[{"date_updated":"2024-10-21T06:02:25Z","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.10451"}],"oa":1,"article_type":"original","oa_version":"Preprint","_id":"177","external_id":{"arxiv":["1711.10451"],"isi":["000526986300004"]},"author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","last_name":"Browning","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","first_name":"Timothy D"},{"first_name":"Will","full_name":"Sawin, Will","last_name":"Sawin"}],"publication_status":"published","publisher":"Princeton University","day":"01","doi":"10.4007/annals.2020.191.3.4","abstract":[{"lang":"eng","text":"We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree."}],"article_processing_charge":"No","publist_id":"7744","intvolume":"       191","page":"893-948","arxiv":1,"date_published":"2020-05-01T00:00:00Z","isi":1,"department":[{"_id":"TiBr"}],"date_created":"2018-12-11T11:45:02Z","scopus_import":"1","quality_controlled":"1","citation":{"chicago":"Browning, Timothy D, and Will Sawin. “A Geometric Version of the Circle Method.” <i>Annals of Mathematics</i>. Princeton University, 2020. <a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">https://doi.org/10.4007/annals.2020.191.3.4</a>.","ieee":"T. D. Browning and W. Sawin, “A geometric version of the circle method,” <i>Annals of Mathematics</i>, vol. 191, no. 3. Princeton University, pp. 893–948, 2020.","apa":"Browning, T. D., &#38; Sawin, W. (2020). A geometric version of the circle method. <i>Annals of Mathematics</i>. Princeton University. <a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">https://doi.org/10.4007/annals.2020.191.3.4</a>","ama":"Browning TD, Sawin W. A geometric version of the circle method. <i>Annals of Mathematics</i>. 2020;191(3):893-948. doi:<a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">10.4007/annals.2020.191.3.4</a>","mla":"Browning, Timothy D., and Will Sawin. “A Geometric Version of the Circle Method.” <i>Annals of Mathematics</i>, vol. 191, no. 3, Princeton University, 2020, pp. 893–948, doi:<a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">10.4007/annals.2020.191.3.4</a>.","ista":"Browning TD, Sawin W. 2020. A geometric version of the circle method. Annals of Mathematics. 191(3), 893–948.","short":"T.D. Browning, W. Sawin, Annals of Mathematics 191 (2020) 893–948."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","volume":191,"type":"journal_article","issue":"3","year":"2020","language":[{"iso":"eng"}],"publication":"Annals of Mathematics","title":"A geometric version of the circle method"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.10715"}],"date_updated":"2024-10-21T06:02:33Z","month":"09","oa_version":"Preprint","oa":1,"article_type":"original","abstract":[{"text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1215/00127094-2020-0031","author":[{"last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D","first_name":"Timothy D"},{"last_name":"Heath Brown","full_name":"Heath Brown, Roger","first_name":"Roger"}],"_id":"179","external_id":{"isi":["000582676300002"],"arxiv":["1805.10715"]},"publication_status":"published","publisher":"Duke University Press","day":"10","page":"3099-3165","arxiv":1,"date_published":"2020-09-10T00:00:00Z","intvolume":"       169","publication_identifier":{"issn":["0012-7094"]},"department":[{"_id":"TiBr"}],"isi":1,"citation":{"short":"T.D. Browning, R. Heath Brown, Duke Mathematical Journal 169 (2020) 3099–3165.","ista":"Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 169(16), 3099–3165.","mla":"Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” <i>Duke Mathematical Journal</i>, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:<a href=\"https://doi.org/10.1215/00127094-2020-0031\">10.1215/00127094-2020-0031</a>.","ama":"Browning TD, Heath Brown R. Density of rational points on a quadric bundle in ℙ3×ℙ3. <i>Duke Mathematical Journal</i>. 2020;169(16):3099-3165. doi:<a href=\"https://doi.org/10.1215/00127094-2020-0031\">10.1215/00127094-2020-0031</a>","apa":"Browning, T. D., &#38; Heath Brown, R. (2020). Density of rational points on a quadric bundle in ℙ3×ℙ3. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-2020-0031\">https://doi.org/10.1215/00127094-2020-0031</a>","ieee":"T. D. Browning and R. Heath Brown, “Density of rational points on a quadric bundle in ℙ3×ℙ3,” <i>Duke Mathematical Journal</i>, vol. 169, no. 16. Duke University Press, pp. 3099–3165, 2020.","chicago":"Browning, Timothy D, and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” <i>Duke Mathematical Journal</i>. Duke University Press, 2020. <a href=\"https://doi.org/10.1215/00127094-2020-0031\">https://doi.org/10.1215/00127094-2020-0031</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":169,"status":"public","date_created":"2018-12-11T11:45:02Z","quality_controlled":"1","scopus_import":"1","language":[{"iso":"eng"}],"title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","publication":"Duke Mathematical Journal","issue":"16","year":"2020","type":"journal_article"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1063/1.5122969"}],"date_updated":"2026-06-18T19:23:35Z","month":"03","oa_version":"Published Version","oa":1,"article_type":"original","abstract":[{"text":"We introduce “state space persistence analysis” for deducing the symbolic dynamics of time series data obtained from high-dimensional chaotic attractors. To this end, we adapt a topological data analysis technique known as persistent homology for the characterization of state space projections of chaotic trajectories and periodic orbits. By comparing the shapes along a chaotic trajectory to those of the periodic orbits, state space persistence analysis quantifies the shape similarity of chaotic trajectory segments and periodic orbits. We demonstrate the method by applying it to the three-dimensional Rössler system and a 30-dimensional discretization of the Kuramoto–Sivashinsky partial differential equation in (1+1) dimensions.\r\nOne way of studying chaotic attractors systematically is through their symbolic dynamics, in which one partitions the state space into qualitatively different regions and assigns a symbol to each such region.1–3 This yields a “coarse-grained” state space of the system, which can then be reduced to a Markov chain encoding all possible transitions between the states of the system. While it is possible to obtain the symbolic dynamics of low-dimensional chaotic systems with standard tools such as Poincaré maps, when applied to high-dimensional systems such as turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5 In this paper, we develop “state space persistence analysis” and demonstrate that it can be utilized to infer the symbolic dynamics in very high-dimensional settings.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1063/1.5122969","_id":"7563","publisher":"AIP Publishing","external_id":{"arxiv":["1910.04584"],"isi":["000519254800002"]},"author":[{"last_name":"Yalniz","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425","first_name":"Gökhan","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan"},{"id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","last_name":"Budanur","full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","first_name":"Nazmi B"}],"publication_status":"published","day":"03","ddc":["530"],"arxiv":1,"date_published":"2020-03-03T00:00:00Z","article_number":"033109","intvolume":"        30","department":[{"_id":"BjHo"}],"publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Yalniz, Gökhan, and Nazmi B Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>. AIP Publishing, 2020. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>.","ieee":"G. Yalniz and N. B. Budanur, “Inferring symbolic dynamics of chaotic flows from persistence,” <i>Chaos</i>, vol. 30, no. 3. AIP Publishing, 2020.","apa":"Yalniz, G., &#38; Budanur, N. B. (2020). Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.5122969\">https://doi.org/10.1063/1.5122969</a>","ama":"Yalniz G, Budanur NB. Inferring symbolic dynamics of chaotic flows from persistence. <i>Chaos</i>. 2020;30(3). doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>","mla":"Yalniz, Gökhan, and Nazmi B. Budanur. “Inferring Symbolic Dynamics of Chaotic Flows from Persistence.” <i>Chaos</i>, vol. 30, no. 3, 033109, AIP Publishing, 2020, doi:<a href=\"https://doi.org/10.1063/1.5122969\">10.1063/1.5122969</a>.","ista":"Yalniz G, Budanur NB. 2020. Inferring symbolic dynamics of chaotic flows from persistence. Chaos. 30(3), 033109.","short":"G. Yalniz, N.B. Budanur, Chaos 30 (2020)."},"volume":30,"status":"public","date_created":"2020-03-04T08:06:25Z","related_material":{"record":[{"relation":"dissertation_contains","id":"19684","status":"public"}]},"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"title":"Inferring symbolic dynamics of chaotic flows from persistence","corr_author":"1","publication":"Chaos","type":"journal_article","year":"2020","issue":"3"},{"ddc":["510"],"ec_funded":1,"_id":"7567","author":[{"last_name":"Choudhary","first_name":"Aruni","full_name":"Choudhary, Aruni"},{"last_name":"Kachanovich","first_name":"Siargey","full_name":"Kachanovich, Siargey"},{"first_name":"Mathijs","orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Springer Nature","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"day":"01","doi":"10.1007/s11786-020-00461-5","abstract":[{"text":"Coxeter triangulations are triangulations of Euclidean space based on a single simplex. By this we mean that given an individual simplex we can recover the entire triangulation of Euclidean space by inductively reflecting in the faces of the simplex. In this paper we establish that the quality of the simplices in all Coxeter triangulations is O(1/d−−√) of the quality of regular simplex. We further investigate the Delaunay property for these triangulations. Moreover, we consider an extension of the Delaunay property, namely protection, which is a measure of non-degeneracy of a Delaunay triangulation. In particular, one family of Coxeter triangulations achieves the protection O(1/d2). We conjecture that both bounds are optimal for triangulations in Euclidean space.