[{"scopus_import":"1","publication":"Scientific Reports","date_published":"2019-11-12T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1038/s41598-019-53049-w","title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","publication_identifier":{"eissn":["2045-2322"]},"pmid":1,"article_number":"16565","year":"2019","intvolume":"         9","article_processing_charge":"No","month":"11","volume":9,"isi":1,"abstract":[{"lang":"eng","text":"BAX, a member of the BCL2 gene family, controls the committed step of the intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed feature of apoptosis, which occurs through the process of mitochondrial fission. BAX has consistently been associated with mitochondrial fission, yet how BAX participates in the process of mitochondrial fragmentation during apoptosis remains to be tested. Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates that rapid mitochondrial fragmentation during apoptosis occurs after the complete recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement of a fully functioning BAX protein for the fission process was demonstrated further in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant performed fusion to restore the mitochondrial network. but was not demonstrably recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial fragmentation was blocked. Additionally, we show that loss of the fission protein, dynamin-like protein 1 (DRP1), does not temporally affect the initiation time or rate of BAX recruitment, but does reduce the final level of BAX recruited to the MOM during the late phase of BAX recruitment. These correlative observations suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial fragmentation machinery in apoptotic cells."}],"department":[{"_id":"SaSi"}],"status":"public","oa_version":"Published Version","file":[{"file_name":"2019_ScientificReports_Maes.pdf","file_size":6467393,"date_updated":"2020-07-14T12:47:49Z","content_type":"application/pdf","checksum":"9ab397ed9c1c454b34bffb8cc863d734","relation":"main_file","date_created":"2019-11-25T07:49:52Z","creator":"dernst","file_id":"7096","access_level":"open_access"}],"citation":{"mla":"Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” <i>Scientific Reports</i>, vol. 9, 16565, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41598-019-53049-w\">10.1038/s41598-019-53049-w</a>.","apa":"Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., &#38; Nickells, R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-019-53049-w\">https://doi.org/10.1038/s41598-019-53049-w</a>","chicago":"Maes, Margaret E, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” <i>Scientific Reports</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41598-019-53049-w\">https://doi.org/10.1038/s41598-019-53049-w</a>.","ieee":"M. E. Maes, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells, “Completion of BAX recruitment correlates with mitochondrial fission during apoptosis,” <i>Scientific Reports</i>, vol. 9. Springer Nature, 2019.","ista":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. 2019. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 9, 16565.","ama":"Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. <i>Scientific Reports</i>. 2019;9. doi:<a href=\"https://doi.org/10.1038/s41598-019-53049-w\">10.1038/s41598-019-53049-w</a>","short":"M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific Reports 9 (2019)."},"article_type":"original","date_created":"2019-11-25T07:45:17Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2023-08-30T07:26:54Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"12","external_id":{"pmid":["31719602"],"isi":["000495857600019"]},"quality_controlled":"1","publication_status":"published","_id":"7095","author":[{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","orcid":"0000-0001-9642-1085","last_name":"Maes","full_name":"Maes, Margaret E"},{"first_name":"J. A.","full_name":"Grosser, J. A.","last_name":"Grosser"},{"last_name":"Fehrman","full_name":"Fehrman, R. L.","first_name":"R. L."},{"first_name":"C. L.","last_name":"Schlamp","full_name":"Schlamp, C. L."},{"first_name":"R. W.","full_name":"Nickells, R. W.","last_name":"Nickells"}],"ddc":["570"],"has_accepted_license":"1","publisher":"Springer Nature","oa":1,"file_date_updated":"2020-07-14T12:47:49Z"},{"date_updated":"2023-08-30T07:27:55Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"15","external_id":{"isi":["000496767800005"]},"quality_controlled":"1","publication_status":"published","_id":"7097","author":[{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"first_name":"Junko Y.","last_name":"Toshima","full_name":"Toshima, Junko Y."},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Toshima","full_name":"Toshima, Jiro","first_name":"Jiro"}],"has_accepted_license":"1","ddc":["570"],"publisher":"Springer Nature","file_date_updated":"2020-07-14T12:47:49Z","oa":1,"scopus_import":"1","date_published":"2019-11-15T00:00:00Z","publication":"Communications Biology","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1038/s42003-019-0670-5","title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","publication_identifier":{"issn":["2399-3642"]},"article_number":"419","issue":"1","year":"2019","intvolume":"         2","article_processing_charge":"No","abstract":[{"text":"Early endosomes, also called sorting endosomes, are known to mature into late endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early endosome existence isthought to be maintained by the continual fusion of transport vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial for the formation of endosomes andthe subsequent endolysosomal traffic regulated by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide exchange on Vps21p arefirst recruited to theTGN  before  transport  to  the  endosome,  namely  the  GEF  Vps9p and  the  epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation and identify the TGN as a critical location forregulating progress through the endolysosomal trafficking pathway.","lang":"eng"}],"volume":2,"month":"11","isi":1,"department":[{"_id":"DaSi"}],"status":"public","oa_version":"Published Version","file":[{"file_name":"2019_CommunicBiology_Nagano.pdf","date_updated":"2020-07-14T12:47:49Z","file_size":2626069,"content_type":"application/pdf","checksum":"c63c69a264fc8a0e52f2b0d482f3bdae","file_id":"7098","relation":"main_file","creator":"dernst","date_created":"2019-11-25T07:58:05Z","access_level":"open_access"}],"citation":{"ieee":"M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome formation is regulated at the trans-Golgi network,” <i>Communications Biology</i>, vol. 2, no. 1. Springer Nature, 2019.","ista":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. 2019. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2(1), 419.","apa":"Nagano, M., Toshima, J. Y., Siekhaus, D. E., &#38; Toshima, J. (2019). Rab5-mediated endosome formation is regulated at the trans-Golgi network. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-019-0670-5\">https://doi.org/10.1038/s42003-019-0670-5</a>","mla":"Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” <i>Communications Biology</i>, vol. 2, no. 1, 419, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s42003-019-0670-5\">10.1038/s42003-019-0670-5</a>.","chicago":"Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” <i>Communications Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s42003-019-0670-5\">https://doi.org/10.1038/s42003-019-0670-5</a>.","ama":"Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation is regulated at the trans-Golgi network. <i>Communications Biology</i>. 2019;2(1). doi:<a href=\"https://doi.org/10.1038/s42003-019-0670-5\">10.1038/s42003-019-0670-5</a>","short":"M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019)."},"article_type":"original","date_created":"2019-11-25T07:55:01Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"20","external_id":{"isi":["000497963500017"],"pmid":["31543297"]},"date_updated":"2023-08-30T07:28:22Z","page":"781-794.e4","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.013","open_access":"1"}],"oa":1,"ddc":["571","599"],"has_accepted_license":"1","author":[{"first_name":"Yu","full_name":"Kasugai, Yu","last_name":"Kasugai"},{"full_name":"Vogel, Elisabeth","last_name":"Vogel","first_name":"Elisabeth"},{"first_name":"Heide","last_name":"Hörtnagl","full_name":"Hörtnagl, Heide"},{"first_name":"Sabine","full_name":"Schönherr, Sabine","last_name":"Schönherr"},{"full_name":"Paradiso, Enrica","last_name":"Paradiso","first_name":"Enrica"},{"full_name":"Hauschild, Markus","last_name":"Hauschild","first_name":"Markus"},{"first_name":"Georg","full_name":"Göbel, Georg","last_name":"Göbel"},{"first_name":"Ivan","full_name":"Milenkovic, Ivan","last_name":"Milenkovic"},{"first_name":"Yvan","last_name":"Peterschmitt","full_name":"Peterschmitt, Yvan"},{"last_name":"Tasan","full_name":"Tasan, Ramon","first_name":"Ramon"},{"full_name":"Sperk, Günther","last_name":"Sperk","first_name":"Günther"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"last_name":"Sieghart","full_name":"Sieghart, Werner","first_name":"Werner"},{"last_name":"Singewald","full_name":"Singewald, Nicolas","first_name":"Nicolas"},{"full_name":"Lüthi, Andreas","last_name":"Lüthi","first_name":"Andreas"},{"full_name":"Ferraguti, Francesco","last_name":"Ferraguti","first_name":"Francesco"}],"_id":"7099","publisher":"Elsevier","publication_status":"published","quality_controlled":"1","issue":"4","acknowledgement":"The authors thank Gabi Schmid for excellent technical support. We also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the specificity\r\nof some of the antibodies used in this study on replicas. Funding was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung) Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.), and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous version of the manuscript.","intvolume":"       104","year":"2019","title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","pmid":1,"publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2019.08.013","publication":"Neuron","language":[{"iso":"eng"}],"date_published":"2019-11-20T00:00:00Z","scopus_import":"1","type":"journal_article","date_created":"2019-11-25T08:02:39Z","article_type":"original","oa_version":"Published Version","citation":{"ama":"Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. <i>Neuron</i>. 