[{"oa":1,"year":"2016","publication":"Journal of Cell Science","date_updated":"2021-01-12T06:51:00Z","page":"367 - 379","department":[{"_id":"DaSi"}],"publist_id":"5720","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-01-15T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:52:14Z","intvolume":"       129","publisher":"Company of Biologists","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","author":[{"full_name":"Toshima, Junko","last_name":"Toshima","first_name":"Junko"},{"first_name":"Chika","last_name":"Horikomi","full_name":"Horikomi, Chika"},{"first_name":"Asuka","full_name":"Okada, Asuka","last_name":"Okada"},{"first_name":"Makiko","last_name":"Hatori","full_name":"Hatori, Makiko"},{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"last_name":"Masuda","full_name":"Masuda, Atsushi","first_name":"Atsushi"},{"last_name":"Yamamoto","full_name":"Yamamoto, Wataru","first_name":"Wataru"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"first_name":"Jiro","last_name":"Toshima","full_name":"Toshima, Jiro"}],"title":"Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis","_id":"1476","issue":"2","abstract":[{"lang":"eng","text":"The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis"}],"doi":"10.1242/jcs.176651","project":[{"_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7"}],"status":"public","publication_status":"published","acknowledgement":"We are grateful to Anthony Bretscher (Cornell University, NY) for providing the bni1-12 bnr1Δ (Y4135) strain. J.Y.T. was supported by a Japan Society for the Promotion of Science (JSPS) KAKENHI grant [grant number 26440067]; the Takeda Science Foundation; and the Novartis Foundation (Japan). J.T. was supported by a JSPS KAKENHI grant [grant number 25440054]; the Takeda Science Foundation; and the Kurata Memorial Hitachi Science and Technology Foundation. D.E.S. was supported by the European Union [grant number PCIG12-GA-2012-334077].","ec_funded":1,"day":"15","pubrep_id":"767","citation":{"ieee":"J. Toshima <i>et al.</i>, “Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis,” <i>Journal of Cell Science</i>, vol. 129, no. 2. Company of Biologists, pp. 367–379, 2016.","apa":"Toshima, J., Horikomi, C., Okada, A., Hatori, M., Nagano, M., Masuda, A., … Toshima, J. (2016). Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.176651\">https://doi.org/10.1242/jcs.176651</a>","ista":"Toshima J, Horikomi C, Okada A, Hatori M, Nagano M, Masuda A, Yamamoto W, Siekhaus DE, Toshima J. 2016. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 129(2), 367–379.","ama":"Toshima J, Horikomi C, Okada A, et al. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. <i>Journal of Cell Science</i>. 2016;129(2):367-379. doi:<a href=\"https://doi.org/10.1242/jcs.176651\">10.1242/jcs.176651</a>","short":"J. Toshima, C. Horikomi, A. Okada, M. Hatori, M. Nagano, A. Masuda, W. Yamamoto, D.E. Siekhaus, J. Toshima, Journal of Cell Science 129 (2016) 367–379.","chicago":"Toshima, Junko, Chika Horikomi, Asuka Okada, Makiko Hatori, Makoto Nagano, Atsushi Masuda, Wataru Yamamoto, Daria E Siekhaus, and Jiro Toshima. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” <i>Journal of Cell Science</i>. Company of Biologists, 2016. <a href=\"https://doi.org/10.1242/jcs.176651\">https://doi.org/10.1242/jcs.176651</a>.","mla":"Toshima, Junko, et al. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” <i>Journal of Cell Science</i>, vol. 129, no. 2, Company of Biologists, 2016, pp. 367–79, doi:<a href=\"https://doi.org/10.1242/jcs.176651\">10.1242/jcs.176651</a>."},"file_date_updated":"2020-07-14T12:44:56Z","ddc":["570","576"],"month":"01","oa_version":"Published Version","file":[{"file_name":"IST-2017-767-v1+1_367.full.pdf","file_size":7176912,"creator":"system","relation":"main_file","date_updated":"2020-07-14T12:44:56Z","access_level":"open_access","checksum":"2da0a09149a9ed956cdf79a95c17f08a","content_type":"application/pdf","file_id":"4861","date_created":"2018-12-12T10:11:08Z"}],"has_accepted_license":"1","volume":129},{"_id":"1477","title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","first_name":"Mathieu","full_name":"Tracol, Mathieu","last_name":"Tracol"}],"doi":"10.1016/j.jcss.2016.02.009","abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples.","lang":"eng"}],"issue":"5","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"publication_status":"published","status":"public","month":"08","citation":{"ista":"Chatterjee K, Chmelik M, Tracol M. 2016. What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. 82(5), 878–911.","short":"K. Chatterjee, M. Chmelik, M. Tracol, Journal of Computer and System Sciences 82 (2016) 878–911.","ama":"Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable Markov decision processes with ω-regular objectives. <i>Journal of Computer and System Sciences</i>. 2016;82(5):878-911. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">10.1016/j.jcss.2016.02.009</a>","ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with ω-regular objectives,” <i>Journal of Computer and System Sciences</i>, vol. 82, no. 5. Elsevier, pp. 878–911, 2016.","apa":"Chatterjee, K., Chmelik, M., &#38; Tracol, M. (2016). What is decidable about partially observable Markov decision processes with ω-regular objectives. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">https://doi.org/10.1016/j.jcss.2016.02.009</a>","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">https://doi.org/10.1016/j.jcss.2016.02.009</a>.","mla":"Chatterjee, Krishnendu, et al. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” <i>Journal of Computer and System Sciences</i>, vol. 82, no. 5, Elsevier, 2016, pp. 878–911, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">10.1016/j.jcss.2016.02.009</a>."},"day":"01","oa_version":"Preprint","arxiv":1,"volume":82,"oa":1,"year":"2016","date_updated":"2023-02-23T12:24:38Z","publication":"Journal of Computer and System Sciences","page":"878 - 911","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2295"},{"relation":"earlier_version","status":"public","id":"5400"}]},"publist_id":"5718","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:52:15Z","scopus_import":1,"external_id":{"arxiv":["1309.2802"]},"date_published":"2016-08-01T00:00:00Z","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1309.2802"}],"intvolume":"        82","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}]},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2020-07-14T12:44:56Z","checksum":"4f959eabc19d2a2f518318a450a4d424","content_type":"application/pdf","access_level":"open_access","file_size":965607,"relation":"main_file","creator":"system","file_name":"IST-2016-579-v1+1_njp_18_3_035002.pdf","date_created":"2018-12-12T10:17:22Z","file_id":"5276"}],"has_accepted_license":"1","volume":18,"citation":{"ieee":"R. Seiringer and S. Warzel, “Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas,” <i>New Journal of Physics</i>, vol. 18, no. 3. IOP Publishing Ltd., 2016.","apa":"Seiringer, R., &#38; Warzel, S. (2016). Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. <i>New Journal of Physics</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">https://doi.org/10.1088/1367-2630/18/3/035002</a>","short":"R. Seiringer, S. Warzel, New Journal of Physics 18 (2016).","ista":"Seiringer R, Warzel S. 2016. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 18(3), 035002.","ama":"Seiringer R, Warzel S. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. <i>New Journal of Physics</i>. 2016;18(3). doi:<a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">10.1088/1367-2630/18/3/035002</a>","chicago":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">https://doi.org/10.1088/1367-2630/18/3/035002</a>.","mla":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” <i>New Journal of Physics</i>, vol. 18, no. 3, 035002, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">10.1088/1367-2630/18/3/035002</a>."},"pubrep_id":"579","day":"29","ddc":["510","530"],"month":"02","file_date_updated":"2020-07-14T12:44:56Z","license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","project":[{"grant_number":"P27533_N27","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF"}],"publication_status":"published","status":"public","title":"Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas","author":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Simone","last_name":"Warzel","full_name":"Warzel, Simone"}],"_id":"1478","abstract":[{"lang":"eng","text":"We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature."}],"issue":"3","doi":"10.1088/1367-2630/18/3/035002","publisher":"IOP Publishing Ltd.","intvolume":"        18","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"RoSe"}],"publist_id":"5716","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-02-29T00:00:00Z","date_created":"2018-12-11T11:52:15Z","scopus_import":1,"publication":"New Journal of Physics","date_updated":"2021-01-12T06:51:01Z","article_number":"035002","oa":1,"year":"2016"},{"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","publisher":"Springer","intvolume":"        25","date_created":"2018-12-11T11:52:16Z","scopus_import":1,"date_published":"2016-09-01T00:00:00Z","publist_id":"5715","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrPi"}],"page":"567 - 605","related_material":{"record":[{"id":"2940","relation":"earlier_version","status":"public"}]},"date_updated":"2023-02-23T11:05:09Z","publication":"Computational Complexity","year":"2016","oa":1,"volume":25,"has_accepted_license":"1","file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"7659296174fa75f5f0364f31f46f4bcf","date_updated":"2020-07-14T12:44:56Z","file_name":"IST-2017-766-v1+1_678.pdf","relation":"main_file","creator":"system","file_size":483258,"file_id":"5012","date_created":"2018-12-12T10:13:29Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:44:56Z","month":"09","ddc":["004"],"citation":{"mla":"Krenn, Stephan, et al. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” <i>Computational Complexity</i>, vol. 25, no. 3, Springer, 2016, pp. 567–605, doi:<a href=\"https://doi.org/10.1007/s00037-015-0120-9\">10.1007/s00037-015-0120-9</a>.","chicago":"Krenn, Stephan, Krzysztof Z Pietrzak, Akshay Wadia, and Daniel Wichs. “A Counterexample to the Chain Rule for Conditional HILL Entropy.” <i>Computational Complexity</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s00037-015-0120-9\">https://doi.org/10.1007/s00037-015-0120-9</a>.","ieee":"S. Krenn, K. Z. Pietrzak, A. Wadia, and D. Wichs, “A counterexample to the chain rule for conditional HILL entropy,” <i>Computational Complexity</i>, vol. 25, no. 3. Springer, pp. 567–605, 2016.","apa":"Krenn, S., Pietrzak, K. Z., Wadia, A., &#38; Wichs, D. (2016). A counterexample to the chain rule for conditional HILL entropy. <i>Computational Complexity</i>. Springer. <a href=\"https://doi.org/10.1007/s00037-015-0120-9\">https://doi.org/10.1007/s00037-015-0120-9</a>","ama":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. A counterexample to the chain rule for conditional HILL entropy. <i>Computational Complexity</i>. 2016;25(3):567-605. doi:<a href=\"https://doi.org/10.1007/s00037-015-0120-9\">10.1007/s00037-015-0120-9</a>","short":"S. Krenn, K.Z. Pietrzak, A. Wadia, D. Wichs, Computational Complexity 25 (2016) 567–605.","ista":"Krenn S, Pietrzak KZ, Wadia A, Wichs D. 2016. A counterexample to the chain rule for conditional HILL entropy. Computational Complexity. 25(3), 567–605."},"pubrep_id":"766","day":"01","ec_funded":1,"acknowledgement":"This work was partly funded by the European Research Council under ERC Starting Grant 259668-PSPC and ERC Advanced Grant 321310-PERCY.\r\n","publication_status":"published","status":"public","project":[{"name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/s00037-015-0120-9","abstract":[{"text":"Most entropy notions H(.) like Shannon or min-entropy satisfy a chain rule stating that for random variables X,Z, and A we have H(X|Z,A)≥H(X|Z)−|A|. That is, by conditioning on A the entropy of X can decrease by at most the bitlength |A| of A. Such chain rules are known to hold for some computational entropy notions like Yao’s and unpredictability-entropy. For HILL entropy, the computational analogue of min-entropy, the chain rule is of special interest and has found many applications, including leakage-resilient cryptography, deterministic encryption, and memory delegation. These applications rely on restricted special cases of the chain rule. Whether the chain rule for conditional HILL entropy holds in general was an open problem for which we give a strong negative answer: we construct joint distributions (X,Z,A), where A is a distribution over a single bit, such that the HILL entropy H HILL (X|Z) is large but H HILL (X|Z,A) is basically zero.\r\n\r\nOur counterexample just makes the minimal assumption that NP⊈P/poly. Under the stronger assumption that injective one-way function exist, we can make all the distributions efficiently samplable.\r\n\r\nFinally, we show that some more sophisticated cryptographic objects like lossy functions can be used to sample a distribution constituting a counterexample to the chain rule making only a single invocation to the underlying object.","lang":"eng"}],"issue":"3","_id":"1479","title":"A counterexample to the chain rule for conditional HILL entropy","author":[{"last_name":"Krenn","full_name":"Krenn, Stephan","first_name":"Stephan","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2835-9093"},{"last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654"},{"last_name":"Wadia","full_name":"Wadia, Akshay","first_name":"Akshay"},{"full_name":"Wichs, Daniel","last_name":"Wichs","first_name":"Daniel"}]},{"date_published":"2016-01-07T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:52:16Z","oa_version":"Preprint","department":[{"_id":"CaUh"}],"day":"07","citation":{"mla":"Michałek, Mateusz, et al. “Exponential Varieties.” <i>Proceedings of the London Mathematical Society</i>, vol. 112, no. 1, Oxford University Press, 2016, pp. 27–56, doi:<a href=\"https://doi.org/10.1112/plms/pdv066\">10.1112/plms/pdv066</a>.","chicago":"Michałek, Mateusz, Bernd Sturmfels, Caroline Uhler, and Piotr Zwiernik. “Exponential Varieties.” <i>Proceedings of the London Mathematical Society</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1112/plms/pdv066\">https://doi.org/10.1112/plms/pdv066</a>.","ieee":"M. Michałek, B. Sturmfels, C. Uhler, and P. Zwiernik, “Exponential varieties,” <i>Proceedings of the London Mathematical Society</i>, vol. 112, no. 1. Oxford University Press, pp. 27–56, 2016.","apa":"Michałek, M., Sturmfels, B., Uhler, C., &#38; Zwiernik, P. (2016). Exponential varieties. <i>Proceedings of the London Mathematical Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1112/plms/pdv066\">https://doi.org/10.1112/plms/pdv066</a>","short":"M. Michałek, B. Sturmfels, C. Uhler, P. Zwiernik, Proceedings of the London Mathematical Society 112 (2016) 27–56.","ama":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. Exponential varieties. <i>Proceedings of the London Mathematical Society</i>. 2016;112(1):27-56. doi:<a href=\"https://doi.org/10.1112/plms/pdv066\">10.1112/plms/pdv066</a>","ista":"Michałek M, Sturmfels B, Uhler C, Zwiernik P. 2016. Exponential varieties. Proceedings of the London Mathematical Society. 112(1), 27–56."},"publist_id":"5714","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"01","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","volume":112,"intvolume":"       112","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1412.6185"}],"publisher":"Oxford University Press","issue":"1","year":"2016","abstract":[{"lang":"eng","text":"Exponential varieties arise from exponential families in statistics. These real algebraic varieties have strong positivity and convexity properties, familiar from toric varieties and their moment maps. Among them are varieties of inverses of symmetric matrices satisfying linear constraints. This class includes Gaussian graphical models. We develop a general theory of exponential varieties. These are derived from hyperbolic polynomials and their integral representations. We compare the multidegrees and ML degrees of the gradient map for hyperbolic polynomials. "}],"doi":"10.1112/plms/pdv066","author":[{"first_name":"Mateusz","full_name":"Michałek, Mateusz","last_name":"Michałek"},{"first_name":"Bernd","full_name":"Sturmfels, Bernd","last_name":"Sturmfels"},{"orcid":"0000-0002-7008-0216","last_name":"Uhler","full_name":"Uhler, Caroline","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zwiernik, Piotr","last_name":"Zwiernik","first_name":"Piotr"}],"oa":1,"title":"Exponential varieties","_id":"1480","publication_status":"published","status":"public","page":"27 - 56","publication":"Proceedings of the London Mathematical Society","date_updated":"2021-01-12T06:51:02Z"},{"status":"public","publication_status":"published","acknowledgement":"We thank J. Traas, B. Müller and V. Reddy for providing seed materials and Y. Deb for advice regarding the laser ablation experiments. We specially thank Thomas Laux for stimulating discussions and support in the initial phase of this project.","_id":"1482","author":[{"first_name":"Milad","last_name":"Adibi","full_name":"Adibi, Milad"},{"full_name":"Yoshida, Saiko","last_name":"Yoshida","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko"},{"last_name":"Weijers","full_name":"Weijers, Dolf","first_name":"Dolf"},{"first_name":"Christian","full_name":"Fleck, Christian","last_name":"Fleck"}],"title":"Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization","doi":"10.1371/journal.pone.0147830","issue":"2","abstract":[{"text":"Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"creator":"system","relation":"main_file","file_size":4297148,"file_name":"IST-2016-521-v1+1_journal.pone.0147830.PDF","checksum":"6066146e527335030f83aa5924ab72a6","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:57Z","date_created":"2018-12-12T10:14:16Z","file_id":"5066"}],"volume":11,"has_accepted_license":"1","ddc":["570"],"month":"02","file_date_updated":"2020-07-14T12:44:57Z","day":"01","citation":{"apa":"Adibi, M., Yoshida, S., Weijers, D., &#38; Fleck, C. (2016). Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0147830\">https://doi.org/10.1371/journal.pone.0147830</a>","ieee":"M. Adibi, S. Yoshida, D. Weijers, and C. Fleck, “Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization,” <i>PLoS One</i>, vol. 11, no. 2. Public Library of Science, 2016.","ama":"Adibi M, Yoshida S, Weijers D, Fleck C. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. <i>PLoS One</i>. 2016;11(2). doi:<a href=\"https://doi.org/10.1371/journal.pone.0147830\">10.1371/journal.pone.0147830</a>","short":"M. Adibi, S. Yoshida, D. Weijers, C. Fleck, PLoS One 11 (2016).","ista":"Adibi M, Yoshida S, Weijers D, Fleck C. 2016. Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization. PLoS One. 11(2), e0147830.","chicago":"Adibi, Milad, Saiko Yoshida, Dolf Weijers, and Christian Fleck. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0147830\">https://doi.org/10.1371/journal.pone.0147830</a>.","mla":"Adibi, Milad, et al. “Centering the Organizing Center in the Arabidopsis Thaliana Shoot Apical Meristem by a Combination of Cytokinin Signaling and Self-Organization.” <i>PLoS One</i>, vol. 11, no. 2, e0147830, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0147830\">10.1371/journal.pone.0147830</a>."},"pubrep_id":"521","oa_version":"Published Version","date_updated":"2021-01-12T06:51:03Z","publication":"PLoS One","article_number":"e0147830","oa":1,"year":"2016","intvolume":"        11","publisher":"Public Library of Science","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publist_id":"5711","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"scopus_import":1,"date_created":"2018-12-11T11:52:17Z","date_published":"2016-02-01T00:00:00Z"},{"status":"public","publication_status":"published","acknowledgement":"We thank Maciek Adamowski for helpful discussions and Qiang Zhu and Israel Ausin for critical reading of the manuscript. We sincerely apologize to colleagues whose work we could not include owing to space limitations.","issue":"6","doi":"10.1016/j.tcb.2016.02.003","author":[{"last_name":"Chen","full_name":"Chen, Xu","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shuang","full_name":"Wu, Shuang","last_name":"Wu"},{"last_name":"Liu","full_name":"Liu, Zengyu","first_name":"Zengyu"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiřĺ","full_name":"Friml, Jiřĺ","last_name":"Friml"}],"title":"Environmental and endogenous control of cortical microtubule orientation","_id":"1484","has_accepted_license":"1","volume":26,"file":[{"date_created":"2018-12-12T10:15:34Z","file_id":"5155","checksum":"b229e5bb4676ec3e27b7b9ea603b3a63","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:57Z","relation":"main_file","file_size":2329117,"creator":"system","file_name":"IST-2018-1002-v1+1_Chen_TICB_2016_proofs.pdf"}],"oa_version":"Submitted Version","day":"01","pubrep_id":"1002","citation":{"mla":"Chen, Xu, et al. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” <i>Trends in Cell Biology</i>, vol. 26, no. 6, Cell Press, 2016, pp. 409–19, doi:<a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">10.1016/j.tcb.2016.02.003</a>.","chicago":"Chen, Xu, Shuang Wu, Zengyu Liu, and Jiří Friml. “Environmental and Endogenous Control of Cortical Microtubule Orientation.” <i>Trends in Cell Biology</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">https://doi.org/10.1016/j.tcb.2016.02.003</a>.","ama":"Chen X, Wu S, Liu Z, Friml J. Environmental and endogenous control of cortical microtubule orientation. <i>Trends in Cell Biology</i>. 2016;26(6):409-419. doi:<a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">10.1016/j.tcb.2016.02.003</a>","ista":"Chen X, Wu S, Liu Z, Friml J. 2016. Environmental and endogenous control of cortical microtubule orientation. Trends in Cell Biology. 26(6), 409–419.","short":"X. Chen, S. Wu, Z. Liu, J. Friml, Trends in Cell Biology 26 (2016) 409–419.","apa":"Chen, X., Wu, S., Liu, Z., &#38; Friml, J. (2016). Environmental and endogenous control of cortical microtubule orientation. <i>Trends in Cell Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tcb.2016.02.003\">https://doi.org/10.1016/j.tcb.2016.02.003</a>","ieee":"X. Chen, S. Wu, Z. Liu, and J. Friml, “Environmental and endogenous control of cortical microtubule orientation,” <i>Trends in Cell Biology</i>, vol. 26, no. 6. Cell Press, pp. 409–419, 2016."},"ddc":["581"],"file_date_updated":"2020-07-14T12:44:57Z","month":"06","article_type":"review","page":"409 - 419","publication":"Trends in Cell Biology","date_updated":"2021-01-12T06:51:04Z","year":"2016","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"        26","publisher":"Cell Press","date_published":"2016-06-01T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:52:17Z","department":[{"_id":"JiFr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5704"},{"oa":1,"year":"2016","publication":"Physical Biology","date_updated":"2021-01-12T06:51:04Z","article_number":"016003","department":[{"_id":"GaTk"}],"publist_id":"5702","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-01-29T00:00:00Z","date_created":"2018-12-11T11:52:18Z","scopus_import":1,"publisher":"IOP Publishing Ltd.","main_file_link":[{"url":"http://arxiv.org/abs/1505.04613","open_access":"1"}],"intvolume":"        13","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"title":"Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","full_name":"De Martino, Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706"}],"_id":"1485","abstract":[{"text":"In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism.","lang":"eng"}],"issue":"1","doi":"10.1088/1478-3975/13/1/016003","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"status":"public","publication_status":"published","ec_funded":1,"citation":{"chicago":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” <i>Physical Biology</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">https://doi.org/10.1088/1478-3975/13/1/016003</a>.","mla":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” <i>Physical Biology</i>, vol. 13, no. 1, 016003, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">10.1088/1478-3975/13/1/016003</a>.","ista":"De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.","ama":"De Martino D. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. <i>Physical Biology</i>. 2016;13(1). doi:<a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">10.1088/1478-3975/13/1/016003</a>","short":"D. De Martino, Physical Biology 13 (2016).","apa":"De Martino, D. (2016). Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. <i>Physical Biology</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">https://doi.org/10.1088/1478-3975/13/1/016003</a>","ieee":"D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” <i>Physical Biology</i>, vol. 13, no. 1. IOP Publishing Ltd., 2016."},"day":"29","month":"01","oa_version":"Preprint","volume":13},{"year":"2016","issue":"2","abstract":[{"text":"We review recent results concerning the mathematical properties of the Bardeen-Cooper-Schrieffer (BCS) functional of superconductivity, which were obtained in a series of papers, partly in collaboration with R. Frank, E. Hamza, S. Naboko, and J. P. Solovej. Our discussion includes, in particular, an investigation of the critical temperature for a general class of interaction potentials, as well as a study of its dependence on external fields. We shall explain how the Ginzburg-Landau model can be derived from the BCS theory in a suitable parameter regime.","lang":"eng"}],"doi":"10.1063/1.4941723","author":[{"last_name":"Hainzl","full_name":"Hainzl, Christian","first_name":"Christian"},{"last_name":"Seiringer","full_name":"Seiringer, Robert","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521"}],"oa":1,"title":"The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties","_id":"1486","status":"public","publication_status":"published","article_number":"021101","publication":"Journal of Mathematical Physics","date_updated":"2021-01-12T06:51:04Z","date_published":"2016-02-24T00:00:00Z","scopus_import":1,"oa_version":"Preprint","date_created":"2018-12-11T11:52:18Z","day":"24","department":[{"_id":"RoSe"}],"citation":{"apa":"Hainzl, C., &#38; Seiringer, R. (2016). The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. <i>Journal of Mathematical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4941723\">https://doi.org/10.1063/1.4941723</a>","ieee":"C. Hainzl and R. Seiringer, “The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties,” <i>Journal of Mathematical Physics</i>, vol. 57, no. 2. American Institute of Physics, 2016.","ama":"Hainzl C, Seiringer R. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. <i>Journal of Mathematical Physics</i>. 2016;57(2). doi:<a href=\"https://doi.org/10.1063/1.4941723\">10.1063/1.4941723</a>","short":"C. Hainzl, R. Seiringer, Journal of Mathematical Physics 57 (2016).","ista":"Hainzl C, Seiringer R. 2016. The Bardeen–Cooper–Schrieffer functional of superconductivity and its mathematical properties. Journal of Mathematical Physics. 57(2), 021101.","chicago":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” <i>Journal of Mathematical Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1063/1.4941723\">https://doi.org/10.1063/1.4941723</a>.","mla":"Hainzl, Christian, and Robert Seiringer. “The Bardeen–Cooper–Schrieffer Functional of Superconductivity and Its Mathematical Properties.” <i>Journal of Mathematical Physics</i>, vol. 57, no. 2, 021101, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1063/1.4941723\">10.1063/1.4941723</a>."