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","oa":1,"article_type":"original","file_date_updated":"2020-11-20T10:18:02Z","oa_version":"Published Version","has_accepted_license":"1","date_updated":"2025-04-14T07:44:03Z","month":"03","type":"journal_article","year":"2020","file":[{"creator":"dernst","success":1,"file_id":"8783","access_level":"open_access","content_type":"application/pdf","date_created":"2020-11-20T10:18:02Z","date_updated":"2020-11-20T10:18:02Z","file_name":"2020_MathCompScie_Choudhary.pdf","checksum":"1d145f3ab50ccee735983cb89236e609","file_size":872275,"relation":"main_file"}],"language":[{"iso":"eng"}],"publication":"Mathematics in Computer Science","corr_author":"1","title":"Coxeter triangulations have good quality","date_created":"2020-03-05T13:30:18Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","quality_controlled":"1","citation":{"apa":"Choudhary, A., Kachanovich, S., &#38; Wintraecken, M. (2020). Coxeter triangulations have good quality. <i>Mathematics in Computer Science</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11786-020-00461-5\">https://doi.org/10.1007/s11786-020-00461-5</a>","ieee":"A. Choudhary, S. Kachanovich, and M. Wintraecken, “Coxeter triangulations have good quality,” <i>Mathematics in Computer Science</i>, vol. 14. Springer Nature, pp. 141–176, 2020.","chicago":"Choudhary, Aruni, Siargey Kachanovich, and Mathijs Wintraecken. “Coxeter Triangulations Have Good Quality.” <i>Mathematics in Computer Science</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11786-020-00461-5\">https://doi.org/10.1007/s11786-020-00461-5</a>.","ista":"Choudhary A, Kachanovich S, Wintraecken M. 2020. Coxeter triangulations have good quality. Mathematics in Computer Science. 14, 141–176.","short":"A. Choudhary, S. Kachanovich, M. Wintraecken, Mathematics in Computer Science 14 (2020) 141–176.","mla":"Choudhary, Aruni, et al. “Coxeter Triangulations Have Good Quality.” <i>Mathematics in Computer Science</i>, vol. 14, Springer Nature, 2020, pp. 141–76, doi:<a href=\"https://doi.org/10.1007/s11786-020-00461-5\">10.1007/s11786-020-00461-5</a>.","ama":"Choudhary A, Kachanovich S, Wintraecken M. Coxeter triangulations have good quality. <i>Mathematics in Computer Science</i>. 2020;14:141-176. doi:<a href=\"https://doi.org/10.1007/s11786-020-00461-5\">10.1007/s11786-020-00461-5</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":14,"license":"https://creativecommons.org/licenses/by/4.0/","publication_identifier":{"eissn":["1661-8289"],"issn":["1661-8270"]},"department":[{"_id":"HeEd"}],"intvolume":"        14","page":"141-176","date_published":"2020-03-01T00:00:00Z"},{"doi":"10.1371/journal.pcbi.1007642","abstract":[{"lang":"eng","text":"Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models."}],"article_processing_charge":"No","_id":"7569","publisher":"Public Library of Science","publication_status":"published","external_id":{"pmid":["32097416"],"isi":["000526725200019"]},"author":[{"last_name":"Grah","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","first_name":"Rok"},{"last_name":"Friedlander","first_name":"Tamar","full_name":"Friedlander, Tamar"}],"day":"25","ddc":["000","570"],"has_accepted_license":"1","date_updated":"2026-04-08T07:25:08Z","month":"02","oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:00Z","article_type":"original","oa":1,"citation":{"mla":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” <i>PLOS Computational Biology</i>, vol. 16, no. 2, e1007642, Public Library of Science, 2020, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">10.1371/journal.pcbi.1007642</a>.","ama":"Grah R, Friedlander T. The relation between crosstalk and gene regulation form revisited. <i>PLOS Computational Biology</i>. 2020;16(2). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">10.1371/journal.pcbi.1007642</a>","short":"R. Grah, T. Friedlander, PLOS Computational Biology 16 (2020).","ista":"Grah R, Friedlander T. 2020. The relation between crosstalk and gene regulation form revisited. PLOS Computational Biology. 16(2), e1007642.","chicago":"Grah, Rok, and Tamar Friedlander. “The Relation between Crosstalk and Gene Regulation Form Revisited.” <i>PLOS Computational Biology</i>. Public Library of Science, 2020. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">https://doi.org/10.1371/journal.pcbi.1007642</a>.","apa":"Grah, R., &#38; Friedlander, T. (2020). The relation between crosstalk and gene regulation form revisited. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1007642\">https://doi.org/10.1371/journal.pcbi.1007642</a>","ieee":"R. Grah and T. Friedlander, “The relation between crosstalk and gene regulation form revisited,” <i>PLOS Computational Biology</i>, vol. 16, no. 2. Public Library of Science, 2020."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":16,"date_created":"2020-03-06T07:39:38Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"status":"deleted","id":"9716","relation":"research_data"},{"relation":"research_data","status":"public","id":"9776"},{"id":"9779","status":"public","relation":"research_data"},{"status":"public","id":"9777","relation":"research_data"},{"relation":"dissertation_contains","id":"8155","status":"public"}]},"file":[{"creator":"dernst","file_id":"7579","access_level":"open_access","date_created":"2020-03-09T15:12:21Z","date_updated":"2020-07-14T12:48:00Z","content_type":"application/pdf","relation":"main_file","file_size":2209325,"file_name":"2020_PlosCompBio_Grah.pdf","checksum":"5239dd134dc6e1c71fe7b3ce2953da37"}],"language":[{"iso":"eng"}],"publication":"PLOS Computational Biology","title":"The relation between crosstalk and gene regulation form revisited","issue":"2","year":"2020","type":"journal_article","pmid":1,"article_number":"e1007642","date_published":"2020-02-25T00:00:00Z","intvolume":"        16","isi":1,"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"publication_identifier":{"issn":["1553-7358"]}},{"publication":"Physical Review X","title":"Slow quantum thermalization and many-body revivals from mixed phase space","file":[{"file_name":"2020_PhysicalReviewX_Michailidis.pdf","checksum":"4b3f2c13873d35230173c73d0e11c408","relation":"main_file","file_size":17828638,"content_type":"application/pdf","date_created":"2020-03-12T12:13:07Z","date_updated":"2020-07-14T12:48:00Z","access_level":"open_access","file_id":"7581","creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"1","type":"journal_article","year":"2020","status":"public","volume":10,"citation":{"mla":"Michailidis, Alexios, et al. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” <i>Physical Review X</i>, vol. 10, no. 1, 011055, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevx.10.011055\">10.1103/physrevx.10.011055</a>.","ama":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. Slow quantum thermalization and many-body revivals from mixed phase space. <i>Physical Review X</i>. 2020;10(1). doi:<a href=\"https://doi.org/10.1103/physrevx.10.011055\">10.1103/physrevx.10.011055</a>","short":"A. Michailidis, C.J. Turner, Z. Papić, D.A. Abanin, M. Serbyn, Physical Review X 10 (2020).","ista":"Michailidis A, Turner CJ, Papić Z, Abanin DA, Serbyn M. 2020. Slow quantum thermalization and many-body revivals from mixed phase space. Physical Review X. 10(1), 011055.","chicago":"Michailidis, Alexios, C. J. Turner, Z. Papić, D. A. Abanin, and Maksym Serbyn. “Slow Quantum Thermalization and Many-Body Revivals from Mixed Phase Space.” <i>Physical Review X</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevx.10.011055\">https://doi.org/10.1103/physrevx.10.011055</a>.","apa":"Michailidis, A., Turner, C. J., Papić, Z., Abanin, D. A., &#38; Serbyn, M. (2020). Slow quantum thermalization and many-body revivals from mixed phase space. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.10.011055\">https://doi.org/10.1103/physrevx.10.011055</a>","ieee":"A. Michailidis, C. J. Turner, Z. Papić, D. A. Abanin, and M. Serbyn, “Slow quantum thermalization and many-body revivals from mixed phase space,” <i>Physical Review X</i>, vol. 10, no. 1. American Physical Society, 2020."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/classical-physics-helps-predict-fate-of-interacting-quantum-systems/","relation":"press_release","description":"News on IST Homepage"}]},"date_created":"2020-03-08T18:02:01Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"isi":1,"publication_identifier":{"issn":["2160-3308"]},"department":[{"_id":"MaSe"}],"date_published":"2020-03-04T00:00:00Z","article_number":"011055","arxiv":1,"intvolume":"        10","ddc":["530"],"doi":"10.1103/physrevx.10.011055","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The relaxation of few-body quantum systems can strongly depend on the initial state when the system’s semiclassical phase space is mixed; i.e., regions of chaotic motion coexist with regular islands. In recent years, there has been much effort to understand the process of thermalization in strongly interacting quantum systems that often lack an obvious semiclassical limit. The time-dependent variational principle (TDVP) allows one to systematically derive an effective classical (nonlinear) dynamical system by projecting unitary many-body dynamics onto a manifold of weakly entangled variational states. We demonstrate that such dynamical systems generally possess mixed phase space. When TDVP errors are small, the mixed phase space leaves a footprint on the exact dynamics of the quantum model. For example, when the system is initialized in a state belonging to a stable periodic orbit or the surrounding regular region, it exhibits persistent many-body quantum revivals. As a proof of principle, we identify new types of “quantum many-body scars,” i.e., initial states that lead to long-time oscillations in a model of interacting Rydberg atoms in one and two dimensions. Intriguingly, the initial states that give rise to most robust revivals are typically entangled states. On the other hand, even when TDVP errors are large, as in the thermalizing tilted-field Ising model, initializing the system in a regular region of phase space leads to a surprising slowdown of thermalization. Our work establishes TDVP as a method for identifying interacting quantum systems with anomalous dynamics in arbitrary dimensions. Moreover, the mixed phase space classical variational equations allow one to find slowly thermalizing initial conditions in interacting models. Our results shed light on a link between classical and quantum chaos, pointing toward possible extensions of the classical Kolmogorov-Arnold-Moser theorem to quantum systems."