2019;104(4):781-794.e4. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">10.1016/j.neuron.2019.08.013</a>","short":"Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild, G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W. Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4.","mla":"Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” <i>Neuron</i>, vol. 104, no. 4, Elsevier, 2019, p. 781–794.e4, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">10.1016/j.neuron.2019.08.013</a>.","apa":"Kasugai, Y., Vogel, E., Hörtnagl, H., Schönherr, S., Paradiso, E., Hauschild, M., … Ferraguti, F. (2019). Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">https://doi.org/10.1016/j.neuron.2019.08.013</a>","chicago":"Kasugai, Yu, Elisabeth Vogel, Heide Hörtnagl, Sabine Schönherr, Enrica Paradiso, Markus Hauschild, Georg Göbel, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.013\">https://doi.org/10.1016/j.neuron.2019.08.013</a>.","ieee":"Y. Kasugai <i>et al.</i>, “Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning,” <i>Neuron</i>, vol. 104, no. 4. Elsevier, p. 781–794.e4, 2019.","ista":"Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4."},"status":"public","volume":104,"isi":1,"month":"11","article_processing_charge":"No","department":[{"_id":"RySh"}]},{"file_date_updated":"2020-07-14T12:47:49Z","oa":1,"author":[{"first_name":"Maximilian","full_name":"Jeblick, Maximilian","last_name":"Jeblick"},{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","last_name":"Leopold"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"}],"_id":"7100","has_accepted_license":"1","ddc":["510"],"publisher":"Springer Nature","publication_status":"published","corr_author":"1","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"08","external_id":{"isi":["000495193700002"]},"project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"date_updated":"2025-04-14T07:27:01Z","page":"1-69","ec_funded":1,"date_created":"2019-11-25T08:08:02Z","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"oa_version":"Published Version","file":[{"access_level":"open_access","creator":"dernst","date_created":"2019-11-25T08:11:11Z","relation":"main_file","file_id":"7101","checksum":"cd283b475dd739e04655315abd46f528","content_type":"application/pdf","file_size":884469,"date_updated":"2020-07-14T12:47:49Z","file_name":"2019_CommMathPhys_Jeblick.pdf"}],"citation":{"ieee":"M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent Gross–Pitaevskii equation in two dimensions,” <i>Communications in Mathematical Physics</i>, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019.","ista":"Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69.","chicago":"Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00220-019-03599-x\">https://doi.org/10.1007/s00220-019-03599-x</a>.","apa":"Jeblick, M., Leopold, N. K., &#38; Pickl, P. (2019). Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03599-x\">https://doi.org/10.1007/s00220-019-03599-x</a>","mla":"Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” <i>Communications in Mathematical Physics</i>, vol. 372, no. 1, Springer Nature, 2019, pp. 1–69, doi:<a href=\"https://doi.org/10.1007/s00220-019-03599-x\">10.1007/s00220-019-03599-x</a>.","short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69.","ama":"Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. <i>Communications in Mathematical Physics</i>. 2019;372(1):1-69. doi:<a href=\"https://doi.org/10.1007/s00220-019-03599-x\">10.1007/s00220-019-03599-x</a>"},"status":"public","article_processing_charge":"Yes (via OA deal)","volume":372,"isi":1,"abstract":[{"text":"We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics.","lang":"eng"}],"month":"11","department":[{"_id":"RoSe"}],"acknowledgement":"OA fund by IST Austria","issue":"1","year":"2019","intvolume":"       372","title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"doi":"10.1007/s00220-019-03599-x","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Communications in Mathematical Physics","date_published":"2019-11-08T00:00:00Z","type":"journal_article"},{"doi":"10.1371/journal.pcbi.1007268","type":"journal_article","scopus_import":"1","publication":"PLoS Computational Biology","date_published":"2019-11-01T00:00:00Z","language":[{"iso":"eng"}],"year":"2019","intvolume":"        15","issue":"11","publication_identifier":{"issn":["1553-7358"]},"pmid":1,"article_number":"e1007268","title":"Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture","status":"public","department":[{"_id":"GaTk"}],"article_processing_charge":"No","isi":1,"month":"11","abstract":[{"lang":"eng","text":"Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics."}],"volume":15,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","ec_funded":1,"date_created":"2019-11-25T08:20:47Z","citation":{"apa":"Wang, J. W. J. L., Lombardi, F., Zhang, X., Anaclet, C., &#38; Ivanov, P. C. (2019). Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">https://doi.org/10.1371/journal.pcbi.1007268</a>","mla":"Wang, Jilin W. J. L., et al. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” <i>PLoS Computational Biology</i>, vol. 15, no. 11, e1007268, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">10.1371/journal.pcbi.1007268</a>.","chicago":"Wang, Jilin W. J. L., Fabrizio Lombardi, Xiyun Zhang, Christelle Anaclet, and Plamen Ch. Ivanov. “Non-Equilibrium Critical Dynamics of Bursts in θ and δ Rhythms as Fundamental Characteristic of Sleep and Wake Micro-Architecture.” <i>PLoS Computational Biology</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">https://doi.org/10.1371/journal.pcbi.1007268</a>.","ieee":"J. W. J. L. Wang, F. Lombardi, X. Zhang, C. Anaclet, and P. C. Ivanov, “Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture,” <i>PLoS Computational Biology</i>, vol. 15, no. 11. Public Library of Science, 2019.","ista":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. 2019. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. PLoS Computational Biology. 15(11), e1007268.","ama":"Wang JWJL, Lombardi F, Zhang X, Anaclet C, Ivanov PC. Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture. <i>PLoS Computational Biology</i>. 2019;15(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007268\">10.1371/journal.pcbi.1007268</a>","short":"J.W.J.L. Wang, F. Lombardi, X. Zhang, C. Anaclet, P.C. Ivanov, PLoS Computational Biology 15 (2019)."},"oa_version":"Published Version","file":[{"access_level":"open_access","date_created":"2019-11-25T08:24:01Z","creator":"dernst","relation":"main_file","file_id":"7104","checksum":"2a096a9c6dcc6eaa94077b2603bc6c12","content_type":"application/pdf","file_name":"2019_PLOSComBio_Wang.pdf","file_size":3982516,"date_updated":"2020-07-14T12:47:49Z"}],"date_updated":"2025-04-14T07:44:06Z","day":"01","external_id":{"pmid":["31725712"],"isi":["000500976100014"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2020-07-14T12:47:49Z","oa":1,"publisher":"Public Library of Science","author":[{"full_name":"Wang, Jilin W. J. L.","last_name":"Wang","first_name":"Jilin W. J. L."},{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi","full_name":"Lombardi, Fabrizio"},{"first_name":"Xiyun","full_name":"Zhang, Xiyun","last_name":"Zhang"},{"full_name":"Anaclet, Christelle","last_name":"Anaclet","first_name":"Christelle"},{"first_name":"Plamen Ch.","last_name":"Ivanov","full_name":"Ivanov, Plamen Ch."}],"_id":"7103","ddc":["570","000"],"has_accepted_license":"1"},{"publisher":"Springer Nature","_id":"7105","author":[{"full_name":"Yolland, Lawrence","last_name":"Yolland","first_name":"Lawrence"},{"first_name":"Mubarik","full_name":"Burki, Mubarik","last_name":"Burki"},{"full_name":"Marcotti, Stefania","last_name":"Marcotti","first_name":"Stefania"},{"full_name":"Luchici, Andrei","last_name":"Luchici","first_name":"Andrei"},{"first_name":"Fiona N.","last_name":"Kenny","full_name":"Kenny, Fiona N."