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5701","month":"02","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","volume":57,"main_file_link":[{"url":"http://arxiv.org/abs/1511.01995","open_access":"1"}],"intvolume":"        57","publisher":"American Institute of Physics"},{"year":"2016","oa":1,"article_number":"e1002384","publication":"PLoS Biology","date_updated":"2021-01-12T06:51:05Z","date_published":"2016-02-18T00:00:00Z","date_created":"2018-12-11T11:52:18Z","scopus_import":1,"department":[{"_id":"JoCs"}],"publist_id":"5700","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Public Library of Science","intvolume":"        14","abstract":[{"text":"Rhythms with time scales of multiple cycles per second permeate the mammalian brain, yet neuroscientists are not certain of their functional roles. One leading idea is that coherent oscillation between two brain regions facilitates the exchange of information between them. In rats, the hippocampus and the vibrissal sensorimotor system both are characterized by rhythmic oscillation in the theta range, 5–12 Hz. Previous work has been divided as to whether the two rhythms are independent or coherent. To resolve this question, we acquired three measures from rats—whisker motion, hippocampal local field potential (LFP), and barrel cortex unit firing—during a whisker-mediated texture discrimination task and during control conditions (not engaged in a whisker-mediated memory task). Compared to control conditions, the theta band of hippocampal LFP showed a marked increase in power as the rats approached and then palpated the texture. Phase synchronization between whisking and hippocampal LFP increased by almost 50% during approach and texture palpation. In addition, a greater proportion of barrel cortex neurons showed firing that was phase-locked to hippocampal theta while rats were engaged in the discrimination task. Consistent with a behavioral consequence of phase synchronization, the rats identified the texture more rapidly and with lower error likelihood on trials in which there was an increase in theta-whisking coherence at the moment of texture palpation. These results suggest that coherence between the whisking rhythm, barrel cortex firing, and hippocampal LFP is augmented selectively during epochs in which the rat collects sensory information and that such coherence enhances the efficiency of integration of stimulus information into memory and decision-making centers.","lang":"eng"}],"issue":"2","doi":"10.1371/journal.pbio.1002384","title":"Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination","author":[{"first_name":"Natalia","last_name":"Grion","full_name":"Grion, Natalia"},{"last_name":"Akrami","full_name":"Akrami, Athena","first_name":"Athena"},{"full_name":"Zuo, Yangfang","last_name":"Zuo","first_name":"Yangfang"},{"orcid":"0000-0001-9439-3148","id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","first_name":"Federico","full_name":"Stella, Federico","last_name":"Stella"},{"first_name":"Mathew","last_name":"Diamond","full_name":"Diamond, Mathew"}],"_id":"1487","status":"public","acknowledgement":"We thank Eric Maris, Demian Battaglia, and Rodrigo Quian Quiroga for useful discussions. We are grateful to Fabrizio Manzino and Marco Gigante for construction of the behavioral apparatus, Igor Perkon for developing custom whisker tracking software and to Francesca Pulecchi for animal care and histological processing.","publication_status":"published","oa_version":"Published Version","pubrep_id":"518","citation":{"short":"N. Grion, A. Akrami, Y. Zuo, F. Stella, M. Diamond, PLoS Biology 14 (2016).","ista":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. 2016. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. PLoS Biology. 14(2), e1002384.","ama":"Grion N, Akrami A, Zuo Y, Stella F, Diamond M. Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. <i>PLoS Biology</i>. 2016;14(2). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002384\">10.1371/journal.pbio.1002384</a>","apa":"Grion, N., Akrami, A., Zuo, Y., Stella, F., &#38; Diamond, M. (2016). Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002384\">https://doi.org/10.1371/journal.pbio.1002384</a>","ieee":"N. Grion, A. Akrami, Y. Zuo, F. Stella, and M. Diamond, “Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination,” <i>PLoS Biology</i>, vol. 14, no. 2. Public Library of Science, 2016.","mla":"Grion, Natalia, et al. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” <i>PLoS Biology</i>, vol. 14, no. 2, e1002384, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002384\">10.1371/journal.pbio.1002384</a>.","chicago":"Grion, Natalia, Athena Akrami, Yangfang Zuo, Federico Stella, and Mathew Diamond. “Coherence between Rat Sensorimotor System and Hippocampus Is Enhanced during Tactile Discrimination.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.1002384\">https://doi.org/10.1371/journal.pbio.1002384</a>."},"day":"18","ddc":["570"],"month":"02","file_date_updated":"2020-07-14T12:44:57Z","has_accepted_license":"1","volume":14,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"3a5ce0d4e4e36bd6ceb4be761f85644a","date_updated":"2020-07-14T12:44:57Z","file_name":"IST-2016-518-v1+1_journal.pbio.1002384.PDF","relation":"main_file","file_size":2879899,"creator":"system","file_id":"5129","date_created":"2018-12-12T10:15:11Z"}]},{"_id":"1488","title":"Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","author":[{"last_name":"Riccio","full_name":"Riccio, Paul","first_name":"Paul"},{"last_name":"Cebrián","full_name":"Cebrián, Cristina","first_name":"Cristina"},{"last_name":"Zong","full_name":"Zong, Hui","first_name":"Hui"},{"orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"},{"last_name":"Costantini","full_name":"Costantini, Frank","first_name":"Frank"}],"doi":"10.1371/journal.pbio.1002382","abstract":[{"text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis.","lang":"eng"}],"issue":"2","status":"public","publication_status":"published","acknowledgement":"We thank Silvia Arber, Thomas Jessell, Kenneth M. Murphy, Carlton Bates, Hideki Enomoto, Liqun Luo and Andrew McMahon for mouse strains; Thomas Jessell for antibodies; and Laura Martinez Prat for experimental assistance.","month":"02","ddc":["570"],"file_date_updated":"2020-07-14T12:44:57Z","pubrep_id":"517","citation":{"chicago":"Riccio, Paul, Cristina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” <i>PLoS Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.1002382\">https://doi.org/10.1371/journal.pbio.1002382</a>.","mla":"Riccio, Paul, et al. “Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” <i>PLoS Biology</i>, vol. 14, no. 2, e1002382, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002382\">10.1371/journal.pbio.1002382</a>.","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., &#38; Costantini, F. (2016). Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002382\">https://doi.org/10.1371/journal.pbio.1002382</a>","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis,” <i>PLoS Biology</i>, vol. 14, no. 2. Public Library of Science, 2016.","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2016. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. PLoS Biology. 14(2), e1002382.","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. <i>PLoS Biology</i>. 2016;14(2). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002382\">10.1371/journal.pbio.1002382</a>","short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, PLoS Biology 14 (2016)."},"day":"19","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_created":"2018-12-12T10:13:42Z","file_id":"5027","checksum":"7f8fa1b3a29f94c0a14dd4465278cdbc","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:57Z","file_size":5904773,"relation":"main_file","creator":"system","file_name":"IST-2016-517-v1+1_journal.pbio.1002382_1_.PDF"}],"volume":14,"has_accepted_license":"1","oa":1,"year":"2016","date_updated":"2023-02-23T10:01:08Z","publication":"PLoS Biology","article_number":"e1002382","related_material":{"record":[{"id":"9703","relation":"research_data","status":"deleted"}]},"publist_id":"5699","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SiHi"}],"date_created":"2018-12-11T11:52:19Z","scopus_import":1,"date_published":"2016-02-19T00:00:00Z","publisher":"Public Library of Science","intvolume":"        14","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}]},{"_id":"1489","author":[{"last_name":"Ajanki","full_name":"Ajanki, Oskari H","first_name":"Oskari H","id":"36F2FB7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-4821-3297","last_name":"Krüger","full_name":"Krüger, Torben H","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"}],"title":"Local spectral statistics of Gaussian matrices with correlated entries","doi":"10.1007/s10955-016-1479-y","issue":"2","abstract":[{"lang":"eng","text":"We prove optimal local law, bulk universality and non-trivial decay for the off-diagonal elements of the resolvent for a class of translation invariant Gaussian random matrix ensembles with correlated entries. "}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). Oskari H. Ajanki was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council. László Erdős was Partially supported by ERC Advanced Grant RANMAT No. 338804. Torben Krüger was Partially supported by ERC Advanced Grant RANMAT No. 338804, and SFB-TR 12 Grant of the German Research Council.","ddc":["510"],"month":"04","file_date_updated":"2020-07-14T12:44:57Z","day":"01","pubrep_id":"516","citation":{"chicago":"Ajanki, Oskari H, László Erdös, and Torben H Krüger. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” <i>Journal of Statistical Physics</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s10955-016-1479-y\">https://doi.org/10.1007/s10955-016-1479-y</a>.","mla":"Ajanki, Oskari H., et al. “Local Spectral Statistics of Gaussian Matrices with Correlated Entries.” <i>Journal of Statistical Physics</i>, vol. 163, no. 2, Springer, 2016, pp. 280–302, doi:<a href=\"https://doi.org/10.1007/s10955-016-1479-y\">10.1007/s10955-016-1479-y</a>.","ieee":"O. H. Ajanki, L. Erdös, and T. H. Krüger, “Local spectral statistics of Gaussian matrices with correlated entries,” <i>Journal of Statistical Physics</i>, vol. 163, no. 2. Springer, pp. 280–302, 2016.","apa":"Ajanki, O. H., Erdös, L., &#38; Krüger, T. H. (2016). Local spectral statistics of Gaussian matrices with correlated entries. <i>Journal of Statistical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s10955-016-1479-y\">https://doi.org/10.1007/s10955-016-1479-y</a>","short":"O.H. Ajanki, L. Erdös, T.H. Krüger, Journal of Statistical Physics 163 (2016) 280–302.","ista":"Ajanki OH, Erdös L, Krüger TH. 2016. Local spectral statistics of Gaussian matrices with correlated entries. Journal of Statistical Physics. 