}],"day":"04","_id":"7570","author":[{"first_name":"Alexios","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis"},{"last_name":"Turner","first_name":"C. J.","full_name":"Turner, C. J."},{"last_name":"Papić","first_name":"Z.","full_name":"Papić, Z."},{"last_name":"Abanin","full_name":"Abanin, D. A.","first_name":"D. A."},{"last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym"}],"external_id":{"arxiv":["1905.08564"],"isi":["000517969300001"]},"publication_status":"published","publisher":"American Physical Society","file_date_updated":"2020-07-14T12:48:00Z","oa_version":"Published Version","oa":1,"article_type":"original","month":"03","has_accepted_license":"1","date_updated":"2023-08-18T07:01:07Z"},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"8358","status":"public"}]},"scopus_import":"1","quality_controlled":"1","date_created":"2020-03-08T23:00:47Z","volume":158,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in <i>Methods in Cell Biology</i>, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161.","apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., &#38; Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), <i>Methods in Cell Biology</i> (Vol. 158, pp. 145–161). Elsevier. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>","chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In <i>Methods in Cell Biology</i>, edited by Phong  Tran, 158:145–61. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>.","ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.","short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161.","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. <i>Methods in Cell Biology</i>. Vol 158. Elsevier; 2020:145-161. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” <i>Methods in Cell Biology</i>, edited by Phong  Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>."},"year":"2020","type":"book_chapter","title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","publication":"Methods in Cell Biology","language":[{"iso":"eng"}],"intvolume":"       158","date_published":"2020-02-27T00:00:00Z","alternative_title":["Methods in Cell Biology"],"page":"145-161","department":[{"_id":"MaLo"}],"publication_identifier":{"issn":["0091-679X"]},"isi":1,"day":"27","project":[{"grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"_id":"7572","external_id":{"isi":["000611826500008"]},"author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","first_name":"Paulo R"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","last_name":"Radler","first_name":"Philipp","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 "},{"first_name":"Christoph M","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Elsevier","publication_status":"published","article_processing_charge":"No","abstract":[{"text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material.","lang":"eng"}],"doi":"10.1016/bs.mcb.2020.01.006","ec_funded":1,"month":"02","date_updated":"2026-04-08T07:26:30Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"oa":1,"editor":[{"last_name":"Tran","full_name":"Tran, Phong ","first_name":"Phong "}],"oa_version":"Preprint"},{"project":[{"name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Differential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"F06504"},{"grant_number":"W1245","call_identifier":"FWF","name":"Dissipation and dispersion in nonlinear partial differential equations","_id":"260788DE-B435-11E9-9278-68D0E5697425"}],"day":"01","external_id":{"isi":["000539439400008"],"arxiv":["1905.05757"]},"_id":"7573","author":[{"last_name":"Gladbach","first_name":"Peter","full_name":"Gladbach, Peter"},{"first_name":"Eva","full_name":"Kopfer, Eva","last_name":"Kopfer"},{"id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","first_name":"Jan","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"},{"last_name":"Portinale","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","full_name":"Portinale, Lorenzo"}],"publication_status":"published","publisher":"Elsevier","doi":"10.1016/j.matpur.2020.02.008","article_processing_charge":"No","abstract":[{"lang":"eng","text":"This paper deals with dynamical optimal transport metrics defined by spatial discretisation of the Benamou–Benamou formula for the Kantorovich metric . Such metrics appear naturally in discretisations of -gradient flow formulations for dissipative PDE. However, it has recently been shown that these metrics do not in general converge to , unless strong geometric constraints are imposed on the discrete mesh. In this paper we prove that, in a 1-dimensional periodic setting, discrete transport metrics converge to a limiting transport metric with a non-trivial effective mobility. This mobility depends sensitively on the geometry of the mesh and on the non-local mobility at the discrete level. Our result quantifies to what extent discrete transport can make use of microstructure in the mesh to reduce the cost of transport."}],"ec_funded":1,"month":"07","date_updated":"2026-04-08T07:00:03Z","acknowledgement":"J.M. gratefully acknowledges support by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No 716117). J.M. and L.P. also acknowledge support from the Austrian Science Fund (FWF), grants No F65 and W1245. E.K. gratefully acknowledges support by the German Research Foundation through the Hausdorff Center for Mathematics and the Collaborative Research Center 1060. P.G. is partially funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 350398276.","main_file_link":[{"url":"https://arxiv.org/abs/1905.05757","open_access":"1"}],"article_type":"original","oa":1,"oa_version":"Preprint","scopus_import":"1","quality_controlled":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10030"}]},"date_created":"2020-03-08T23:00:47Z","status":"public","volume":139,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Gladbach, Peter, Eva Kopfer, Jan Maas, and Lorenzo Portinale. “Homogenisation of One-Dimensional Discrete Optimal Transport.” <i>Journal de Mathematiques Pures et Appliquees</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">https://doi.org/10.1016/j.matpur.2020.02.008</a>.","ieee":"P. Gladbach, E. Kopfer, J. Maas, and L. Portinale, “Homogenisation of one-dimensional discrete optimal transport,” <i>Journal de Mathematiques Pures et Appliquees</i>, vol. 139, no. 7. Elsevier, pp. 204–234, 2020.","apa":"Gladbach, P., Kopfer, E., Maas, J., &#38; Portinale, L. (2020). Homogenisation of one-dimensional discrete optimal transport. <i>Journal de Mathematiques Pures et Appliquees</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">https://doi.org/10.1016/j.matpur.2020.02.008</a>","ama":"Gladbach P, Kopfer E, Maas J, Portinale L. Homogenisation of one-dimensional discrete optimal transport. <i>Journal de Mathematiques Pures et Appliquees</i>. 2020;139(7):204-234. doi:<a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">10.1016/j.matpur.2020.02.008</a>","mla":"Gladbach, Peter, et al. “Homogenisation of One-Dimensional Discrete Optimal Transport.” <i>Journal de Mathematiques Pures et Appliquees</i>, vol. 139, no. 7, Elsevier, 2020, pp. 204–34, doi:<a href=\"https://doi.org/10.1016/j.matpur.2020.02.008\">10.1016/j.matpur.2020.02.008</a>.","short":"P. Gladbach, E. Kopfer, J. Maas, L. Portinale, Journal de Mathematiques Pures et Appliquees 139 (2020) 204–234.","ista":"Gladbach P, Kopfer E, Maas J, Portinale L. 2020. Homogenisation of one-dimensional discrete optimal transport. Journal de Mathematiques Pures et Appliquees. 139(7), 204–234."},"issue":"7","year":"2020","type":"journal_article","publication":"Journal de Mathematiques Pures et Appliquees","title":"Homogenisation of one-dimensional discrete optimal transport","language":[{"iso":"eng"}],"intvolume":"       139","date_published":"2020-07-01T00:00:00Z","arxiv":1,"page":"204-234","isi":1,"department":[{"_id":"JaMa"}],"publication_identifier":{"issn":["0021-7824"]}},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"isi":1,"department":[{"_id":"MaLo"},{"_id":"CaBe"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"intvolume":"       117","page":"6504-6549","date_published":"2020-03-24T00:00:00Z","year":"2020","type":"journal_article","issue":"12","pmid":1,"language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","title":"Stochastic activation and bistability in a Rab GTPase regulatory network","date_created":"2020-03-12T05:32:26Z","quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"status":"public","id":"8341","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","relation":"press_release","description":"News on IST Homepage"}]},"citation":{"short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 6504–6549.","ista":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences of the United States of America. 117(12), 6504–6549.","mla":"Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 12, National Academy of Sciences, 2020, pp. 6504–49, doi:<a href=\"https://doi.org/10.1073/pnas.1921027117\">10.1073/pnas.1921027117</a>.","ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(12):6504-6549. doi:<a href=\"https://doi.org/10.1073/pnas.1921027117\">10.1073/pnas.1921027117</a>","apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., &#38; Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921027117\">https://doi.org/10.1073/pnas.1921027117</a>","ieee":"U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 12. National Academy of Sciences, pp. 6504–6549, 2020.","chicago":"Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921027117\">https://doi.org/10.1073/pnas.1921027117</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":117,"oa":1,"article_type":"original","oa_version":"Preprint","date_updated":"2026-04-08T07:24:55Z","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/776567"}],"_id":"7580","external_id":{"isi":["000521821800040"],"pmid":["32161136"]},"publication_status":"published","author":[{"orcid":"0000-0003-1365-5631","full_name":"Bezeljak, Urban","first_name":"Urban","last_name":"Bezeljak","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Loya","full_name":"Loya, Hrushikesh","first_name":"Hrushikesh"},{"full_name":"Kaczmarek, Beata M","first_name":"Beata M","last_name":"Kaczmarek","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Timothy E.","full_name":"Saunders, Timothy E.","last_name":"Saunders"},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"publisher":"National Academy of Sciences","project":[{"name":"Reconstitution of cell polarity and axis determination in a cell-free system","_id":"2599F062-B435-11E9-9278-68D0E5697425","grant_number":"RGY0083/2016"}],"day":"24","doi":"10.1073/pnas.1921027117","article_processing_charge":"No","abstract":[{"lang":"eng","text":"The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell."}]},{"scopus_import":"1","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2020-03-15T23:00:52Z","status":"public","volume":9,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"apa":"Moturu, T. R., Sinha, S., Salava, H., Thula, S., Nodzyński, T., Vařeková, R. S., … Simon, S. (2020). Molecular evolution and diversification of proteins involved in miRNA maturation pathway. <i>Plants</i>. MDPI. <a href=\"https://doi.org/10.3390/plants9030299\">https://doi.org/10.3390/plants9030299</a>","ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of proteins involved in miRNA maturation pathway,” <i>Plants</i>, vol. 9, no. 3. MDPI, 2020.","chicago":"Moturu, Taraka Ramji, Sansrity Sinha, Hymavathi Salava, Sravankumar Thula, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” <i>Plants</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/plants9030299\">https://doi.org/10.3390/plants9030299</a>.","short":"T.R. Moturu, S. Sinha, H. Salava, S. Thula, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Plants 9 (2020).","ista":"Moturu TR, Sinha S, Salava H, Thula S, Nodzyński T, Vařeková RS, Friml J, Simon S. 2020. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. Plants. 9(3), 299.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of Proteins Involved in MiRNA Maturation Pathway.” <i>Plants</i>, vol. 9, no. 3, 299, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/plants9030299\">10.3390/plants9030299</a>.","ama":"Moturu TR, Sinha S, Salava H, et al. Molecular evolution and diversification of proteins involved in miRNA maturation pathway. <i>Plants</i>. 2020;9(3). doi:<a href=\"https://doi.org/10.3390/plants9030299\">10.3390/plants9030299</a>"},"pmid":1,"year":"2020","type":"journal_article","issue":"3","corr_author":"1","publication":"Plants","title":"Molecular evolution and diversification of proteins involved in miRNA maturation pathway","file":[{"checksum":"6d5af3e17266a48996b4af4e67e88a85","file_name":"2020_Plants_Moturu.pdf","file_size":2373484,"relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-23T13:37:00Z","file_id":"7614","access_level":"open_access","creator":"dernst"}],"language":[{"iso":"eng"}],"intvolume":"         9","article_number":"299","date_published":"2020-03-01T00:00:00Z","isi":1,"department":[{"_id":"JiFr"}],"publication_identifier":{"eissn":["2223-7747"]},"project":[{"call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"day":"01","_id":"7582","publication_status":"published","author":[{"full_name":"Moturu, Taraka Ramji","first_name":"Taraka Ramji","last_name":"Moturu"},{"last_name":"Sinha","full_name":"Sinha, Sansrity","first_name":"Sansrity"},{"last_name":"Salava","full_name":"Salava, Hymavathi","first_name":"Hymavathi"},{"full_name":"Thula, Sravankumar","first_name":"Sravankumar","last_name":"Thula"},{"last_name":"Nodzyński","full_name":"Nodzyński, Tomasz","first_name":"Tomasz"},{"last_name":"Vařeková","first_name":"Radka Svobodová","full_name":"Vařeková, Radka Svobodová"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"last_name":"Simon","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","first_name":"Sibu"}],"external_id":{"isi":["000525315000035"],"pmid":["32121542"]},"publisher":"MDPI","doi":"10.3390/plants9030299","abstract":[{"text":"Small RNAs (smRNA, 19–25 nucleotides long), which are transcribed by RNA polymerase II, regulate the expression of genes involved in a multitude of processes in eukaryotes. miRNA biogenesis and the proteins involved in the biogenesis pathway differ across plant and animal lineages. The major proteins constituting the biogenesis pathway, namely, the Dicers (DCL/DCR) and Argonautes (AGOs), have been extensively studied. However, the accessory proteins (DAWDLE (DDL), SERRATE (SE), and TOUGH (TGH)) of the pathway that differs across the two lineages remain largely uncharacterized. We present the first detailed report on the molecular evolution and divergence of these proteins across eukaryotes. Although DDL is present in eukaryotes and prokaryotes, SE and TGH appear to be specific to eukaryotes. The addition/deletion of specific domains and/or domain-specific sequence divergence in the three proteins points to the observed functional divergence of these proteins across the two lineages, which correlates with the differences in miRNA length across the two lineages. Our data enhance the current understanding of the structure–function relationship of these proteins and reveals previous unexplored crucial residues in the three proteins that can be used as a basis for further functional characterization. The data presented here on the number of miRNAs in crown eukaryotic lineages are consistent with the notion of the expansion of the number of miRNA-coding genes in animal and plant lineages correlating with organismal complexity. Whether this difference in functionally correlates with the diversification (or presence/absence) of the three proteins studied here or the miRNA signaling in the plant and animal lineages is unclear. Based on our results of the three proteins studied here and previously available data concerning the evolution of miRNA genes in the plant and animal lineages, we believe that miRNAs probably evolved once in the ancestor to crown eukaryotes and have diversified independently in the eukaryotes.","lang":"eng"}],"article_processing_charge":"No","ddc":["580"],"ec_funded":1,"month":"03","has_accepted_license":"1","date_updated":"2026-04-02T14:35:47Z","article_type":"original","oa":1,"file_date_updated":"2020-07-14T12:48:00Z","oa_version":"Published Version"},{"ddc":["570"],"article_processing_charge":"No","abstract":[{"lang":"eng","text":"CLC chloride/proton exchangers may support acidification of endolysosomes and raise their luminal Cl− concentration. Disruption of endosomal ClC‐3 causes severe neurodegeneration. To assess the importance of ClC‐3 Cl−/H+ exchange, we now generate Clcn3unc/unc mice in which ClC‐3 is converted into a Cl− channel. Unlike Clcn3−/− mice, Clcn3unc/unc mice appear normal owing to compensation by ClC‐4 with which ClC‐3 forms heteromers. ClC‐4 protein levels are strongly reduced in Clcn3−/−, but not in Clcn3unc/unc mice because ClC‐3unc binds and stabilizes ClC‐4 like wild‐type ClC‐3. Although mice lacking ClC‐4 appear healthy, its absence in Clcn3unc/unc/Clcn4−/− mice entails even stronger neurodegeneration than observed in Clcn3−/− mice. A fraction of ClC‐3 is found on synaptic vesicles, but miniature postsynaptic currents and synaptic vesicle acidification are not affected in Clcn3unc/unc or Clcn3−/− mice before neurodegeneration sets in. Both, Cl−/H+‐exchange activity and the stabilizing effect on ClC‐4, are central to the biological function of ClC‐3."}],"doi":"10.15252/embj.2019103358","day":"02","external_id":{"pmid":["32118314"],"isi":["000517335000001"]},"_id":"7586","publisher":"EMBO Press","author":[{"last_name":"Weinert","first_name":"Stefanie","full_name":"Weinert, Stefanie"},{"last_name":"Gimber","first_name":"Niclas","full_name":"Gimber, Niclas"},{"full_name":"Deuschel, Dorothea","first_name":"Dorothea","last_name":"Deuschel"},{"first_name":"Till","full_name":"Stuhlmann, Till","last_name":"Stuhlmann"},{"full_name":"Puchkov, Dmytro","first_name":"Dmytro","last_name":"Puchkov"},{"last_name":"Farsi","full_name":"Farsi, Zohreh","first_name":"Zohreh"},{"last_name":"Ludwig","full_name":"Ludwig, Carmen F.","first_name":"Carmen F."},{"first_name":"Gaia","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Karen I.","full_name":"López-Cayuqueo, Karen I.","last_name":"López-Cayuqueo"},{"full_name":"Planells-Cases, Rosa","first_name":"Rosa","last_name":"Planells-Cases"},{"last_name":"Jentsch","first_name":"Thomas J.","full_name":"Jentsch, Thomas J."}],"publication_status":"published","file_date_updated":"2020-07-14T12:48:00Z","oa_version":"Published Version","oa":1,"article_type":"original","acknowledgement":"We thank T. Stauber and T. Breiderhoff for cloning expression constructs; K. Räbel, S. Hohensee, and C. Backhaus for technical assistance; R. Jahn (MPIbpc, Göttingen) for providing the equipment required for SV purification; and A\r\nWoehler (MDC, Berlin) for assistance with SV imaging. Supported, in part, by grants from the Deutsche Forschungsgemeinschaft (JE164/9-2, SFB740 TP C5, FOR 2625 (JE164/14-1), NeuroCure Cluster of Excellence), the European Research Council Advanced Grant CYTOVOLION (ERC 294435) and the Prix Louis-Jeantet de Médecine to TJJ, and Peter and Traudl Engelhorn fellowship to ZF.","month":"03","date_updated":"2026-04-16T09:35:48Z","has_accepted_license":"1","title":"Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration","publication":"EMBO Journal","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_id":"7615","access_level":"open_access","date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-23T13:51:11Z","content_type":"application/pdf","file_size":12243278,"relation":"main_file","checksum":"82750a7a93e3740decbce8474004111a","file_name":"2020_EMBO_Weinert.pdf"}],"pmid":1,"type":"journal_article","year":"2020","volume":39,"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"apa":"Weinert, S., Gimber, N., Deuschel, D., Stuhlmann, T., Puchkov, D., Farsi, Z., … Jentsch, T. J. (2020). Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. <i>EMBO Journal</i>. EMBO Press. <a href=\"https://doi.org/10.15252/embj.2019103358\">https://doi.org/10.15252/embj.2019103358</a>","ieee":"S. Weinert <i>et al.