},{"full_name":"Davis, John Robert","last_name":"Davis","first_name":"John Robert"},{"full_name":"Serna-Morales, Eduardo","last_name":"Serna-Morales","first_name":"Eduardo"},{"first_name":"Jan","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","last_name":"Müller","full_name":"Müller, Jan"},{"orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Andrew","full_name":"Davidson, Andrew","last_name":"Davidson"},{"last_name":"Wood","full_name":"Wood, Will","first_name":"Will"},{"full_name":"Schumacher, Linus J.","last_name":"Schumacher","first_name":"Linus J."},{"last_name":"Endres","full_name":"Endres, Robert G.","first_name":"Robert G."},{"last_name":"Miodownik","full_name":"Miodownik, Mark","first_name":"Mark"},{"last_name":"Stramer","full_name":"Stramer, Brian M.","first_name":"Brian M."}],"oa":1,"quality_controlled":"1","publication_status":"published","day":"01","external_id":{"isi":["000495888300009"],"pmid":["31685997"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891"}],"page":"1370-1381","date_updated":"2023-09-06T11:08:52Z","citation":{"chicago":"Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” <i>Nature Cell Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41556-019-0411-5\">https://doi.org/10.1038/s41556-019-0411-5</a>.","mla":"Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” <i>Nature Cell Biology</i>, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:<a href=\"https://doi.org/10.1038/s41556-019-0411-5\">10.1038/s41556-019-0411-5</a>.","apa":"Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. <i>Nature Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41556-019-0411-5\">https://doi.org/10.1038/s41556-019-0411-5</a>","ieee":"L. Yolland <i>et al.</i>, “Persistent and polarized global actin flow is essential for directionality during cell migration,” <i>Nature Cell Biology</i>, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019.","ista":"Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381.","short":"L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381.","ama":"Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. <i>Nature Cell Biology</i>. 2019;21(11):1370-1381. doi:<a href=\"https://doi.org/10.1038/s41556-019-0411-5\">10.1038/s41556-019-0411-5</a>"},"oa_version":"Submitted Version","date_created":"2019-11-25T08:55:00Z","article_type":"original","department":[{"_id":"MiSi"}],"month":"11","volume":21,"abstract":[{"text":"Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence.","lang":"eng"}],"isi":1,"article_processing_charge":"No","status":"public","pmid":1,"publication_identifier":{"issn":["1465-7392"],"eissn":["1476-4679"]},"title":"Persistent and polarized global actin flow is essential for directionality during cell migration","intvolume":"        21","year":"2019","issue":"11","type":"journal_article","publication":"Nature Cell Biology","date_published":"2019-11-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":"1","doi":"10.1038/s41556-019-0411-5"},{"page":"1114-1119","date_updated":"2025-04-14T07:45:04Z","external_id":{"isi":["000496526100010"],"pmid":["31712756"]},"day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2020-10-14T08:54:49Z","oa":1,"publisher":"Springer Nature","author":[{"first_name":"Roman","full_name":"Skokan, Roman","last_name":"Skokan"},{"first_name":"Eva","last_name":"Medvecká","full_name":"Medvecká, Eva"},{"first_name":"Tom","last_name":"Viaene","full_name":"Viaene, Tom"},{"last_name":"Vosolsobě","full_name":"Vosolsobě, Stanislav","first_name":"Stanislav"},{"last_name":"Zwiewka","full_name":"Zwiewka, Marta","first_name":"Marta"},{"full_name":"Müller, Karel","last_name":"Müller","first_name":"Karel"},{"last_name":"Skůpa","full_name":"Skůpa, Petr","first_name":"Petr"},{"first_name":"Michal","last_name":"Karady","full_name":"Karady, Michal"},{"full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou"},{"first_name":"Dorina P.","full_name":"Janacek, Dorina P.","last_name":"Janacek"},{"last_name":"Hammes","full_name":"Hammes, Ulrich Z.","first_name":"Ulrich Z."},{"first_name":"Karin","last_name":"Ljung","full_name":"Ljung, Karin"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"_id":"7106","ddc":["580"],"has_accepted_license":"1","doi":"10.1038/s41477-019-0542-5","type":"journal_article","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","publication":"Nature Plants","language":[{"iso":"eng"}],"year":"2019","intvolume":"         5","issue":"11","pmid":1,"publication_identifier":{"issn":["2055-0278"]},"title":"PIN-driven auxin transport emerged early in streptophyte evolution","status":"public","department":[{"_id":"JiFr"}],"article_processing_charge":"No","isi":1,"abstract":[{"lang":"eng","text":"PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes."}],"month":"11","volume":5,"article_type":"original","date_created":"2019-11-25T09:08:04Z","ec_funded":1,"citation":{"short":"R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119.","ama":"Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. <i>Nature Plants</i>. 2019;5(11):1114-1119. doi:<a href=\"https://doi.org/10.1038/s41477-019-0542-5\">10.1038/s41477-019-0542-5</a>","ista":"Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119.","ieee":"R. Skokan <i>et al.</i>, “PIN-driven auxin transport emerged early in streptophyte evolution,” <i>Nature Plants</i>, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019.","chicago":"Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” <i>Nature Plants</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41477-019-0542-5\">https://doi.org/10.1038/s41477-019-0542-5</a>.","mla":"Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” <i>Nature Plants</i>, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:<a href=\"https://doi.org/10.1038/s41477-019-0542-5\">10.1038/s41477-019-0542-5</a>.","apa":"Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-019-0542-5\">https://doi.org/10.1038/s41477-019-0542-5</a>"},"oa_version":"Submitted Version","file":[{"file_name":"2019_NaturePlants_Skokan_accepted.pdf","date_updated":"2020-10-14T08:54:49Z","file_size":1980851,"content_type":"application/pdf","checksum":"94e0426856aad9a9bd0135d5436efbf1","success":1,"file_id":"8660","relation":"main_file","creator":"dernst","date_created":"2020-10-14T08:54:49Z","access_level":"open_access"}]},{"article_type":"original","date_created":"2019-11-26T10:13:59Z","oa_version":"Preprint","citation":{"ama":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. <i>Journal of the ACM</i>. 2019;66(3). doi:<a href=\"https://doi.org/10.1145/3314024\">10.1145/3314024</a>","short":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019).","ista":"Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21.","ieee":"X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” <i>Journal of the ACM</i>, vol. 66, no. 3. ACM, 2019.","apa":"Goaoc, X., Patak, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2019). Shellability is NP-complete. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3314024\">https://doi.org/10.1145/3314024</a>","mla":"Goaoc, Xavier, et al. “Shellability Is NP-Complete.” <i>Journal of the ACM</i>, vol. 66, no. 3, 21, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3314024\">10.1145/3314024</a>.","chicago":"Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” <i>Journal of the ACM</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3314024\">https://doi.org/10.1145/3314024</a>."},"related_material":{"record":[{"status":"public","id":"184","relation":"earlier_version"}]},"status":"public","article_processing_charge":"No","volume":66,"isi":1,"abstract":[{"text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable.","lang":"eng"}],"month":"06","department":[{"_id":"UlWa"}],"issue":"3","year":"2019","intvolume":"        66","title":"Shellability is NP-complete","publication_identifier":{"issn":["0004-5411"]},"article_number":"21","arxiv":1,"doi":"10.1145/3314024","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Journal of the ACM","date_published":"2019-06-01T00:00:00Z","type":"journal_article","oa":1,"_id":"7108","author":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"first_name":"Pavel","id":"B593B804-1035-11EA-B4F1-947645A5BB83","last_name":"Patak","full_name":"Patak, Pavel"},{"orcid":"0000-0002-3975-1683","last_name":"Patakova","full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana"},{"first_name":"Martin","full_name":"Tancer, Martin","last_name":"Tancer"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","last_name":"Wagner","full_name":"Wagner, Uli"}],"publisher":"ACM","publication_status":"published","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","external_id":{"isi":["000495406300007"],"arxiv":["1711.08436"]},"date_updated":"2025-06-04T07:49:03Z","main_file_link":[{"url":"https://arxiv.org/abs/1711.08436","open_access":"1"}]},{"page":"2759-2771.e5","date_updated":"2021-01-12T08:11:56Z","keyword":["cardiomyocyte","cell