163(2), 280–302.","ama":"Ajanki OH, Erdös L, Krüger TH. Local spectral statistics of Gaussian matrices with correlated entries. <i>Journal of Statistical Physics</i>. 2016;163(2):280-302. doi:<a href=\"https://doi.org/10.1007/s10955-016-1479-y\">10.1007/s10955-016-1479-y</a>"},"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"4869","date_created":"2018-12-12T10:11:16Z","file_name":"IST-2016-516-v1+1_s10955-016-1479-y.pdf","file_size":660602,"creator":"system","relation":"main_file","date_updated":"2020-07-14T12:44:57Z","access_level":"open_access","checksum":"7139598dcb1cafbe6866bd2bfd732b33","content_type":"application/pdf"}],"volume":163,"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","oa":1,"year":"2016","date_updated":"2021-01-12T06:51:05Z","publication":"Journal of Statistical Physics","page":"280 - 302","publist_id":"5698","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"LaEr"}],"scopus_import":1,"date_created":"2018-12-11T11:52:19Z","date_published":"2016-04-01T00:00:00Z","intvolume":"       163","publisher":"Springer","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1"},{"date_published":"2016-02-23T00:00:00Z","date_created":"2018-12-11T11:52:19Z","scopus_import":1,"department":[{"_id":"MiSi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5697","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Cell Press","intvolume":"        14","year":"2016","oa":1,"page":"1723 - 1734","publication":"Cell Reports","date_updated":"2021-01-12T06:51:07Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","pubrep_id":"515","citation":{"ista":"Russo E, Teijeira A, Vaahtomeri K, Willrodt A, Bloch J, Nitschké M, Santambrogio L, Kerjaschki D, Sixt MK, Halin C. 2016. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. Cell Reports. 14(7), 1723–1734.","ama":"Russo E, Teijeira A, Vaahtomeri K, et al. Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. <i>Cell Reports</i>. 2016;14(7):1723-1734. doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.01.048\">10.1016/j.celrep.2016.01.048</a>","short":"E. Russo, A. Teijeira, K. Vaahtomeri, A. Willrodt, J. Bloch, M. Nitschké, L. Santambrogio, D. Kerjaschki, M.K. Sixt, C. Halin, Cell Reports 14 (2016) 1723–1734.","apa":"Russo, E., Teijeira, A., Vaahtomeri, K., Willrodt, A., Bloch, J., Nitschké, M., … Halin, C. (2016). Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2016.01.048\">https://doi.org/10.1016/j.celrep.2016.01.048</a>","ieee":"E. Russo <i>et al.</i>, “Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels,” <i>Cell Reports</i>, vol. 14, no. 7. Cell Press, pp. 1723–1734, 2016.","chicago":"Russo, Erica, Alvaro Teijeira, Kari Vaahtomeri, Ann Willrodt, Joël Bloch, Maximilian Nitschké, Laura Santambrogio, Dontscho Kerjaschki, Michael K Sixt, and Cornelia Halin. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” <i>Cell Reports</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.celrep.2016.01.048\">https://doi.org/10.1016/j.celrep.2016.01.048</a>.","mla":"Russo, Erica, et al. “Intralymphatic CCL21 Promotes Tissue Egress of Dendritic Cells through Afferent Lymphatic Vessels.” <i>Cell Reports</i>, vol. 14, no. 7, Cell Press, 2016, pp. 1723–34, doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.01.048\">10.1016/j.celrep.2016.01.048</a>."},"day":"23","ddc":["570"],"file_date_updated":"2020-07-14T12:44:58Z","month":"02","has_accepted_license":"1","volume":14,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"file_id":"4948","date_created":"2018-12-12T10:12:30Z","access_level":"open_access","content_type":"application/pdf","checksum":"c98c1151d5f1e5ce1643a83d8d7f3c29","date_updated":"2020-07-14T12:44:58Z","file_name":"IST-2016-515-v1+1_1-s2.0-S2211124716300262-main.pdf","creator":"system","relation":"main_file","file_size":5489897}],"abstract":[{"text":"To induce adaptive immunity, dendritic cells (DCs) migrate through afferent lymphatic vessels (LVs) to draining lymph nodes (dLNs). This process occurs in several consecutive steps. Upon entry into lymphatic capillaries, DCs first actively crawl into downstream collecting vessels. From there, they are next passively and rapidly transported to the dLN by lymph flow. Here, we describe a role for the chemokine CCL21 in intralymphatic DC crawling. Performing time-lapse imaging in murine skin, we found that blockade of CCL21-but not the absence of lymph flow-completely abolished DC migration from capillaries toward collecting vessels and reduced the ability of intralymphatic DCs to emigrate from skin. Moreover, we found that in vitro low laminar flow established a CCL21 gradient along lymphatic endothelial monolayers, thereby inducing downstream-directed DC migration. These findings reveal a role for intralymphatic CCL21 in promoting DC trafficking to dLNs, through the formation of a flow-induced gradient.","lang":"eng"}],"issue":"7","doi":"10.1016/j.celrep.2016.01.048","title":"Intralymphatic CCL21 promotes tissue egress of dendritic cells through afferent lymphatic vessels","author":[{"first_name":"Erica","full_name":"Russo, Erica","last_name":"Russo"},{"last_name":"Teijeira","full_name":"Teijeira, Alvaro","first_name":"Alvaro"},{"orcid":"0000-0001-7829-3518","first_name":"Kari","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","full_name":"Vaahtomeri, Kari"},{"last_name":"Willrodt","full_name":"Willrodt, Ann","first_name":"Ann"},{"first_name":"Joël","full_name":"Bloch, Joël","last_name":"Bloch"},{"full_name":"Nitschké, Maximilian","last_name":"Nitschké","first_name":"Maximilian"},{"last_name":"Santambrogio","full_name":"Santambrogio, Laura","first_name":"Laura"},{"first_name":"Dontscho","full_name":"Kerjaschki, Dontscho","last_name":"Kerjaschki"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"},{"first_name":"Cornelia","full_name":"Halin, Cornelia","last_name":"Halin"}],"_id":"1490","status":"public","publication_status":"published"},{"oa_version":"Submitted Version","day":"01","citation":{"chicago":"Lewin, Mathieu, Phan Nam, and Nicolas Rougerie. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” <i>Transactions of the American Mathematical Society</i>. American Mathematical Society, 2016. <a href=\"https://doi.org/10.1090/tran/6537\">https://doi.org/10.1090/tran/6537</a>.","mla":"Lewin, Mathieu, et al. “The Mean-Field Approximation and the Non-Linear Schrödinger Functional for Trapped Bose Gases.” <i>Transactions of the American Mathematical Society</i>, vol. 368, no. 9, American Mathematical Society, 2016, pp. 6131–57, doi:<a href=\"https://doi.org/10.1090/tran/6537\">10.1090/tran/6537</a>.","ieee":"M. Lewin, P. Nam, and N. Rougerie, “The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases,” <i>Transactions of the American Mathematical Society</i>, vol. 368, no. 9. American Mathematical Society, pp. 6131–6157, 2016.","apa":"Lewin, M., Nam, P., &#38; Rougerie, N. (2016). The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. <i>Transactions of the American Mathematical Society</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/tran/6537\">https://doi.org/10.1090/tran/6537</a>","ista":"Lewin M, Nam P, Rougerie N. 2016. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. Transactions of the American Mathematical Society. 368(9), 6131–6157.","short":"M. Lewin, P. Nam, N. Rougerie, Transactions of the American Mathematical Society 368 (2016) 6131–6157.","ama":"Lewin M, Nam P, Rougerie N. The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases. <i>Transactions of the American Mathematical Society</i>. 2016;368(9):6131-6157. doi:<a href=\"https://doi.org/10.1090/tran/6537\">10.1090/tran/6537</a>"},"month":"01","volume":368,"issue":"9","abstract":[{"text":"We study the ground state of a trapped Bose gas, starting from the full many-body Schrödinger Hamiltonian, and derive the non-linear Schrödinger energy functional in the limit of a large particle number, when the interaction potential converges slowly to a Dirac delta function. Our method is based on quantitative estimates on the discrepancy between the full many-body energy and its mean-field approximation using Hartree states. These are proved using finite dimensional localization and a quantitative version of the quantum de Finetti theorem. Our approach covers the case of attractive interactions in the regime of stability. In particular, our main new result is a derivation of the 2D attractive non-linear Schrödinger ground state.","lang":"eng"}],"doi":"10.1090/tran/6537","author":[{"last_name":"Lewin","full_name":"Lewin, Mathieu","first_name":"Mathieu"},{"full_name":"Nam, Phan","last_name":"Nam","id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan"},{"first_name":"Nicolas","last_name":"Rougerie","full_name":"Rougerie, Nicolas"}],"title":"The mean-field approximation and the non-linear Schrödinger functional for trapped Bose gases","_id":"1491","publication_status":"published","acknowledgement":"The authors acknowledge financial support from the European Research Council (FP7/2007-2013 Grant Agreement MNIQS 258023) and the ANR (Mathostaq project, ANR-13-JS01-0005-01). The second