</i>, “Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration,” <i>EMBO Journal</i>, vol. 39. EMBO Press, 2020.","chicago":"Weinert, Stefanie, Niclas Gimber, Dorothea Deuschel, Till Stuhlmann, Dmytro Puchkov, Zohreh Farsi, Carmen F. Ludwig, et al. “Uncoupling Endosomal CLC Chloride/Proton Exchange Causes Severe Neurodegeneration.” <i>EMBO Journal</i>. EMBO Press, 2020. <a href=\"https://doi.org/10.15252/embj.2019103358\">https://doi.org/10.15252/embj.2019103358</a>.","ista":"Weinert S, Gimber N, Deuschel D, Stuhlmann T, Puchkov D, Farsi Z, Ludwig CF, Novarino G, López-Cayuqueo KI, Planells-Cases R, Jentsch TJ. 2020. Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. EMBO Journal. 39, e103358.","short":"S. Weinert, N. Gimber, D. Deuschel, T. Stuhlmann, D. Puchkov, Z. Farsi, C.F. Ludwig, G. Novarino, K.I. López-Cayuqueo, R. Planells-Cases, T.J. Jentsch, EMBO Journal 39 (2020).","mla":"Weinert, Stefanie, et al. “Uncoupling Endosomal CLC Chloride/Proton Exchange Causes Severe Neurodegeneration.” <i>EMBO Journal</i>, vol. 39, e103358, EMBO Press, 2020, doi:<a href=\"https://doi.org/10.15252/embj.2019103358\">10.15252/embj.2019103358</a>.","ama":"Weinert S, Gimber N, Deuschel D, et al. Uncoupling endosomal CLC chloride/proton exchange causes severe neurodegeneration. <i>EMBO Journal</i>. 2020;39. doi:<a href=\"https://doi.org/10.15252/embj.2019103358\">10.15252/embj.2019103358</a>"},"quality_controlled":"1","scopus_import":"1","date_created":"2020-03-15T23:00:55Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"department":[{"_id":"GaNo"}],"isi":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","date_published":"2020-03-02T00:00:00Z","article_number":"e103358","intvolume":"        39"},{"quality_controlled":"1","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2020-03-20T13:16:41Z","volume":9,"status":"public","citation":{"chicago":"Moon, Hyang Mi, Simon Hippenmeyer, Liqun Luo, and Anthony Wynshaw-Boris. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/elife.51512\">https://doi.org/10.7554/elife.51512</a>.","ieee":"H. M. Moon, S. Hippenmeyer, L. Luo, and A. Wynshaw-Boris, “LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","apa":"Moon, H. M., Hippenmeyer, S., Luo, L., &#38; Wynshaw-Boris, A. (2020). LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.51512\">https://doi.org/10.7554/elife.51512</a>","ama":"Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/elife.51512\">10.7554/elife.51512</a>","mla":"Moon, Hyang Mi, et al. “LIS1 Determines Cleavage Plane Positioning by Regulating Actomyosin-Mediated Cell Membrane Contractility.” <i>ELife</i>, vol. 9, 51512, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/elife.51512\">10.7554/elife.51512</a>.","short":"H.M. Moon, S. Hippenmeyer, L. Luo, A. Wynshaw-Boris, ELife 9 (2020).","ista":"Moon HM, Hippenmeyer S, Luo L, Wynshaw-Boris A. 2020. LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility. eLife. 9, 51512."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"type":"journal_article","year":"2020","title":"LIS1 determines cleavage plane positioning by regulating actomyosin-mediated cell membrane contractility","publication":"eLife","language":[{"iso":"eng"}],"file":[{"file_id":"8567","access_level":"open_access","success":1,"creator":"dernst","relation":"main_file","file_size":15089438,"file_name":"2020_elife_Moon.pdf","checksum":"396ceb2dd10b102ef4e699666b9342c3","date_created":"2020-09-24T07:03:20Z","date_updated":"2020-09-24T07:03:20Z","content_type":"application/pdf"}],"intvolume":"         9","article_number":"51512","date_published":"2020-03-11T00:00:00Z","publication_identifier":{"issn":["2050-084X"]},"department":[{"_id":"SiHi"}],"isi":1,"day":"11","_id":"7593","publisher":"eLife Sciences Publications","author":[{"full_name":"Moon, Hyang Mi","first_name":"Hyang Mi","last_name":"Moon"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer"},{"last_name":"Luo","first_name":"Liqun","full_name":"Luo, Liqun"},{"last_name":"Wynshaw-Boris","full_name":"Wynshaw-Boris, Anthony","first_name":"Anthony"}],"publication_status":"published","external_id":{"pmid":["32159512"],"isi":["000522835800001"]},"abstract":[{"lang":"eng","text":"Heterozygous loss of human PAFAH1B1 (coding for LIS1) results in the disruption of neurogenesis and neuronal migration via dysregulation of microtubule (MT) stability and dynein motor function/localization that alters mitotic spindle orientation, chromosomal segregation, and nuclear migration. Recently, human induced pluripotent stem cell (iPSC) models revealed an important role for LIS1 in controlling the length of terminal cell divisions of outer radial glial (oRG) progenitors, suggesting cellular functions of LIS1 in regulating neural progenitor cell (NPC) daughter cell separation. Here we examined the late mitotic stages NPCs in vivo and mouse embryonic fibroblasts (MEFs) in vitro from Pafah1b1-deficient mutants. Pafah1b1-deficient neocortical NPCs and MEFs similarly exhibited cleavage plane displacement with mislocalization of furrow-associated markers, associated with actomyosin dysfunction and cell membrane hyper-contractility. Thus, it suggests LIS1 acts as a key molecular link connecting MTs/dynein and actomyosin, ensuring that cell membrane contractility is tightly controlled to execute proper daughter cell separation."}],"article_processing_charge":"No","doi":"10.7554/elife.51512","ddc":["570"],"month":"03","date_updated":"2023-08-18T07:06:31Z","has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.1101/751958","open_access":"1"}],"oa":1,"article_type":"original","oa_version":"Published Version","file_date_updated":"2020-09-24T07:03:20Z"},{"type":"journal_article","issue":"1","year":"2020","title":"How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator","publication":"Physical Review Research","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","file_id":"7610","creator":"dernst","relation":"main_file","file_size":1436735,"checksum":"1be551fd5f5583635076017d7391ffdc","file_name":"2020_PhysRevResearch_Gotfryd.pdf","date_updated":"2020-07-14T12:48:00Z","date_created":"2020-03-23T10:18:38Z","content_type":"application/pdf"}],"quality_controlled":"1","scopus_import":"1","date_created":"2020-03-20T15:21:10Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":2,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Gotfryd, D., Paerschke, E., Chaloupka, J., Oles, A. M., &#38; Wohlfeld, K. (2020). How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.2.013353\">https://doi.org/10.1103/PhysRevResearch.2.013353</a>","ieee":"D. Gotfryd, E. Paerschke, J. Chaloupka, A. M. Oles, and K. Wohlfeld, “How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator,” <i>Physical Review Research</i>, vol. 2, no. 1. American Physical Society, 2020.","chicago":"Gotfryd, Dorota, Ekaterina Paerschke, Jiri Chaloupka, Andrzej M. Oles, and Krzysztof Wohlfeld. “How Spin-Orbital Entanglement Depends on the Spin-Orbit Coupling in a Mott Insulator.” <i>Physical Review Research</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevResearch.2.013353\">https://doi.org/10.1103/PhysRevResearch.2.013353</a>.","short":"D. Gotfryd, E. Paerschke, J. Chaloupka, A.M. Oles, K. Wohlfeld, Physical Review Research 2 (2020).","ista":"Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. 2020. How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator. Physical Review Research. 2(1), 013353.","mla":"Gotfryd, Dorota, et al. “How Spin-Orbital Entanglement Depends on the Spin-Orbit Coupling in a Mott Insulator.” <i>Physical Review Research</i>, vol. 2, no. 1, 013353, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.2.013353\">10.1103/PhysRevResearch.2.013353</a>.","ama":"Gotfryd D, Paerschke E, Chaloupka J, Oles AM, Wohlfeld K. How spin-orbital entanglement depends on the spin-orbit coupling in a Mott insulator. <i>Physical Review Research</i>. 2020;2(1). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.2.013353\">10.1103/PhysRevResearch.2.013353</a>"},"department":[{"_id":"MiLe"}],"intvolume":"         2","article_number":"013353","date_published":"2020-03-20T00:00:00Z","ddc":["530"],"ec_funded":1,"day":"20","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publisher":"American Physical Society","_id":"7594","publication_status":"published","author":[{"last_name":"Gotfryd","first_name":"Dorota","full_name":"Gotfryd, Dorota"},{"last_name":"Paerschke","id":"8275014E-6063-11E9-9B7F-6338E6697425","first_name":"Ekaterina","orcid":"0000-0003-0853-8182","full_name":"Paerschke, Ekaterina"},{"last_name":"Chaloupka","full_name":"Chaloupka, Jiri","first_name":"Jiri"},{"first_name":"Andrzej M.","full_name":"Oles, Andrzej M.","last_name":"Oles"},{"full_name":"Wohlfeld, Krzysztof","first_name":"Krzysztof","last_name":"Wohlfeld"}],"abstract":[{"text":"The concept of the entanglement between spin and orbital degrees of freedom plays a crucial role in our understanding of various phases and exotic ground states in a broad class of materials, including orbitally ordered materials and spin liquids. We investigate how the spin-orbital entanglement in a Mott insulator depends on the value of the spin-orbit coupling of the relativistic origin. To this end, we numerically diagonalize a one-dimensional spin-orbital model with Kugel-Khomskii exchange interactions between spins and orbitals on different sites supplemented by the on-site spin-orbit coupling. In the regime of small spin-orbit coupling with regard to the spin-orbital exchange, the ground state to a large extent resembles the one obtained in the limit of vanishing spin-orbit coupling. On the other hand, for large spin-orbit coupling the ground state can, depending on the model parameters, either still show negligible spin-orbital entanglement or evolve to a highly spin-orbitally-entangled phase with completely distinct properties that are described by an effective XXZ model. The presented results suggest that (i) the spin-orbital entanglement may be induced by large on-site spin-orbit coupling, as found in the 5d transition metal oxides, such as the iridates; (ii) for Mott insulators with weak spin-orbit coupling of Ising type, such as, e.g., the alkali hyperoxides, the effects of the spin-orbit coupling on the ground state can, in the first order of perturbation theory, be neglected.