cycle","Cofilin2","cytoskeleton","Hippo","microRNA","regeneration","YAP"],"day":"28","external_id":{"pmid":["31141697"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication_status":"published","publisher":"Elsevier","ddc":["576"],"has_accepted_license":"1","author":[{"full_name":"Torrini, Consuelo","last_name":"Torrini","first_name":"Consuelo"},{"last_name":"Cubero","orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J"},{"last_name":"Dirkx","full_name":"Dirkx, Ellen","first_name":"Ellen"},{"last_name":"Braga","full_name":"Braga, Luca","first_name":"Luca"},{"full_name":"Ali, Hashim","last_name":"Ali","first_name":"Hashim"},{"first_name":"Giulia","full_name":"Prosdocimo, Giulia","last_name":"Prosdocimo"},{"last_name":"Gutierrez","full_name":"Gutierrez, Maria Ines","first_name":"Maria Ines"},{"first_name":"Chiara","full_name":"Collesi, Chiara","last_name":"Collesi"},{"full_name":"Licastro, Danilo","last_name":"Licastro","first_name":"Danilo"},{"first_name":"Lorena","full_name":"Zentilin, Lorena","last_name":"Zentilin"},{"first_name":"Miguel","full_name":"Mano, Miguel","last_name":"Mano"},{"first_name":"Serena","full_name":"Zacchigna, Serena","last_name":"Zacchigna"},{"first_name":"Michele","full_name":"Vendruscolo, Michele","last_name":"Vendruscolo"},{"first_name":"Matteo","full_name":"Marsili, Matteo","last_name":"Marsili"},{"last_name":"Samal","full_name":"Samal, Areejit","first_name":"Areejit"},{"full_name":"Giacca, Mauro","last_name":"Giacca","first_name":"Mauro"}],"_id":"7128","oa":1,"file_date_updated":"2020-07-14T12:47:50Z","type":"journal_article","language":[{"iso":"eng"}],"date_published":"2019-05-28T00:00:00Z","publication":"Cell Reports","doi":"10.1016/j.celrep.2019.05.005","publication_identifier":{"issn":["2211-1247"]},"pmid":1,"title":"Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation","intvolume":"        27","year":"2019","issue":"9","month":"05","volume":27,"abstract":[{"lang":"eng","text":"Loss of functional cardiomyocytes is a major determinant of heart failure after myocardial infarction. Previous high throughput screening studies have identified a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate cardiac regeneration in mice. Here, we show that all of the most effective of these miRNAs activate nuclear localization of the master transcriptional cofactor Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization by targeting Cofilin2, a process that by itself activates YAP nuclear translocation. Thus, activation of YAP and modulation of the actin cytoskeleton are major components of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte proliferation."}],"article_processing_charge":"Yes","status":"public","citation":{"ista":"Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI, Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili M, Samal A, Giacca M. 2019. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. Cell Reports. 27(9), 2759–2771.e5.","ieee":"C. Torrini <i>et al.</i>, “Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation,” <i>Cell Reports</i>, vol. 27, no. 9. Elsevier, p. 2759–2771.e5, 2019.","chicago":"Torrini, Consuelo, Ryan J Cubero, Ellen Dirkx, Luca Braga, Hashim Ali, Giulia Prosdocimo, Maria Ines Gutierrez, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">https://doi.org/10.1016/j.celrep.2019.05.005</a>.","mla":"Torrini, Consuelo, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>, vol. 27, no. 9, Elsevier, 2019, p. 2759–2771.e5, doi:<a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">10.1016/j.celrep.2019.05.005</a>.","apa":"Torrini, C., Cubero, R. J., Dirkx, E., Braga, L., Ali, H., Prosdocimo, G., … Giacca, M. (2019). Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">https://doi.org/10.1016/j.celrep.2019.05.005</a>","short":"C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I. Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo, M. Marsili, A. Samal, M. Giacca, Cell Reports 27 (2019) 2759–2771.e5.","ama":"Torrini C, Cubero RJ, Dirkx E, et al. Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte proliferation. <i>Cell Reports</i>. 2019;27(9):2759-2771.e5. doi:<a href=\"https://doi.org/10.1016/j.celrep.2019.05.005\">10.1016/j.celrep.2019.05.005</a>"},"extern":"1","file":[{"content_type":"application/pdf","file_size":4650750,"file_name":"torrini_cellreports_2019.pdf","date_updated":"2020-07-14T12:47:50Z","checksum":"c5d855d07263bfec718673385d0ea2d7","date_created":"2019-11-26T22:30:43Z","creator":"rcubero","relation":"main_file","file_id":"7129","access_level":"open_access"}],"oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"article_type":"original","date_created":"2019-11-26T22:30:07Z"},{"date_updated":"2021-01-12T08:11:57Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.00249"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"17","external_id":{"arxiv":["1808.00249"]},"keyword":["optimization under uncertainty","source coding","large deviation"],"publication_status":"published","quality_controlled":"1","oa":1,"_id":"7130","author":[{"full_name":"Cubero, Ryan J","last_name":"Cubero","orcid":"0000-0003-0002-1867","first_name":"Ryan J","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"last_name":"Jo","full_name":"Jo, Junghyo","first_name":"Junghyo"},{"last_name":"Marsili","full_name":"Marsili, Matteo","first_name":"Matteo"},{"last_name":"Roudi","full_name":"Roudi, Yasser","first_name":"Yasser"},{"first_name":"Juyong","full_name":"Song, Juyong","last_name":"Song"}],"publisher":"IOP Publishing","doi":"10.1088/1742-5468/ab16c8","publication":"Journal of Statistical Mechanics: Theory and Experiment","language":[{"iso":"eng"}],"date_published":"2019-06-17T00:00:00Z","type":"journal_article","acknowledgement":"We acknowledge interesting discussions with M Abbott, E Aurell, J Barbier, R Monasson, T Mora, I Nemenman, N Tishby and R Zecchina. This research was supported by the Kavli Foundation and the Centre of Excellence scheme of the Research Council of Norway (Centre for Neural Computation) (RJC and YR), by the Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education (2016R1D1A1B03932264) (JJ), and, in part, by the ICTP through the OEA-AC-98 (JS).","issue":"6","year":"2019","intvolume":"      2019","title":"Statistical criticality arises in most informative representations","arxiv":1,"publication_identifier":{"issn":["1742-5468"]},"article_number":"063402","status":"public","article_processing_charge":"No","volume":2019,"month":"06","abstract":[{"lang":"eng","text":"We show that statistical criticality, i.e. the occurrence of power law frequency distributions, arises in samples that are maximally informative about the underlying generating process. In order to reach this conclusion, we first identify the frequency with which different outcomes occur in a sample, as the variable carrying useful information on the generative process. The entropy of the frequency, that we call relevance, provides an upper bound to the number of informative bits. This differs from the entropy of the data, that we take as a measure of resolution. Samples that maximise relevance at a given resolution—that we call maximally informative samples—exhibit statistical criticality. In particular, Zipf's law arises at the optimal trade-off between resolution (i.e. compression) and relevance. As a byproduct, we derive a bound of the maximal number of parameters that can be estimated from a dataset, in the absence of prior knowledge on the generative model.\r\n\r\nFurthermore, we relate criticality to the statistical properties of the representation of the data generating process. We show that, as a consequence of the concentration property of the asymptotic equipartition property, representations that are maximally informative about the data generating process are characterised by an exponential distribution of energy levels. This arises from a principle of minimal entropy, that is conjugate of the maximum entropy principle in statistical mechanics. This explains why statistical criticality requires no parameter fine tuning in maximally informative samples."}],"article_type":"original","date_created":"2019-11-26T22:36:09Z","oa_version":"Preprint","extern":"1","citation":{"short":"R.J. Cubero, J. Jo, M. Marsili, Y. Roudi, J. Song, Journal of Statistical Mechanics: Theory and Experiment 2019 (2019).","ama":"Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. Statistical criticality arises in most informative representations. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2019;2019(6). doi:<a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">10.1088/1742-5468/ab16c8</a>","chicago":"Cubero, Ryan J, Junghyo Jo, Matteo Marsili, Yasser Roudi, and Juyong Song. “Statistical Criticality Arises in Most Informative Representations.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2019. <a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">https://doi.org/10.1088/1742-5468/ab16c8</a>.","apa":"Cubero, R. J., Jo, J., Marsili, M., Roudi, Y., &#38; Song, J. (2019). Statistical criticality arises in most informative representations. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">https://doi.org/10.1088/1742-5468/ab16c8</a>","mla":"Cubero, Ryan J., et al. “Statistical Criticality Arises in Most Informative Representations.