and third authors have benefited from the hospitality of the Institute for Mathematical Science of the National University of Singapore.","status":"public","date_published":"2016-01-01T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:52:20Z","department":[{"_id":"RoSe"}],"publist_id":"5692","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1405.3220"}],"intvolume":"       368","publisher":"American Mathematical Society","year":"2016","oa":1,"page":"6131 - 6157","publication":"Transactions of the American Mathematical Society","date_updated":"2021-01-12T06:51:07Z"},{"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc/4.0/","pmid":1,"ddc":["570"],"month":"03","file_date_updated":"2020-07-14T12:44:58Z","day":"01","citation":{"chicago":"Marhavý, Peter, Juan C Montesinos López, Anas Abuzeineh, Daniël Van Damme, Joop Vermeer, Jérôme Duclercq, Hana Rakusova, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press, 2016. <a href=\"https://doi.org/10.1101/gad.276964.115\">https://doi.org/10.1101/gad.276964.115</a>.","mla":"Marhavý, Peter, et al. “Targeted Cell Elimination Reveals an Auxin-Guided Biphasic Mode of Lateral Root Initiation.” <i>Genes and Development</i>, vol. 30, no. 4, Cold Spring Harbor Laboratory Press, 2016, pp. 471–83, doi:<a href=\"https://doi.org/10.1101/gad.276964.115\">10.1101/gad.276964.115</a>.","apa":"Marhavý, P., Montesinos López, J. C., Abuzeineh, A., Van Damme, D., Vermeer, J., Duclercq, J., … Benková, E. (2016). Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. <i>Genes and Development</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gad.276964.115\">https://doi.org/10.1101/gad.276964.115</a>","ieee":"P. Marhavý <i>et al.</i>, “Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation,” <i>Genes and Development</i>, vol. 30, no. 4. Cold Spring Harbor Laboratory Press, pp. 471–483, 2016.","ista":"Marhavý P, Montesinos López JC, Abuzeineh A, Van Damme D, Vermeer J, Duclercq J, Rakusova H, Marhavá P, Friml J, Geldner N, Benková E. 2016. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. Genes and Development. 30(4), 471–483.","ama":"Marhavý P, Montesinos López JC, Abuzeineh A, et al. Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation. <i>Genes and Development</i>. 2016;30(4):471-483. doi:<a href=\"https://doi.org/10.1101/gad.276964.115\">10.1101/gad.276964.115</a>","short":"P. Marhavý, J.C. Montesinos López, A. Abuzeineh, D. Van Damme, J. Vermeer, J. Duclercq, H. Rakusova, P. Marhavá, J. Friml, N. Geldner, E. Benková, Genes and Development 30 (2016) 471–483."},"volume":30,"has_accepted_license":"1","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"date_updated":"2020-07-14T12:44:58Z","checksum":"ea394498ee56270e021d1028a29358a0","content_type":"application/pdf","access_level":"open_access","creator":"kschuh","file_size":2757636,"relation":"main_file","file_name":"2016_GeneDev_Marhavy.pdf","date_created":"2019-01-25T09:56:11Z","file_id":"5883"}],"doi":"10.1101/gad.276964.115","issue":"4","abstract":[{"lang":"eng","text":"To sustain a lifelong ability to initiate organs, plants retain pools of undifferentiated cells with a preserved prolif eration capacity. The root pericycle represents a unique tissue with conditional meristematic activity, and its tight control determines initiation of lateral organs. Here we show that the meristematic activity of the pericycle is constrained by the interaction with the adjacent endodermis. Release of these restraints by elimination of endo dermal cells by single-cell ablation triggers the pericycle to re-enter the cell cycle. We found that endodermis removal substitutes for the phytohormone auxin-dependent initiation of the pericycle meristematic activity. However, auxin is indispensable to steer the cell division plane orientation of new organ-defining divisions. We propose a dual, spatiotemporally distinct role for auxin during lateral root initiation. In the endodermis, auxin releases constraints arising from cell-to-cell interactions that compromise the pericycle meristematic activity, whereas, in the pericycle, auxin defines the orientation of the cell division plane to initiate lateral roots."}],"_id":"1492","author":[{"last_name":"Marhavy","full_name":"Marhavy, Peter","first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741"},{"orcid":"0000-0001-9179-6099","last_name":"Montesinos López","full_name":"Montesinos López, Juan C","first_name":"Juan C","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anas","last_name":"Abuzeineh","full_name":"Abuzeineh, Anas"},{"full_name":"Van Damme, Daniël","last_name":"Van Damme","first_name":"Daniël"},{"first_name":"Joop","full_name":"Vermeer, Joop","last_name":"Vermeer"},{"first_name":"Jérôme","full_name":"Duclercq, Jérôme","last_name":"Duclercq"},{"first_name":"Hana","last_name":"Rakusova","full_name":"Rakusova, Hana"},{"first_name":"Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá","full_name":"Marhavá, Petra"},{"full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","orcid":"0000-0002-8302-7596"},{"last_name":"Geldner","full_name":"Geldner, Niko","first_name":"Niko"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"title":"Targeted cell elimination reveals an auxin-guided biphasic mode of lateral root initiation","publication_status":"published","acknowledgement":"This work was supported by a European Research Council Starting Inde-pendent Research grant (ERC-2007-Stg-207362-HCPO to J.D.), Research Foundation-Flanders (G033711N to A.A.), and the Austrian Science Fund (FWF01_I1774S to E.B.). P.M. is indebted to the Federation of European Biochemical Sciences for a Long-Term Fellowship. ","status":"public","acknowledged_ssus":[{"_id":"LifeSc"}],"scopus_import":1,"date_created":"2018-12-11T11:52:20Z","external_id":{"pmid":["    26883363"]},"date_published":"2016-03-01T00:00:00Z","publist_id":"5691","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EvBe"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"intvolume":"        30","publisher":"Cold Spring Harbor Laboratory Press","year":"2016","oa":1,"page":"471 - 483","date_updated":"2021-01-12T06:51:08Z","publication":"Genes and Development"},{"oa":1,"year":"2016","publication":"Mathematical Physics, Analysis and Geometry","date_updated":"2021-01-12T06:51:08Z","article_number":"3","department":[{"_id":"RoSe"}],"publist_id":"5690","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2016-03-01T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:52:20Z","intvolume":"        19","publisher":"Springer","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","author":[{"first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrat","full_name":"Petrat, Sören P","orcid":"0000-0002-9166-5889"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"}],"title":"A new method and a new scaling for deriving fermionic mean-field dynamics","_id":"1493","issue":"1","abstract":[{"text":"We introduce a new method for deriving the time-dependent Hartree or Hartree-Fock equations as an effective mean-field dynamics from the microscopic Schrödinger equation for fermionic many-particle systems in quantum mechanics. The method is an adaption of the method used in Pickl (Lett. Math. Phys. 97 (2) 151–164 2011) for bosonic systems to fermionic systems. It is based on a Gronwall type estimate for a suitable measure of distance between the microscopic solution and an antisymmetrized product state. We use this method to treat a new mean-field limit for fermions with long-range interactions in a large volume. Some of our results hold for singular attractive or repulsive interactions. We can also treat Coulomb interaction assuming either a mild singularity cutoff or certain regularity conditions on the solutions to the Hartree(-Fock) equations. In the considered limit, the kinetic and interaction energy are of the same order, while the average force is subleading. For some interactions, we prove that the Hartree(-Fock) dynamics is a more accurate approximation than a simpler dynamics that one would expect from the subleading force. With our method we also treat the mean-field limit coupled to a semiclassical limit, which was discussed in the literature before, and we recover some of the previous results. All results hold for initial data close (but not necessarily equal) to antisymmetrized product states and we always provide explicit rates of convergence.","lang":"eng"}],"doi":"10.1007/s11040-016-9204-2","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication_status":"published","status":"public","acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). ","ec_funded":1,"day":"01","citation":{"mla":"Petrat, Sören P., and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 19, no. 1, 3, Springer, 2016, doi:<a href=\"https://doi.org/10.1007/s11040-016-9204-2\">10.1007/s11040-016-9204-2</a>.","chicago":"Petrat, Sören P, and Peter Pickl. “A New Method and a New Scaling for Deriving Fermionic Mean-Field Dynamics.” <i>Mathematical Physics, Analysis and Geometry</i>. Springer, 2016. <a href=\"https://doi.org/10.1007/s11040-016-9204-2\">https://doi.org/10.1007/s11040-016-9204-2</a>.","ieee":"S. P. Petrat and P. Pickl, “A new method and a new scaling for deriving fermionic mean-field dynamics,” <i>Mathematical Physics, Analysis and Geometry</i>, vol. 19, no. 1. Springer, 2016.","apa":"Petrat, S. P., &#38; Pickl, P. (2016). A new method and a new scaling for deriving fermionic mean-field dynamics. <i>Mathematical Physics, Analysis and Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s11040-016-9204-2\">https://doi.org/10.1007/s11040-016-9204-2</a>","ama":"Petrat SP, Pickl P. A new method and a new scaling for deriving fermionic mean-field dynamics. <i>Mathematical Physics, Analysis and Geometry</i>. 