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1103/PhysRevResearch.2.013353","oa":1,"article_type":"original","oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:00Z","month":"03","date_updated":"2024-10-21T06:02:21Z","has_accepted_license":"1"},{"doi":"10.1038/s41477-020-0648-9","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Directional intercellular transport of the phytohormone auxin mediated by PIN FORMED (PIN) efflux carriers plays essential roles in both coordinating patterning processes and integrating multiple external cues by rapidly redirecting auxin fluxes. Multilevel regulations of PIN activity under internal and external cues are complicated; however, the underlying molecular mechanism remains elusive. Here we demonstrate that 3’-Phosphoinositide-Dependent Protein Kinase1 (PDK1), which is conserved in plants and mammals, functions as a molecular hub integrating the upstream lipid signalling and the downstream substrate activity through phosphorylation. Genetic analysis uncovers that loss-of-function Arabidopsis mutant pdk1.1 pdk1.2 exhibits a plethora of abnormalities in organogenesis and growth, due to the defective PIN-dependent auxin transport. Further cellular and biochemical analyses reveal that PDK1 phosphorylates D6 Protein Kinase to facilitate its activity towards PIN proteins. Our studies establish a lipid-dependent phosphorylation cascade connecting membrane composition-based cellular signalling with plant growth and patterning by regulating morphogenetic auxin fluxes."}],"_id":"7600","author":[{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang"},{"first_name":"Xixi","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang"},{"first_name":"Wei","full_name":"Kong, Wei","last_name":"Kong"},{"first_name":"Xiao-Li","full_name":"Yang, Xiao-Li","last_name":"Yang"},{"last_name":"Molnar","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Molnar, Gergely","first_name":"Gergely"},{"last_name":"Vondráková","full_name":"Vondráková, Zuzana","first_name":"Zuzana"},{"first_name":"Roberta","full_name":"Filepová, Roberta","last_name":"Filepová"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"last_name":"Xue","first_name":"Hong-Wei","full_name":"Xue, Hong-Wei"}],"publisher":"Springer Nature","publication_status":"published","external_id":{"pmid":["32393881"],"isi":["000531787500006"]},"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"},{"grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanism underlying Salicylic Acid Regulation of Endocytic Trafficking in Arabidopsis"}],"day":"01","ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/755504"}],"date_updated":"2026-04-02T11:50:26Z","month":"05","oa_version":"Preprint","oa":1,"article_type":"original","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"short":"S. Tan, X. Zhang, W. Kong, X.-L. Yang, G. Molnar, Z. Vondráková, R. Filepová, J. Petrášek, J. Friml, H.-W. Xue, Nature Plants 6 (2020) 556–569.","ista":"Tan S, Zhang X, Kong W, Yang X-L, Molnar G, Vondráková Z, Filepová R, Petrášek J, Friml J, Xue H-W. 2020. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nature Plants. 6, 556–569.","ama":"Tan S, Zhang X, Kong W, et al. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. <i>Nature Plants</i>. 2020;6:556-569. doi:<a href=\"https://doi.org/10.1038/s41477-020-0648-9\">10.1038/s41477-020-0648-9</a>","mla":"Tan, Shutang, et al. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” <i>Nature Plants</i>, vol. 6, Springer Nature, 2020, pp. 556–69, doi:<a href=\"https://doi.org/10.1038/s41477-020-0648-9\">10.1038/s41477-020-0648-9</a>.","ieee":"S. Tan <i>et al.</i>, “The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis,” <i>Nature Plants</i>, vol. 6. Springer Nature, pp. 556–569, 2020.","apa":"Tan, S., Zhang, X., Kong, W., Yang, X.-L., Molnar, G., Vondráková, Z., … Xue, H.-W. (2020). The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-020-0648-9\">https://doi.org/10.1038/s41477-020-0648-9</a>","chicago":"Tan, Shutang, Xixi Zhang, Wei Kong, Xiao-Li Yang, Gergely Molnar, Zuzana Vondráková, Roberta Filepová, Jan Petrášek, Jiří Friml, and Hong-Wei Xue. “The Lipid Code-Dependent Phosphoswitch PDK1–D6PK Activates PIN-Mediated Auxin Efflux in Arabidopsis.” <i>Nature Plants</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41477-020-0648-9\">https://doi.org/10.1038/s41477-020-0648-9</a>."},"status":"public","volume":6,"date_created":"2020-03-21T16:34:16Z","quality_controlled":"1","scopus_import":"1","related_material":{"link":[{"url":"https://doi.org/10.1038/s41477-020-0719-y","relation":"erratum"}]},"language":[{"iso":"eng"}],"publication":"Nature Plants","title":"The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis","type":"journal_article","year":"2020","pmid":1,"page":"556-569","date_published":"2020-05-01T00:00:00Z","intvolume":"         6","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"isi":1,"publication_identifier":{"eissn":["2055-0278"]},"department":[{"_id":"JiFr"}]},{"department":[{"_id":"JiFr"}],"oa":1,"oa_version":"Preprint","month":"02","date_updated":"2021-01-12T08:14:26Z","date_published":"2020-02-19T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1101/791137","open_access":"1"}],"page":"22","type":"preprint","year":"2020","title":"Plasmodesmata-like intercellular connections by plant remorin in animal cells","publication":"bioRxiv","language":[{"iso":"eng"}],"day":"19","publication_status":"published","_id":"7601","date_created":"2020-03-21T16:34:42Z","author":[{"last_name":"Wei","full_name":"Wei, Zhuang","first_name":"Zhuang"},{"orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang","first_name":"Shutang","last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tao","full_name":"Liu, Tao","last_name":"Liu"},{"last_name":"Wu","full_name":"Wu, Yuan","first_name":"Yuan"},{"first_name":"Ji-Gang","full_name":"Lei, Ji-Gang","last_name":"Lei"},{"last_name":"Chen","full_name":"Chen, ZhengJun","first_name":"ZhengJun"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hong-Wei","full_name":"Xue, Hong-Wei","last_name":"Xue"},{"full_name":"Liao, Kan","first_name":"Kan","last_name":"Liao"}],"publisher":"Cold Spring Harbor Laboratory","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Plasmodesmata (PD) are crucial structures for intercellular communication in multicellular plants with remorins being their crucial plant-specific structural and functional constituents. The PD biogenesis is an intriguing but poorly understood process. By expressing an Arabidopsis remorin protein in mammalian cells, we have reconstituted a PD-like filamentous structure, termed remorin filament (RF), connecting neighboring cells physically and physiologically. Notably, RFs are capable of transporting macromolecules intercellularly, in a way similar to plant PD. With further super-resolution microscopic analysis and biochemical characterization, we found that RFs are also composed of actin filaments, forming the core skeleton structure, aligned with the remorin protein. This unique heterologous filamentous structure might explain the molecular mechanism for remorin function as well as PD construction. Furthermore, remorin protein exhibits a specific distribution manner in the plasma membrane in mammalian cells, representing a lipid nanodomain, depending on its lipid modification status. Our studies not only provide crucial insights into the mechanism of PD biogenesis, but also uncovers unsuspected fundamental mechanistic and evolutionary links between intercellular communication systems of plants and animals."}],"doi":"10.1101/791137","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wei, Zhuang, et al. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2020, doi:<a href=\"https://doi.org/10.1101/791137\">10.1101/791137</a>.","ama":"Wei Z, Tan S, Liu T, et al. Plasmodesmata-like intercellular connections by plant remorin in animal cells. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/791137\">10.1101/791137</a>","short":"Z. Wei, S. Tan, T. Liu, Y. Wu, J.-G. Lei, Z. Chen, J. Friml, H.-W. Xue, K. Liao, BioRxiv (2020).","ista":"Wei Z, Tan S, Liu T, Wu Y, Lei J-G, Chen Z, Friml J, Xue H-W, Liao K. 2020. Plasmodesmata-like intercellular connections by plant remorin in animal cells. bioRxiv, <a href=\"https://doi.org/10.1101/791137\">10.1101/791137</a>.","chicago":"Wei, Zhuang, Shutang Tan, Tao Liu, Yuan Wu, Ji-Gang Lei, ZhengJun Chen, Jiří Friml, Hong-Wei Xue, and Kan Liao. “Plasmodesmata-like Intercellular Connections by Plant Remorin in Animal Cells.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2020. <a href=\"https://doi.org/10.1101/791137\">https://doi.org/10.1101/791137</a>.","apa":"Wei, Z., Tan, S., Liu, T., Wu, Y., Lei, J.-G., Chen, Z., … Liao, K. (2020). Plasmodesmata-like intercellular connections by plant remorin in animal cells. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/791137\">https://doi.org/10.1101/791137</a>","ieee":"Z. Wei <i>et al.</i>, “Plasmodesmata-like intercellular connections by plant remorin in animal cells,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020."}},{"month":"02","has_accepted_license":"1","date_updated":"2026-04-16T08:28:17Z","file_date_updated":"2020-07-14T12:48:01Z","oa_version":"Published Version","oa":1,"article_type":"original","doi":"10.3389/fpls.2020.00091","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants."}],"day":"19","author":[{"last_name":"Nimeth","first_name":"Barbara Anna","full_name":"Nimeth, Barbara Anna"},{"full_name":"Riegler, Stefan","orcid":"0000-0003-3413-1343","first_name":"Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","last_name":"Riegler"},{"full_name":"Kalyna, Maria","first_name":"Maria","last_name":"Kalyna"}],"_id":"7603","external_id":{"isi":["000518903600001"]},"publisher":"Frontiers","publication_status":"published","ddc":["580"],"article_number":"91","date_published":"2020-02-19T00:00:00Z","intvolume":"        11","isi":1,"publication_identifier":{"eissn":["1664-462X"]},"department":[{"_id":"FyKo"}],"status":"public","volume":11,"citation":{"ieee":"B. A. Nimeth, S. Riegler, and M. Kalyna, “Alternative splicing and DNA damage response in plants,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020.","apa":"Nimeth, B. A., Riegler, S., &#38; Kalyna, M. (2020). Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>","chicago":"Nimeth, Barbara Anna, Stefan Riegler, and Maria Kalyna. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fpls.2020.00091\">https://doi.org/10.3389/fpls.2020.00091</a>.","ista":"Nimeth BA, Riegler S, Kalyna M. 2020. Alternative splicing and DNA damage response in plants. Frontiers in Plant Science. 