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2019, no. 6, 063402, IOP Publishing, 2019, doi:<a href=\"https://doi.org/10.1088/1742-5468/ab16c8\">10.1088/1742-5468/ab16c8</a>.","ieee":"R. J. Cubero, J. Jo, M. Marsili, Y. Roudi, and J. Song, “Statistical criticality arises in most informative representations,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2019, no. 6. IOP Publishing, 2019.","ista":"Cubero RJ, Jo J, Marsili M, Roudi Y, Song J. 2019. Statistical criticality arises in most informative representations. Journal of Statistical Mechanics: Theory and Experiment. 2019(6), 063402."}},{"quality_controlled":"1","publication_status":"published","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skórski","full_name":"Skórski, Maciej"}],"_id":"7136","publisher":"IEEE","oa":1,"conference":{"location":"Paris, France","end_date":"2019-07-12","start_date":"2019-07-07","name":"ISIT: International Symposium on Information Theory"},"main_file_link":[{"url":"https://arxiv.org/abs/1702.08476","open_access":"1"}],"date_updated":"2023-09-06T11:15:41Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"arxiv":["1702.08476"],"isi":["000489100301043"]},"day":"01","article_processing_charge":"No","isi":1,"month":"07","abstract":[{"lang":"eng","text":"It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X<i are ϵ-close to be nearly flat (only a constant factor away). The argument is combinatorial (based on simplex coverings).\r\nThis result may be used as a generic tool for \\emph{exhibiting block-source structures}. We demonstrate this by reproving the fundamental converter due to Nisan and Zuckermann (\\emph{J. Computer and System Sciences, 1996}), which shows that sampling blocks from a min-entropy source roughly preserves the entropy rate. Our bound implies, only by straightforward chain rules, an additive loss of o(1) (for sufficiently many samples), which qualitatively meets the first tighter analysis of this problem due to Vadhan (\\emph{CRYPTO'03}), obtained by large deviation techniques. "}],"department":[{"_id":"KrPi"}],"status":"public","oa_version":"Preprint","citation":{"ieee":"M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in <i>2019 IEEE International Symposium on Information Theory</i>, Paris, France, 2019.","ista":"Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240.","mla":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” <i>2019 IEEE International Symposium on Information Theory</i>, 8849240, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/isit.2019.8849240\">10.1109/isit.2019.8849240</a>.","apa":"Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In <i>2019 IEEE International Symposium on Information Theory</i>. Paris, France: IEEE. <a href=\"https://doi.org/10.1109/isit.2019.8849240\">https://doi.org/10.1109/isit.2019.8849240</a>","chicago":"Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In <i>2019 IEEE International Symposium on Information Theory</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/isit.2019.8849240\">https://doi.org/10.1109/isit.2019.8849240</a>.","ama":"Skórski M. Strong chain rules for min-entropy under few bits spoiled. In: <i>2019 IEEE International Symposium on Information Theory</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/isit.2019.8849240\">10.1109/isit.2019.8849240</a>","short":"M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019."},"date_created":"2019-11-28T10:19:21Z","scopus_import":"1","date_published":"2019-07-01T00:00:00Z","publication":"2019 IEEE International Symposium on Information Theory","language":[{"iso":"eng"}],"type":"conference","doi":"10.1109/isit.2019.8849240","title":"Strong chain rules for min-entropy under few bits spoiled","publication_identifier":{"isbn":["9781538692912"]},"arxiv":1,"article_number":"8849240","year":"2019"},{"volume":29,"month":"12","abstract":[{"lang":"eng","text":"Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content."}],"isi":1,"article_processing_charge":"No","department":[{"_id":"JiFr"}],"status":"public","oa_version":"Published Version","citation":{"ama":"Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. <i>Cell Research</i>. 2019;29:965-966. doi:<a href=\"https://doi.org/10.1038/s41422-019-0254-4\">10.1038/s41422-019-0254-4</a>","short":"S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966.","ieee":"S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” <i>Cell Research</i>, vol. 29. Springer Nature, pp. 965–966, 2019.","ista":"Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966.","apa":"Sinclair, S. A., &#38; Friml, J. (2019). Defying gravity: a plant’s quest for moisture. <i>Cell Research</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41422-019-0254-4\">https://doi.org/10.1038/s41422-019-0254-4</a>","mla":"Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” <i>Cell Research</i>, vol. 29, Springer Nature, 2019, pp. 965–66, doi:<a href=\"https://doi.org/10.1038/s41422-019-0254-4\">10.1038/s41422-019-0254-4</a>.","chicago":"Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” <i>Cell Research</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41422-019-0254-4\">https://doi.org/10.1038/s41422-019-0254-4</a>."},"date_created":"2019-12-02T12:30:48Z","article_type":"original","language":[{"iso":"eng"}],"date_published":"2019-12-01T00:00:00Z","publication":"Cell Research","scopus_import":"1","type":"journal_article","doi":"10.1038/s41422-019-0254-4","title":"Defying gravity: a plant's quest for moisture","pmid":1,"publication_identifier":{"issn":["1001-0602"],"eissn":["1748-7838"]},"intvolume":"        29","year":"2019","quality_controlled":"1","publication_status":"published","ddc":["580"],"author":[{"orcid":"0000-0002-4566-0593","last_name":"Sinclair","full_name":"Sinclair, Scott A","id":"2D99FE6A-F248-11E8-B48F-1D18A9856A87","first_name":"Scott A"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"_id":"7143","publisher":"Springer Nature","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41422-019-0254-4"}],"date_updated":"2026-06-18T19:16:44Z","page":"965-966","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","external_id":{"pmid":["31745287"],"isi":["000500749600001"]}},{"doi":"10.1103/physrevb.100.205412","scopus_import":"1","date_published":"2019-11-15T00:00:00Z","language":[{"iso":"eng"}],"publication":"Physical Review B","type":"journal_article","issue":"20","year":"2019","intvolume":"       100","title":"End-to-end correlated subgap states in hybrid nanowires","article_number":"205412","arxiv":1,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"status":"public","article_processing_charge":"No","month":"11","volume":100,"isi":1,"abstract":[{"lang":"eng","text":"End-to-end correlated bound states are investigated in superconductor-semiconductor hybrid nanowires at zero magnetic field. Peaks in subgap conductance are independently identified from each wire end, and a cross-correlation function is computed that counts end-to-end coincidences, averaging over thousands of subgap features. Strong correlations in a short, 300-nm device are reduced by a factor of 4 in a long, 900-nm device. In addition, subgap conductance distributions are investigated, and correlations between the left and right distributions are identified based on their mutual information."}],"department":[{"_id":"AnHi"}],"article_type":"original","date_created":"2019-12-04T16:02:25Z","oa_version":"Preprint","citation":{"ama":"Anselmetti GLR, Martinez EA, Ménard GC, et al. End-to-end correlated subgap states in hybrid nanowires. <i>Physical Review B</i>. 2019;100(20). doi:<a href=\"https://doi.org/10.1103/physrevb.100.205412\">10.1103/physrevb.100.205412</a>","short":"G.L.R. Anselmetti, E.A. Martinez, G.C. Ménard, D. Puglia, F.K. Malinowski, J.S. Lee, S. Choi, M. Pendharkar, C.J. Palmstrøm, C.M. Marcus, L. Casparis, A.P. Higginbotham, Physical Review B 100 (2019).","ista":"Anselmetti GLR, Martinez EA, Ménard GC, Puglia D, Malinowski FK, Lee JS, Choi S, Pendharkar M, Palmstrøm CJ, Marcus CM, Casparis L, Higginbotham AP. 2019. End-to-end correlated subgap states in hybrid nanowires. Physical Review B. 100(20), 205412.","ieee":"G. L. R. Anselmetti <i>et al.</i>, “End-to-end correlated subgap states in hybrid nanowires,” <i>Physical Review B</i>, vol. 100, no. 20. American Physical Society, 2019.","mla":"Anselmetti, G. L. R., et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” <i>Physical Review B</i>, vol. 100, no. 20, 205412, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/physrevb.100.205412\">10.1103/physrevb.100.205412</a>.","apa":"Anselmetti, G. L. R., Martinez, E. A., Ménard, G. C., Puglia, D., Malinowski, F. K., Lee, J. S., … Higginbotham, A. P. (2019). End-to-end correlated subgap states in hybrid nanowires. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.100.205412\">https://doi.org/10.1103/physrevb.100.205412</a>","chicago":"Anselmetti, G. L. R., E. A. Martinez, G. C. Ménard, D. Puglia, F. K. Malinowski, J. S. Lee, S. Choi, et al. “End-to-End Correlated Subgap States in Hybrid Nanowires.” <i>Physical Review B</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/physrevb.100.205412\">https://doi.org/10.1103/physrevb.100.205412</a>."