2016;19(1). doi:<a href=\"https://doi.org/10.1007/s11040-016-9204-2\">10.1007/s11040-016-9204-2</a>","ista":"Petrat SP, Pickl P. 2016. A new method and a new scaling for deriving fermionic mean-field dynamics. Mathematical Physics, Analysis and Geometry. 19(1), 3.","short":"S.P. Petrat, P. Pickl, Mathematical Physics, Analysis and Geometry 19 (2016)."},"pubrep_id":"514","month":"03","ddc":["510","530"],"file_date_updated":"2020-07-14T12:44:58Z","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_name":"IST-2016-514-v1+1_s11040-016-9204-2.pdf","relation":"main_file","file_size":911310,"creator":"system","access_level":"open_access","checksum":"eb5d2145ef0d377c4f78bf06e18f4529","content_type":"application/pdf","date_updated":"2020-07-14T12:44:58Z","file_id":"5246","date_created":"2018-12-12T10:16:55Z"}],"has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","volume":19},{"date_updated":"2021-01-12T06:51:08Z","publication":"Nature Physics","page":"254 - 258","year":"2016","publisher":"Nature Publishing Group","intvolume":"        12","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5685","department":[{"_id":"BjHo"}],"date_created":"2018-12-11T11:52:21Z","scopus_import":1,"date_published":"2016-02-15T00:00:00Z","project":[{"name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589"},{"name":"Astrophysical instability of currents and turbulences","_id":"2511D90C-B435-11E9-9278-68D0E5697425","grant_number":"SFB 963  TP A8"}],"ec_funded":1,"status":"public","acknowledgement":"We thank P. Maier for providing valuable ideas and supporting us in the technical aspects. Discussions with D. Barkley, Y. Duguet, B. Eckhart, N. Goldenfeld, P. Manneville and K. Takeuchi are gratefully acknowledged. We acknowledge the Deutsche Forschungsgemeinschaft (Project No. FOR 1182), and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589 for financial support. L.S. and B.H. acknowledge research funding by Deutsche Forschungsgemeinschaft (DFG) under Grant No. SFB 963/1 (project A8). Numerical simulations were performed thanks to the CPU time allocations of JUROPA in Juelich Supercomputing Center (project HGU17) and of the Max Planck Computing and Data Facility (Garching, Germany). Excellent technical support from M. Rampp on the hybrid code nsCouette is appreciated.","publication_status":"published","_id":"1494","title":"Directed percolation phase transition to sustained turbulence in Couette flow","author":[{"full_name":"Lemoult, Grégoire M","last_name":"Lemoult","id":"4787FE80-F248-11E8-B48F-1D18A9856A87","first_name":"Grégoire M"},{"full_name":"Shi, Liang","last_name":"Shi","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","first_name":"Liang"},{"first_name":"Kerstin","full_name":"Avila, Kerstin","last_name":"Avila"},{"full_name":"Jalikop, Shreyas V","last_name":"Jalikop","id":"44A1D772-F248-11E8-B48F-1D18A9856A87","first_name":"Shreyas V"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"doi":"10.1038/nphys3675","abstract":[{"text":"Turbulence is one of the most frequently encountered non-equilibrium phenomena in nature, yet characterizing the transition that gives rise to turbulence in basic shear flows has remained an elusive task. Although, in recent studies, critical points marking the onset of sustained turbulence have been determined for several such flows, the physical nature of the transition could not be fully explained. In extensive experimental and computational studies we show for the example of Couette flow that the onset of turbulence is a second-order phase transition and falls into the directed percolation universality class. Consequently, the complex laminar–turbulent patterns distinctive for the onset of turbulence in shear flows result from short-range interactions of turbulent domains and are characterized by universal critical exponents. More generally, our study demonstrates that even high-dimensional systems far from equilibrium such as turbulence exhibit universality at onset and that here the collective dynamics obeys simple rules.","lang":"eng"}],"issue":"3","volume":12,"month":"02","citation":{"mla":"Lemoult, Grégoire M., et al. “Directed Percolation Phase Transition to Sustained Turbulence in Couette Flow.” <i>Nature Physics</i>, vol. 12, no. 3, Nature Publishing Group, 2016, pp. 254–58, doi:<a href=\"https://doi.org/10.1038/nphys3675\">10.1038/nphys3675</a>.","chicago":"Lemoult, Grégoire M, Liang Shi, Kerstin Avila, Shreyas V Jalikop, Marc Avila, and Björn Hof. “Directed Percolation Phase Transition to Sustained Turbulence in Couette Flow.” <i>Nature Physics</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nphys3675\">https://doi.org/10.1038/nphys3675</a>.","ama":"Lemoult GM, Shi L, Avila K, Jalikop SV, Avila M, Hof B. Directed percolation phase transition to sustained turbulence in Couette flow. <i>Nature Physics</i>. 2016;12(3):254-258. doi:<a href=\"https://doi.org/10.1038/nphys3675\">10.1038/nphys3675</a>","short":"G.M. Lemoult, L. Shi, K. Avila, S.V. Jalikop, M. Avila, B. Hof, Nature Physics 12 (2016) 254–258.","ista":"Lemoult GM, Shi L, Avila K, Jalikop SV, Avila M, Hof B. 2016. Directed percolation phase transition to sustained turbulence in Couette flow. Nature Physics. 12(3), 254–258.","ieee":"G. M. Lemoult, L. Shi, K. Avila, S. V. Jalikop, M. Avila, and B. Hof, “Directed percolation phase transition to sustained turbulence in Couette flow,” <i>Nature Physics</i>, vol. 12, no. 3. Nature Publishing Group, pp. 254–258, 2016.","apa":"Lemoult, G. M., Shi, L., Avila, K., Jalikop, S. V., Avila, M., &#38; Hof, B. (2016). Directed percolation phase transition to sustained turbulence in Couette flow. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys3675\">https://doi.org/10.1038/nphys3675</a>"},"day":"15","oa_version":"None"},{"month":"03","citation":{"chicago":"Amaro, Pedro, Filippo Fratini, Laleh Safari, Jorge Machado, Mauro Guerra, Paul Indelicato, and José Santos. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society, 2016. <a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">https://doi.org/10.1103/PhysRevA.93.032502</a>.","mla":"Amaro, Pedro, et al. “Relativistic Evaluation of the Two-Photon Decay of the Metastable 1s22s2p3P0 State in Berylliumlike Ions with an Effective-Potential Model.” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3, 032502, American Physical Society, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">10.1103/PhysRevA.93.032502</a>.","ista":"Amaro P, Fratini F, Safari L, Machado J, Guerra M, Indelicato P, Santos J. 2016. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. Physical Review A - Atomic, Molecular, and Optical Physics. 93(3), 032502.","ama":"Amaro P, Fratini F, Safari L, et al. Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. 2016;93(3). doi:<a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">10.1103/PhysRevA.93.032502</a>","short":"P. Amaro, F. Fratini, L. Safari, J. Machado, M. Guerra, P. Indelicato, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 93 (2016).","ieee":"P. Amaro <i>et al.</i>, “Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model,” <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>, vol. 93, no. 3. American Physical Society, 2016.","apa":"Amaro, P., Fratini, F., Safari, L., Machado, J., Guerra, M., Indelicato, P., &#38; Santos, J. (2016). Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model. <i>Physical Review A - Atomic, Molecular, and Optical Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.93.032502\">https://doi.org/10.1103/PhysRevA.93.032502</a>"},"day":"07","oa_version":"Preprint","volume":93,"_id":"1496","title":"Relativistic evaluation of the two-photon decay of the metastable 1s22s2p3P0 state in berylliumlike ions with an effective-potential model","author":[{"last_name":"Amaro","full_name":"Amaro, Pedro","first_name":"Pedro"},{"first_name":"Filippo","last_name":"Fratini","full_name":"Fratini, Filippo"},{"first_name":"Laleh","id":"3C325E5E-F248-11E8-B48F-1D18A9856A87","last_name":"Safari","full_name":"Safari, Laleh"},{"last_name":"Machado","full_name":"Machado, Jorge","first_name":"Jorge"},{"first_name":"Mauro","full_name":"Guerra, Mauro","last_name":"Guerra"},{"first_name":"Paul","last_name":"Indelicato","full_name":"Indelicato, Paul"},{"first_name":"José","last_name":"Santos","full_name":"Santos, José"}],"doi":"10.1103/PhysRevA.93.032502","abstract":[{"lang":"eng","text":"The two-photon 1s2 2s 2p 3P0 1s22s2 1S0 transition in berylliumlike ions is theoretically investigated within a fully relativistic framework and a second-order perturbation theory. We focus our analysis on how electron correlation, as well as the negative-energy spectrum, can affect the forbidden E1M1 decay rate. For this purpose, we include the electronic correlation via an effective local potential and within a single configuration-state model. Due to its experimental interest, evaluations of decay rates are performed for berylliumlike xenon and uranium. We find that the negative-energy contribution can be neglected at the present level of accuracy in the evaluation of the decay rate. On the other hand, if contributions of electronic correlation are not carefully taken into account, it may change the lifetime of the metastable state by up to 20%. By performing a full-relativistic jj-coupling calculation, we found a decrease of the decay rate by two orders of magnitude compared to non-relativistic LS-coupling calculations, for the selected heavy ions."