11, 91.","short":"B.A. Nimeth, S. Riegler, M. Kalyna, Frontiers in Plant Science 11 (2020).","ama":"Nimeth BA, Riegler S, Kalyna M. Alternative splicing and DNA damage response in plants. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>","mla":"Nimeth, Barbara Anna, et al. “Alternative Splicing and DNA Damage Response in Plants.” <i>Frontiers in Plant Science</i>, vol. 11, 91, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2020.00091\">10.3389/fpls.2020.00091</a>."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","quality_controlled":"1","date_created":"2020-03-22T23:00:46Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Frontiers in Plant Science","title":"Alternative splicing and DNA damage response in plants","file":[{"date_created":"2020-03-23T09:03:40Z","date_updated":"2020-07-14T12:48:01Z","content_type":"application/pdf","relation":"main_file","file_size":507414,"file_name":"2020_FrontiersPlants_Nimeth.pdf","checksum":"57c37209f7b6712ced86c0f11b2be74e","creator":"dernst","file_id":"7607","access_level":"open_access"}],"language":[{"iso":"eng"}],"year":"2020","type":"journal_article"},{"intvolume":"       153","page":"15:1-15:16","arxiv":1,"date_published":"2020-02-01T00:00:00Z","alternative_title":["LIPIcs"],"license":"https://creativecommons.org/licenses/by/3.0/","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959771337"]},"department":[{"_id":"DaAl"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"date_created":"2020-03-22T23:00:46Z","scopus_import":"1","quality_controlled":"1","citation":{"ieee":"D.-A. Alistarh, A. Fedorov, and N. Koval, “In search of the fastest concurrent union-find algorithm,” in <i>23rd International Conference on Principles of Distributed Systems</i>, Neuchatal, Switzerland, 2020, vol. 153, p. 15:1-15:16.","apa":"Alistarh, D.-A., Fedorov, A., &#38; Koval, N. (2020). In search of the fastest concurrent union-find algorithm. In <i>23rd International Conference on Principles of Distributed Systems</i> (Vol. 153, p. 15:1-15:16). Neuchatal, Switzerland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.15</a>","chicago":"Alistarh, Dan-Adrian, Alexander Fedorov, and Nikita Koval. “In Search of the Fastest Concurrent Union-Find Algorithm.” In <i>23rd International Conference on Principles of Distributed Systems</i>, 153:15:1-15:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. <a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.15\">https://doi.org/10.4230/LIPIcs.OPODIS.2019.15</a>.","ista":"Alistarh D-A, Fedorov A, Koval N. 2020. In search of the fastest concurrent union-find algorithm. 23rd International Conference on Principles of Distributed Systems. OPODIS: International Conference on Principles of Distributed Systems, LIPIcs, vol. 153, 15:1-15:16.","short":"D.-A. Alistarh, A. Fedorov, N. Koval, in:, 23rd International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 15:1-15:16.","ama":"Alistarh D-A, Fedorov A, Koval N. In search of the fastest concurrent union-find algorithm. In: <i>23rd International Conference on Principles of Distributed Systems</i>. Vol 153. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2020:15:1-15:16. doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.15\">10.4230/LIPIcs.OPODIS.2019.15</a>","mla":"Alistarh, Dan-Adrian, et al. “In Search of the Fastest Concurrent Union-Find Algorithm.” <i>23rd International Conference on Principles of Distributed Systems</i>, vol. 153, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020, p. 15:1-15:16, doi:<a href=\"https://doi.org/10.4230/LIPIcs.OPODIS.2019.15\">10.4230/LIPIcs.OPODIS.2019.15</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":153,"status":"public","type":"conference","year":"2020","language":[{"iso":"eng"}],"file":[{"file_size":13074131,"relation":"main_file","file_name":"2019_LIPIcs_Alistarh.pdf","checksum":"d66f07ecb609d9f02433e39f80a447e9","date_created":"2020-03-23T09:22:48Z","date_updated":"2020-07-14T12:48:01Z","content_type":"application/pdf","access_level":"open_access","file_id":"7609","creator":"dernst"}],"title":"In search of the fastest concurrent union-find algorithm","corr_author":"1","publication":"23rd International Conference on Principles of Distributed Systems","date_updated":"2025-07-10T11:54:46Z","has_accepted_license":"1","month":"02","oa":1,"file_date_updated":"2020-07-14T12:48:01Z","oa_version":"Published Version","publication_status":"published","_id":"7605","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","author":[{"last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian"},{"last_name":"Fedorov","first_name":"Alexander","full_name":"Fedorov, Alexander"},{"first_name":"Nikita","full_name":"Koval, Nikita","last_name":"Koval","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1911.06347"]},"day":"01","conference":{"name":"OPODIS: International Conference on Principles of Distributed Systems","start_date":"2019-12-17","location":"Neuchatal, Switzerland","end_date":"2019-12-19"},"article_processing_charge":"No","abstract":[{"text":"Union-Find (or Disjoint-Set Union) is one of the fundamental problems in computer science; it has been well-studied from both theoretical and practical perspectives in the sequential case. Recently, there has been mounting interest in analyzing this problem in the concurrent scenario, and several asymptotically-efficient algorithms have been proposed. Yet, to date, there is very little known about the practical performance of concurrent Union-Find. This work addresses this gap. We evaluate and analyze the performance of several concurrent Union-Find algorithms and optimization strategies across a wide range of platforms (Intel, AMD, and ARM) and workloads (social, random, and road networks, as well as integrations into more complex algorithms). We first observe that, due to the limited computational cost, the number of induced cache misses is the critical determining factor for the performance of existing algorithms. We introduce new techniques to reduce this cost by storing node priorities implicitly and by using plain reads and writes in a way that does not affect the correctness of the algorithms. Finally, we show that Union-Find implementations are an interesting application for Transactional Memory (TM): one of the fastest algorithm variants we discovered is a sequential one that uses coarse-grained locking with the lock elision optimization to reduce synchronization cost and increase scalability. ","lang":"eng"}],"doi":"10.4230/LIPIcs.OPODIS.2019.15","ddc":["000"]},{"page":"2143-2174","date_published":"2020-03-12T00:00:00Z","intvolume":"       110","department":[{"_id":"RoSe"}],"publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Rademacher, S. A. E. (2020). Central limit theorem for Bose gases interacting through singular potentials. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-020-01286-w\">https://doi.org/10.1007/s11005-020-01286-w</a>","ieee":"S. A. E. Rademacher, “Central limit theorem for Bose gases interacting through singular potentials,” <i>Letters in Mathematical Physics</i>, vol. 110. Springer Nature, pp. 2143–2174, 2020.","chicago":"Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11005-020-01286-w\">https://doi.org/10.1007/s11005-020-01286-w</a>.","ista":"Rademacher SAE. 2020. Central limit theorem for Bose gases interacting through singular potentials. Letters in Mathematical Physics. 110, 2143–2174.","short":"S.A.E. Rademacher, Letters in Mathematical Physics 110 (2020) 2143–2174.","mla":"Rademacher, Simone Anna Elvira. “Central Limit Theorem for Bose Gases Interacting through Singular Potentials.” <i>Letters in Mathematical Physics</i>, vol. 110, Springer Nature, 2020, pp. 2143–74, doi:<a href=\"https://doi.org/10.1007/s11005-020-01286-w\">10.1007/s11005-020-01286-w</a>.","ama":"Rademacher SAE. Central limit theorem for Bose gases interacting through singular potentials. <i>Letters in Mathematical Physics</i>. 2020;110:2143-2174. doi:<a href=\"https://doi.org/10.1007/s11005-020-01286-w\">10.1007/s11005-020-01286-w</a>"},"volume":110,"status":"public","date_created":"2020-03-23T11:11:47Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","quality_controlled":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","access_level":"open_access","file_id":"8784","success":1,"date_created":"2020-11-20T12:04:26Z","date_updated":"2020-11-20T12:04:26Z","content_type":"application/pdf","file_size":478683,"relation":"main_file","file_name":"2020_LettersMathPhysics_Rademacher.pdf","checksum":"3bdd41f10ad947b67a45b98f507a7d4a"}],"title":"Central limit theorem for Bose gases interacting through singular potentials","corr_author":"1","publication":"Letters in Mathematical Physics","year":"2020","type":"journal_article","acknowledgement":"Simone Rademacher acknowledges partial support from the NCCR SwissMAP. This project has received\r\nfunding from the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSkłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).\r\nS.R. would like to thank Benjamin Schlein for many fruitful discussions.","date_updated":"2025-04-14T07:44:03Z","has_accepted_license":"1","month":"03","oa_version":"Published Version","file_date_updated":"2020-11-20T12:04:26Z","oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"We consider a system of N bosons in the limit N→∞, interacting through singular potentials. For initial data exhibiting Bose–Einstein condensation, the many-body time evolution is well approximated through a quadratic fluctuation dynamics around a cubic nonlinear Schrödinger equation of the condensate wave function. We show that these fluctuations satisfy a (multi-variate) central limit theorem."