","ama":"Bollenbach MT, Heisenberg C-PJ. Gradients are shaping up. <i>Cell</i>. 2015;161(3):431-432. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.04.009\">10.1016/j.cell.2015.04.009</a>","short":"M.T. Bollenbach, C.-P.J. Heisenberg, Cell 161 (2015) 431–432.","chicago":"Bollenbach, Mark Tobias, and Carl-Philipp J Heisenberg. “Gradients Are Shaping Up.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.04.009\">https://doi.org/10.1016/j.cell.2015.04.009</a>.","ieee":"M. T. Bollenbach and C.-P. J. Heisenberg, “Gradients are shaping up,” <i>Cell</i>, vol. 161, no. 3. Cell Press, pp. 431–432, 2015."},"language":[{"iso":"eng"}],"status":"public","date_published":"2015-04-23T00:00:00Z","doi":"10.1016/j.cell.2015.04.009","quality_controlled":"1","publication_status":"published","_id":"1581","publication":"Cell","article_processing_charge":"No","scopus_import":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Cell Press","department":[{"_id":"ToBo"},{"_id":"CaHe"}],"year":"2015","volume":161,"title":"Gradients are shaping up","publist_id":"5590","date_created":"2018-12-11T11:52:50Z","author":[{"last_name":"Bollenbach","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"page":"431 - 432","month":"04","oa_version":"None","type":"journal_article","day":"23","abstract":[{"lang":"eng","text":"In animal embryos, morphogen gradients determine tissue patterning and morphogenesis. Shyer et al. provide evidence that, during vertebrate gut formation, tissue folding generates graded activity of signals required for subsequent steps of gut growth and differentiation, thereby revealing an intriguing link between tissue morphogenesis and morphogen gradient formation."}],"date_updated":"2022-08-25T13:56:10Z"},{"language":[{"iso":"eng"}],"issue":"2","quality_controlled":"1","doi":"10.1016/j.comgeo.2014.08.006","pubrep_id":"474","scopus_import":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Computational Geometry: Theory and Applications","department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","publist_id":"5589","title":"Weighted straight skeletons in the plane","day":"01","file":[{"file_id":"5215","date_updated":"2020-07-14T12:45:02Z","checksum":"c1ef67f6ec925e12f73a96b8fe285ab4","date_created":"2018-12-12T10:16:28Z","access_level":"open_access","file_name":"IST-2016-474-v1+1_1-s2.0-S0925772114000807-main.pdf","file_size":505987,"content_type":"application/pdf","relation":"main_file","creator":"system"}],"author":[{"first_name":"Therese","last_name":"Biedl","full_name":"Biedl, Therese"},{"first_name":"Martin","last_name":"Held","full_name":"Held, Martin"},{"last_name":"Huber","first_name":"Stefan","full_name":"Huber, Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814"},{"full_name":"Kaaser, Dominik","first_name":"Dominik","last_name":"Kaaser"},{"last_name":"Palfrader","first_name":"Peter","full_name":"Palfrader, Peter"}],"citation":{"ieee":"T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Weighted straight skeletons in the plane,” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 2. Elsevier, pp. 120–133, 2015.","chicago":"Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Weighted Straight Skeletons in the Plane.” <i>Computational Geometry: Theory and Applications</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.006\">https://doi.org/10.1016/j.comgeo.2014.08.006</a>.","short":"T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 120–133.","ama":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Weighted straight skeletons in the plane. <i>Computational Geometry: Theory and Applications</i>. 2015;48(2):120-133. doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.006\">10.1016/j.comgeo.2014.08.006</a>","mla":"Biedl, Therese, et al. “Weighted Straight Skeletons in the Plane.” <i>Computational Geometry: Theory and Applications</i>, vol. 48, no. 2, Elsevier, 2015, pp. 120–33, doi:<a href=\"https://doi.org/10.1016/j.comgeo.2014.08.006\">10.1016/j.comgeo.2014.08.006</a>.","ista":"Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(2), 120–133.","apa":"Biedl, T., Held, M., Huber, S., Kaaser, D., &#38; Palfrader, P. (2015). Weighted straight skeletons in the plane. <i>Computational Geometry: Theory and Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.comgeo.2014.08.006\">https://doi.org/10.1016/j.comgeo.2014.08.006</a>"},"intvolume":"        48","related_material":{"record":[{"relation":"other","id":"1584","status":"public"}]},"status":"public","date_published":"2015-02-01T00:00:00Z","ddc":["000"],"has_accepted_license":"1","publication_status":"published","oa":1,"_id":"1582","year":"2015","file_date_updated":"2020-07-14T12:45:02Z","date_created":"2018-12-11T11:52:51Z","volume":48,"date_updated":"2023-02-23T10:05:27Z","abstract":[{"lang":"eng","text":"We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights."}],"type":"journal_article","month":"02","oa_version":"Published Version","page":"120 - 133"}]