}],"issue":"3","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"ec_funded":1,"publication_status":"published","acknowledgement":"This  research  was  supported  in  part  by  FCT, Portugal, through Project No. PTDC/FIS/117606/2010, financed by the European Community  Fund  FEDER  through  the  COMPETE. ","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5683","department":[{"_id":"MiLe"}],"date_created":"2018-12-11T11:52:21Z","scopus_import":1,"date_published":"2016-03-07T00:00:00Z","publisher":"American Physical Society","intvolume":"        93","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1508.06169"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","oa":1,"year":"2016","date_updated":"2021-01-12T06:51:09Z","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","article_number":"032502"},{"date_updated":"2025-05-28T11:42:48Z","publication":"Genetics","page":"775 - 786","article_type":"original","oa":1,"year":"2016","publisher":"Genetics Society of America","intvolume":"       202","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5658","department":[{"_id":"KrCh"},{"_id":"NiBa"}],"date_created":"2018-12-11T11:52:29Z","scopus_import":"1","external_id":{"pmid":["26715666"]},"date_published":"2016-02-01T00:00:00Z","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"ec_funded":1,"acknowledgement":"We thank Lynsey Bunnefeld for discussions throughout the project and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on an earlier version of this manuscript. This work was supported by funding from the\r\nUnited Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant from the European\r\nResearch Council (250152) (to N.H.B.).","publication_status":"published","status":"public","_id":"1518","title":"Efficient strategies for calculating blockwise likelihoods under the coalescent","author":[{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"last_name":"Martin","full_name":"Martin, Simon","first_name":"Simon"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"doi":"10.1534/genetics.115.183814","abstract":[{"lang":"eng","text":"The inference of demographic history from genome data is hindered by a lack of efficient computational approaches. In particular, it has proved difficult to exploit the information contained in the distribution of genealogies across the genome. We have previously shown that the generating function (GF) of genealogies can be used to analytically compute likelihoods of demographic models from configurations of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has a simple, recursive form, the size of such likelihood calculations explodes quickly with the number of individuals and applications of this framework have so far been mainly limited to small samples (pairs and triplets) for which the GF can be written by hand. Here we investigate several strategies for exploiting the inherent symmetries of the coalescent. In particular, we show that the GF of genealogies can be decomposed into a set of equivalence classes that allows likelihood calculations from nontrivial samples. Using this strategy, we automated blockwise likelihood calculations for a general set of demographic scenarios in Mathematica. These histories may involve population size changes, continuous migration, discrete divergence, and admixture between multiple populations. To give a concrete example, we calculate the likelihood for a model of isolation with migration (IM), assuming two diploid samples without phase and outgroup information. We demonstrate the new inference scheme with an analysis of two individual butterfly genomes from the sister species Heliconius melpomene rosina and H. cydno."}],"issue":"2","file":[{"date_created":"2018-12-12T10:16:51Z","file_id":"5241","date_updated":"2020-07-14T12:45:00Z","checksum":"41c9b5d72e7fe4624dd22dfe622337d5","content_type":"application/pdf","access_level":"open_access","file_size":957466,"creator":"system","relation":"main_file","file_name":"IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf"}],"volume":202,"article_processing_charge":"No","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:00Z","ddc":["570"],"pmid":1,"month":"02","citation":{"mla":"Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>, vol. 202, no. 2, Genetics Society of America, 2016, pp. 775–86, doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>.","chicago":"Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient Strategies for Calculating Blockwise Likelihoods under the Coalescent.” <i>Genetics</i>. Genetics Society of America, 2016. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>.","short":"K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.","ama":"Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. 2016;202(2):775-786. doi:<a href=\"https://doi.org/10.1534/genetics.115.183814\">10.1534/genetics.115.183814</a>","ista":"Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.","ieee":"K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for calculating blockwise likelihoods under the coalescent,” <i>Genetics</i>, vol. 202, no. 2. Genetics Society of America, pp. 775–786, 2016.","apa":"Lohse, K., Chmelik, M., Martin, S., &#38; Barton, N. H. (2016). Efficient strategies for calculating blockwise likelihoods under the coalescent. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.115.183814\">https://doi.org/10.1534/genetics.115.183814</a>"},"pubrep_id":"561","day":"01","oa_version":"Preprint"},{"date_published":"2016-07-01T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:52:30Z","oa_version":"None","day":"01","department":[{"_id":"LeSa"}],"citation":{"short":"J. Berrisford, R. Baradaran, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1857 (2016) 892–901.","ista":"Berrisford J, Baradaran R, Sazanov LA. 2016. Structure of bacterial respiratory complex I. Biochimica et Biophysica Acta - Bioenergetics. 1857(7), 892–901.","ama":"Berrisford J, Baradaran R, Sazanov LA. Structure of bacterial respiratory complex I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. 2016;1857(7):892-901. doi:<a href=\"https://doi.org/10.1016/j.bbabio.2016.01.012\">10.1016/j.bbabio.2016.01.012</a>","ieee":"J. Berrisford, R. Baradaran, and L. A. Sazanov, “Structure of bacterial respiratory complex I,” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1857, no. 7. Elsevier, pp. 892–901, 2016.","apa":"Berrisford, J., Baradaran, R., &#38; Sazanov, L. A. (2016). Structure of bacterial respiratory complex I. <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbabio.2016.01.012\">https://doi.org/10.1016/j.bbabio.2016.01.012</a>","chicago":"Berrisford, John, Rozbeh Baradaran, and Leonid A Sazanov. “Structure of Bacterial Respiratory Complex I.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.bbabio.2016.01.012\">https://doi.org/10.1016/j.bbabio.2016.01.012</a>.","mla":"Berrisford, John, et al. “Structure of Bacterial Respiratory Complex I.” <i>Biochimica et Biophysica Acta - Bioenergetics</i>, vol. 1857, no. 7, Elsevier, 2016, pp. 892–901, doi:<a href=\"https://doi.org/10.1016/j.bbabio.2016.01.012\">10.1016/j.bbabio.2016.01.012</a>."},"publist_id":"5654","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"07","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","volume":1857,"intvolume":"      1857","publisher":"Elsevier","year":"2016","issue":"7","abstract":[{"text":"Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. It is the largest protein assembly of respiratory chains and one of the most elaborate redox membrane proteins known. Bacterial enzyme is about half the size of mitochondrial and thus provides its important &quot;minimal&quot; model. Dysfunction of mitochondrial complex I is implicated in many human neurodegenerative diseases. The L-shaped complex consists of a hydrophilic arm, where electron transfer occurs, and a membrane arm, where proton translocation takes place. We have solved the crystal structures of the hydrophilic domain of complex I from Thermus thermophilus, the membrane domain from Escherichia coli and recently of the intact, entire complex I from T. thermophilus (536. kDa, 16 subunits, 9 iron-sulphur clusters, 64 transmembrane helices). The 95. Å long electron transfer pathway through the enzyme proceeds from the primary electron acceptor flavin mononucleotide through seven conserved Fe-S clusters to the unusual elongated quinone-binding site at the interface with the membrane domain. Four putative proton translocation channels are found in the membrane domain, all linked by the central flexible axis containing charged residues. The redox energy of electron transfer is coupled to proton translocation by the as yet undefined mechanism proposed to involve long-range conformational changes. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.","lang":"eng"}],"doi":"10.1016/j.bbabio.2016.01.012","author":[{"full_name":"Berrisford, John","last_name":"Berrisford","first_name":"John"},{"full_name":"Baradaran, Rozbeh","last_name":"Baradaran","first_name":"Rozbeh"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"}],"title":"Structure of bacterial respiratory complex I","_id":"1521","publication_status":"published","acknowledgement":"funded by the Medical Research Council (Grant number MC_U105674180)","status":"public","page":"892 - 901","publication":"Biochimica et Biophysica Acta - Bioenergetics","date_updated":"2021-01-12T06:51:21Z"}]