}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1007/s11005-020-01286-w","_id":"7611","publisher":"Springer Nature","external_id":{"isi":["000551556000006"]},"publication_status":"published","author":[{"last_name":"Rademacher","id":"856966FE-A408-11E9-977E-802DE6697425","first_name":"Simone Anna Elvira","orcid":"0000-0001-5059-4466","full_name":"Rademacher, Simone Anna Elvira"}],"day":"12","project":[{"call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"ec_funded":1,"ddc":["510"]},{"main_file_link":[{"url":"https://arxiv.org/abs/1903.10455","open_access":"1"}],"acknowledgement":"J. Pitrik was supported by the Hungarian Academy of Sciences Lendület-Momentum Grant for Quantum\r\nInformation Theory, No. 96 141, and by the Hungarian National Research, Development and Innovation\r\nOffice (NKFIH) via Grants Nos. K119442, K124152 and KH129601. D. Virosztek was supported by the\r\nISTFELLOW program of the Institute of Science and Technology Austria (Project Code IC1027FELL01),\r\nby the European Union’s Horizon 2020 research and innovation program under the Marie\r\nSklodowska-Curie Grant Agreement No. 846294, and partially supported by the Hungarian National\r\nResearch, Development and Innovation Office (NKFIH) via Grants Nos. K124152 and KH129601.\r\nWe are grateful to Milán Mosonyi for drawing our attention to Ref.’s [6,14,15,17,\r\n20,21], for comments on earlier versions of this paper, and for several discussions on the topic. We are\r\nalso grateful to Miklós Pálfia for several discussions; to László Erdös for his essential suggestions on the\r\nstructure and highlights of this paper, and for his comments on earlier versions; and to the anonymous\r\nreferee for his/her valuable comments and suggestions.","date_updated":"2025-10-09T08:23:15Z","month":"08","oa_version":"Preprint","oa":1,"article_type":"original","abstract":[{"text":"This short note aims to study quantum Hellinger distances investigated recently by Bhatia et al. (Lett Math Phys 109:1777–1804, 2019) with a particular emphasis on barycenters. We introduce the family of generalized quantum Hellinger divergences that are of the form ϕ(A,B)=Tr((1−c)A+cB−AσB), where σ is an arbitrary Kubo–Ando mean, and c∈(0,1) is the weight of σ. We note that these divergences belong to the family of maximal quantum f-divergences, and hence are jointly convex, and satisfy the data processing inequality. We derive a characterization of the barycenter of finitely many positive definite operators for these generalized quantum Hellinger divergences. We note that the characterization of the barycenter as the weighted multivariate 1/2-power mean, that was claimed in Bhatia et al. (2019), is true in the case of commuting operators, but it is not correct in the general case. ","lang":"eng"}],"article_processing_charge":"No","doi":"10.1007/s11005-020-01282-0","_id":"7618","publication_status":"published","publisher":"Springer Nature","author":[{"last_name":"Pitrik","full_name":"Pitrik, Jozsef","first_name":"Jozsef"},{"first_name":"Daniel","full_name":"Virosztek, Daniel","orcid":"0000-0003-1109-5511","id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","last_name":"Virosztek"}],"external_id":{"arxiv":["1903.10455"],"isi":["000551556000002"]},"day":"01","project":[{"grant_number":"846294","call_identifier":"H2020","name":"Geometric study of Wasserstein spaces and free probability","_id":"26A455A6-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"ec_funded":1,"page":"2039-2052","arxiv":1,"date_published":"2020-08-01T00:00:00Z","intvolume":"       110","department":[{"_id":"LaEr"}],"publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"isi":1,"citation":{"apa":"Pitrik, J., &#38; Virosztek, D. (2020). Quantum Hellinger distances revisited. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-020-01282-0\">https://doi.org/10.1007/s11005-020-01282-0</a>","ieee":"J. Pitrik and D. Virosztek, “Quantum Hellinger distances revisited,” <i>Letters in Mathematical Physics</i>, vol. 110, no. 8. Springer Nature, pp. 2039–2052, 2020.","chicago":"Pitrik, Jozsef, and Daniel Virosztek. “Quantum Hellinger Distances Revisited.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11005-020-01282-0\">https://doi.org/10.1007/s11005-020-01282-0</a>.","short":"J. Pitrik, D. Virosztek, Letters in Mathematical Physics 110 (2020) 2039–2052.","ista":"Pitrik J, Virosztek D. 2020. Quantum Hellinger distances revisited. Letters in Mathematical Physics. 110(8), 2039–2052.","mla":"Pitrik, Jozsef, and Daniel Virosztek. “Quantum Hellinger Distances Revisited.” <i>Letters in Mathematical Physics</i>, vol. 110, no. 8, Springer Nature, 2020, pp. 2039–52, doi:<a href=\"https://doi.org/10.1007/s11005-020-01282-0\">10.1007/s11005-020-01282-0</a>.","ama":"Pitrik J, Virosztek D. Quantum Hellinger distances revisited. <i>Letters in Mathematical Physics</i>. 2020;110(8):2039-2052. doi:<a href=\"https://doi.org/10.1007/s11005-020-01282-0\">10.1007/s11005-020-01282-0</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":110,"status":"public","date_created":"2020-03-25T15:57:48Z","quality_controlled":"1","scopus_import":"1","language":[{"iso":"eng"}],"title":"Quantum Hellinger distances revisited","publication":"Letters in Mathematical Physics","corr_author":"1","year":"2020","type":"journal_article","issue":"8"},{"intvolume":"        32","date_published":"2020-05-01T00:00:00Z","page":"1644-1664","isi":1,"publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"department":[{"_id":"JiFr"}],"acknowledged_ssus":[{"_id":"Bio"}],"scopus_import":"1","quality_controlled":"1","date_created":"2020-03-28T07:39:22Z","status":"public","volume":32,"citation":{"short":"X. Zhang, M. Adamowski, P. Marhavá, S. Tan, Y. Zhang, L. Rodriguez Solovey, M. Zwiewka, V. Pukyšová, A.S. Sánchez, V.K. Raxwal, C.S. Hardtke, T. Nodzynski, J. Friml, The Plant Cell 32 (2020) 1644–1664.","ista":"Zhang X, Adamowski M, Marhavá P, Tan S, Zhang Y, Rodriguez Solovey L, Zwiewka M, Pukyšová V, Sánchez AS, Raxwal VK, Hardtke CS, Nodzynski T, Friml J. 2020. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. The Plant Cell. 32(5), 1644–1664.","mla":"Zhang, Xixi, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” <i>The Plant Cell</i>, vol. 32, no. 5, American Society of Plant Biologists, 2020, pp. 1644–64, doi:<a href=\"https://doi.org/10.1105/tpc.19.00869\">10.1105/tpc.19.00869</a>.","ama":"Zhang X, Adamowski M, Marhavá P, et al. Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. <i>The Plant Cell</i>. 2020;32(5):1644-1664. doi:<a href=\"https://doi.org/10.1105/tpc.19.00869\">10.1105/tpc.19.00869</a>","apa":"Zhang, X., Adamowski, M., Marhavá, P., Tan, S., Zhang, Y., Rodriguez Solovey, L., … Friml, J. (2020). Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters. <i>The Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.19.00869\">https://doi.org/10.1105/tpc.19.00869</a>","ieee":"X. Zhang <i>et al.</i>, “Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters,” <i>The Plant Cell</i>, vol. 32, no. 5. American Society of Plant Biologists, pp. 1644–1664, 2020.","chicago":"Zhang, Xixi, Maciek Adamowski, Petra Marhavá, Shutang Tan, Yuzhou Zhang, Lesia Rodriguez Solovey, Marta Zwiewka, et al. “Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters.” <i>The Plant Cell</i>. American Society of Plant Biologists, 2020. <a href=\"https://doi.org/10.1105/tpc.19.00869\">https://doi.org/10.1105/tpc.19.00869</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"issue":"5","type":"journal_article","year":"2020","corr_author":"1","publication":"The Plant Cell","title":"Arabidopsis flippases cooperate with ARF GTPase exchange factors to regulate the trafficking and polarity of PIN auxin transporters","language":[{"iso":"eng"}],"month":"05","date_updated":"2026-06-18T19:24:19Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1105/tpc.19.00869"}],"article_type":"original","oa":1,"oa_version":"Published Version","project":[{"grant_number":"742985","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"day":"01","_id":"7619","author":[{"id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","last_name":"Zhang","first_name":"Xixi","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627"},{"id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","first_name":"Maciek"},{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","last_name":"Marhavá","full_name":"Marhavá, Petra","first_name":"Petra"},{"last_name":"Tan","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang","orcid":"0000-0002-0471-8285","full_name":"Tan, Shutang"},{"orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","first_name":"Lesia","full_name":"Rodriguez Solovey, Lesia","orcid":"0000-0002-7244-7237"},{"first_name":"Marta","full_name":"Zwiewka, Marta","last_name":"Zwiewka"},{"first_name":"Vendula","full_name":"Pukyšová, Vendula","last_name":"Pukyšová"},{"first_name":"Adrià Sans","full_name":"Sánchez, Adrià Sans","last_name":"Sánchez"},{"last_name":"Raxwal","first_name":"Vivek Kumar","full_name":"Raxwal, Vivek Kumar"},{"last_name":"Hardtke","first_name":"Christian S.","full_name":"Hardtke, Christian S."},{"full_name":"Nodzynski, Tomasz","first_name":"Tomasz","last_name":"Nodzynski"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"external_id":{"isi":["000545741500030"],"pmid":["32193204"]},"publisher":"American Society of Plant Biologists","publication_status":"published","doi":"10.1105/tpc.19.00869","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Cell polarity is a fundamental feature of all multicellular organisms. In plants, prominent cell polarity markers are PIN auxin transporters crucial for plant development. To identify novel components involved in cell polarity establishment and maintenance, we carried out a forward genetic screening with PIN2:PIN1-HA;pin2 Arabidopsis plants, which ectopically express predominantly basally localized PIN1 in the root epidermal cells leading to agravitropic root growth. From the screen, we identified the regulator of PIN polarity 12 (repp12) mutation, which restored gravitropic root growth and caused PIN1-HA polarity switch from basal to apical side of root epidermal cells. Complementation experiments established the repp12 causative mutation as an amino acid substitution in Aminophospholipid ATPase3 (ALA3), a phospholipid flippase with predicted function in vesicle formation. ala3 T-DNA mutants show defects in many auxin-regulated processes, in asymmetric auxin distribution and in PIN trafficking. Analysis of quintuple and sextuple mutants confirmed a crucial role of ALA proteins in regulating plant development and in PIN trafficking and polarity. Genetic and physical interaction studies revealed that ALA3 functions together with GNOM and BIG3 ARF GEFs. Taken together, our results identified ALA3 flippase as an important interactor and regulator of ARF GEF functioning in PIN polarity, trafficking and auxin-mediated development."}],"ddc":["580"],"ec_funded":1}]