},"date_updated":"2024-02-28T13:13:51Z","main_file_link":[{"url":"https://arxiv.org/abs/1908.05549","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","external_id":{"isi":["000495967500006"],"arxiv":["1908.05549"]},"publication_status":"published","quality_controlled":"1","oa":1,"author":[{"first_name":"G. L. R.","full_name":"Anselmetti, G. L. R.","last_name":"Anselmetti"},{"full_name":"Martinez, E. A.","last_name":"Martinez","first_name":"E. A."},{"first_name":"G. C.","last_name":"Ménard","full_name":"Ménard, G. C."},{"first_name":"D.","last_name":"Puglia","full_name":"Puglia, D."},{"first_name":"F. K.","full_name":"Malinowski, F. K.","last_name":"Malinowski"},{"full_name":"Lee, J. S.","last_name":"Lee","first_name":"J. S."},{"first_name":"S.","full_name":"Choi, S.","last_name":"Choi"},{"last_name":"Pendharkar","full_name":"Pendharkar, M.","first_name":"M."},{"full_name":"Palmstrøm, C. J.","last_name":"Palmstrøm","first_name":"C. J."},{"full_name":"Marcus, C. M.","last_name":"Marcus","first_name":"C. M."},{"first_name":"L.","last_name":"Casparis","full_name":"Casparis, L."},{"full_name":"Higginbotham, Andrew P","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87"}],"_id":"7145","publisher":"American Physical Society"},{"month":"12","abstract":[{"lang":"eng","text":"In this work, we use algebraic methods for studying distance computation and subgraph detection tasks in the congested clique model. Specifically, we adapt parallel matrix multiplication implementations to the congested clique, obtaining an O(n1−2/ω) round matrix multiplication algorithm, where ω<2.3728639 is the exponent of matrix multiplication. In conjunction with known techniques from centralised algorithmics, this gives significant improvements over previous best upper bounds in the congested clique model. The highlight results include:\r\n\r\n1.    triangle and 4-cycle counting in O(n0.158) rounds, improving upon the O(n1/3) algorithm of Dolev et al. [DISC 2012],\r\n2. a (1+o(1))-approximation of all-pairs shortest paths in O(n0.158) rounds, improving upon the O~(n1/2)-round (2+o(1))-approximation algorithm given by Nanongkai [STOC 2014], and\r\n 3. computing the girth in O(n0.158) rounds, which is the first non-trivial solution in this model.\r\n   \r\nIn addition, we present a novel constant-round combinatorial algorithm for detecting 4-cycles."}],"volume":32,"article_processing_charge":"No","status":"public","citation":{"ista":"Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. 2019. Algebraic methods in the congested clique. Distributed Computing. 32(6), 461–478.","ieee":"K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, and J. Suomela, “Algebraic methods in the congested clique,” <i>Distributed Computing</i>, vol. 32, no. 6. Springer Nature, pp. 461–478, 2019.","chicago":"Censor-Hillel, Keren, Petteri Kaski, Janne Korhonen, Christoph Lenzen, Ami Paz, and Jukka Suomela. “Algebraic Methods in the Congested Clique.” <i>Distributed Computing</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/s00446-016-0270-2\">https://doi.org/10.1007/s00446-016-0270-2</a>.","mla":"Censor-Hillel, Keren, et al. “Algebraic Methods in the Congested Clique.” <i>Distributed Computing</i>, vol. 32, no. 6, Springer Nature, 2019, pp. 461–78, doi:<a href=\"https://doi.org/10.1007/s00446-016-0270-2\">10.1007/s00446-016-0270-2</a>.","apa":"Censor-Hillel, K., Kaski, P., Korhonen, J., Lenzen, C., Paz, A., &#38; Suomela, J. (2019). Algebraic methods in the congested clique. <i>Distributed Computing</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00446-016-0270-2\">https://doi.org/10.1007/s00446-016-0270-2</a>","short":"K. Censor-Hillel, P. Kaski, J. Korhonen, C. Lenzen, A. Paz, J. Suomela, Distributed Computing 32 (2019) 461–478.","ama":"Censor-Hillel K, Kaski P, Korhonen J, Lenzen C, Paz A, Suomela J. Algebraic methods in the congested clique. <i>Distributed Computing</i>. 2019;32(6):461-478. doi:<a href=\"https://doi.org/10.1007/s00446-016-0270-2\">10.1007/s00446-016-0270-2</a>"},"extern":"1","oa_version":"Preprint","article_type":"original","date_created":"2019-12-05T09:49:49Z","type":"journal_article","publication":"Distributed Computing","date_published":"2019-12-01T00:00:00Z","language":[{"iso":"eng"}],"doi":"10.1007/s00446-016-0270-2","publication_identifier":{"issn":["0178-2770","1432-0452"]},"arxiv":1,"title":"Algebraic methods in the congested clique","intvolume":"        32","year":"2019","issue":"6","quality_controlled":"1","publication_status":"published","publisher":"Springer Nature","_id":"7150","author":[{"last_name":"Censor-Hillel","full_name":"Censor-Hillel, Keren","first_name":"Keren"},{"last_name":"Kaski","full_name":"Kaski, Petteri","first_name":"Petteri"},{"last_name":"Korhonen","full_name":"Korhonen, Janne","first_name":"Janne","id":"C5402D42-15BC-11E9-A202-CA2BE6697425"},{"full_name":"Lenzen, Christoph","last_name":"Lenzen","first_name":"Christoph"},{"first_name":"Ami","full_name":"Paz, Ami","last_name":"Paz"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1503.04963"}],"page":"461-478","date_updated":"2021-01-12T08:12:05Z","day":"01","external_id":{"arxiv":["1503.04963"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.15479/AT:ISTA:7154","date_updated":"2025-06-12T06:58:31Z","type":"research_data","date_published":"2019-12-06T00:00:00Z","year":"2019","day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"title":"Supplementary data for \"Programming temporal morphing of self-actuated shells\"","status":"public","related_material":{"record":[{"id":"8433","status":"deleted","relation":"used_in_publication"},{"status":"public","id":"7262","relation":"used_in_publication"}]},"department":[{"_id":"BeBi"}],"article_processing_charge":"No","month":"12","file_date_updated":"2020-07-14T12:47:50Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"date_created":"2019-12-09T07:52:46Z","ec_funded":1,"publisher":"Institute of Science and Technology Austria","citation":{"ama":"Guseinov R. Supplementary data for “Programming temporal morphing of self-actuated shells.” 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7154\">10.15479/AT:ISTA:7154</a>","short":"R. Guseinov, (2019).","ieee":"R. Guseinov, “Supplementary data for ‘Programming temporal morphing of self-actuated shells.’” Institute of Science and Technology Austria, 2019.","ista":"Guseinov R. 2019. Supplementary data for ‘Programming temporal morphing of self-actuated shells’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7154\">10.15479/AT:ISTA:7154</a>.","mla":"Guseinov, Ruslan. <i>Supplementary Data for “Programming Temporal Morphing of Self-Actuated Shells.”</i> Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7154\">10.15479/AT:ISTA:7154</a>.","apa":"Guseinov, R. (2019). Supplementary data for “Programming temporal morphing of self-actuated shells.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7154\">https://doi.org/10.15479/AT:ISTA:7154</a>","chicago":"Guseinov, Ruslan. “Supplementary Data for ‘Programming Temporal Morphing of Self-Actuated Shells.’” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7154\">https://doi.org/10.15479/AT:ISTA:7154</a>."},"author":[{"orcid":"0000-0001-9819-5077","last_name":"Guseinov","full_name":"Guseinov, Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ruslan"}],"_id":"7154","oa_version":"Published Version","file":[{"access_level":"open_access","relation":"main_file","date_created":"2019-12-09T07:52:17Z","creator":"dernst","file_id":"7155","checksum":"155133e6e188e85b3c0676a5e70b9341","file_size":65307107,"file_name":"temporal_morphing_supp_data.zip","date_updated":"2020-07-14T12:47:50Z","content_type":"application/x-zip-compressed"}],"has_accepted_license":"1","ddc":["000"],"contributor":[{"last_name":"Guseinov","orcid":"0000-0001-9819-5077","first_name":"Ruslan","id":"3AB45EE2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Connor","last_name":"McMahan"},{"id":"2DC83906-F248-11E8-B48F-1D18A9856A87","first_name":"Jesus","last_name":"Perez Rodriguez"},{"first_name":"Chiara","last_name":"Daraio"},{"orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}]},{"doi":"10.1038/s41534-019-0220-5","type":"journal_article","scopus_import":"1","language":[{"iso":"eng"}],"date_published":"2019-12-01T00:00:00Z","publication":"npj Quantum Information","year":"2019","intvolume":"         5","publication_identifier":{"issn":["2056-6387"]},"arxiv":1,"article_number":"108","title":"Electro-optic entanglement source for microwave to telecom quantum state transfer","status":"public","department":[{"_id":"JoFi"}],"article_processing_charge":"No","isi":1,"month":"12","abstract":[{"lang":"eng","text":"We propose an efficient microwave-photonic modulator as a resource for stationary entangled microwave-optical fields and develop the theory for deterministic entanglement generation and quantum state transfer in multi-resonant electro-optic systems. The device is based on a single crystal whispering gallery mode resonator integrated into a 3D-microwave cavity. The specific design relies on a new combination of thin-film technology and conventional machining that is optimized for the lowest dissipation rates in the microwave, optical, and mechanical domains. We extract important device properties from finite-element simulations and predict continuous variable entanglement generation rates on the order of a Mebit/s for optical pump powers of only a few tens of microwatts. We compare the quantum state transfer fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation and direct conversion protocols under realistic conditions. Combining the unique capabilities of circuit quantum electrodynamics with the resilience of fiber optic communication could facilitate long-distance solid-state qubit networks, new methods for quantum signal synthesis, quantum key distribution, and quantum enhanced detection, as well as more power-efficient classical sensing and modulation."}],"volume":5,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2019-12-09T08:18:56Z","article_type":"original","ec_funded":1,"citation":{"chicago":"Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” <i>Npj Quantum Information</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41534-019-0220-5\">https://doi.org/10.1038/s41534-019-0220-5</a>.","mla":"Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” <i>Npj Quantum Information</i>, vol. 5, 108, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41534-019-0220-5\">10.1038/s41534-019-0220-5</a>.","apa":"Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., &#38; Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. <i>Npj Quantum Information</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41534-019-0220-5\">https://doi.org/10.1038/s41534-019-0220-5</a>","ista":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 5, 108.","ieee":"A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic entanglement source for microwave to telecom quantum state transfer,” <i>npj Quantum Information</i>, vol. 5. Springer Nature, 2019.","short":"A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019).","ama":"Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. <i>npj Quantum Information</i>. 2019;5. doi:<a href=\"https://doi.org/10.1038/s41534-019-0220-5\">10.1038/s41534-019-0220-5</a>"},"oa_version":"Published Version","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:47:50Z","file_name":"2019_NPJ_Rueda.pdf","file_size":1580132,"checksum":"13e0ea1d4f9b5f5710780d9473364f58","creator":"dernst","date_created":"2019-12-09T08:25:06Z","relation":"main_file","file_id":"7157","access_level":"open_access"}],"date_updated":"2026-04-15T06:43:52Z","external_id":{"arxiv":["1909.01470"],"isi":["000502996200003"]},"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"call_identifier":"H2020","grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","_id":"258047B6-B435-11E9-9278-68D0E5697425","grant_number":"707438","call_identifier":"H2020"},{"grant_number":"732894","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","call_identifier":"H2020"},{"grant_number":"F07105","name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"publication_status":"published","quality_controlled":"1","corr_author":"1","file_date_updated":"2020-07-14T12:47:50Z","oa":1,"publisher":"Springer Nature","_id":"7156","author":[{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","last_name":"Rueda Sanchez","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Hease, William J","orcid":"0000-0001-9868-2166","last_name":"Hease","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir","first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink","orcid":"0000-0001-8112-028X"}],"ddc":["530"],"has_accepted_license":"1"},{"publication":"Development","language":[{"iso":"eng"}],"date_published":"2019-12-04T00:00:00Z","scopus_import":"1","type":"journal_article","doi":"10.1242/dev.176297","title":"Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium","article_number":"dev176297","pmid":1,"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"issue":"23","intvolume":"       146","year":"2019","isi":1,"abstract":[{"lang":"eng","text":"Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube."}],"volume":146,"month":"12","article_processing_charge":"No","department":[{"_id":"AnKi"}],"status":"public","file":[{"access_level":"open_access","file_id":"7177","relation":"main_file","date_created":"2019-12-13T07:34:06Z","creator":"dernst","checksum":"b6533c37dc8fbd803ffeca216e0a8b8a","date_updated":"2020-07-14T12:47:50Z","file_name":"2019_Development_Guerrero.pdf","file_size":7797881,"content_type":"application/pdf"}],"oa_version":"Published Version","citation":{"apa":"Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., &#38; Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>","mla":"Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>.","chicago":"Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>. The Company of Biologists, 2019. <a href=\"https://doi.org/10.1242/dev.176297\">https://doi.org/10.1242/dev.176297</a>.","ista":"Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297.","ieee":"P. Guerrero <i>et al.</i>, “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” <i>Development</i>, vol. 146, no. 23. The Company of Biologists, 2019.","ama":"Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>. 2019;146(23). doi:<a href=\"https://doi.org/10.1242/dev.176297\">10.1242/dev.176297</a>","short":"P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019)."},"date_created":"2019-12-10T14:39:50Z","article_type":"original","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_updated":"2025-04-14T07:27:30Z","project":[{"call_identifier":"H2020","grant_number":"680037","_id":"B6FC0238-B512-11E9-945C-1524E6697425","name":"Coordination of Patterning And Growth In the Spinal Cord"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"04","external_id":{"isi":["000507575700004"],"pmid":["31784457"]},"corr_author":"1","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","ddc":["570"],"_id":"7165","author":[{"first_name":"Pilar","full_name":"Guerrero, Pilar","last_name":"Guerrero"},{"full_name":"Perez-Carrasco, Ruben","last_name":"Perez-Carrasco","first_name":"Ruben"},{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"first_name":"David","full_name":"Page, David","last_name":"Page"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","last_name":"Kicheva"},{"first_name":"James","full_name":"Briscoe, James","last_name":"Briscoe"},{"last_name":"Page","full_name":"Page, Karen M.","first_name":"Karen M."}],"publisher":"The Company of Biologists","oa":1,"file_date_updated":"2020-07-14T12:47:50Z"},{"doi":"10.15479/AT:ISTA:7172","date_published":"2019-12-12T00:00:00Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"type":"dissertation","year":"2019","title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","publication_identifier":{"eissn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"449","relation":"part_of_dissertation"},{"id":"6377","status":"public","relation":"part_of_dissertation"},{"id":"1346","status":"public","relation":"part_of_dissertation"}]},"status":"public","month":"12","abstract":[{"lang":"eng","text":"The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.\r\nThe first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.\r\nThe second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.\r\nThe third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.\r\nIn the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.\r\nIn the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes."}],"article_processing_charge":"No","department":[{"_id":"JiFr"}],"date_created":"2019-12-11T21:24:39Z","file":[{"access_level":"closed","file_id":"7175","creator":"mvasilev","date_created":"2019-12-12T09:32:36Z","relation":"source_file","checksum":"ef981c1a3b1d9da0edcbedcff4970d37","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":20454014,"file_name":"Thesis_Mina_final_upload_7.docx","date_updated":"2020-07-14T12:47:51Z"},{"file_id":"7176","creator":"mvasilev","date_created":"2019-12-12T09:33:10Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_Mina_final_upload_7.pdf","date_updated":"2020-07-14T12:47:51Z","file_size":11565025,"checksum":"3882c4585e46c9cfb486e4225cad54ab"}],"oa_version":"Published Version","citation":{"chicago":"Vasileva, Mina K. “Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7172\">https://doi.org/10.15479/AT:ISTA:7172</a>.","mla":"Vasileva, Mina K. <i>Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7172\">10.15479/AT:ISTA:7172</a>.","apa":"Vasileva, M. K. (2019). <i>Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7172\">https://doi.org/10.15479/AT:ISTA:7172</a>","ista":"Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","ieee":"M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019.","short":"M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019.","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7172\">10.15479/AT:ISTA:7172</a>"},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"OA_place":"publisher","alternative_title":["ISTA Thesis"],"date_updated":"2026-04-08T13:54:45Z","page":"192","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"12","publication_status":"published","corr_author":"1","file_date_updated":"2020-07-14T12:47:51Z","oa":1,"has_accepted_license":"1","ddc":["570"],"_id":"7172","author":[{"first_name":"Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87","last_name":"Vasileva","full_name":"Vasileva, Mina K"}],"publisher":"Institute of Science and Technology Austria"},{"article_processing_charge":"No","isi":1,"month":"12","abstract":[{"lang":"eng","text":"Glutamate is the major excitatory neurotransmitter in the CNS binding to a variety of glutamate receptors. Metabotropic glutamate receptors (mGluR1 to mGluR8) can act excitatory or inhibitory, depending on associated signal cascades. Expression and localization of inhibitory acting mGluRs at inner hair cells (IHCs) in the cochlea are largely unknown. Here, we analyzed expression of mGluR2, mGluR3, mGluR4, mGluR6, mGluR7, and mGluR8 and investigated their localization with respect to the presynaptic ribbon of IHC synapses. We detected transcripts for mGluR2, mGluR3, and mGluR4 as well as for mGluR7a, mGluR7b, mGluR8a, and mGluR8b splice variants. Using receptor-specific antibodies in cochlear wholemounts, we found expression of mGluR2, mGluR4, and mGluR8b close to presynaptic ribbons. Super resolution and confocal microscopy in combination with 3-dimensional reconstructions indicated a postsynaptic localization of mGluR2 that overlaps with postsynaptic density protein 95 on dendrites of afferent type I spiral ganglion neurons. In contrast, mGluR4 and mGluR8b were expressed at the presynapse close to IHC ribbons. In summary, we localized in detail 3 mGluR types at IHC ribbon synapses, providing a fundament for new therapeutical strategies that could protect the cochlea against noxious stimuli and excitotoxicity."}],"volume":33,"department":[{"_id":"RySh"}],"status":"public","oa_version":"Submitted Version","file":[{"access_level":"open_access","file_id":"8922","date_created":"2020-12-06T17:30:09Z","creator":"shigemot","relation":"main_file","checksum":"79e3b72481dc32489911121cf3b7d8d0","success":1,"content_type":"application/pdf","file_name":"Klotz et al 2019 EMBO Reports.pdf","date_updated":"2020-12-06T17:30:09Z","file_size":4766789}],"citation":{"short":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, R. Enz, FASEB Journal 33 (2019) 13734–13746.","ama":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. <i>FASEB Journal</i>. 2019;33(12):13734-13746. doi:<a href=\"https://doi.org/10.1096/fj.201901543R\">10.1096/fj.201901543R</a>","chicago":"Klotz, Lisa, Olaf Wendler, Renato Frischknecht, Ryuichi Shigemoto, Holger Schulze, and Ralf Enz. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” <i>FASEB Journal</i>. FASEB, 2019. <a href=\"https://doi.org/10.1096/fj.201901543R\">https://doi.org/10.1096/fj.201901543R</a>.","apa":"Klotz, L., Wendler, O., Frischknecht, R., Shigemoto, R., Schulze, H., &#38; Enz, R. (2019). Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. <i>FASEB Journal</i>. FASEB. <a href=\"https://doi.org/10.1096/fj.201901543R\">https://doi.org/10.1096/fj.201901543R</a>","mla":"Klotz, Lisa, et al. “Localization of Group II and III Metabotropic Glutamate Receptors at Pre- and Postsynaptic Sites of Inner Hair Cell Ribbon Synapses.” <i>FASEB Journal</i>, vol. 33, no. 12, FASEB, 2019, pp. 13734–46, doi:<a href=\"https://doi.org/10.1096/fj.201901543R\">10.1096/fj.201901543R</a>.","ista":"Klotz L, Wendler O, Frischknecht R, Shigemoto R, Schulze H, Enz R. 2019. Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses. FASEB Journal. 33(12), 13734–13746.","ieee":"L. Klotz, O. Wendler, R. Frischknecht, R. Shigemoto, H. Schulze, and R. Enz, “Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses,” <i>FASEB Journal</i>, vol. 33, no. 12. FASEB, pp. 13734–13746, 2019."},"date_created":"2019-12-15T23:00:42Z","article_type":"original","scopus_import":"1","date_published":"2019-12-01T00:00:00Z","publication":"FASEB Journal","language":[{"iso":"eng"}],"type":"journal_article","doi":"10.1096/fj.201901543R","title":"Localization of group II and III metabotropic glutamate receptors at pre- and postsynaptic sites of inner hair cell ribbon synapses","pmid":1,"publication_identifier":{"eissn":["1530-6860"]},"issue":"12","year":"2019","intvolume":"        33","quality_controlled":"1","publication_status":"published","_id":"7179","author":[{"full_name":"Klotz, Lisa","last_name":"Klotz","first_name":"Lisa"},{"first_name":"Olaf","last_name":"Wendler","full_name":"Wendler, Olaf"},{"first_name":"Renato","full_name":"Frischknecht, Renato","last_name":"Frischknecht"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"first_name":"Holger","full_name":"Schulze, Holger","last_name":"Schulze"},{"last_name":"Enz","full_name":"Enz, Ralf","first_name":"Ralf"}],"has_accepted_license":"1","ddc":["571","599"],"publisher":"FASEB","file_date_updated":"2020-12-06T17:30:09Z","oa":1,"date_updated":"2026-04-03T09:44:03Z","page":"13734-13746","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"pmid":["31585509"],"isi":["000507466100054"]},"day":"01"},{"article_processing_charge":"No","abstract":[{"text":"Arabidopsis PIN2 protein directs transport of the phytohormone auxin from the root tip into the root elongation zone. Variation in hormone transport, which depends on a delicate interplay between PIN2 sorting to and from polar plasma membrane domains, determines root growth. By employing a constitutively degraded version of PIN2, we identify brassinolides as antagonists of PIN2 endocytosis. This response does not require de novo protein synthesis, but involves early events in canonical brassinolide signaling. Brassinolide-controlled adjustments in PIN2 sorting and intracellular distribution governs formation of a lateral PIN2 gradient in gravistimulated roots, coinciding with adjustments in auxin signaling and directional root growth. Strikingly, simulations indicate that PIN2 gradient formation is no prerequisite for root bending but rather dampens asymmetric auxin flow and signaling. Crosstalk between brassinolide signaling and endocytic PIN2 sorting, thus, appears essential for determining the rate of gravity-induced root curvature via attenuation of differential cell elongation.","lang":"eng"}],"volume":10,"month":"12","isi":1,"department":[{"_id":"DaSi"}],"status":"public","oa_version":"Published Version","file":[{"file_id":"7184","date_created":"2019-12-16T07:37:50Z","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:52Z","file_name":"2019_NatureComm_Retzer.pdf","file_size":5156533,"checksum":"77e8720a8e0f3091b98159f85be40893"}],"citation":{"ieee":"K. Retzer <i>et al.</i>, “Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","ista":"Retzer K, Akhmanova M, Konstantinova N, Malínská K, Leitner J, Petrášek J, Luschnig C. 2019. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. Nature Communications. 10, 5516.","mla":"Retzer, Katarzyna, et al. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” <i>Nature Communications</i>, vol. 10, 5516, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13543-1\">10.1038/s41467-019-13543-1</a>.","apa":"Retzer, K., Akhmanova, M., Konstantinova, N., Malínská, K., Leitner, J., Petrášek, J., &#38; Luschnig, C. (2019). Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13543-1\">https://doi.org/10.1038/s41467-019-13543-1</a>","chicago":"Retzer, Katarzyna, Maria Akhmanova, Nataliia Konstantinova, Kateřina Malínská, Johannes Leitner, Jan Petrášek, and Christian Luschnig. “Brassinosteroid Signaling Delimits Root Gravitropism via Sorting of the Arabidopsis PIN2 Auxin Transporter.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13543-1\">https://doi.org/10.1038/s41467-019-13543-1</a>.","ama":"Retzer K, Akhmanova M, Konstantinova N, et al. Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13543-1\">10.1038/s41467-019-13543-1</a>","short":"K. Retzer, M. Akhmanova, N. Konstantinova, K. Malínská, J. Leitner, J. Petrášek, C. Luschnig, Nature Communications 10 (2019)."},"date_created":"2019-12-15T23:00:43Z","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"date_published":"2019-12-01T00:00:00Z","type":"journal_article","doi":"10.1038/s41467-019-13543-1","title":"Brassinosteroid signaling delimits root gravitropism via sorting of the Arabidopsis PIN2 auxin transporter","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"article_number":"5516","year":"2019","intvolume":"        10","quality_controlled":"1","publication_status":"published","_id":"7180","author":[{"last_name":"Retzer","full_name":"Retzer, Katarzyna","first_name":"Katarzyna"},{"full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162","last_name":"Akhmanova","first_name":"Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Konstantinova, Nataliia","last_name":"Konstantinova","first_name":"Nataliia"},{"first_name":"Kateřina","last_name":"Malínská","full_name":"Malínská, Kateřina"},{"first_name":"Johannes","full_name":"Leitner, Johannes","last_name":"Leitner"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"}],"ddc":["570"],"has_accepted_license":"1","publisher":"Springer Nature","oa":1,"file_date_updated":"2020-07-14T12:47:52Z","date_updated":"2026-04-03T09:46:19Z","project":[{"call_identifier":"FWF","name":"Modeling epithelial tissue mechanics during cell invasion","_id":"264CBBAC-B435-11E9-9278-68D0E5697425","grant_number":"M02379"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"pmid":["31797871"],"isi":["000500508100001"]},"day":"01"}]